diff --git a/docs/cluster_guides/backup.md b/docs/cluster_guides/backup.md index 4b8112cd0..36503f684 100644 --- a/docs/cluster_guides/backup.md +++ b/docs/cluster_guides/backup.md @@ -7,6 +7,7 @@ As PI, you and your academic institution are ultimately responsible for your dat While UPPMAX systems may have backup, these are not designed to act as the sole repository of primary data, e.g. raw data or originals. ## What does "backup" mean for my data? + The type of backup that is generally available for project storage at UPPMAX is incremental backup with 30 day retention. This means that any file that was deleted more than 30 days ago is irretrievably gone. Changes in a file are kept for 30 days, so we can potentially retrieve an old version up to a month after you edited it. The backup service tries to backup all changes as often as they occur, but rapid changes will not register. Due to the large amounts of files in the file systems, a single backup session may take upwards of a week or more. This means that if you create a file and delete it the next day, it will probably not be backed up. @@ -18,6 +19,7 @@ To ensure timely backups, it is very important to reduce the workload of the bac - It is especially important that temporary files and files that are changed often are placed in nobackup directories. ## Which directories are backed up? + Backup is done on: - Home directories (on Rackham these also have snapshots) @@ -28,13 +30,16 @@ Backup is done on: - SNIC projects (named snicYYYY-X-ZZZZ) # What should I put in directories with backup? + - In short, irreplaceable data should be placed there. This includes especially raw sequencing data and any other data that cannot be recreated by any effort. Scripts and other files that are needed to reproduce or repeat the analyses should also be placed on backup. ## What should I not put in directories with backup? + - Directories where you are actively working, especially if you are creating or modifying many files. The backup mechanisms cannot keep up with large amounts of files changing on a rapid basis. ## How robust is uppmax storage? + - All UPPMAX storage systems use RAID technology to make storage more robust through redundancy. - This means that two or more disks must fail in the same "RAID volume" before there is a risk of data loss. @@ -42,9 +47,11 @@ Backup is done on: - Off-site backup is crucial. ## How can I access my backups? + You must contact UPPMAX support and ask for help. Provide as much information as possible, especially directory and file names. ## What about "snapshots"? + - In addition to the regular backup service, the home directories on Rackham have a feature called "snapshots". - Snapshot makes a frozen "picture" of some file structure as it looks at the time the snapshot was taken. - This allows you to restore a particular file as it was at some time point. diff --git a/docs/cluster_guides/bianca.md b/docs/cluster_guides/bianca.md index bb8e515c5..84de51d32 100644 --- a/docs/cluster_guides/bianca.md +++ b/docs/cluster_guides/bianca.md @@ -11,13 +11,13 @@ suitable for working with sensitive data. - [Submitting jobs, using Slurm](slurm.md) - [Starting an interactive node](start_interactive_node_on_bianca.md) - [File transfer](transfer_bianca.md) - - [File transfer using a graphical program](bianca_file_transfer_using_gui.md) + - [File transfer using a graphical program](bianca_file_transfer_using_gui.md) - [The module system](bianca_modules.md) - [IDEs](ides_on_bianca.md) - - [Jupyter](../software/jupyter.md) - - [RStudio](rstudio_on_bianca.md) - - :no_entry: [VSCode](vscode_on_bianca.md) - - [VSCodium](vscodium_on_bianca.md) + - [Jupyter](../software/jupyter.md) + - [RStudio](rstudio_on_bianca.md) + - :no_entry: [VSCode](vscode_on_bianca.md) + - [VSCodium](vscodium_on_bianca.md) - [Workshops and courses](../workshops_courses/workshops_courses.md) - NAISS-sens - Best practices diff --git a/docs/cluster_guides/bianca_file_transfer_using_filezilla.md b/docs/cluster_guides/bianca_file_transfer_using_filezilla.md index 68592f48c..a1d66cf0c 100644 --- a/docs/cluster_guides/bianca_file_transfer_using_filezilla.md +++ b/docs/cluster_guides/bianca_file_transfer_using_filezilla.md @@ -49,7 +49,7 @@ In the 'Site Manager' dialog, click 'New site' ![](./img/filezilla_site_manager.png) -## 5. Create a name for the site, e.g. `bianca-sens123456`. +## 5. Create a name for the site, e.g. `bianca-sens123456` In the 'New Site' dialog, create a name for the site, e.g. `bianca-sens123456`. @@ -57,9 +57,9 @@ In the 'New Site' dialog, create a name for the site, e.g. `bianca-sens123456`. In the 'New Site' dialog, use all standards, except: - * Set protocol to 'SFTP - SSH File Transfer Protocol' - * Set host to `bianca-sftp.uppmax.uu.se` - * Set user to `[username]-[project]`, e.g. `richel-sens123456` +* Set protocol to 'SFTP - SSH File Transfer Protocol' +* Set host to `bianca-sftp.uppmax.uu.se` +* Set user to `[username]-[project]`, e.g. `richel-sens123456` ???- tip "How does that look like?" diff --git a/docs/cluster_guides/bianca_file_transfer_using_gui.md b/docs/cluster_guides/bianca_file_transfer_using_gui.md index 6f8a25cdd..5ca27a4af 100644 --- a/docs/cluster_guides/bianca_file_transfer_using_gui.md +++ b/docs/cluster_guides/bianca_file_transfer_using_gui.md @@ -98,8 +98,8 @@ Here, we show how to transfer files using a graphical tool called FileZilla. In general, one can pick any graphical tools with these constraints: - * the tool must support SFTP - * the tool must not store a password +* the tool must support SFTP +* the tool must not store a password Whatever tool one picks, it must do secure file transfer. For secure file transfer, Bianca supports the SFTP protocol. diff --git a/docs/cluster_guides/bianca_file_transfer_using_winscp.md b/docs/cluster_guides/bianca_file_transfer_using_winscp.md index 256e45c57..a289f97db 100644 --- a/docs/cluster_guides/bianca_file_transfer_using_winscp.md +++ b/docs/cluster_guides/bianca_file_transfer_using_winscp.md @@ -23,9 +23,10 @@ Start WinSCP. In WinSCP, click on 'Create new site'. For that site, use all standards, except: - * Set file protocol to 'SFTP' - * Set host name to `bianca-sftp.uppmax.uu.se` - * Set user name to `[username]-[project]`, e.g. `richel-sens123456` + +* Set file protocol to 'SFTP' +* Set host name to `bianca-sftp.uppmax.uu.se` +* Set user name to `[username]-[project]`, e.g. `richel-sens123456` ???- tip "How does that look like?" diff --git a/docs/cluster_guides/bianca_modules.md b/docs/cluster_guides/bianca_modules.md index 09ab6d5dc..08117c429 100644 --- a/docs/cluster_guides/bianca_modules.md +++ b/docs/cluster_guides/bianca_modules.md @@ -8,4 +8,3 @@ do their work independently and undisturbed. Because this is the same for nearly all UPPMAX clusters, there is a general page on modules [here](modules.md) - diff --git a/docs/cluster_guides/compiling_parallel.md b/docs/cluster_guides/compiling_parallel.md index 01a21b28f..5df27f446 100644 --- a/docs/cluster_guides/compiling_parallel.md +++ b/docs/cluster_guides/compiling_parallel.md @@ -18,14 +18,14 @@ This is a short tutorial about how to use the queuing system, and how to compile For serial programs, see a short version of this page at [Compiling source code](compiling_serial.md). -## Compiling and running parallel programs on UPPMAX clusters. +## Compiling and running parallel programs on UPPMAX clusters + ### Introduction These notes show by brief examples how to compile and run serial and parallel programs on the clusters at UPPMAX. All programs are of the trivial "hello, world" type. The point is to demonstrate how to compile and execute the programs, not how to write parallel programs! - ## Running serial programs on execution nodes Jobs are submitted to execution nodes through the resource manager. @@ -57,7 +57,7 @@ The last line in the script is the command used to start the program. Submit the job to the batch queue: ```console -$ sbatch hello.sh +sbatch hello.sh ``` The program's output to stdout is saved in the file named at the -o flag. @@ -98,7 +98,6 @@ Before compiling a program for MPI we must choose, in addition to the compiler, Check this compatibility page for a more complete picture of compatible versions. - ### C programs Enter the following mpi program in c and save in the file hello.c @@ -123,13 +122,13 @@ Before compiling a program for MPI we must choose which version of MPI. At UPPMA To load the openmpi module, enter the command below or choose other versions according to the lists above. ```console -$ module load gcc/10.3.0 openmpi/3.1.6 +module load gcc/10.3.0 openmpi/3.1.6 ``` To check that the openmpi modules is loaded, use the command: ```console -$ module list +module list ``` The command to compile a c program for mpi is mpicc. Which compiler is used when this command is issued depends on what compiler module was loaded before openmpi @@ -137,13 +136,13 @@ The command to compile a c program for mpi is mpicc. Which compiler is used when To compile, enter the command: ```console -$ mpicc -o hello-mpi hello-mpi.c +mpicc -o hello-mpi hello-mpi.c ``` You should add optimization and other flags to the mpicc command, just as you would to the compiler used. So if the gcc compiler is used and you wish to compile an mpi program written in C with good, fast optimization you should use a command similar to the following: ```console -$ mpicc -fast -o hello-mpi hello-mpi.c +mpicc -fast -o hello-mpi hello-mpi.c ``` To run the mpi program hello using the batch system, we make a batch script with name ``hello-mpi.sh`` @@ -171,7 +170,7 @@ The last word on the last line is the program name hello. Submit the job to the batch queue: ```console -$ sbatch hello-mpi.sh +sbatch hello-mpi.sh ``` The program's output to stdout is saved in the file named at the -o flag. @@ -233,8 +232,8 @@ end program testampi The program can be compiled by this procedure, using mpif90: ```console -$ module load intel/20.4 openmpi/3.1.6 -$ mpif90 -Ofast -o testampi testampi.f90 +module load intel/20.4 openmpi/3.1.6 +mpif90 -Ofast -o testampi testampi.f90 ``` The program can be run by creating a submit script sub.sh: @@ -309,13 +308,13 @@ OpenMP uses threads that use shared memory. OpenMP is supported by both the gcc Depending on your preferences load the chosen compiler: ```console -$ module load gcc/12.1.0 +module load gcc/12.1.0 ``` or ```console -$ module load intel/20.4 +module load intel/20.4 ``` ### C programs @@ -342,13 +341,13 @@ int main() To compile, enter the command (note the -fopenmp or -qopenmp flag depending on compiler): ```console -$ gcc -fopenmp -o hello_omp hello_omp.c +gcc -fopenmp -o hello_omp hello_omp.c ``` or ```console -$ icc qfopenmp -o hello_omp hello_omp.c +icc qfopenmp -o hello_omp hello_omp.c ``` Also here you should add optimization flags such as -fast as appropriate. @@ -382,7 +381,7 @@ The last line in the script is the command used to start the program. Submit the job to the batch queue: ```console -$ sbatch hello.sh +sbatch hello.sh ``` The program's output to stdout is saved in the file named at the -o flag. @@ -427,13 +426,13 @@ END With gcc compiler: ```console -$ gfortran hello_omp.f90 -o hello_omp -fopenmp +gfortran hello_omp.f90 -o hello_omp -fopenmp ``` and with Intel compiler: ```console -$ ifort hello_omp.f90 -o hello_omp -qopenmp +ifort hello_omp.f90 -o hello_omp -qopenmp ``` Run with: @@ -448,7 +447,6 @@ $ ./hello_omp Number of threads = 4 ``` - A batch file would look similar to the C version, above. ## Pthreads @@ -493,8 +491,8 @@ int main() To compile, enter the commands ```console -$ module load gcc/10.2.0 -$ gcc -pthread -o hello_pthread hello_pthread.c +module load gcc/10.2.0 +gcc -pthread -o hello_pthread hello_pthread.c ``` To run the pthread program hello using the batch system, enter the following shell script in the file hello.sh: @@ -521,8 +519,9 @@ The last line in the script is the command used to start the program. Submit the job to the batch queue: ```console -$ sbatch hello.sh +sbatch hello.sh ``` + The program's output to stdout is saved in the file named at the -o flag. A test run of the above program yelds the following output file: diff --git a/docs/cluster_guides/compiling_serial.md b/docs/cluster_guides/compiling_serial.md index 7aad2b813..efd7fa0a9 100644 --- a/docs/cluster_guides/compiling_serial.md +++ b/docs/cluster_guides/compiling_serial.md @@ -12,6 +12,7 @@ C HELLO.F : PRINT MESSAGE ON SCREEN WRITE(*,*) "hello, world"; END ``` + - To compile this you should decide on which compilers to use. At UPPMAX there are two different Fortran compilers installed gcc (gfortran) and Intel (ifort). - For this example we will use Gnu Compiler Collection (gcc) compilers installed on UPPMAX, so the gfortran command can be used to compile fortran code. The GFortran compiler is fully compliant with the Fortran 95 Standard and includes legacy F77 support. In addition, a significant number of Fortran 2003 and Fortran 2008 features are implemented. Fortran2008 and Fortran2018 has full support from gcc/9. @@ -19,16 +20,17 @@ C HELLO.F : PRINT MESSAGE ON SCREEN - A module must first be loaded to use the compilers. You can check what is available and then load a specific version. Choose one recent or one you know will work for your needs. ``` console -$ module avail gcc +module avail gcc -$ module load gcc/10.3.0 +module load gcc/10.3.0 ``` To compile, enter the command: ``` console -$ gfortran -o hello hello.f +gfortran -o hello hello.f ``` + to run, enter: ``` console @@ -45,31 +47,36 @@ hello, world For Intel versions up to 20.4 you do as follows: ``` console -$ module avail intel +module avail intel -$ module load intel/20.4 +module load intel/20.4 ``` + To compile, enter the command: ``` console -$ ifort -o hello hello.f +ifort -o hello hello.f ``` + For Intel versions from year 2021, do like this instead: ``` console -$ module load intel-oneapi compiler -$ module av compiler +module load intel-oneapi compiler +module av compiler ``` + Choose the version you need, like ``` console -$ module load compiler/2023.1.0 +module load compiler/2023.1.0 ``` + To compile, enter the command: ``` console -$ ifx -o hello hello.f +ifx -o hello hello.f ``` + to run, enter: ``` console @@ -94,19 +101,20 @@ int main() To compile using gcc installed with the system (4.8.5, 2015) and with no optimization, use the gcc command. ``` console -$ gcc -o hello hello.c +gcc -o hello hello.c ``` To use a newer version of ggc we load a module: ``` console -$ module load gcc/10.3.0 -$ gcc -o hello hello.c +module load gcc/10.3.0 +gcc -o hello hello.c ``` + with basic optimization: ``` console -$ gcc -O3 -o hello hello.c +gcc -O3 -o hello hello.c ``` c11 standard has full support from gcc/4.8, c17 standard (bug-fix) from gcc/8. @@ -114,32 +122,35 @@ c11 standard has full support from gcc/4.8, c17 standard (bug-fix) from gcc/8. To use the intel compiler, first load the intel module: ``` console -$ module load intel/20.4 +module load intel/20.4 ``` + or for newer Intel versions (2021-, see above): ``` console -$ module load intel-oneapi compiler -$ module load compiler/2023.1.0 +module load intel-oneapi compiler +module load compiler/2023.1.0 ``` and then compile with the command icc, or icx: ``` console -$ icc -o hello hello.c +icc -o hello hello.c ``` or for newer versions: ``` console -$ icx -o hello hello.c +icx -o hello hello.c ``` + To run, enter: ``` console $ ./hello hello, world ``` + c11 and c17 (bug fix) standards have support from intel/17+ (fully from 19). ## Java programs @@ -155,11 +166,12 @@ public static void main(String[] args) } } ``` + Before compiling a java program, the module java has to be loaded. To load the java module, enter the command: ``` console -$ module load java +module load java ``` To check that the java module is loaded, use the command: @@ -177,7 +189,7 @@ The java module is not always needed to run the program. To verify this, unload the java module: ``` console -$ module unload java +module unload java ``` to run, enter: @@ -216,8 +228,9 @@ The last line in the script is the command used to start the program. Submit the job to the batch queue: ``` console -$ sbatch hello.sh +sbatch hello.sh ``` + The program's output to stdout is saved in the file named at the -o flag. ``` console diff --git a/docs/cluster_guides/conda.md b/docs/cluster_guides/conda.md index 93b00edbd..dabc00e1a 100644 --- a/docs/cluster_guides/conda.md +++ b/docs/cluster_guides/conda.md @@ -5,7 +5,7 @@ If you want to see a video how to use Conda on Rackham, go [here](https://youtu.be/SMhawXQhtls?si=_2t6T2Vn2B10M6LW) -## Install packages or not? Check it! +## Install packages or not? Check it ### Python @@ -13,7 +13,7 @@ - load a python version like: ``ml python/3.10.8`` - from the Python shell with the ``import`` command - from BASH shell with the - + - ``pip list`` command - ``ml help python/3.9.5`` (or other version) at UPPMAX @@ -143,15 +143,14 @@ both Rackham and Bianca. These are updated every third day. See above for these - Since python or other packages are dependent on each-other expect solving the versions takes some time. - use an interactive session! -1. ```bash +1. ```bash module load conda ``` - This grants you access to the latest version of Conda and all major repositories on all UPPMAX systems. - Check the text output as ``conda`` is loaded, especially the first time, see below - -2. Create the Conda environment +2. Create the Conda environment - Example: @@ -182,6 +181,7 @@ both Rackham and Bianca. These are updated every third day. See above for these # # $ conda deactivate ``` + - or ```bash @@ -194,8 +194,7 @@ both Rackham and Bianca. These are updated every third day. See above for these # $ mamba deactivate ``` - -4. Activate the conda environment by `source activate` if you have not enabled ``conda/mamba activate``, see above: +4. Activate the conda environment by `source activate` if you have not enabled ``conda/mamba activate``, see above: ```bash source activate python36-env @@ -209,15 +208,18 @@ both Rackham and Bianca. These are updated every third day. See above for these conda list pip list ``` + - you can also add more packages within the environment by exact version (use `=`) or latest (?) compatible version: + ```bash conda install --prefix $CONDA_ENVS_PATH/python36-env pandas ``` + - that may have given you ``pandas=1.1.5`` which would be the newest version compatible with ``python3.6`` and ``numpy=1.13.1`` -5. Now do your work! +5. Now do your work! -6. Deactivate with ``conda``/``mamba deactivate`` (this will work in any case!) +6. Deactivate with ``conda``/``mamba deactivate`` (this will work in any case!) ```bash (python-36-env) $ conda deactivate @@ -231,14 +233,14 @@ both Rackham and Bianca. These are updated every third day. See above for these ## Working with Conda environments defined by files -- Create an environment based on dependencies given in an environment +- Create an environment based on dependencies given in an environment file: - $ conda env create --file environment.yml + conda env create --file environment.yml -- Create file from present conda environment: +- Create file from present conda environment: - $ conda env export > environment.yml + conda env export > environment.yml `environments.yml` (for conda) is a yaml-file which looks like this: @@ -271,7 +273,6 @@ dependencies: - Dependency management from course [Python for Scientific computing](https://aaltoscicomp.github.io/python-for-scicomp/dependencies/) - !!! abstract "keypoints" - Conda is an installer of packages but also bigger toolkits @@ -285,6 +286,7 @@ dependencies: - That is, you cannot load the python module and use the packages therein inside your Conda environment. ## Conda in batch scripts + If you already have setup the CONDA_ENVS_PATH path and run 'conda init bash' a batch script containing a conda environment shall include ```bash @@ -293,6 +295,7 @@ conda activate ``` ## Packages on Bianca + Since we have mirrored conda repositories locally conda will work also on Bianca! First try Conda! There is a mirrored repository with many available packages. @@ -308,7 +311,7 @@ You may have to: in source directory: ``` -$ cp –a +cp –a ``` you may want to tar before copying to include all possible symbolic links: @@ -320,4 +323,4 @@ $ tar xfz #if there is a tar file! $ mv –a ~/.local/lib/python/site-packages/ ``` -If problems arise, send an email to support@uppmax.uu.se and we'll help you. +If problems arise, send an email to and we'll help you. diff --git a/docs/cluster_guides/dardel_migration.md b/docs/cluster_guides/dardel_migration.md index 7ea1ad567..8aba308d7 100644 --- a/docs/cluster_guides/dardel_migration.md +++ b/docs/cluster_guides/dardel_migration.md @@ -36,8 +36,6 @@ The really short description is: See the rest of this guide for more information about these steps. - - ## Long version ???- question "Prefer a video?" @@ -159,7 +157,6 @@ This step is optional, yet may help against possible problems. Running `darsync check` will make Darsync prompt for questions: - ```bash darsync check ``` @@ -242,7 +239,6 @@ or try to fix them yourself. # the the command above finished without error messages and you have a folder.tar.gz file that seems about right in size, rm -r /path/to/folder - #### 5.3 Generate script In this third step, the [Slurm](slurm.md) script is created. @@ -254,7 +250,6 @@ In this third step, the [Slurm](slurm.md) script is created. Running `darsync gen` will make Darsync prompt for questions: - ```bash darsync gen ``` @@ -395,7 +390,6 @@ rm ~/id_ed25519_pdc* ## Troubleshooting - ???- question "I get the error: `ssh: connect to host dardel.pdc.kth.se port 22: No route to host`. How do I fix this?" ``` @@ -410,6 +404,3 @@ rm ~/id_ed25519_pdc* Check https://www.pdc.kth.se/about/pdc-news if there are any problems with Dardel. You can do nothing, except wait until Dardel is up again. - - - diff --git a/docs/cluster_guides/darsync.md b/docs/cluster_guides/darsync.md index c8b69fb5e..b3f14db65 100644 --- a/docs/cluster_guides/darsync.md +++ b/docs/cluster_guides/darsync.md @@ -21,7 +21,6 @@ flowchart TD > The Darsync workflow - !!! warning "Temporarily add a `PATH`" Until the darsync script is added to the `/sw/uppmax/bin` folder @@ -31,7 +30,7 @@ flowchart TD export PATH=$PATH:/proj/staff/dahlo/testarea/darsync ``` -## TLDR; +## TLDR If you know your way around Linux, here is the short version. @@ -116,7 +115,7 @@ darsync check -l /path/to/dir The warnings you can get are: -### Too many uncompressed files. +### Too many uncompressed files It looks for files with file endings matching common uncompressed file formats, like `.fq`, `.sam`, `.vcf`, `.txt`. If the combined file size of these files are above a threshold it will trigger the warning. Most programs that uses these formats can also read the compressed version of them. @@ -136,6 +135,7 @@ samtools view -b file.sam > file.bam ``` For examples on how to compress other file formats, use an internet search engine to look for + ``` how to compress file ``` @@ -156,22 +156,21 @@ tar -xzvf folder.tar.gz Once you have mitigated any warnings you got you are ready to generate the Slurm script that will preform the data transfer. - ## Gen mode To generate a transfer script you will need to supply Darsync with some information. Make sure to have this readily available: * **ID of the UPPMAX project** that will run the transfer job, e.g. `naiss2099-23-99` - - If you don't remember if, find the name of the project you want to transfer by looking in [the list of active project in SUPR](https://supr.naiss.se/project/). + * If you don't remember if, find the name of the project you want to transfer by looking in [the list of active project in SUPR](https://supr.naiss.se/project/). * **Path to the folder you want to transfer**, .e.g. `/proj/naiss2099-23-999` - - Either transfer your whole project, or put the files and folder your want to transfer into a new folder in your project folder and transfer that folder. - - The project's folder on UPPMAX will be located in the `/proj/` folder, most likely a folder with the same name as the project's ID, `/proj/`, e.g. `/proj/naiss2024-23-999`. If your project has picked a custom *directory name* when it was created it will have that name instead of the project ID, e.g. `/proj/directory_name`. Check which directory name your project has by looking at the project's page in [SUPR](https://supr.naiss.se/project/) and look at the field called `Directory name:` + * Either transfer your whole project, or put the files and folder your want to transfer into a new folder in your project folder and transfer that folder. + * The project's folder on UPPMAX will be located in the `/proj/` folder, most likely a folder with the same name as the project's ID, `/proj/`, e.g. `/proj/naiss2024-23-999`. If your project has picked a custom *directory name* when it was created it will have that name instead of the project ID, e.g. `/proj/directory_name`. Check which directory name your project has by looking at the project's page in [SUPR](https://supr.naiss.se/project/) and look at the field called `Directory name:` * **Your Dardel username**. - - You can see your Dardel username in [SUPR](https://supr.naiss.se/account/) + * You can see your Dardel username in [SUPR](https://supr.naiss.se/account/) * **The path on Dardel** where you want to put your data, e.g. `/cfs/klemming/projects/snic/naiss2099-23-999` - - Check which project ID you have for your project on Dardel in [the list of active project in SUPR](https://supr.naiss.se/project/). + * Check which project ID you have for your project on Dardel in [the list of active project in SUPR](https://supr.naiss.se/project/). * The **path to the SSH key** you have prepared to be used to login from Rackham to Dardel, e.g. `~/.ssh/id_rsa` - - Check + * Check * The path to where you want to **save the generated transfer script**. To initiate the gen mode you run Darsync with the `gen` argument. If you run it without any other arguments it will ask you interactive questions to get the information it needs. @@ -195,7 +194,6 @@ bash ~/dardel_transfer_script.sh If you start see progress reports from `rsync` you know it works and you can press `ctrl+c` to stop. - Example of how it can look when it works: ``` @@ -228,12 +226,10 @@ rsync: connection unexpectedly closed (0 bytes received so far) [sender] rsync error: unexplained error (code 255) at io.c(231) [sender=3.2.7] ``` - ## Troubleshooting Apart from getting the username or paths wrong, we foresee that the most common problem will be to get the SSH keys generated, added to the [PDC login portal](https://loginportal.pdc.kth.se/), and adding the UPPMAX ip/hostname as authorized for that SSH key. Please see the [PDC user guide on how to set up SSH keys](https://www.pdc.kth.se/support/documents/login/ssh_login.html#ssh-login). Once you have your key created and added to the login portal, go to the login portal again and add the address `*.uppmax.uu.se` to your key to make it work from Rackham. - ## Links - * [darsync GitHub repository](https://github.com/uppmax/darsync) +* [darsync GitHub repository](https://github.com/uppmax/darsync) diff --git a/docs/cluster_guides/empty.md b/docs/cluster_guides/empty.md index 8b1378917..e69de29bb 100644 --- a/docs/cluster_guides/empty.md +++ b/docs/cluster_guides/empty.md @@ -1 +0,0 @@ - diff --git a/docs/cluster_guides/file_transfer.md b/docs/cluster_guides/file_transfer.md index 7e07d6e18..81be2352e 100644 --- a/docs/cluster_guides/file_transfer.md +++ b/docs/cluster_guides/file_transfer.md @@ -2,7 +2,7 @@ [File transfer](file_transfer.md) is the process of getting files from one place to the other. - * [File transfer to/from Bianca](transfer_bianca.md) - * [File transfer to/from Dardel](transfer_dardel.md) - * [File transfer to/from Rackham](transfer_rackham.md) - * [File transfer to/from Transit](transfer_transit.md) +* [File transfer to/from Bianca](transfer_bianca.md) +* [File transfer to/from Dardel](transfer_dardel.md) +* [File transfer to/from Rackham](transfer_rackham.md) +* [File transfer to/from Transit](transfer_transit.md) diff --git a/docs/cluster_guides/install.md b/docs/cluster_guides/install.md index c2c6e96ed..ef363164f 100644 --- a/docs/cluster_guides/install.md +++ b/docs/cluster_guides/install.md @@ -3,13 +3,13 @@ ## Install software yourself ### Build from source + - To build from source use a **compiler module** - We have several compiler versions from GNU and INTEL - check with: ``$ ml avail gcc`` and ``$ ml avail intel`` - [Guide for compiling **serial** programs](compiling_serial.md) - [Guide for compiling **parallel** programs](compiling_parallel.md) - - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries) - + - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries) ## Packages and libraries to scripting programs @@ -17,7 +17,6 @@ - R has a special module called ``R_packages``, and some Machine Learning python packages are included in the ``python_ML_packages`` module. - If not found there you can try to install those by yourself. - !!! info "Tip Python packages" - Try Conda first directly on Bianca and PyPI on Rackham. @@ -53,8 +52,8 @@ - On UPPMAX the module ``R_packages`` is an omnibus package library containing almost all packages in the CRAN and BioConductor repositories. - As of 2023-05-31, there were a total of 23100 R packages installed in ``R_packages/4.2.1``. - - A total of 23109 packages were available in CRAN and BioConductor, and 23000 of these were installed in ``R_packages/4.2.1`` - - The additional 100 R packages available in this module were installed from the CRAN/BioConductor archives, or were hosted on github, gitlab or elsewhere. + - A total of 23109 packages were available in CRAN and BioConductor, and 23000 of these were installed in ``R_packages/4.2.1`` + - The additional 100 R packages available in this module were installed from the CRAN/BioConductor archives, or were hosted on github, gitlab or elsewhere. - [Installing R packages](../software/r.md) @@ -92,6 +91,7 @@ - [Singularity user guide](../cluster_guides/singularity.md) #### Docker + - Docker will unfortunately not work on the clusters, since it requires root permission. !!! info "More info" @@ -105,16 +105,17 @@ - Please use Spack only if other ways to install your tool is not possible or very difficult, e.g. requiring very many dependencies and it is not available through, e.g. Easybuild. - [UPPMAX Spack user guide](../software/spack.md) -### Own development... +### Own development - You may have your own code that you want to run on UPPMAX. - [Guide for compiling **serial** programs](compiling_serial.md) - [Guide for compiling **parallel** programs](compiling_parallel.md) - - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries) + - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries) - [User guide for debuggers](../cluster_guides/debuggers.md) - [User guide for profilers](../cluster_guides/profilers.md) ## Run own scripts or programs + - Unless your script or program is in the active path, you run it by the full path or `./` if you are in the present directory. ## Summary diff --git a/docs/cluster_guides/lftp_with_bianca.md b/docs/cluster_guides/lftp_with_bianca.md index 09929630d..5df0cba69 100644 --- a/docs/cluster_guides/lftp_with_bianca.md +++ b/docs/cluster_guides/lftp_with_bianca.md @@ -17,8 +17,8 @@ lftp sftp://[user_name]-[project_id]@bianca-sftp.uppmax.uu.se/[user_name]-[proje where - * `[project_id]` is the ID of your [NAISS project](../getting_started/project.md) - * `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md) +* `[project_id]` is the ID of your [NAISS project](../getting_started/project.md) +* `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md) For example: diff --git a/docs/cluster_guides/modules.md b/docs/cluster_guides/modules.md index a6eb4acb5..2b9d9bd89 100644 --- a/docs/cluster_guides/modules.md +++ b/docs/cluster_guides/modules.md @@ -241,7 +241,6 @@ Of the module shown, also the different versions are reported. so that you can spend time on your research and we figure this out :-) - To load a module, use `module load [module]`, for example `module load cowsay`. This will load the default version of that module, @@ -387,10 +386,10 @@ Full command |Shorthand syntax ## Links - * [Almost all installed software on UPPMAX](../software/overview.md) - * [Almost all installed databases on UPPMAX](../databases/overview.md) - * [Wikipedia page on environment modules](https://en.wikipedia.org/wiki/Environment_Modules_(software)) - * [lmod homepage](https://www.tacc.utexas.edu/research/tacc-research/lmod/) +- [Almost all installed software on UPPMAX](../software/overview.md) +- [Almost all installed databases on UPPMAX](../databases/overview.md) +- [Wikipedia page on environment modules](https://en.wikipedia.org/wiki/Environment_Modules_(software)) +- [lmod homepage](https://www.tacc.utexas.edu/research/tacc-research/lmod/) ## Extra materials @@ -411,8 +410,9 @@ though, especially when searching for a specific tool, or a bioinformatics tool. It only reports modules that are immediately available. ``` -$ module avail R +module avail R ``` + outputs everything that has an `r` in the name... not useful. ``` diff --git a/docs/cluster_guides/old/disk_quota_more.md b/docs/cluster_guides/old/disk_quota_more.md index 7a7f60297..b924a9ca6 100644 --- a/docs/cluster_guides/old/disk_quota_more.md +++ b/docs/cluster_guides/old/disk_quota_more.md @@ -6,7 +6,7 @@ You can display your current usage with the command 'uquota'. When you exceed your quota, the system will not let you write any more data and you have to either remove some files or request more quota. The 'uquota' command will also show the date and to what limit your quota will change to, if you have been given a larger quota. -To get more quota, send a mail to support (support@uppmax.uu.se) and state how much, for how long time, and why you need it. See the storage project application page for more information on how we handle and prioritise storage requests. +To get more quota, send a mail to support () and state how much, for how long time, and why you need it. See the storage project application page for more information on how we handle and prioritise storage requests. Here are two commands. The first results in a list of subdirectories ordered by size and proportion of total size. The second produces a list of the files in the current directory that take up most space. These may take a long time to complete, use 'ctrl-c' to stop the process if you change your mind. @@ -14,4 +14,5 @@ Here are two commands. The first results in a list of subdirectories ordered by du -b $PWD | sort -rn | awk 'NR==1 {ALL=$1} {print int($1*100/ALL) "% " $0}' find $PWD -print0 -type f | xargs -0 stat -c "%s %n" | sort -rn ``` + You should also read the Disk Storage Guide. **LINK** diff --git a/docs/cluster_guides/old/webexport.md b/docs/cluster_guides/old/webexport.md index daa20055b..35c13f2db 100644 --- a/docs/cluster_guides/old/webexport.md +++ b/docs/cluster_guides/old/webexport.md @@ -3,6 +3,7 @@ In IG: Support User guides Webexport guide ## Rackham + You can enable webexport by creating a publicly readable folder called **webexport** in your project directory (``/proj/[project id]``). The contents of that folder will be accessible through `https://export.uppmax.uu.se/[project id]/`. A publicly readable folder has the execute permission set for "other" users. Run the command chmod o+x webexport to ensure that the webexport directory has the correct permissions. diff --git a/docs/cluster_guides/profilers.md b/docs/cluster_guides/profilers.md index a16689cc4..b4431da38 100644 --- a/docs/cluster_guides/profilers.md +++ b/docs/cluster_guides/profilers.md @@ -47,7 +47,6 @@ For more options you run gprof like this: gprof options [executable-file [profile-data-files…]] [> outfile] - ### Valgrind Valgrind is a suite of simulation-based debugging and profiling tools for programs. @@ -78,11 +77,10 @@ How to use valgrind with mpi programs Load your compiler, openmpi and the valgrind module as before: - $ module load gcc/10.3.0 openmpi/3.1.6 or - $ module load intel/20.4 openmpi/3.1.6 + module load intel/20.4 openmpi/3.1.6 As of now, Valgrind seems not compatible with openmpi/4.X.X. Then run: diff --git a/docs/cluster_guides/project_management.md b/docs/cluster_guides/project_management.md index 1b2cc08a3..9116a3540 100644 --- a/docs/cluster_guides/project_management.md +++ b/docs/cluster_guides/project_management.md @@ -1,9 +1,7 @@ # Manage you projects - ## CPU hours - ## Storage - [Disk storage guide](../storage/disk_storage_guide.md) diff --git a/docs/cluster_guides/rackham.md b/docs/cluster_guides/rackham.md index 362f4b0f4..3dd1647e6 100644 --- a/docs/cluster_guides/rackham.md +++ b/docs/cluster_guides/rackham.md @@ -17,17 +17,17 @@ Rackham is one of the [UPPMAX clusters](uppmax_cluster.md). - [Log in](../getting_started/login_rackham.md) - [Starting an interactive node](start_interactive_node_on_rackham.md) - [File transfer](transfer_rackham.md) - - [using a graphical program](rackham_file_transfer_using_gui.md) - - [using SCP](rackham_file_transfer_using_scp.md) - - [using SFTP](rackham_file_transfer_using_sftp.md) + - [using a graphical program](rackham_file_transfer_using_gui.md) + - [using SCP](rackham_file_transfer_using_scp.md) + - [using SFTP](rackham_file_transfer_using_sftp.md) - [The module system](rackham_modules.md) - [IDEs](ides_on_rackham.md) - - [Jupyter](../software/jupyter.md) - - [RStudio](rstudio_on_rackham.md) - - [VSCode](vscode_on_rackham.md) - - :no_entry: [VSCodium](vscodium_on_rackham.md) + - [Jupyter](../software/jupyter.md) + - [RStudio](rstudio_on_rackham.md) + - [VSCode](vscode_on_rackham.md) + - :no_entry: [VSCodium](vscodium_on_rackham.md) - Isolated environments - - [venv](venv_on_rackham.md) + - [venv](venv_on_rackham.md) - Best practices - Rackham installation guides - Rackham workshops diff --git a/docs/cluster_guides/rackham_file_transfer_using_gui.md b/docs/cluster_guides/rackham_file_transfer_using_gui.md index b7ff85300..2d4a29e8b 100644 --- a/docs/cluster_guides/rackham_file_transfer_using_gui.md +++ b/docs/cluster_guides/rackham_file_transfer_using_gui.md @@ -50,9 +50,9 @@ To transfer files to/from Rackham using FileZilla, do: - Create a name for the site, e.g. `rackham`. - For that site, use all standards, except: - - Set protocol to 'SFTP - SSH File Transfer Protocol' - - Set host to `rackham.uppmax.uu.se` - - Set user to `[username]`, e.g. `richel` + - Set protocol to 'SFTP - SSH File Transfer Protocol' + - Set host to `rackham.uppmax.uu.se` + - Set user to `[username]`, e.g. `richel` ???- tip "How does that look like?" @@ -103,9 +103,9 @@ To transfer files to/from Rackham using WinSCP, do: - Start WinSCP - Create a new site - For that site, use all standards, except: - - Set file protocol to 'SFTP' - - Set host name to `rackham.uppmax.uu.se` - - Set user name to `[username]`, e.g. `richel` + - Set file protocol to 'SFTP' + - Set host name to `rackham.uppmax.uu.se` + - Set user name to `[username]`, e.g. `richel` ### File transfer overview diff --git a/docs/cluster_guides/rackham_file_transfer_using_scp.md b/docs/cluster_guides/rackham_file_transfer_using_scp.md index b48b2bd9c..56e39f867 100644 --- a/docs/cluster_guides/rackham_file_transfer_using_scp.md +++ b/docs/cluster_guides/rackham_file_transfer_using_scp.md @@ -56,7 +56,6 @@ scp sven@rackham.uppmax.uu.se:/home/sven/my_remote_file.txt /home/sven 3. If asked, give your UPPMAX password. You can get rid of this prompt if you have setup SSH keys - ```mermaid flowchart TD @@ -98,4 +97,3 @@ flowchart TD > The purple nodes are about file transfer, > the blue nodes are about 'doing other things'. > The user can be either inside or outside SUNET. - diff --git a/docs/cluster_guides/rackham_file_transfer_using_transit.md b/docs/cluster_guides/rackham_file_transfer_using_transit.md index e3247235c..555af5127 100644 --- a/docs/cluster_guides/rackham_file_transfer_using_transit.md +++ b/docs/cluster_guides/rackham_file_transfer_using_transit.md @@ -20,8 +20,8 @@ This page assumes your files are 'posted' to Transit. To transfer files between Rackham and Transit can be done in multiple ways too: - * [Using SCP](#using-scp) - * [Using SFTP](#using-sftp) +* [Using SCP](#using-scp) +* [Using SFTP](#using-sftp) ## Using SCP @@ -75,6 +75,7 @@ yet the file will not be found on Transit. #### 3b. Run `scp` to copy files from Transit to Rackham In the terminal, run `scp` to copy files from Transit to Rackham by doing: + ``` scp [file_on_rackham] [username]@transit.uppmax.uu.se ``` @@ -120,6 +121,7 @@ In the terminal, run `scp` to copy files from Transit to Rackham by doing: ``` scp [username]@rackham.uppmax.uu.se:/home/[username]/[file_on_rackham] [path_on_transit] ``` + where `[file_on_rackham]` is the name of a file on Rackham, `[username]` is your UPPMAX username, and `[path_on_transit]` is the target path on Transit, @@ -131,7 +133,6 @@ scp sven@rackham.uppmax.uu.se:/home/sven/my_rackham_file.txt . Where `.` means 'the directory where I am now on Transit'. - #### 3b. :no_entry: Run `scp` to copy files from Rackham to Transit This is how you **would** copy a file from Rackham to Transit: @@ -152,7 +153,7 @@ However, [Transit is a service, not a file server](transit.md). The `scp` command will complete successfully, yet the file will not be found on Transit. -#### 4. If asked, give your UPPMAX password. +#### 4. If asked, give your UPPMAX password You can get rid of this prompt if you have setup SSH keys diff --git a/docs/cluster_guides/rstudio_on_bianca.md b/docs/cluster_guides/rstudio_on_bianca.md index 32ed56419..9be9362ca 100644 --- a/docs/cluster_guides/rstudio_on_bianca.md +++ b/docs/cluster_guides/rstudio_on_bianca.md @@ -71,7 +71,6 @@ Within that terminal, start an interactive session with 2 cores. Instead, load RStudio from the module system instead. - ### 4. Load the modules needed In the terminal of the interactive session, do: diff --git a/docs/cluster_guides/rsync_on_bianca.md b/docs/cluster_guides/rsync_on_bianca.md index d19581563..17259c40e 100644 --- a/docs/cluster_guides/rsync_on_bianca.md +++ b/docs/cluster_guides/rsync_on_bianca.md @@ -14,35 +14,34 @@ One cannot `rsync` directly to `wharf`. However, this is how it looks like: - ``` - richel@richel-N141CU:~$ rsync my_local_file.txt richel-sens2016001@bianca-sftp.uppmax.uu.se:/richel-sens2016001 + ``` + richel@richel-N141CU:~$ rsync my_local_file.txt richel-sens2016001@bianca-sftp.uppmax.uu.se:/richel-sens2016001 - Hi! + Hi! - You are connected to the bianca wharf (sftp service) at - bianca-sftp.uppmax.uu.se. + You are connected to the bianca wharf (sftp service) at + bianca-sftp.uppmax.uu.se. - Note that we only support SFTP, which is not exactly the - same as SSH (rsync and scp will not work). + Note that we only support SFTP, which is not exactly the + same as SSH (rsync and scp will not work). - Please see our homepage and the Bianca User Guide - for more information: + Please see our homepage and the Bianca User Guide + for more information: - https://www.uppmax.uu.se/support/user-guides/bianca-user-guide/ + https://www.uppmax.uu.se/support/user-guides/bianca-user-guide/ - If you have any questions not covered by the User Guide, you are - welcome to contact us at support@uppmax.uu.se. + If you have any questions not covered by the User Guide, you are + welcome to contact us at support@uppmax.uu.se. - Best regards, - UPPMAX - - richel-sens2016001@bianca-sftp.uppmax.uu.se's password: - protocol version mismatch -- is your shell clean? - (see the rsync manpage for an explanation) - rsync error: protocol incompatibility (code 2) at compat.c(622) [sender=3.2.7] - ``` + Best regards, + UPPMAX + richel-sens2016001@bianca-sftp.uppmax.uu.se's password: + protocol version mismatch -- is your shell clean? + (see the rsync manpage for an explanation) + rsync error: protocol incompatibility (code 2) at compat.c(622) [sender=3.2.7] + ``` ## Links - * [`rsync` homepage](https://rsync.samba.org/) +* [`rsync` homepage](https://rsync.samba.org/) diff --git a/docs/cluster_guides/rsync_on_rackham.md b/docs/cluster_guides/rsync_on_rackham.md index 437a0c0ed..2f18e66be 100644 --- a/docs/cluster_guides/rsync_on_rackham.md +++ b/docs/cluster_guides/rsync_on_rackham.md @@ -60,4 +60,4 @@ Where `.` means 'the folder where I am now'. ## Links - * [`rsync` homepage](https://rsync.samba.org/) +* [`rsync` homepage](https://rsync.samba.org/) diff --git a/docs/cluster_guides/running_jobs/interactive_more.md b/docs/cluster_guides/running_jobs/interactive_more.md index b0bf3e475..c4cab7fff 100644 --- a/docs/cluster_guides/running_jobs/interactive_more.md +++ b/docs/cluster_guides/running_jobs/interactive_more.md @@ -42,5 +42,4 @@ interactive -A p2010099 -n 16 -C fat -t 15:00:00 but no "priority lane" can be used, you get your normal queue priority, and you might have to wait for a very long time for your session to start. Please note that you need to keep watch over when the job starts, because you are accounted for all the time from job start even if you are sleeping, and because an allocated and unused node is a waste of expensive resources. - NB. You can not launch an interactive job from an other cluster with the flag -M, which otherwise is a common flag to other SLURM commands. You must launch it from a login node to the cluster you want to use. diff --git a/docs/cluster_guides/running_jobs/nodes_own_disk.md b/docs/cluster_guides/running_jobs/nodes_own_disk.md index e9d801350..14b1a8cdb 100644 --- a/docs/cluster_guides/running_jobs/nodes_own_disk.md +++ b/docs/cluster_guides/running_jobs/nodes_own_disk.md @@ -62,4 +62,4 @@ cp $SNIC_TMP/sample.bam /proj/snic2022-X-YYY/nobackup/results/ It's not harder than that. This way, the index files are copied to $SNIC_TMP in a single operation, which is much less straining for the file system than small random read/writes. The network filesystem is used when gathering reads for alignment, and streaming reads are easy for that filesystem. When the alignment is finished the results is copied back to project directory so that it can be used in other analysis. -One problem that can happen is if your files and the results are too large for the node's hard drive. The drive is 2TiB on Rackham and 4TiB on Bianca, so it is unusual for the hard drive to be too small for the results of such analyses. If you run into this problem, please email UPPMAX at support@uppmax.uu.se and we can look into the problem. +One problem that can happen is if your files and the results are too large for the node's hard drive. The drive is 2TiB on Rackham and 4TiB on Bianca, so it is unusual for the hard drive to be too small for the results of such analyses. If you run into this problem, please email UPPMAX at and we can look into the problem. diff --git a/docs/cluster_guides/running_jobs/runtime_tips.md b/docs/cluster_guides/running_jobs/runtime_tips.md index a169e6481..dbe6b04a0 100644 --- a/docs/cluster_guides/running_jobs/runtime_tips.md +++ b/docs/cluster_guides/running_jobs/runtime_tips.md @@ -32,7 +32,6 @@ (NOTE: The actual number above might be different for you, and should be changed accordingly!) - ???- question "I want my program to send data to both stdout and to a file but nothing comes until the program ends" There is a program called unbuffer. You could try using it like (tee takes care of sending both to stdout and to a file): @@ -57,7 +56,6 @@ - Then, the original executable file can be safely deleted. - - Alternatively, rename the currently executing file to something new and unique (using the mv command) before recompiling/reinstalling your program. - ???- question "I have strange problems with my text-files / scripts when they have been copied from other computers" ???- info "For UPPMAX staff" @@ -119,11 +117,8 @@ - [Start an interactive node](../start_interactive_node.md) - [More about interactive](interactive_more.md) - - ## Related to Batch jobs - ???- question "Looking at "jobinfo" output, PRIORITY and REASON for my waiting jobs change over time. Please explain what is going on!" [What do the fields PRIORITY and REASON mean in "jobinfo" output?](jobinfo_reason.md) @@ -166,7 +161,6 @@ i.e. notice the trailing "-l". This tells bash to load the correct environment settings, which makes the module system usable. - ???- question "How can I see my job's memory usage?" - Historical information can first of all be found by issuing the command ``finishedjobinfo -j``. That will print out the maximum memory used by your job. @@ -201,11 +195,8 @@ - RSS is the number reported in "top" and "ps"; i.e. including ALL shared buffered/cached memory. - And then there's also the PSS figure which tries to calculate a proportional memory usage per user for all shared memory buffers and caches (i.e. the figure will fall between USS and RSS). - - ???- question "My job has very low priority! What can be wrong?" - - One reason could be that your project has consumed its allocated hours. - Background: Every job is associated with a project. @@ -245,4 +236,3 @@ - If your job priority is zero or one, there are more serious problems, for example that you asked for more resources than the batch system finds on the system. - If you ask for a longer run time (TimeLimit) than the maximum on the system, your job will not run. The maximum is currently ten days. If you must run a longer job, submit it with a ten-day runtime and contact UPPMAX support. - diff --git a/docs/cluster_guides/running_jobs/storage_compression.md b/docs/cluster_guides/running_jobs/storage_compression.md index 3c6cef8ac..6bdd2831b 100644 --- a/docs/cluster_guides/running_jobs/storage_compression.md +++ b/docs/cluster_guides/running_jobs/storage_compression.md @@ -21,8 +21,8 @@ - You might also be interested in our [disk storage guide](../storage/disk_storage_guide.md). - ## Compression + ???- question "File compression guide" [Compression guide](../storage/compress_guide.md) diff --git a/docs/cluster_guides/screen.md b/docs/cluster_guides/screen.md index d933823d4..de4eb507a 100644 --- a/docs/cluster_guides/screen.md +++ b/docs/cluster_guides/screen.md @@ -6,6 +6,7 @@ When you run the `interactive` command, you get a command prompt in the _screen_ When running the screen program in other environments, you can detach from your screen and later reattach to it. Within the environment of the `interactive` command, you lose this ability: Your job is terminated when you detach. (This is a design decision and not a bug.) In case you want the best of both worlds, i.e. to be able to detach and reattach to your screen program within a job, you need to start a job in some other way and start your screen session from a separate ssh login. Here is an example of how you can do this: + ```bash $ salloc -A project_ID -t 15:00 -n 1 --qos=short --bell --no-shell salloc: Pending job allocation 46964140 @@ -15,15 +16,19 @@ salloc: Granted job allocation 46964140 salloc: Waiting for resource configuration salloc: Nodes r174 are ready for job ``` + Check the queue manager for the allocated node. In the example bellow, one core was allocated on `r174` compute node. + ```bash $ squeue -j 46964140 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46964140 core no-shell user R 0:44 1 r174 ``` + You can start `xterm` terminal in this allocated session like this: + ```bash -$ xterm -e ssh -AX r174 & +xterm -e ssh -AX r174 & ``` `salloc` command gives you a job allocation of one node for 15 minutes (the "--no-shell" option is important here). Instead you can log in to any node of any of your running jobs, started with e.g. the `sbatch` command. @@ -33,12 +38,15 @@ You get a job number and from that you can find out the node name, in this examp When you log in to the node with the `ssh` command, start the screen program: ```bash -$ screen +screen ``` + When you detach from the screen program, with e.g. the "d" command, you can later in the same ssh session or in another ssh session reattach to your screen session: + ```bash -$ screen -r +screen -r ``` + When your job has terminated, you can neither reattach to your screen session nor log in to the node. The screen session of the `interactive` command is integrated into your job, so e.g. all environment variables for the job is correctly assigned. For a separate ssh session, as in this example, that is not the case. @@ -48,32 +56,41 @@ Please note that it is the job allocation that determines your core hour usage a ## Tips - Start a new screen session with a command: + ``` screen -dm your_command ``` + This will start a new screen session, run the command, and then detach from the session. - If you want to run multiple commands, you can do so like this: + ``` screen -dm bash -c "command1; command2" ``` + This will run `command1` and `command2` in order. - To reattach to the screen session, use: + ``` screen -r ``` + If you have multiple sessions, you'll need to specify the session ID. - To list your current screen sessions, use: + ``` screen -ls ``` Please note that when a program terminates, `screen` (by default) kills the window that contained it. If you don't want your session to get killed after the script is finished, add `exec sh` at the end. For example: + ``` screen -dm bash -c 'your_command; exec sh' ``` + This will keep the screen session alive after `your_command` has finished executing. YouTube : [How to use GNU SCREEN - the Terminal Multiplexer](https://www.youtube.com/watch?v=I4xVn6Io5Nw) diff --git a/docs/cluster_guides/sftp_with_bianca.md b/docs/cluster_guides/sftp_with_bianca.md index 71379ace1..7a9e7ddbb 100644 --- a/docs/cluster_guides/sftp_with_bianca.md +++ b/docs/cluster_guides/sftp_with_bianca.md @@ -18,8 +18,8 @@ sftp [user_name]-[project_id]@bianca-sftp.uppmax.uu.se:/[user_name]-[project_id] where - * `[project_id]` is the ID of your [NAISS project](../getting_started/project.md) - * `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md) +* `[project_id]` is the ID of your [NAISS project](../getting_started/project.md) +* `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md) For example: @@ -48,27 +48,27 @@ and the `sftp` prompt. ``` Hi! - You are connected to the bianca wharf (sftp service) at - bianca-sftp.uppmax.uu.se. + You are connected to the bianca wharf (sftp service) at + bianca-sftp.uppmax.uu.se. - Note that we only support SFTP, which is not exactly the - same as SSH (rsync and scp will not work). + Note that we only support SFTP, which is not exactly the + same as SSH (rsync and scp will not work). - Please see our homepage and the Bianca User Guide - for more information: + Please see our homepage and the Bianca User Guide + for more information: - https://www.uppmax.uu.se/support/user-guides/bianca-user-guide/ + https://www.uppmax.uu.se/support/user-guides/bianca-user-guide/ - If you have any questions not covered by the User Guide, you are - welcome to contact us at support@uppmax.uu.se. + If you have any questions not covered by the User Guide, you are + welcome to contact us at support@uppmax.uu.se. - Best regards, - UPPMAX + Best regards, + UPPMAX - richel-sens2016001@bianca-sftp.uppmax.uu.se's password: - Connected to bianca-sftp.uppmax.uu.se. - sftp> - ``` + richel-sens2016001@bianca-sftp.uppmax.uu.se's password: + Connected to bianca-sftp.uppmax.uu.se. + sftp> + ``` ???- question "How do I get rid of the welcome message?" @@ -78,8 +78,7 @@ and the `sftp` prompt. sftp -q sven-sens2016001@bianca-sftp.uppmax.uu.se ``` -The last line, `sftp> ` is the `sftp` prompt. - +The last line, `sftp>` is the `sftp` prompt. Once connected you will have to type the `sftp` commands to upload/download files. See [the UPPMAX page on `sftp`](../software/sftp.md) how to do so. diff --git a/docs/cluster_guides/singularity.md b/docs/cluster_guides/singularity.md index 7a1bd4f77..924d4efb7 100644 --- a/docs/cluster_guides/singularity.md +++ b/docs/cluster_guides/singularity.md @@ -7,11 +7,13 @@ One of the ways in which Singularity is more suitable for HPC is that it very ac Singularity is installed and usable to run custom container images on the clusters bianca and rackham. ## Running an existing image + It's possible to download and run pre-built images from the Singularity hub [https://singularity-hub.org](https://singularity-hub.org) and the singularity library ([https://cloud.sylabs.io](https://cloud.sylabs.io) library) using the singularity pull sub command such as: ```bash singularity pull library://ubuntu ``` + Which will download the requested image and place it in the current directory. You can also upload and run image directly your self. Once you have an image, you can "run" it with a command such as @@ -19,9 +21,11 @@ Once you have an image, you can "run" it with a command such as ```bash singularity run singularityhub-ubuntu-14.04.img ``` + which will try to execute a "run" target in the container. There are also the shell and exec subcommands for starting a shell and running a specific command respectively. -## Access to UPPMAX file systems. +## Access to UPPMAX file systems + By default, singularity will try to help and map the UPPMAX file systems from the current cluster so that they can be accessed from within the container. For CentOS7 based clusters (snowy, rackham, bianca), this works as expected. Singularity is installed on the system (on each separate node) and does not require any module load to be available. @@ -34,10 +38,12 @@ singularity shell docker://debian:stretch but note that Docker containers are typically designed to run with more privileges than are allowed with Singularity, so it's quite possible things do not work as expected. -## Not all images may work everywhere! +## Not all images may work everywhere + Images run with the same linux kernel as the rest of the system. For HPC we systems, the kernel used tend to be quite old for stability reasons (with milou using very old kernels). This is not normally a problem, but can cause issues if the libraries of the images you try to run expects functionality added in newer kernels. How and what works is difficult to know without trying, but we have successfully started a shell in an image for the currently most recent Ubuntu release (17.04). ## Creating your own images + If you have singularity on your own machine, you can create your own images and upload and run them from UPPMAX. Creating images directly on UPPMAX is not possible as it requires administrator (root) privileges (but see below). Singularity provides functionality to create and bootstrap images, and the installation contains example definitions for bootstrapping various images you can use as a start (like Ubuntu, Scientific Linux and so on). If you normally run Linux and have administrative access, you can install Singularity and build images locally, typical usage would be: @@ -45,10 +51,10 @@ Singularity provides functionality to create and bootstrap images, and the insta ```bash sudo singularity build myimage.img examples/ubuntu.def ``` -Look for more examples on the [UPPMAX Singularity workshop](https://pmitev.github.io/UPPMAX-Singularity-workshop/) page - "Case Studies" section. +Look for more examples on the [UPPMAX Singularity workshop](https://pmitev.github.io/UPPMAX-Singularity-workshop/) page - "Case Studies" section. -## Building images on Rackham. +## Building images on Rackham On Rackham, the singularity capabilities are instead provided by [Apptainer](https://apptainer.org/). The differences are beyond the scope of this material, but you can safely assume you are working with Singularity. Apptainer, also allows you to build containers without sudo/administrative rights. In most of the cases, you can simply start building directly without sudo i.e. `singularity build myimage.img examples/ubuntu.def`. Here are some precautions that will allow you to safely build images on Rackham. @@ -72,11 +78,12 @@ mkdir -p $APPTAINER_CACHEDIR $APPTAINER_TMPDIR ``` ## Using the sylabs cloud remote builder, an example + Even if you don't run Linux on your desktop system, you can still build your own images. Typically software pages contain enough information as installation instructions to create a modified recipe to build images for software. [Sylabs](https://www.sylabs.io/) (the company currently developing singularity) offer an experimental cloud service for building images from recipes. Here's an example on how to use that to build an image for a software (for this example, we picked [sortmerna](https://github.com/biocore/sortmerna) as it was the first user software request that came up). -- First, we need to sign in to the sylabs remote builder, available at https://cloud.sylabs.io. It allows sign in through various providers (currently Google, Microsoft, GitHub, GitLab). If you don't have an account with one of these, at least one of them is likely to offer free registration. +- First, we need to sign in to the sylabs remote builder, available at . It allows sign in through various providers (currently Google, Microsoft, GitHub, GitLab). If you don't have an account with one of these, at least one of them is likely to offer free registration. - Once signed in, we want to create a project for this software, so we click on "Singularity Library" in the top menu and select "Create a new project", set ourselves as owner and enter sortmerna as project name. We also select to make images for this project public. @@ -195,26 +202,34 @@ From: ubuntu:18.04 ``` ## Using the sylabs cloud remote builder from the UPPMAX shell + The remote builder service provided by sylabs also supports remote builds through an API. This means you can call on it from the shell at UPPMAX. Using this service also requires you to register/log in to the Sylabs cloud service. To use this, simply run + ```bash singularity remote login SylabsCloud ``` + and you should see + ``` Generate an API Key at https://cloud.sylabs.io/auth/tokens, and paste here: API Key: ``` if you visit that link and give a name, a text-token will be created for you. Copy and paste this to the prompt at UPPMAX. You should see + ``` INFO: API Key Verified! ``` + once you've done this, you can go on and build images almost as normal, using commands like + ```bash singularity build --remote testcontainer.sif testdefinition.def ``` + which will build the container from testdefinition.def remotely and transfer it to your directory, storing it as testcontainer.sif Running your container in jobs @@ -236,6 +251,7 @@ singularity run ./anotherimage some parameters here ``` ## Another example; building a container from conda + To build a container from a conda environment, here we demonstrate for `qiime2` ```singularity @@ -261,4 +277,4 @@ From: centos:7 # OPTIONAL CLEANUP rm qiime2-2019.7-py36-linux-conda.yml /miniconda/bin/conda clean -a -``` \ No newline at end of file +``` diff --git a/docs/cluster_guides/slurm.md b/docs/cluster_guides/slurm.md index 610e1563c..6d8a6ca93 100644 --- a/docs/cluster_guides/slurm.md +++ b/docs/cluster_guides/slurm.md @@ -28,13 +28,13 @@ For information specific to clusters, see: The Slurm system is accessed using the following commands: -* `interactive` - Start an interactive session. This is described +- `interactive` - Start an interactive session. This is described in-depth for [Bianca](start_interactive_node_on_bianca.md) and [Rackham](start_interactive_node_on_rackham.md) -* `sbatch` - Submit and run a batch job script -* `srun` - Typically used inside batch job scripts for running parallel jobs +- `sbatch` - Submit and run a batch job script +- `srun` - Typically used inside batch job scripts for running parallel jobs (See examples further down) -* `scancel` - Cancel one or more of your jobs. +- `scancel` - Cancel one or more of your jobs. ```mermaid flowchart TD @@ -129,7 +129,6 @@ sbatch -A sens2017625 --partition core my_script.sh To specify multiple cores, use `--ntasks` (or `-n`) like this: - ```bash sbatch -A [project_code] --partition core --ntasks [number_of_cores] [script_filename] ``` @@ -152,9 +151,6 @@ Here, two cores are used. sbatch -A [project_code] --partition core --ntasks [number_of_cores] --ntasks-per-core 1 [script_filename] ``` - - - This is especially important if you might adjust core usage of the job to be something less than a full node. @@ -171,8 +167,6 @@ to ensure that only 8 cores (less than a single node) are allocated for such a j ### The `devcore` partition - - ### Specifying job parameters Whether you use the UPPMAX clusters interactively or in batch mode, you always diff --git a/docs/cluster_guides/slurm_troubleshooting.md b/docs/cluster_guides/slurm_troubleshooting.md index 86ef1728e..b32396c89 100644 --- a/docs/cluster_guides/slurm_troubleshooting.md +++ b/docs/cluster_guides/slurm_troubleshooting.md @@ -10,6 +10,3 @@ The full error message is: ``` sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified ``` - - - diff --git a/docs/cluster_guides/snowy.md b/docs/cluster_guides/snowy.md index e74378916..690ecdd16 100644 --- a/docs/cluster_guides/snowy.md +++ b/docs/cluster_guides/snowy.md @@ -40,24 +40,24 @@ as is discussed in more detail there. **Note:** When accessing snowy from Rackhams login nodes you must always use the flag -M for all Slurm commands. Examples: -* squeue -M snowy -* jobinfo -M snowy -* sbatch -M snowy slurm\_script\_file -* scancel -u username -M snowy -* interactive -A projectname -M snowy -p node -n 32 -t 01:00:00 +- squeue -M snowy +- jobinfo -M snowy +- sbatch -M snowy slurm\_script\_file +- scancel -u username -M snowy +- interactive -A projectname -M snowy -p node -n 32 -t 01:00:00 **Note:** We always recommend loading all your modules in your job script file, This is even more important when running on Snowy since the module environment is not the same on the Rackham login nodes as on Snowy compute nodes. ### Some Limits -* There is a job walltime limit of 30 days (720 hours). -* We restrict each user to at most 5000 running and waiting jobs in total. -* Each project has a 30 days running allocation of CPU hours. We do not forbid running jobs after the allocation is overdrafted, but instead allow to submit jobs with a very low queue priority, so that you may be able to run your jobs anyway, if a sufficient number of nodes happens to be free on the system. -* Very wide jobs will only be started within a maintenance window (just before the maintenance window or at the end of the maintenance window). These are planned for the first Wednesday of each month. On Snowy a "very wide" job asks for 100 nodes or more. +- There is a job walltime limit of 30 days (720 hours). +- We restrict each user to at most 5000 running and waiting jobs in total. +- Each project has a 30 days running allocation of CPU hours. We do not forbid running jobs after the allocation is overdrafted, but instead allow to submit jobs with a very low queue priority, so that you may be able to run your jobs anyway, if a sufficient number of nodes happens to be free on the system. +- Very wide jobs will only be started within a maintenance window (just before the maintenance window or at the end of the maintenance window). These are planned for the first Wednesday of each month. On Snowy a "very wide" job asks for 100 nodes or more. ### Convenience Variables -* **$SNIC\_TMP - Path to node-local temporary disk space** +- **$SNIC\_TMP - Path to node-local temporary disk space** The **$SNIC\_TMP** variable contains the path to a node-local temporary file directory that you can use when running your jobs, in order to get maximum disk performance (since the disks are local to the current compute node). This directory will be automatically created on your (first) compute node before the job starts and automatically deleted when the job has finished. @@ -75,21 +75,17 @@ Some serial jobs must run as "**node**" jobs. You tell Slurm that you need a "no A "**core**" job: -* Will use a part of the resources on a node, from a 1/16 share to a 15/16 share of a node. +- Will use a part of the resources on a node, from a 1/16 share to a 15/16 share of a node. -* Must specify less cores than 16, i.e.between "**\-n 1**" to "**\-n 15**". +- Must specify less cores than 16, i.e.between "**\-n 1**" to "**\-n 15**". +- Must not demand "-N", "--nodes", or "--exclusive". -* Must not demand "-N", "--nodes", or "--exclusive". +- Is recommended not to demand "--mem" -* Is recommended not to demand "--mem" - - -* Must not demand to run on a fat node (see below, for an explanation of "fat"), a devel node. - - -* Must not use more than 8 GB of RAM for each core it demands. If a job needs half of the RAM, i.e. 64 GB, you need to reserve also at least half of the cores on the node, i.e. 8 cores, with the "-n 8" flag. +- Must not demand to run on a fat node (see below, for an explanation of "fat"), a devel node. +- Must not use more than 8 GB of RAM for each core it demands. If a job needs half of the RAM, i.e. 64 GB, you need to reserve also at least half of the cores on the node, i.e. 8 cores, with the "-n 8" flag. A "**core**" job is accounted on your project as one "core hour" (sometimes also named as a "CPU hour") per core you have been allocated, for each wallclock hour that it runs. On the other hand, a "**node**" job is accounted on your project as sixteen core hours for each wallclock hour that it runs, multiplied with the number of nodes that you have asked for. @@ -97,9 +93,9 @@ A "**core**" job is accounted on your project as one "core hour" (sometimes also Rackham has two node types, _thin_ being the typical cluster node and _fat_ nodes having double the amount of memory available normally (256 GB). You may specify a node with more RAM, by adding the words "**\-C mem256GB**" or "**\-C fat**" to your job submission line and thus making sure that you will get 256 GB of RAM on each node in your job. If you need even more memory you can request a 512 GB memory node by adding "**\-C mem512GB**". Please note that there are only 13 nodes with 256GB and 17 with 512GB of RAM. -**To request a fat node, use -C mem256GB or -C fat in your Slurm command.**  +**To request a fat node, use -C mem256GB or -C fat in your Slurm command.** -**To request the fattest nodes, use -C mem512GB in your Slurm command.**  +**To request the fattest nodes, use -C mem512GB in your Slurm command.** ## File storage and disk space @@ -111,19 +107,12 @@ see [Disk Storage User Guide](../cluster_guides/uppmax_systems.md) for more info If you have very long jobs that require more than 10 days of CPU-time. We recommend using Snowy. But in order for our job to successfully run for severay weeks you should implement the following; -* Use only local disk for your job. Copy all input and data files needed to **$SNIC\_TMP** at the start of your job and at the end, copy all output back to your project directory. -* Book a full node with the Slurm flags **\-p node** (you won't be able to submit these jobs in the core partition). -* If possible make sure you do not rely on files stored outside the node. One way of achieving this may be to copy program files to $SNIC\_TMP. +- Use only local disk for your job. Copy all input and data files needed to **$SNIC\_TMP** at the start of your job and at the end, copy all output back to your project directory. +- Book a full node with the Slurm flags **\-p node** (you won't be able to submit these jobs in the core partition). +- If possible make sure you do not rely on files stored outside the node. One way of achieving this may be to copy program files to $SNIC\_TMP. Even if you do this we can't promise that a 20 or 30 day long job will finish without being interrupted by the global file systems, the network or problems on the node, - - - - - - - ## Snowy's design Snowy is an (general-purpose) high-performance computing (HPC) cluster, @@ -164,8 +153,8 @@ There are several compilers available through the [module system](modules.md) on Snowy. This gives you flexibility to obtain programs that run optimally on Snowy. -* gcc - the newest version usually generates the best code, if you tell it to use the new instructions. Check which version is the newest by doing **module avail**. +- gcc - the newest version usually generates the best code, if you tell it to use the new instructions. Check which version is the newest by doing **module avail**. The compiler executable is named gcc for C, g++ for C++, and gfortran for Fortran. To use the new instructions available on Snowy (AVX2 and FMA3), give the additional options "**\-mavx2 -mfma3**" to gcc. For good performance with this compiler you should also specify optimization at least at level **\-O2** or **\-O3**. Also try using **\-march=broadwell** for GCC >= 4.9.0 or **\-march=core-avx2** for GCC 4.8.x, which will enable all the instructions on the CPU. -* Intel+MKL - usually generates the fastest code. As with gcc, it is good to use the latest version. The compiler executable is named icc for C, icpc for C++, and ifort for Fortran. You should give optimization options at least **\-O2**, preferably **\-O3** or **\-fast**. You can also try to use the **\-xCORE-AVX2** option to the compiler to output AVX2 instructions. -* pgi - often generates somewhat slower code, but it is stable so often it is easier to obtain working code, even with quite advanced optimizations. The compiler executable is named pgcc for C, pgCC for C++, and pgfortran, pgf77, pgf90, or pgf95 for Fortran. For this compiler, you can generate code for Snowy using the following options "**UPDATES NEEDED**". Also give optimization options at least **\-O2**, preferably **\-Ofast**, even though the compile times are much longer, the result is often worth the wait. +- Intel+MKL - usually generates the fastest code. As with gcc, it is good to use the latest version. The compiler executable is named icc for C, icpc for C++, and ifort for Fortran. You should give optimization options at least **\-O2**, preferably **\-O3** or **\-fast**. You can also try to use the **\-xCORE-AVX2** option to the compiler to output AVX2 instructions. +- pgi - often generates somewhat slower code, but it is stable so often it is easier to obtain working code, even with quite advanced optimizations. The compiler executable is named pgcc for C, pgCC for C++, and pgfortran, pgf77, pgf90, or pgf95 for Fortran. For this compiler, you can generate code for Snowy using the following options "**UPDATES NEEDED**". Also give optimization options at least **\-O2**, preferably **\-Ofast**, even though the compile times are much longer, the result is often worth the wait. diff --git a/docs/cluster_guides/software_on_transit.md b/docs/cluster_guides/software_on_transit.md index 3fc3c2d26..655d18be2 100644 --- a/docs/cluster_guides/software_on_transit.md +++ b/docs/cluster_guides/software_on_transit.md @@ -13,7 +13,7 @@ is available on [Transit](../cluster_guides/transit.md). In addition, some modules are available. - * SciLifeLab Data Delivery System - [https://delivery.scilifelab.se/](https://delivery.scilifelab.se/) +* SciLifeLab Data Delivery System - [https://delivery.scilifelab.se/](https://delivery.scilifelab.se/) ```bash # Load the tool from the software module tree @@ -22,6 +22,7 @@ In addition, some modules are available. # Run the tool dds ``` + ![dds-cli](../img/dds-cli.png) To download data from TCGA, diff --git a/docs/cluster_guides/start_interactive_node.md b/docs/cluster_guides/start_interactive_node.md index ceeb57d44..c4b4c9dae 100644 --- a/docs/cluster_guides/start_interactive_node.md +++ b/docs/cluster_guides/start_interactive_node.md @@ -76,7 +76,6 @@ with such code: use an interactive node. An interactive node is a type of calculation node, where one can run heavy calculations directly. - ```mermaid flowchart TD UPPMAX(What to run on which node?) diff --git a/docs/cluster_guides/start_interactive_node_on_bianca.md b/docs/cluster_guides/start_interactive_node_on_bianca.md index beddc8794..2a342a952 100644 --- a/docs/cluster_guides/start_interactive_node_on_bianca.md +++ b/docs/cluster_guides/start_interactive_node_on_bianca.md @@ -25,4 +25,3 @@ that uses 2 cores and has a maximum duration of 8 hours. It can take tens of minutes before an interactive node is allocated. Bianca has not frozen, go ahead and have a coffee break :-) - diff --git a/docs/cluster_guides/start_interactive_node_on_rackham.md b/docs/cluster_guides/start_interactive_node_on_rackham.md index c0b2c0bb5..27363a21a 100644 --- a/docs/cluster_guides/start_interactive_node_on_rackham.md +++ b/docs/cluster_guides/start_interactive_node_on_rackham.md @@ -56,4 +56,3 @@ that has a maximum duration of 8 hours. It can take tens of seconds before an interactive node is allocated. Rackham has not frozen, just be a bit more patient. - diff --git a/docs/cluster_guides/start_interactive_node_on_snowy.md b/docs/cluster_guides/start_interactive_node_on_snowy.md index 07c37af46..6b835222b 100644 --- a/docs/cluster_guides/start_interactive_node_on_snowy.md +++ b/docs/cluster_guides/start_interactive_node_on_snowy.md @@ -56,4 +56,3 @@ that has a maximum duration of 8 hours. It can take tens of seconds before an interactive node is allocated. Snowy has not frozen, just be a bit more patient. - diff --git a/docs/cluster_guides/storage/compress_fastQ.md b/docs/cluster_guides/storage/compress_fastQ.md index f7c9733e3..1fe8eab35 100644 --- a/docs/cluster_guides/storage/compress_fastQ.md +++ b/docs/cluster_guides/storage/compress_fastQ.md @@ -3,6 +3,7 @@ **Short answer: The best compression using a widely available format is provided by bzip2 and its parallel equivalent pbzip2. The best compression ratio for FastQ is provided by fqz_comp in the fqzcomp/4.6 module. However, this tool is experimental and is not recommended for general, everyday use.** ## Long answer + We conducted an informal examination of two specialty FastQ compression tools by recompressing an existing fastq.gz file. The first tool fqzcomp (available in the module fqzcomp/4.6) uses a compiled executable (fqz_comp) that works similar to e.g., gzip, while the second tool (LFQC in the module lfqc/1.1) uses separate ruby-language scripts for compression (lfqc.rb) and decompression (lfqcd.rb). It does not appear the LFQC scripts accept piping but the documentation is limited. ``` @@ -51,8 +52,8 @@ We also compared against bzip2 and xz, which are general-use compressors. These Neither of these improved general-use compressors did as well with FastQ as the specialty compressors. This makes sense given the specialty compressors can take advantages of the restrictions of the format. - ### Which is the best method in this trial? + From the results of this trial, the tool that provides the best compression ratio in a reasonable amount of time is fqz_comp in the fqzcomp/4.6 module. It is as fast as bzip2 which is also much better than gzip but does a much better job of compressing FastQ. However, fqz_comp is experimental so we do not recommend using fqz_comp for everyday use. We recommend using bzip2 or its parallel equivalent, pbzip2. The fqz_comp executable could be used to decompress FastQ within a named pipe if FastQ is required for input: @@ -63,6 +64,6 @@ The fqz_comp executable could be used to decompress FastQ within a named pipe if Note that fqz_comp is designed to compress FastQ files alone, and neither method here provides the blocked compression format suitable for random access that bgzip does; see [which-compression-format-should-i-use-for-ngs-related-files](../storage/compress_format.md) for more on that subject. - ### Why not LFQC? + Though LFQC has the best compression of FastQ, there are some strong disadvantages. First, it takes quite a long time, perhaps 50x longer than fqz_comp. Second, it apparently cannot be used easily within a pipe like many other compressors. Third, it contains multiple scripts with multiple auxiliary programs, rather than a single executable. Fourth, it is quite verbose during operation, which can be helpful but cannot be turned off. Finally, it was difficult to track down for installation; two different links were provided in the publications and neither worked. It was finally found in a github repository, the location of which is provided in the module help. diff --git a/docs/cluster_guides/storage/compress_guide.md b/docs/cluster_guides/storage/compress_guide.md index def76ca62..76bb8437b 100644 --- a/docs/cluster_guides/storage/compress_guide.md +++ b/docs/cluster_guides/storage/compress_guide.md @@ -3,6 +3,7 @@ To avoid filling up the storage at UPPMAX, we all users to do their part and store their files in a good way. The best way to store files is of course to delete everything you don't need anymore, like temporary and intermediate files. For everything else you need to keep, here are some useful commands to know (section about biological data below). ## General files + We have several compression programs installed and you are free to chose whichever you want (any better than none). Examples: ### gzip (fast, good compression) @@ -44,6 +45,7 @@ $ unzstd --rm file.txt.zst ``` ## Compressing lots of files + The commands above work on a single file at a time, and if you have 1000s of files it is quite boring to go through them manually. If you want to combine all the files into a single compressed archive, you can use a program named tar. ``` @@ -71,6 +73,7 @@ $ find . \( -iname '*.fq' -o -iname '*.fastq' \) -print0 | xargs -0 -P 4 gzip ``` ## Biological data + There are some compression algorithms that have become standard practice to use in the realm of biological data. Most programs can read the compressed versions of files as long as it's compressed with the correct program. Leaving out the decompression commands, mostly because they are already described in the General files section about, but also because there is little reason to ever decompress biological data. ### fastq files @@ -108,6 +111,7 @@ $ tabix sample.vcf.gz ``` ## Programs that don't read compressed files + There are clever ways to get around programs that don't support reading compressed files. Let's say you have a program that only reads plain text files. You can use something called process substitution (also known as anonymous named pipes) to be able to decompress the data on-the-fly while feeding it to the program. ### How you normally would run the program diff --git a/docs/cluster_guides/storage/disk_storage_guide.md b/docs/cluster_guides/storage/disk_storage_guide.md index 42c961418..73af02b07 100644 --- a/docs/cluster_guides/storage/disk_storage_guide.md +++ b/docs/cluster_guides/storage/disk_storage_guide.md @@ -13,7 +13,8 @@ Temporary virtual filesystem Users have access to shared network storage on various cluster file systems, and backup home directories and some project storages to tape. ### If you need more quota -If more quota is needed, contact support (support@uppmax.uu.se) for advice. The uquota command is used to check current disk usage and limits. This command is available in the 'uppmax' module, which is loaded by default. + +If more quota is needed, contact support () for advice. The uquota command is used to check current disk usage and limits. This command is available in the 'uppmax' module, which is loaded by default. We do not extend quotas for home directories or SNIC project directories, but it's possible to apply for storage projects. @@ -23,9 +24,11 @@ du -b $PWD | sort -rn | awk 'NR==1 {ALL=$1} {print int($1*100/ALL) "% " $0}' find $PWD -print0 -type f | xargs -0 stat -c "%s %n" | sort -rn ### If you need even more quota for archiving -Please contact UPPMAX support at support@uppmax.uu.se. We have a previously been able to provide users with a low-cost moderate performant storage solution for a cost of 500SEK/TB/year, for a commitment of four years and 50TB. + +Please contact UPPMAX support at . We have a previously been able to provide users with a low-cost moderate performant storage solution for a cost of 500SEK/TB/year, for a commitment of four years and 50TB. ### Environmental variables + We have defines several environment variables to help our users. They are: $HOME (or $SNIC_BACKUP) is a traditional one, pointing to the users home directory. @@ -33,7 +36,9 @@ $TMPDIR or ($SNIC_TMP) points to node-local storage, suitable for temporary file $SNIC_NOBACKUP points to an UPPMAX-wide storage suitable for temporary files (not deleted when the job is finished) ## Types of storage + ### User Home directories + Paths: $HOME or $SNIC_BACKUP Permanent storage of users files during the lifetime of the accounts. Shared access on all cluster nodes. Snapshots are normally enabled on this file system, and you can access the snapshots in every directory by 'ls .snapshot' or 'cd .snapshot'. The quota is 32GB per user. We provide backup of this volume, and we keep the files on tape up to 90 days after they are deleted from disk. If you have files you do not want to back up place them in a folder called 'nobackup'. @@ -41,11 +46,13 @@ Permanent storage of users files during the lifetime of the accounts. Shared acc We recommend you do not use your home directory for running jobs. Our general recommendation is to keep everything related to a specific research project in its project directory. ### Local Scratch + Paths: $TMPDIR or $SNIC_TMP Each node has a /scratch volume for local access providing the most efficient disk storage for temporary files. Users have read/write access to this file system. SLURM defines the environment variable TMPDIR which you may use in job scripts. On clusters with SLURM you may use /scratch/$SLURM_JOB_ID. This area is for local access only, and is not directly reachable from other nodes or from the front node. There is no backup of the data and the lifetime of any file created is limited to the current user session or batch job. Files are automatically erased when space is needed by other users. ### Projects global (network) storage + Paths: /proj/[proj-id] The project global storage is permanent storage of project's files during the lifetime of the project. Disk quota on this volume is shared by all project members. Default quota allocation is determined by your project type. @@ -63,6 +70,7 @@ On Bianca and in SLLStore and UppStore projects, all temporary files, and files More information about backup at UPPMAX. ### Temporary virtual filesystem + Paths: /dev/shm/[job-id] On all our clusters we have a temporary virtual filesystem implemented as a shared memory area. I.e. it uses primarily the RAM for storage (until it eventually might have to swap out to physical disk), and can be accessed via the path /dev/shm/[job-id]. diff --git a/docs/cluster_guides/thinlinc.md b/docs/cluster_guides/thinlinc.md index 389ab186c..890962d2f 100644 --- a/docs/cluster_guides/thinlinc.md +++ b/docs/cluster_guides/thinlinc.md @@ -28,11 +28,13 @@ Bianca is handled a bit special. ## Connecting ### Login node connection + Just as you can log in via ssh to a login node to get a text session, you can connect with ThinLinc to get a graphical desktop session on a login node. These are subject to the same limitations normal login sessions are (memory and run time limits, don't do anything that might disturb other users). In addition to the normal limitations, login node connections may have short (10-15) minute idle timeouts meaning your session may disappear if you leave it. ### Making the connection + After downloading and installing, you can launch the ThinLinc client, and should see a form where you can enter your username and password (and possibly a server name). If you only see the simple form: ![Login](img/c_555890-l_1-k_thinlincsimple.png) @@ -40,9 +42,11 @@ After downloading and installing, you can launch the ThinLinc client, and should you can click Advanced to be able to set the server name to connect to. Provided you have set it up earlier, you can also use key based authentication. ## Two factor authentication + The ThinLinc client connects over SSH which means it may be required to present a code from two factor authentication (**FIX LINK**). The ThinLinc client does not know to ask for this so you will need to use the grace time feature, similar to file transfers with SFTP/rsync. To do this, first you have to connect with regular SSH and present the required code. Once you have logged in over SSH you can safely exit again. The login server will remember that you just logged in for a few minutes and not ask for two factor authentication again, so make sure you do not wait too long to connect with the ThinLinc client. ## Server names + The server name to connect to is CLUSTERNAME-gui.uppmax.uu.se to make a login node connection. This means possible servers to connect to are currently ``rackham-gui.uppmax.uu.se (fingerprint 94:c6:66:db:16:b2:95:7d:d1:53:5d:75:f6:3c:e8:cf)`` @@ -50,11 +54,13 @@ The server name to connect to is CLUSTERNAME-gui.uppmax.uu.se to make a login no If you are using the web interface do note that the server only accepts secure connections, so do not forget the s in https://. ## ThinLinc client options + Under the "Screen" tab, you can set the starting size of the session and choose to enable/disable Full screen mode. Typically, users prefer to turn off full screen mode. Normally you don't have to change anything else here, and we have also disabled all "local devices" (USB-sticks, sound and printers) on server side. So no point to fiddle with these specific options. ## Web interface + The servers listed above also offer a HTML5 client available at the according https URLs: diff --git a/docs/cluster_guides/transfer_bianca.md b/docs/cluster_guides/transfer_bianca.md index 3ced220f8..9b99fcc05 100644 --- a/docs/cluster_guides/transfer_bianca.md +++ b/docs/cluster_guides/transfer_bianca.md @@ -22,8 +22,8 @@ the [Bianca](bianca.md) UPPMAX cluster. For all file transfer on Bianca: - * [The user needs to be inside of SUNET](../getting_started/get_inside_sunet.md) - * The files are moved from/to [the `wharf` folder](wharf.md) +* [The user needs to be inside of SUNET](../getting_started/get_inside_sunet.md) +* The files are moved from/to [the `wharf` folder](wharf.md) ## File transfer methods @@ -37,7 +37,6 @@ Method |Features Transit server from/to Rackham, see below |Terminal, can be used to transfer data between clusters in general [Mounting `wharf` on your local computer](#mounting-wharf) |Both graphical and terminal, need a computer with `sshfs` installed - ## Using a graphical program ![FileZilla connected to Bianca](./img/filezilla_login_to_bianca_236_x_266.png) @@ -69,16 +68,16 @@ via SSH at `transit.uppmax.uu.se`. See [the UPPMAX documentation on the Transit server](transit.md). -- Note that your home directory is mounted _read-only_, any changes you do to your "local" home directory (on transit) will be lost upon logging out. +* Note that your home directory is mounted _read-only_, any changes you do to your "local" home directory (on transit) will be lost upon logging out. -- You can use commands like ``rsync``, ``scp`` to fetch data and transfer it to your bianca wharf. - - You can use cp to copy from Rackham to the wharf -- Remember that you cannot make lasting changes to anything except for mounted wharf directories. Therefore you have to use rsync and scp to transfer from the ``wharf`` to Rackham. -- The mounted directory will be kept for later sessions. +* You can use commands like ``rsync``, ``scp`` to fetch data and transfer it to your bianca wharf. + * You can use cp to copy from Rackham to the wharf +* Remember that you cannot make lasting changes to anything except for mounted wharf directories. Therefore you have to use rsync and scp to transfer from the ``wharf`` to Rackham. +* The mounted directory will be kept for later sessions. ### Moving data from transit to Rackham -- **On Rackham:** (_or other computer_) copy files to Bianca via transit: +* **On Rackham:** (_or other computer_) copy files to Bianca via transit: ```bash # scp @@ -88,7 +87,8 @@ scp path/my_files my_user@transit.uppmax.uu.se:sens2023531/ rsync -avh path/my_files my_user@transit.uppmax.uu.se:sens2023531/ ``` -- **On transit:** copy files to Bianca from Rackham (_or other computer_) +* **On transit:** copy files to Bianca from Rackham (_or other computer_) + ```bash # scp scp my_user@rackham.uppmax.uu.se:path/my_files ~/sens2023531/ @@ -103,10 +103,10 @@ rsync -avh my_user@rackham.uppmax.uu.se:path/my_files ~/sens2023531/ ### Moving data between projects -- You can use transit to transfer data between projects +* You can use transit to transfer data between projects by mounting the wharfs for the different projects and transferring data with `rsync`. -- Note that you may of course only do this if this is allowed +* Note that you may of course only do this if this is allowed (agreements, permissions, etc.) ## Mounting `wharf` on your local computer @@ -128,4 +128,3 @@ See [the UPPMAX documentation of `wharf`](wharf.md) on how to do so. ## Bianca file transfer as image ![Bianca](../img/Bianca-transfer.png) - diff --git a/docs/cluster_guides/transfer_dardel.md b/docs/cluster_guides/transfer_dardel.md index be9d446a5..05d5854ff 100644 --- a/docs/cluster_guides/transfer_dardel.md +++ b/docs/cluster_guides/transfer_dardel.md @@ -61,7 +61,6 @@ and you have created a SSH key pair. ssh-ed25519 AAAA63Nz1C1lZkI1NdE5ABAAIA7RHe4jVBRTEvHVbEYxV8lnOQl22N+4QcUK+rDv1gPS user@rackham2.uppmax.uu.se ``` - ### 5. Add the public SSH key to PDC:s Login Portal How to add the SSH public key is described @@ -70,7 +69,7 @@ in detail in [the PDC documentation on how to add SSH keys](https://www.pdc.kth. You will need to get the public part of the key in order to complete this step.i On Rackham, in a terminal, type: ``` -$ cat ~/.ssh/id_ed25519_pdc.pub +cat ~/.ssh/id_ed25519_pdc.pub ``` This will show a text similar to: @@ -184,6 +183,7 @@ rm ~/.ssh/id_ed25519_pdc* ``` Create new ones if you still need to connect to Dardel from UPPMAX. To create new keys with password on them, simply run: + ``` ssh-keygen -t ed25519 ``` @@ -194,4 +194,4 @@ Once you are sure your data has been transferred, we recommend that you switch o ## Link - * [PDC's page on getting access to Dardel](https://www.pdc.kth.se/support/documents/getting_access/get_access.html) +* [PDC's page on getting access to Dardel](https://www.pdc.kth.se/support/documents/getting_access/get_access.html) diff --git a/docs/cluster_guides/transfer_rackham.md b/docs/cluster_guides/transfer_rackham.md index af85ca268..aa6fedfff 100644 --- a/docs/cluster_guides/transfer_rackham.md +++ b/docs/cluster_guides/transfer_rackham.md @@ -5,8 +5,8 @@ There are multiple ways to transfer files to/from Rackham: Method |Features --------------------------------------------------------------|--------------------------------------------- [Using a graphical program](#using-a-graphical-program) |Graphical interface, intuitive, for small amounts of data only -[Using SCP](#using-SCP) |Terminal, easy to learn, can be used in scripts -[Using SFTP](#using-SFTP) |Terminal, easy to learn, secure +[Using SCP](#using-scp) |Terminal, easy to learn, can be used in scripts +[Using SFTP](#using-sftp) |Terminal, easy to learn, secure [Using transit](#using-transit) |Terminal, easy to learn, secure, can transfer between HPC clusters Each of these methods is discussed below. @@ -108,4 +108,3 @@ flowchart TD > The purple nodes are about file transfer, > the blue nodes are about 'doing other things'. > The user can be either inside or outside SUNET. - diff --git a/docs/cluster_guides/transfer_transit.md b/docs/cluster_guides/transfer_transit.md index e1be2edc1..b64052f5f 100644 --- a/docs/cluster_guides/transfer_transit.md +++ b/docs/cluster_guides/transfer_transit.md @@ -9,12 +9,11 @@ There are multiple ways to transfer files to/from [Transit](../cluster_guides/tr See [the page about Transit](transit.md) for more detailed information. - Method |Features --------------------------------------------------------------|--------------------------------------------- [Using a graphical program](#using-a-graphical-program) |Graphical interface, intuitive, for small amounts of data only -[Using SFTP](#using-SFTP) |Terminal, easy to learn, secure -[Using SCP](#using-SCP) |:no_entry: only download, terminal, easy to learn, can be used in scripts +[Using SFTP](#using-sftp) |Terminal, easy to learn, secure +[Using SCP](#using-scp) |:no_entry: only download, terminal, easy to learn, can be used in scripts Each of these methods is discussed below. @@ -106,4 +105,3 @@ flowchart TD ``` > Overview of file transfer on Transit - diff --git a/docs/cluster_guides/transit.md b/docs/cluster_guides/transit.md index 55025f85f..6a4bb8f81 100644 --- a/docs/cluster_guides/transit.md +++ b/docs/cluster_guides/transit.md @@ -31,6 +31,6 @@ is an UPPMAX service that can be used to securely transfer files. Here, 'putting an address on the letter' is to copy the file to the desired location. - * [how to log in to Transit](../cluster_guides/login_transit.md) - * [file transfer using Transit](../cluster_guides/transfer_transit.md). - * [software on Transit](../cluster_guides/software_on_transit.md) +* [how to log in to Transit](../cluster_guides/login_transit.md) +* [file transfer using Transit](../cluster_guides/transfer_transit.md). +* [software on Transit](../cluster_guides/software_on_transit.md) diff --git a/docs/cluster_guides/transit_file_transfer_using_gui.md b/docs/cluster_guides/transit_file_transfer_using_gui.md index b03d7eb2e..f99972562 100644 --- a/docs/cluster_guides/transit_file_transfer_using_gui.md +++ b/docs/cluster_guides/transit_file_transfer_using_gui.md @@ -79,7 +79,7 @@ For that site, use all standards, except: ### 7. Click 'Connect' -### 8. You will be asked for your password, +### 8. You will be asked for your password You will be asked for your password, hence type `[your password]`, e.g. `VerySecret`. @@ -122,8 +122,8 @@ You do need to transfer these files to other HPC clusters before closing FileZilla. For detailed instructions, see the guides at the respective cluster, among others: - * Bianca file transfer using Transit - * [Rackham file transfer using Transit](rackham_file_transfer_using_transit.md) +- Bianca file transfer using Transit +- [Rackham file transfer using Transit](rackham_file_transfer_using_transit.md) ## Extra material @@ -136,9 +136,9 @@ To transfer files to/from Transit using WinSCP, do: - Start WinSCP - Create a new site - For that site, use all standards, except: - - Set file protocol to 'SFTP' - - Set host name to `transit.uppmax.uu.se` - - Set user name to `[username]`, e.g. `richel` + - Set file protocol to 'SFTP' + - Set host name to `transit.uppmax.uu.se` + - Set user name to `[username]`, e.g. `richel` ### File transfer overview diff --git a/docs/cluster_guides/transit_file_transfer_using_scp.md b/docs/cluster_guides/transit_file_transfer_using_scp.md index 8c6e7d281..df976ad95 100644 --- a/docs/cluster_guides/transit_file_transfer_using_scp.md +++ b/docs/cluster_guides/transit_file_transfer_using_scp.md @@ -118,4 +118,3 @@ flowchart TD > The purple nodes are about file transfer, > the blue nodes are about 'doing other things'. > The user can be either inside or outside SUNET. - diff --git a/docs/cluster_guides/transit_file_transfer_using_sftp.md b/docs/cluster_guides/transit_file_transfer_using_sftp.md index 55e637436..40171b790 100644 --- a/docs/cluster_guides/transit_file_transfer_using_sftp.md +++ b/docs/cluster_guides/transit_file_transfer_using_sftp.md @@ -82,7 +82,7 @@ You do need to transfer these files to other HPC clusters before closing `sftp`. For detailed instructions, see the guides at the respective cluster, among others: - * [Rackham file transfer using SFTP](rackham_file_transfer_using_sftp.md) +* [Rackham file transfer using SFTP](rackham_file_transfer_using_sftp.md) ## Overview diff --git a/docs/cluster_guides/uppmax_cloud.md b/docs/cluster_guides/uppmax_cloud.md index d9f5a20de..2223b7a97 100644 --- a/docs/cluster_guides/uppmax_cloud.md +++ b/docs/cluster_guides/uppmax_cloud.md @@ -9,4 +9,3 @@ has a service called 'Dis' (the Swedish word for 'haze'). See [here](https://www.uu.se/en/centre/uppmax/resources/clusters/cloud-service-dis) for more information. - diff --git a/docs/cluster_guides/uppmax_cluster.md b/docs/cluster_guides/uppmax_cluster.md index e4a7415f2..4f2ae6cc3 100644 --- a/docs/cluster_guides/uppmax_cluster.md +++ b/docs/cluster_guides/uppmax_cluster.md @@ -36,7 +36,6 @@ Another cluster UPPMAX is involved in: - [Dardel](dardel.md): a general purpose HPC cluster in Stockholm. Consider moving your files to it already - ```mermaid flowchart TD UPPMAX(Which UPPMAX cluster?) @@ -226,7 +225,6 @@ Bianca |Yes Rackham |No Snowy |No - On a sensitive data cluster, (sensitive) data must be protected to remain there, due to which there are these additional restrictions to users: diff --git a/docs/cluster_guides/uppmax_history.md b/docs/cluster_guides/uppmax_history.md index 2d18ed041..b0868a1d9 100644 --- a/docs/cluster_guides/uppmax_history.md +++ b/docs/cluster_guides/uppmax_history.md @@ -1,6 +1,6 @@ # UPPMAX history - * On January 12, 2024, the Irham nodes `r[1001-1072,1179-1250]` +* On January 12, 2024, the Irham nodes `r[1001-1072,1179-1250]` have been decommissioned. In 2021, the NGI HPC system Irma was replaced by Miarka, freeing up Irma nodes. In later part of 2021 a research group expressed interest in diff --git a/docs/cluster_guides/uppmax_systems.md b/docs/cluster_guides/uppmax_systems.md index e4271c7d6..e78196f88 100644 --- a/docs/cluster_guides/uppmax_systems.md +++ b/docs/cluster_guides/uppmax_systems.md @@ -124,7 +124,6 @@ are restricted in some ways: This is done by requesting an interactive node from the SLURM scheduler. - - Users cannot install software directly. Instead, users need to use pre-installed software or learn techniques how to run custom software anyway @@ -200,13 +199,10 @@ There are three types of nodes: This is done by requesting an interactive node from the SLURM scheduler. - Each node contains several CPU/GPU cores, RAM and local storage space. A user logs in to a login node via the Internet. - - ## Summary !!! abstract "keypoints" diff --git a/docs/cluster_guides/vscodium_on_bianca.md b/docs/cluster_guides/vscodium_on_bianca.md index 3246f225a..bbf1aca77 100644 --- a/docs/cluster_guides/vscodium_on_bianca.md +++ b/docs/cluster_guides/vscodium_on_bianca.md @@ -71,7 +71,6 @@ With the modules loaded, in that same terminal, start VSCodium: - ``` code ``` diff --git a/docs/cluster_guides/vscodium_on_rackham.md b/docs/cluster_guides/vscodium_on_rackham.md index ddee12d38..be4f0b978 100644 --- a/docs/cluster_guides/vscodium_on_rackham.md +++ b/docs/cluster_guides/vscodium_on_rackham.md @@ -69,7 +69,6 @@ With the modules loaded, in that same terminal, start VSCodium: - ``` code ``` diff --git a/docs/cluster_guides/wharf.md b/docs/cluster_guides/wharf.md index 74c2a682d..b7cb284e7 100644 --- a/docs/cluster_guides/wharf.md +++ b/docs/cluster_guides/wharf.md @@ -5,10 +5,10 @@ for [file transfer on Bianca](transfer_bianca.md). He it is described: - * [What is `wharf`?](#what-is-wharf) - * [The `wharf` location](#the-wharf-location) - * [`wharf` use](#wharf-use) - * [mounting `wharf`](#mounting-wharf) +* [What is `wharf`?](#what-is-wharf) +* [The `wharf` location](#the-wharf-location) +* [`wharf` use](#wharf-use) +* [mounting `wharf`](#mounting-wharf) ## What is `wharf`? @@ -28,8 +28,8 @@ The path to this special folder is: where - * `[project_id]` is the ID of your [NAISS project](../getting_started/project.md) - * `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md) +* `[project_id]` is the ID of your [NAISS project](../getting_started/project.md) +* `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md) For example: @@ -69,8 +69,8 @@ RHEL7/CentOS7 [1] | `fuse-sshfs` RHEL8 [2] | `fuse-sshfs` CentOS8 [3] | `fuse-sshfs` - * [1] Enable EPEL repository - * [2] Enable `codeready-builder` repository - * [3] Enable `powertools` repository +* [1] Enable EPEL repository +* [2] Enable `codeready-builder` repository +* [3] Enable `powertools` repository UPPMAX does not have `sshfs` installed for security reasons. diff --git a/docs/databases/1000-genome_project.md b/docs/databases/1000-genome_project.md index cdff93e09..e99b094cd 100644 --- a/docs/databases/1000-genome_project.md +++ b/docs/databases/1000-genome_project.md @@ -6,4 +6,4 @@ The main archive is stored at /sw/data/KGP/central. Within this folder, "low" ho One level up in the file system, /sw/data/KGP/regional holds sequence data for some individual countries outside the 1000-genome project. So far, very little data has been stored but this may be expanded. -Users interesting in any of this data should request membership in the "KGP" group (via support@uppmax.uu.se). This requirement is not intended to restrict the resource in any way but makes it easier to inform interested users of possible changes. Considering the large storage space used, it is possible that the data would need to be reorganized or possibly even reduced in the future, depending of course on the perceived need for the resource by the members of the KGP group. +Users interesting in any of this data should request membership in the "KGP" group (via ). This requirement is not intended to restrict the resource in any way but makes it easier to inform interested users of possible changes. Considering the large storage space used, it is possible that the data would need to be reorganized or possibly even reduced in the future, depending of course on the perceived need for the resource by the members of the KGP group. diff --git a/docs/databases/blast.md b/docs/databases/blast.md index 8e3c19f98..e0e5b6e3e 100644 --- a/docs/databases/blast.md +++ b/docs/databases/blast.md @@ -1,7 +1,5 @@ # Blast databases available locally - - Many pipelines involving annotation/assembly comparison involve Blast. Several Blast versions are available as modules, for example: blast/2.12.0+, etc. : the Blast+ suites (blastp, tblastn, etc.), recommended @@ -37,51 +35,51 @@ Each NCBI-hosted database also includes a JSON file containing additional metada cat /sw/data/blast_databases/nr*.json The Blast databases available at UPPMAX are: -Name Type Source Notes -16S_ribosomal_RNA nucleotide NCBI 16S ribosomal RNA (Bacteria and Archaea type strains) -18S_fungal_sequences nucleotide NCBI 18S ribosomal RNA sequences (SSU) from Fungi type and reference material (BioProject PRJNA39195) -28S_fungal_sequences nucleotide NCBI 28S ribosomal RNA sequences (LSU) from Fungi type and reference material (BioProject PRJNA51803) -Betacoronavirus nucleotide NCBI Betacoronavirus nucleotide sequences -cdd_delta protein NCBI Conserved domain database for use with delta-blast -env_nr protein NCBI Protein sequences for metagenomes (EXCLUDED from nr) -env_nt nucleotide NCBI Nucleotide sequences for metagenomes -human_genome nucleotide NCBI Current RefSeq human genome assembly with various database masking -ITS_eukaryote_sequences nucleotide NCBI Internal transcribed spacer region (ITS) for eukaryotic sequences -ITS_RefSeq_Fungi nucleotide NCBI Internal transcribed spacer region (ITS) from Fungi type and reference material (BioProject PRJNA177353) -landmark protein NCBI Proteomes of 27 model organisms. The landmark database includes complete proteomes from a few selected representative genomes spanning a wide taxonomic range, the main database used by the SmartBLAST services. -LSU_eukaryote_rRNA nucleotide NCBI Large subunit ribosomal RNA sequences for eukaryotic sequences -LSU_prokaryote_rRNA nucleotide NCBI Large subunit ribosomal RNA sequences for prokaryotic sequences -mito nucleotide NCBI NCBI Genomic Mitochondrial Reference Sequences -mouse_genome nucleotide NCBI Current RefSeq mouse genome assembly with various database masking -nr protein NCBI Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSe -nt nucleotide NCBI Partially non-redundant nucleotide sequences from all traditional divisions of GenBank, EMBL, and DDBJ -pataa protein NCBI Patent protein sequences -patnt nucleotide NCBI Patent nucleotide sequences. Both patent databases are directly from the USPTO, or from the EPO/JPO via EMBL/DDBJ -pdbaa protein NCBI Sequences for the protein structure from the Protein Data Bank -pdbnt nucleitide NCBI Sequences for the nucleotide structure from the Protein Data Bank. They are NOT the protein coding sequences for the corresponding pdbaa entries. -ref_euk_rep_genomes nucleotide NCBI Refseq Representative Eukaryotic genomes (1000+ organisms) -ref_prok_rep_genomes nucleotide NCBI Refseq Representative Prokaryotic genomes (5700+ organisms) -ref_viroid_rep_genomes nucleotide NCBI Refseq Representative Viroid genomes (46 organisms) -ref_viruses_rep_genomes nucleotide NCBI Refseq Representative Virus genomes (9000+ organisms) -refseq_protein protein NCBI NCBI protein reference sequences -refseq_rna nucleotide NCBI NCBI Transcript reference sequences -refseq_select_prot protein NCBI NCBI RefSeq protein sequences from human, mouse, and prokaryotes, restricted to the RefSeq Select set of proteins. RefSeq Select includes one representative protein per protein-coding gene for human and mouse, and RefSeq proteins annotated on reference and representative genomes for prokaryotes -refseq_select_rna nucleotide NCBI NCBI RefSeq transcript sequences from human and mouse, restricted to the RefSeq Select set with one representative transcript per protein-coding gene -SSU_eukaryote_rRNA nucleotide NCBI Small subunit ribosomal RNA sequences for eukaryotic sequences -swissprot protein NCBI Swiss-Prot sequence database (last major update) -tsa_nr protein NCBI Protein sequences from the Transcriptome Shotgun Assembly. Its entries are EXCLUDED from the nr database. -tsa_nt nucleotide NCBI A database with earlier non-project based Transcriptome Shotgun Assembly (TSA) entries. Project-based TSA entries are NOT included. Entries are EXCLUDED from the nt database. -uniprot_sprot protein UniProt Swiss-Prot high quality manually annotated and non-redundant protein sequence database -uniprot_trembl protein UniProt TrEMBL high quality but unreviewed protein sequence database -uniprot_sptrembl protein uniprot_sprot and uniprot_trembl combined -uniprot_all protein alias for uniprot_sptrembl -uniprot_all.fasta protein alias for uniprot_sptrembl -uniprot_sprot_varsplic protein UniProt UniProt canonical and isoform sequences (see link) -uniprot_uniref50 protein UniProt Clustered sets of 50%-similar protein sequences (see link) -uniprot_uniref90 protein UniProt Clustered sets of 90%-similar protein sequences (see link) -uniprot_uniref100 protein UniProt Clustered sets of identical protein sequences (see link) -UniVec nucleotide UniVec Sequences commonly attached to cDNA/genomic DNA during the cloning process -UniVec_Core nucleotide UniVec A subset of UniVec chosen to minimise false positives +Name Type Source Notes +16S_ribosomal_RNA nucleotide NCBI 16S ribosomal RNA (Bacteria and Archaea type strains) +18S_fungal_sequences nucleotide NCBI 18S ribosomal RNA sequences (SSU) from Fungi type and reference material (BioProject PRJNA39195) +28S_fungal_sequences nucleotide NCBI 28S ribosomal RNA sequences (LSU) from Fungi type and reference material (BioProject PRJNA51803) +Betacoronavirus nucleotide NCBI Betacoronavirus nucleotide sequences +cdd_delta protein NCBI Conserved domain database for use with delta-blast +env_nr protein NCBI Protein sequences for metagenomes (EXCLUDED from nr) +env_nt nucleotide NCBI Nucleotide sequences for metagenomes +human_genome nucleotide NCBI Current RefSeq human genome assembly with various database masking +ITS_eukaryote_sequences nucleotide NCBI Internal transcribed spacer region (ITS) for eukaryotic sequences +ITS_RefSeq_Fungi nucleotide NCBI Internal transcribed spacer region (ITS) from Fungi type and reference material (BioProject PRJNA177353) +landmark protein NCBI Proteomes of 27 model organisms. The landmark database includes complete proteomes from a few selected representative genomes spanning a wide taxonomic range, the main database used by the SmartBLAST services. +LSU_eukaryote_rRNA nucleotide NCBI Large subunit ribosomal RNA sequences for eukaryotic sequences +LSU_prokaryote_rRNA nucleotide NCBI Large subunit ribosomal RNA sequences for prokaryotic sequences +mito nucleotide NCBI NCBI Genomic Mitochondrial Reference Sequences +mouse_genome nucleotide NCBI Current RefSeq mouse genome assembly with various database masking +nr protein NCBI Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSe +nt nucleotide NCBI Partially non-redundant nucleotide sequences from all traditional divisions of GenBank, EMBL, and DDBJ +pataa protein NCBI Patent protein sequences +patnt nucleotide NCBI Patent nucleotide sequences. Both patent databases are directly from the USPTO, or from the EPO/JPO via EMBL/DDBJ +pdbaa protein NCBI Sequences for the protein structure from the Protein Data Bank +pdbnt nucleitide NCBI Sequences for the nucleotide structure from the Protein Data Bank. They are NOT the protein coding sequences for the corresponding pdbaa entries. +ref_euk_rep_genomes nucleotide NCBI Refseq Representative Eukaryotic genomes (1000+ organisms) +ref_prok_rep_genomes nucleotide NCBI Refseq Representative Prokaryotic genomes (5700+ organisms) +ref_viroid_rep_genomes nucleotide NCBI Refseq Representative Viroid genomes (46 organisms) +ref_viruses_rep_genomes nucleotide NCBI Refseq Representative Virus genomes (9000+ organisms) +refseq_protein protein NCBI NCBI protein reference sequences +refseq_rna nucleotide NCBI NCBI Transcript reference sequences +refseq_select_prot protein NCBI NCBI RefSeq protein sequences from human, mouse, and prokaryotes, restricted to the RefSeq Select set of proteins. RefSeq Select includes one representative protein per protein-coding gene for human and mouse, and RefSeq proteins annotated on reference and representative genomes for prokaryotes +refseq_select_rna nucleotide NCBI NCBI RefSeq transcript sequences from human and mouse, restricted to the RefSeq Select set with one representative transcript per protein-coding gene +SSU_eukaryote_rRNA nucleotide NCBI Small subunit ribosomal RNA sequences for eukaryotic sequences +swissprot protein NCBI Swiss-Prot sequence database (last major update) +tsa_nr protein NCBI Protein sequences from the Transcriptome Shotgun Assembly. Its entries are EXCLUDED from the nr database. +tsa_nt nucleotide NCBI A database with earlier non-project based Transcriptome Shotgun Assembly (TSA) entries. Project-based TSA entries are NOT included. Entries are EXCLUDED from the nt database. +uniprot_sprot protein UniProt Swiss-Prot high quality manually annotated and non-redundant protein sequence database +uniprot_trembl protein UniProt TrEMBL high quality but unreviewed protein sequence database +uniprot_sptrembl protein uniprot_sprot and uniprot_trembl combined +uniprot_all protein alias for uniprot_sptrembl +uniprot_all.fasta protein alias for uniprot_sptrembl +uniprot_sprot_varsplic protein UniProt UniProt canonical and isoform sequences (see link) +uniprot_uniref50 protein UniProt Clustered sets of 50%-similar protein sequences (see link) +uniprot_uniref90 protein UniProt Clustered sets of 90%-similar protein sequences (see link) +uniprot_uniref100 protein UniProt Clustered sets of identical protein sequences (see link) +UniVec nucleotide UniVec Sequences commonly attached to cDNA/genomic DNA during the cloning process +UniVec_Core nucleotide UniVec A subset of UniVec chosen to minimise false positives Additionally, taxdb.btd and taxdb.bti are downloaded, which provide additional taxonomy information for these databases. Local copies of the NCBI Taxonomy databases are also available; further details are available on a separate page. diff --git a/docs/databases/diamond.md b/docs/databases/diamond.md index 0c299f499..06fb10aa8 100644 --- a/docs/databases/diamond.md +++ b/docs/databases/diamond.md @@ -25,38 +25,39 @@ According to DIAMOND's developer, these are faster to load than DIAMOND's own .d Diamond-format NCBI Protein Databases Downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA. These are updated frequently at NCBI, so they are versioned here by the monthly download date. There is no longer a separate FASTA version of env_nr, so its Blast database is downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db and FASTA sequences are extracted using blastdbcmd -entry all from module blast/2.12.0+. -Database Environment variable for diamond --db UPPMAX path -nr DIAMOND_NR /sw/data/diamond_databases/Blast/latest/nr -env_nr DIAMOND_ENV_NR /sw/data/diamond_databases/Blast/latest/env_nr -swissprot DIAMOND_SWISSPROT /sw/data/diamond_databases/Blast/latest/swissprot -pdbaa DIAMOND_PDBAA /sw/data/diamond_databases/Blast/latest/pdbaa +Database Environment variable for diamond --db UPPMAX path +nr DIAMOND_NR /sw/data/diamond_databases/Blast/latest/nr +env_nr DIAMOND_ENV_NR /sw/data/diamond_databases/Blast/latest/env_nr +swissprot DIAMOND_SWISSPROT /sw/data/diamond_databases/Blast/latest/swissprot +pdbaa DIAMOND_PDBAA /sw/data/diamond_databases/Blast/latest/pdbaa NCBI RefSeq Proteins RefSeq protein databases are downloaded from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/complete/, with an update occurring if there is a new release as indicated by the contents of ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER. -Database Environment variable for diamond --db UPPMAX path -complete.nonredundant_protein.protein DIAMOND_REFSEQ_NONREDUNDANT /sw/data/diamond_databases/RefSeq/latest/complete.nonredundant_protein.protein -complete.protein DIAMOND_REFSEQ /sw/data/diamond_databases/RefSeq/latest/complete.protein +Database Environment variable for diamond --db UPPMAX path +complete.nonredundant_protein.protein DIAMOND_REFSEQ_NONREDUNDANT /sw/data/diamond_databases/RefSeq/latest/complete.nonredundant_protein.protein +complete.protein DIAMOND_REFSEQ /sw/data/diamond_databases/RefSeq/latest/complete.protein UniRef90 The UniRef90 protein database is downloaded as Fasta from its UK mirror at ftp://ftp.expasy.org/databases/uniprot/current_release/uniref/uniref90/, with an update occurring if there is a new version as indicated by the tag in the XML description available at ftp://ftp.expasy.org/databases/uniprot/current_release/uniref/uniref90/RELEASE.metalink. -Database Environment variable for diamond --db UPPMAX path -uniref90 DIAMOND_UNIREF90 /sw/data/diamond_databases/UniRef90/latest/uniref90 +Database Environment variable for diamond --db UPPMAX path +uniref90 DIAMOND_UNIREF90 /sw/data/diamond_databases/UniRef90/latest/uniref90 UniProt Reference Proteomes The UniProt Reference Proteomes protein database is downloaded as Fasta from its UK mirror at ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/reference_proteomes, with an update occurring if there is a new version as indicated by the tag in the XML description available at ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/reference_proteomes/RELEASE.metalink. If there is a new release, then the file Reference_Proteomes_RELEASE.tar.gz is downladed, with RELEASE replaced by the release number. The reference_proteomes.dmnd database is created from this file using the protocol described after the table. -Database Environment variable for diamond --db UPPMAX path -UniProt Reference Proteomes DIAMOND_REFERENCE_PROTEOMES /sw/data/diamond_databases/reference_proteomes/latest/reference_proteomes +Database Environment variable for diamond --db UPPMAX path +UniProt Reference Proteomes DIAMOND_REFERENCE_PROTEOMES /sw/data/diamond_databases/reference_proteomes/latest/reference_proteomes The reference_proteomes.dmnd database is created using the following protocol for the BlobToolKit. This uses UPPMAX's most recently downloaded NCBI taxonomy database for its taxonomic metadata. module load bioinfo-tools module load diamond/2.0.14 module load ncbi_taxonomy/latest + # after downloading + tar xf Reference_Proteomes_RELEASE.tar.gz touch reference_proteomes.fasta.gz find . -mindepth 2 | grep "fasta.gz" | grep -v 'DNA' | grep -v 'additional' | xargs cat >> reference_proteomes.fasta.gz printf "accession\taccession.version\ttaxid\tgi\n" > reference_proteomes.taxid_map zcat */*/*.idmapping.gz | grep "NCBI_TaxID" | awk '{print $1 "\t" $1 "\t" $3 "\t" 0}' >> reference_proteomes.taxid_map diamond makedb --db reference_proteomes.dmnd --in reference_proteomes.fasta.gz --threads 10 --taxonmap reference_proteomes.taxid_map --taxonnames $NCBI_TAXONOMY_ROOT/names.dmp --taxonnodes $NCBI_TAXONOMY_ROOT/nodes.dmp - diff --git a/docs/databases/ncbi.md b/docs/databases/ncbi.md index 81eeff05b..ee061f295 100644 --- a/docs/databases/ncbi.md +++ b/docs/databases/ncbi.md @@ -14,32 +14,32 @@ Uppmax maintains local copies of the full set of NCBI Taxonomy databases. Note t See the links for each database for specifics on file format and contents. Many tools know how to make use of these databases; follow each tool's specific instructions. The files can be found in the indicated directories. The databases available within /sw/data/ncbi_taxonomy/latest are below. For more on each, see the links. -Name Source Notes -taxdump NCBI NCBI taxonomic database, in multiple .dmp files (see taxdump_readme.txt or link) -taxcat NCBI NCBI taxonomic categories, in categories.dmp (see taxcat_readme.txt or link) -taxdump_readme.txt NCBI NCBI taxdump file description -taxcat_readme.txt NCBI NCBI taxcat file description -gi_taxid_nucl.dmp NCBI Mappings of nucleotide GI to taxid (DEPRECATED) -gi_taxid_prot.dmp NCBI Mappings of protein GI to taxid (DEPRECATED) +Name Source Notes +taxdump NCBI NCBI taxonomic database, in multiple .dmp files (see taxdump_readme.txt or link) +taxcat NCBI NCBI taxonomic categories, in categories.dmp (see taxcat_readme.txt or link) +taxdump_readme.txt NCBI NCBI taxdump file description +taxcat_readme.txt NCBI NCBI taxcat file description +gi_taxid_nucl.dmp NCBI Mappings of nucleotide GI to taxid (DEPRECATED) +gi_taxid_prot.dmp NCBI Mappings of protein GI to taxid (DEPRECATED) The databases available within /sw/data/ncbi_taxonomy/latest/new_taxdump are below. For more on each, see the links. -Name Source Notes -new_taxdump NCBI NCBI new-format taxonomic database, in multiple .dmp files (see this taxdump_readme.txt or link) -taxdump_readme.txt NCBI NCBI new-format taxonomic database file description +Name Source Notes +new_taxdump NCBI NCBI new-format taxonomic database, in multiple .dmp files (see this taxdump_readme.txt or link) +taxdump_readme.txt NCBI NCBI new-format taxonomic database file description The databases available within /sw/data/ncbi_taxonomy/latest/accession2taxid are below. The dead_ files contain accession-to-TaxID mappings for dead (suppressed or withdrawn) sequence records. For more on each, see the links. -Name Source Notes -nucl_wgs.accession2taxid NCBI TaxID mapping for nucleotide records of type WGS or TSA -nucl_gb.accession2taxid NCBI TaxID mapping for nucleotide records not of the above types -prot.accession2taxid NCBI TaxID mapping for protein records -pdb.accession2taxid NCBI TaxID mapping for PDB protein records -dead_nucl.accession2taxid NCBI TaxID mapping for dead nucleotide records -dead_prot.accession2taxid NCBI TaxID mapping for dead protein records -dead_wgs.accession2taxid NCBI TaxID mapping for dead WGS or TSA records +Name Source Notes +nucl_wgs.accession2taxid NCBI TaxID mapping for nucleotide records of type WGS or TSA +nucl_gb.accession2taxid NCBI TaxID mapping for nucleotide records not of the above types +prot.accession2taxid NCBI TaxID mapping for protein records +pdb.accession2taxid NCBI TaxID mapping for PDB protein records +dead_nucl.accession2taxid NCBI TaxID mapping for dead nucleotide records +dead_prot.accession2taxid NCBI TaxID mapping for dead protein records +dead_wgs.accession2taxid NCBI TaxID mapping for dead WGS or TSA records The biocollections databases contain collections location information. coll_dump.txt is located within the /sw/data/ncbi_taxonomy/latest directory. Those marked biocollections are located within the /sw/data/ncbi_taxonomy/latest/biocollections directory. -Name Source Notes -coll_dump.txt NCBI -Collection_codes.txt NCBI biocollections -Institution_codes.txt NCBI biocollections -Unique_institution_codes.txt NCBI biocollections +Name Source Notes +coll_dump.txt NCBI +Collection_codes.txt NCBI biocollections +Institution_codes.txt NCBI biocollections +Unique_institution_codes.txt NCBI biocollections diff --git a/docs/databases/other_local.md b/docs/databases/other_local.md index fe06aa84f..ff92d44cb 100644 --- a/docs/databases/other_local.md +++ b/docs/databases/other_local.md @@ -1,6 +1,5 @@ # Other bioinformatics-oriented local data resources - Haplotype Reference Consortium The Haplotype Reference Consortium VCF database is a large reference panel of human haplotypes produced by combining together sequencing data from multiple cohorts. Version r1.1 is installed on all systems as data module HaplotypeReferenceConsortium/r1.1. @@ -37,7 +36,7 @@ CDD - Position-Specific Scoring Matrices for CD-Search The CDD database versions 3.14 and 3.16 are downloaded in their entirety and are available at /sw/data/cdd/{3.14,3.16}. These directories contains collections of position-specific scoring matrices (PSSMs) that have been created for the CD-Search service. -The PSSMs are meant to be used for compiling RPS-BLAST search databases, which can be used with the standalone RPS-BLAST programs (rpsblast and rpsblastn). These programs, as well as the makeprofiledb application needed to convert files in this directory, are part of the BLAST+ executables (available on Uppmax as part of bioinfo-tools, e.g., module blast/2.2.31+). The makeprofiledb application is described at http://www.ncbi.nlm.nih.gov/books/NBK1763. +The PSSMs are meant to be used for compiling RPS-BLAST search databases, which can be used with the standalone RPS-BLAST programs (rpsblast and rpsblastn). These programs, as well as the makeprofiledb application needed to convert files in this directory, are part of the BLAST+ executables (available on Uppmax as part of bioinfo-tools, e.g., module blast/2.2.31+). The makeprofiledb application is described at . More information is available in the CDD README either via FTP or its local copy /sw/data/cdd/README. iGenomes - Collection of reference sequences and annotation files diff --git a/docs/databases/overview.md b/docs/databases/overview.md index 33377836f..2af407d73 100644 --- a/docs/databases/overview.md +++ b/docs/databases/overview.md @@ -11,4 +11,4 @@ Available databases: - [Simons Genome Diversity Project datasets](../databases/simons_genome.md) - [Other bioinformatics-oriented local data resources](../databases/other_local.md) -In order for you to access **Swegen** or **1000-genomes** you must first send an email to datacentre@scilifelab.se and ask for access. When they approve you, they will contact UPPMAX and we will grant access to Swegen. +In order for you to access **Swegen** or **1000-genomes** you must first send an email to and ask for access. When they approve you, they will contact UPPMAX and we will grant access to Swegen. diff --git a/docs/databases/reference_genomes.md b/docs/databases/reference_genomes.md index aa4787b3d..86af192b7 100644 --- a/docs/databases/reference_genomes.md +++ b/docs/databases/reference_genomes.md @@ -1,24 +1,22 @@ # Reference genomes - - NOTE: The Illumina igenomes are also available at UPPMAX, with additional indices built for Bismarck and STAR. The scripts used to build the additional indices are available at the UPPMAX/bio-data github repository. Many next-generation sequencing applications involves alignment of the sequence reads to a reference genome. We store reference sequences in a directory that is accessible for all users in the system. The table below shows all currently available genomes. -Reference genome Assembly version -Homo sapiens Feb. 2009 (GRCh37/hg19) -Pan troglodytes Mar. 2006 (CGSC2.1/PanTro2) -Macaca mulatta Jan. 2006 (RheMac2) -Sus scrofa Apr. 2009 (Sscrofa9) -Canis familiaris Sep. 2011 (CanFam3) -Mus musculus July 2007 (NCBIM37/mm9), Jan. 2012 (GRCm38) -Gallus gallus May 2006 (WASHUC2/galGal3) -Taeniopygia guttata Mar. 2010 (TaeGut3.2.4) -Saccharomyces cerevisiae Mar 2010 (ScereEF2) -Equus caballus Sep. 2007 (EquCab2) -Pichia stipitis Picst3 -Rattus norvegicus Nov. 2004 (RGSC3.4.61) -Schizosaccharomyces pombe 20090701 +Reference genome Assembly version +Homo sapiens Feb. 2009 (GRCh37/hg19) +Pan troglodytes Mar. 2006 (CGSC2.1/PanTro2) +Macaca mulatta Jan. 2006 (RheMac2) +Sus scrofa Apr. 2009 (Sscrofa9) +Canis familiaris Sep. 2011 (CanFam3) +Mus musculus July 2007 (NCBIM37/mm9), Jan. 2012 (GRCm38) +Gallus gallus May 2006 (WASHUC2/galGal3) +Taeniopygia guttata Mar. 2010 (TaeGut3.2.4) +Saccharomyces cerevisiae Mar 2010 (ScereEF2) +Equus caballus Sep. 2007 (EquCab2) +Pichia stipitis Picst3 +Rattus norvegicus Nov. 2004 (RGSC3.4.61) +Schizosaccharomyces pombe 20090701 Directory structure @@ -38,5 +36,4 @@ concat_rm contains most of the fasta files in "chromosome_rm" concatenated into program_files contains index files and metadata for software packages used to work with reference genomes, e.g. SAMtools and aligners such as Bowtie, BWA. - Requests for additional reference genomes or software data/index files should be directed to UPPMAX support. diff --git a/docs/databases/simons_genome.md b/docs/databases/simons_genome.md index 8b30af69b..fb53c2488 100644 --- a/docs/databases/simons_genome.md +++ b/docs/databases/simons_genome.md @@ -25,4 +25,4 @@ total 34529204 -rw-r----- 1 douglas kgp 35355769475 Nov 30 2020 SAMEA3302732.alt_bwamem_GRCh38DH.20200922.Greek.simons.cram -rw-r----- 1 douglas kgp 2079029 Dec 1 2020 SAMEA3302732.alt_bwamem_GRCh38DH.20200922.Greek.simons.cram.crai -To access this data, please request membership in the kgp group by emailing support@uppmax.uu.se. As for the 1000 Genomes Project, this is not to restrict access in any way, but rather to make it easier to inform UPPMAX users using the datasets of any relevant changes. Because the local copies of these datasets are hosted on UPPMAX systems, access is restricted to UPPMAX users; non-UPPMAX users will need to follow the procedures described on the SGDP website to download their own copies of the datasets. +To access this data, please request membership in the kgp group by emailing . As for the 1000 Genomes Project, this is not to restrict access in any way, but rather to make it easier to inform UPPMAX users using the datasets of any relevant changes. Because the local copies of these datasets are hosted on UPPMAX systems, access is restricted to UPPMAX users; non-UPPMAX users will need to follow the procedures described on the SGDP website to download their own copies of the datasets. diff --git a/docs/databases/swegen.md b/docs/databases/swegen.md index 776f23db7..8d02262be 100644 --- a/docs/databases/swegen.md +++ b/docs/databases/swegen.md @@ -1,3 +1,3 @@ # Access to Swegen -In order for you to access Swegen (or 1000 genomes) you must first send an email to datacentre@scilifelab.se and ask for access. When they approve you, they will contact UPPMAX and we will grant access to Swegen. +In order for you to access Swegen (or 1000 genomes) you must first send an email to and ask for access. When they approve you, they will contact UPPMAX and we will grant access to Swegen. diff --git a/docs/getting_started/first_job.md b/docs/getting_started/first_job.md index 47b258ad4..33a097a32 100644 --- a/docs/getting_started/first_job.md +++ b/docs/getting_started/first_job.md @@ -11,11 +11,9 @@ - writing batch script - view your CPU hours and disk usage - ## Transferring some files -### Graphical file manager - +### Graphical file manager ???- question "Want more detailed information of file transfer to/from Rackham using a graphical tool?" @@ -54,14 +52,8 @@ - [Filezilla](https://filezilla-project.org/download.php?type=client) - !!! example "Type-along" TODO - - - - ## Using the compute nodes - diff --git a/docs/getting_started/get_started.md b/docs/getting_started/get_started.md index aaa4394a7..b976afd55 100644 --- a/docs/getting_started/get_started.md +++ b/docs/getting_started/get_started.md @@ -5,15 +5,17 @@ In order to use UPPMAX resources, you need to be a member of a project and a use ## PIs Do you or members in your research group need compute and storage resources on a HPC cluster or Infrastructure-as-a-Service cloud? Learn how to apply for a project by following the link below. + - [Project apply](project_apply.md) Are you interested in other services, e.g. large volume data storage? -Let us know by contacting UPPMAX Support at support@uppmax.uu.se ! +Let us know by contacting UPPMAX Support at ! ## Users Once you or someone in your group or collaboration has a project, you must apply for a user account by following the link below. + - [User account](user_account.md) Have an account already? Then check out these basic user guides: @@ -22,15 +24,13 @@ Have an account already? Then check out these basic user guides: - [Rackham first steps](login_rackham.md) - [Snowy first steps](login_snowy.md) - ## Students Are you taking a university course that uses UPPMAX and need help? Ask your instructor! If they can't help, contact us through IT Support. - ## Getting started: First login to UPPMAX -N.B. You are NOT supposed to log in to any webpage with the password and username you get via UPPMAX support, with the exception of the ThinLinc web interface.  +N.B. You are NOT supposed to log in to any webpage with the password and username you get via UPPMAX support, with the exception of the ThinLinc web interface. In order to use the UPPMAX resources you must login to a dedicated login computer (or 'login node') using ssh ("secure shell"). On Linux/Unix computers this is done in the terminal with the 'ssh' command. On Windows you can download a small free program called [MobaXterm](https://mobaxterm.mobatek.net/) (or an alternative of your choice) to connect via ssh. @@ -81,7 +81,6 @@ Now you are logged in! To log out again, type 'exit'. Note: The information displayed in the welcome screen contains very important information about the usage of UPPMAX, which might affect your jobs, such as scheduled downtime etc, so please read very carefully, and look out for any announcements! - ## Changing your password You should regularly change your password. This is done in the standard Linux way. Type: @@ -90,8 +89,8 @@ You should regularly change your password. This is done in the standard Linux wa The system will prompt you for your current password, after which it will ask you for a new password and a confirmation of the new password. If you lose your password and need to reset it, follow this link (which you can also find on our homepage). - ## Copying files from/to your UPPMAX account + ### From a Linux or Unix computer Copy a file from you computer to your home directory on UPPMAX: @@ -104,7 +103,7 @@ Copy a file from your home directory on UPPMAX to your computer: To place the file in the directory you are currently standing in, use a dot ('.') as the local directory: -scp user@milou.uppmax.uu.se:/home/username/some-file . +scp :/home/username/some-file . ### From a Windows computer @@ -152,6 +151,7 @@ The default permission of your home directory is 750, i.e. you can do everything Also note the private sub-folder. Here you can put files that you want only you, and no one else, to be able to access. Each day we have a job that ensures that all users's private folders still can't be accessed by anyone else, even if the permissions somehow accidentally would change. ## Creating and editing files + ### The nano text editor There are several editors installed at UPPMAX. The one that is considered easiest to use for new users without graphics is nano. @@ -194,7 +194,7 @@ You can read a tutorial in emacs by doing: Control-h t -For a tutorial on emacs: http://www.gnu.org/software/emacs/tour/ +For a tutorial on emacs: ### The Gedit text editor diff --git a/docs/getting_started/linux.md b/docs/getting_started/linux.md index b653ed305..e5efde762 100644 --- a/docs/getting_started/linux.md +++ b/docs/getting_started/linux.md @@ -1,4 +1,5 @@ # Linux + - The "operating system" of the UPPMAX and most of the other clusters is **Linux**. !!! questions @@ -6,8 +7,6 @@ - What is Linux? - How to use the command line? - - !!! objectives - We'll briefly get an overview of Linux @@ -30,29 +29,19 @@ ![Content](./img/images.jfif) - - - Actually, for it to be an OS, it is supplied with GNU software and other additions giving us the name **GNU/Linux**. - [Linux naming controversy](https://en.wikipedia.org/wiki/GNU/Linux_naming_controversy) - - ![Content](./img/gnu.png) - - - Linux has a multiuser platform at its base which means permissions and security comes easy. +### Linux comes in different distributions, dialects or, say, flavours -### Linux comes in different distributions, dialects or, say, flavours. - UPPMAX runs CentOS and RedHat - - ![Content](./img/flavours.png) - - ## Using the command line Below usage of the command line is discussed in text. @@ -60,6 +49,7 @@ If you prefer video, [here](https://youtu.be/kjqLAx2bgJI) is how to use the command-line on the UPPMAX Bianca cluster. ### Command line with bash (Bourne Again Shell) + - A Unix shell and command language. - Often default shell @@ -72,7 +62,6 @@ is how to use the command-line on the UPPMAX Bianca cluster. ![Content](./img/unix_architecture.jpg) - ### The prompt [info]$ program word1 word2 word3 […] @@ -94,7 +83,6 @@ is how to use the command-line on the UPPMAX Bianca cluster. ### Example bash command - ![mv inbox](./img/mv_inbox.png){: style="width:300px"}
@@ -102,29 +90,23 @@ is how to use the command-line on the UPPMAX Bianca cluster. ![program flags](./img/program_flags.png){ : style="width:200px" } -
- Terminal screen shows ![Content](./img/screen.png){ : style="width:500px" } - ### Tab Completion - ![Content](./img/tab.png){ : style="width:200px" } -
< - - Whenever you’re writing a path or filename on the bash prompt, you can strike the ‘tab’ key to ask Bash to complete what you’re writing. - Get in the habit of this — it will save you many hours! - ## Editing files ![](./img/edit.png) @@ -143,7 +125,6 @@ which are described at the UPPMAX 'Text editors' page [here](../software/text_ed - Type `test text` - End and save with ``-X`` followed by `Y` and ``. - ## Typical sources of error ![Content](./img/cross.png) @@ -156,12 +137,10 @@ which are described at the UPPMAX 'Text editors' page [here](../software/text_ed - Check that you are in the right place in the file system. - File permissions. Check that the right read, write and execute permission are set. See next session. - -## Caution!! +## Caution ![Content](./img/caution.png) - !!! Warning - There is no undo for: @@ -170,7 +149,6 @@ which are described at the UPPMAX 'Text editors' page [here](../software/text_ed - remove (`rm`). - **Beware of overwriting files and deleting the wrong ones.** - !!! tip - **Tip: make "`rm`" ask if you really want to erase:** @@ -189,7 +167,6 @@ which are described at the UPPMAX 'Text editors' page [here](../software/text_ed - If you do destroy your data, email UPPMAX support, we may be able to help. - !!! keypoints - Linux Operating system is a UNIX-like and UNIX compatible Operating system. @@ -202,8 +179,6 @@ which are described at the UPPMAX 'Text editors' page [here](../software/text_ed - no undo:s for copying, moving and removing - Solution: ``alias rm='rm -i' `` - - ## Links - * A free online book about Linux: ['The Linux Command Line'](https://linuxcommand.org/tlcl.php). +- A free online book about Linux: ['The Linux Command Line'](https://linuxcommand.org/tlcl.php). diff --git a/docs/getting_started/linux_basics.md b/docs/getting_started/linux_basics.md index 4972e9309..ce7e04af4 100644 --- a/docs/getting_started/linux_basics.md +++ b/docs/getting_started/linux_basics.md @@ -1,14 +1,11 @@ # Basic toolkit - ![Caption](./img/terminal.png) - !!! objectives - Let's dig into the most important BASH commands - We'll do a type-along session - ???- question "Like videos?" Below usage of the command line is discussed in text. @@ -17,8 +14,6 @@ ## We will cover these commands - - ### Navigation and file management 1. `pwd`   present directory @@ -42,54 +37,56 @@ 16. `man`  info about a command ## File system Navigation + ### pwd — where are you now? “Print name of current/Working Directory” ```console -$ pwd +pwd -$ pwd -P +pwd -P ``` + - ``-P`` gives you the physical path, - ignores how you got there - ### ls — list directory contents Type ``ls`` to display the contents of the current directory. ```console -$ ls -a +ls -a ``` ``-a`` also shows hidden files and directories. ```console -$ ls -l +ls -l ``` + ``-l`` gives you listed and detailed information. ```console -$ ls -lt +ls -lt ``` ``-lt`` sorts things by time modified. ```console -$ ls –lrt +ls –lrt ``` ``-r`` gives reversed order, so in this case newest in last line. ```console -$ man ls +man ls ``` - for complete information about a command. - TIP: `-$ man ` works for almost any command! - scroll with arrows and quit with ``q``. - ### cd — Change the shell working Directory + - To change directory, use ``cd `` !!! warning @@ -98,15 +95,15 @@ $ man ls - These involve the `/proj/introtouppmax`` directory ```console -$ cd /proj/introtouppmax +cd /proj/introtouppmax -$ pwd +pwd -$ ls +ls -$ cd labs +cd labs -$ pwd +pwd ``` !!! challenge Experiment with cd @@ -137,43 +134,40 @@ $ pwd - `cd ~` : also goes to home directory - - - ## Copy, Create, Move + ### mkdir — make directories !!! warning - Make sure you’re in your home directory by `cd ~` - - Create a new directory ``uppmax-intro`` ```console -$ cd ~ -$ mkdir uppmax-intro +cd ~ +mkdir uppmax-intro ``` - Go in there: ```console -$ cd uppmax-intro/ +cd uppmax-intro/ ``` - ### cp — copy files and directories - Copy files with: `cp ` - Set target to ``.`` to keep name and to point at present directory. ```console -$ cp /proj/introtouppmax/labs/linux_tutorial/ . +cp /proj/introtouppmax/labs/linux_tutorial/ . ``` - Well, that didn’t work. What does the error say? - So... try + ```console -$ cp -r /proj/introtouppmax/labs/linux_tutorial/ . +cp -r /proj/introtouppmax/labs/linux_tutorial/ . ``` ``-r`` is for recursive, meaning including files and subdirectories! @@ -181,12 +175,13 @@ $ cp -r /proj/introtouppmax/labs/linux_tutorial/ . - Move to your just created ``linux_tutorial/`` ```console -$ cd linux_tutorial +cd linux_tutorial ``` + - Make a copy of the file “newfile” in the same directory: ```console -$ cp newfile copyfile +cp newfile copyfile ``` ### scp — secure copy (remote file copy program) @@ -194,14 +189,15 @@ $ cp newfile copyfile - Linux/MacOS: To copy data to/from Rackham, you can use ``scp`` **from the terminal on your local machine**: #### Download from Rackham + - Download + ```console [bob@macbook]$ scp bob@rackham.uppmax.uu.se:~/mydata copyofmydata [bob@macbook]$ scp bob@rackham.uppmax.uu.se:~/mydata . # (keeping file name) ``` - !!! example **Download the file ``first.txt``** @@ -213,6 +209,7 @@ $ cp newfile copyfile ``` #### Upload to Rackham + - Upload from present directory on local machine to your home directory on cluster. - Example: @@ -239,28 +236,32 @@ $ cp newfile copyfile - [Rackham file transfer using scp](http://docs.uppmax.uu.se/cluster_guides/rackham_file_transfer_using_scp/) - ### mv — move/rename file - Moving files works just like copying files: - `mv ` - Move the copy you just made to another place: + ```console -$ mv copyfile ../ +mv copyfile ../ ``` + - Rename it. + ```console -$ mv ../copyfile ../renamedfile +mv ../copyfile ../renamedfile ``` ## Archiving + **tar — archiving and compression** - We’re going to need more files. Let's extract the tar.gz file (tared and gzipped file) ```console -$ tar -vxzf files.tar.gz +tar -vxzf files.tar.gz ``` + - The flags mean: - verbosely - extract @@ -278,6 +279,7 @@ $ tar -vxzf files.tar.gz ``` ## Deleting + ### rm — delete files or directories !!! Note @@ -296,28 +298,26 @@ $ tar -vxzf files.tar.gz - Edit file ".bashrc" in /home directory by adding the above alias line on any but the first line. - These steps will also work for ``mv`` and ``cp``. - - Deleting files works just like copying or moving them: `rm ` - Try it out: ```console -$ rm ../renamedfile +rm ../renamedfile -$ rm this_is_empty +rm this_is_empty ``` - hmmmm... - ### rmdir — delete an empty directory - We need another command to delete directories ```console -$ rmdir this_is_empty +rmdir this_is_empty -$ rmdir this_has_a_file +rmdir this_has_a_file ``` - Problem again?? @@ -331,14 +331,14 @@ $ rmdir this_has_a_file $ rm -r this_has_a_file ``` - ## Help + ### man — manual, look up the right flags - Nobody can remember whether it’s ``-R`` or `-r` for recursive, or if ``-f`` lets you choose a file or forces an action. ```console -$ man ls +man ls ``` - shows you how to use ``ls`` and all its options @@ -349,8 +349,6 @@ $ man ls !!! challenge - Spend some time now to browse the man pages for the commands you’ve just learned! - - ## Let’s get wild with Wildcards + ![Caption](./img/wildcards_bear.png) ```console -$ ls many_files +ls many_files -$ ls many_files/*.txt +ls many_files/*.txt -$ ls many_files/file_1*1.docx +ls many_files/file_1*1.docx ``` - Want to clean out temporary files ending in .tmp in all the subdirectories? @@ -401,20 +400,18 @@ $ ls many_files/file_1*1.docx !!! challenge Exercise - Exercise: Create a new directory and move all .txt files in many_files to it. - ## Reading files - In Linux, you can (if you wish) also display files without being able to change them ```console -$ cd old_project +cd old_project -$ ls +ls ``` - Hmm, which of these files are useful? - ### cat - concatenate files and print on the standard output ![Caption](./img/cat.png) @@ -422,13 +419,13 @@ $ ls - ``cat`` dumps the contents of files to the terminal as text ```console -$ cat the_best +cat the_best ``` - Yummy! ```console -$ cat a +cat a ``` - What's this???? @@ -436,46 +433,43 @@ $ cat a - **Concatenate** files with this wizardry: ```console -$ cat a the_best > combinedfiles.txt +cat a the_best > combinedfiles.txt ``` - File ``a`` is written first and ``the_best`` is appended ### head — display the top (heading) of a file - ![Caption](./img/head.png) ```console -$ head a +head a ``` + - You can choose how many lines to display (default 10) ```console -$ head -n 4 a +head -n 4 a ``` - ### tail — display the end of a file - ![Caption](./img/tail.png) - Tail is the same as head, but for the other end. ```console -$ tail -n 5 a +tail -n 5 a ``` - Handy to look at log files or to figure out the structure of a text file. - ### less — read a whole file - cat doesn’t really work for long files ```console - $ less a + less a ``` - Search with `/` and `n`/`N` @@ -489,19 +483,14 @@ $ tail -n 5 a - ``history`` shows previous commands - You can rerun earlier commands by: - - copy-pasting and pressing ```` - - ``!990`` will run the command of line 990 of last `history` output. + - copy-pasting and pressing ```` + - ``!990`` will run the command of line 990 of last `history` output. - Search for earlier commands you just remember parts of: - - history | grep 'jobstats' + - history | grep 'jobstats' - [More info](https://www.redswitches.com/blog/linux-history-command/) - - - - ## File permissions - ![Caption](./img/permission.png) ### Example @@ -545,8 +534,8 @@ $ ls -l - Files: Run the file as a program - Directories: Traverse the directory (e.g. with “cd”) - ## Changing permissions + **chmod** — change file mode bits **If you own, i.e. created, the file or directory, you can modify the content** @@ -557,38 +546,37 @@ $ ls -l - If you want to share data or scripts with a person not in your project (e.g. support staff like me), you can! - If you want to keep non-members from even seeing which files you have, you can! - ### Syntax `chmod ` - `` is of the form: For whom, Modify, What permission(s) - For whom? - - `u`: user/owner - - `g`: group, often the members to a certain project - - `o`: others - - `a`: all - - if not set changes are applied for user AND group + - `u`: user/owner + - `g`: group, often the members to a certain project + - `o`: others + - `a`: all + - if not set changes are applied for user AND group - Modify? - - `+`: add permissions, - - `-`: remove - - `=`: set equal to - - `=` usually causes unmentioned bits to be removed except that a directory's unmentioned set user and group ID bits are not affected. + - `+`: add permissions, + - `-`: remove + - `=`: set equal to + - `=` usually causes unmentioned bits to be removed except that a directory's unmentioned set user and group ID bits are not affected. - What permissions? - - `r`, `w`, `x`, i.e. the actual permission + - `r`, `w`, `x`, i.e. the actual permission #### Examples - `` can be e.g.: - - `u+x` : lets You (owner) run a script you just wrote - - `-w` : no write permissions for **owner+group** - - warning: if `w` was already set for *others* it will be kept!! - - `+rw` : let user and group members read and edit this file, not others if not already set - - `=xw` : let group members go into your directory and put files there, but not see which files are there, others are not affected - - `a=xw` : set xw for everyone + - `u+x` : lets You (owner) run a script you just wrote + - `-w` : no write permissions for **owner+group** + - warning: if `w` was already set for *others* it will be kept!! + - `+rw` : let user and group members read and edit this file, not others if not already set + - `=xw` : let group members go into your directory and put files there, but not see which files are there, others are not affected + - `a=xw` : set xw for everyone - chmod takes flags as usual, e.g. - - `-R` for recursive (i.e. all files and sub-directories therein) + - `-R` for recursive (i.e. all files and sub-directories therein) !!! admonition "chmod 755 style — binary sum — octal bit mask" @@ -606,8 +594,6 @@ $ ls -l ??? solution 6 - - ???+ challenge "chmod — Hands-on" - In your *locally created* ``linux_tutorial`` directory, find important files and old saved data that you wouldn’t want to lose (*imagine*). @@ -624,5 +610,4 @@ $ ls -l ## Links - * A free online book about Linux: ['The Linux Command Line'](https://linuxcommand.org/tlcl.php). - +- A free online book about Linux: ['The Linux Command Line'](https://linuxcommand.org/tlcl.php). diff --git a/docs/getting_started/login_bianca.md b/docs/getting_started/login_bianca.md index 7c317f5d6..b02b54e8d 100644 --- a/docs/getting_started/login_bianca.md +++ b/docs/getting_started/login_bianca.md @@ -14,8 +14,8 @@ Here it is described how to log in to [Bianca](../cluster_guides/bianca.md): - [The two Bianca environments](#the-two-bianca-environments) shows the two ways to use Bianca - [Get within the university networks](#get-within-the-university-networks) shows how *to be allowed to* access Bianca - [Get inside the Bianca environment](#get-inside-the-bianca-environment) show how to get inside the Bianca environments: - - [Login to the Bianca remote desktop environment](#login-to-the-bianca-remote-desktop-environment) - - [Login to the Bianca console environment](#login-to-the-Bianca-console-environment) + - [Login to the Bianca remote desktop environment](#login-to-the-bianca-remote-desktop-environment) + - [Login to the Bianca console environment](#login-to-the-bianca-console-environment) ## Prerequisites for using Bianca @@ -144,7 +144,6 @@ The [remote desktop environment](../cluster_guides/thinlinc.md) is considered th new users, as it has most similarities with what a new user is familiar with. However, one must always use a terminal to some extent. - ```mermaid flowchart TD @@ -197,7 +196,7 @@ When inside SUNET, one can access the Bianca environments. - For a remote desktop environment, go to [login to the Bianca remote desktop environment](#login-to-the-bianca-remote-desktop-environment) - For a console environment, - go to [login to the Bianca console environment](#login-to-the-Bianca-console-environment) + go to [login to the Bianca console environment](#login-to-the-bianca-console-environment) Below, the ways to access these Bianca environments are discussed @@ -342,7 +341,7 @@ When picking a remote desktop flavor, pick GNOME or XFCE, avoid picking KDE. Instead, we recommend GNOME or XFCE. -#### 5. You are in! +#### 5. You are in Enjoy! You are in! You are on a Bianca login node! @@ -445,7 +444,7 @@ You can also have multiple log-ins active at once. There are multiple ways to set this up: - [Using an SSH password](#login-to-the-bianca-console-environment-using-an-ssh-password). -- [Using SSH keys](#login-to-the-Bianca-console-environment-using-ssh-keys) +- [Using SSH keys](#login-to-the-bianca-console-environment-using-ssh-keys) Using an SSH password is considered easiest, where using an SSH key is considered more elegant. @@ -504,8 +503,7 @@ using SSH with an SSH password. This is considered the easier one to setup, but one will have to type a password twice to login. To get rid of one password and setup SHH keys, -see [here](#login-to-the-Bianca-console-environment-using-ssh-keys). - +see [here](#login-to-the-bianca-console-environment-using-ssh-keys). #### 1. Use `ssh` to log in @@ -555,7 +553,6 @@ ssh sven-sens2023598@bianca.uppmax.uu.se [X forwarding](../software/ssh_x_forwarding.md) is disabled. Hence, we do not teach it :-) - #### 2. Type your UPPMAX password with 2FA Type your UPPMAX password, @@ -599,7 +596,7 @@ which may take some minutes. Type your UPPMAX password, for example `verysecret` -#### 4. You are in! +#### 4. You are in Enjoy! You are in! Or, to be precise, you are on the login node of your own virtual project cluster. @@ -681,7 +678,7 @@ for example `verysecret678123`, then press enter. In this case, the password is `verysecret` and `678123` is the 2FA number. -### 3. You are in! +### 3. You are in Enjoy! You are in! To be precise, you are on a Bianca login node. @@ -736,7 +733,6 @@ Enjoy! You are in! To be precise, you are on a Bianca login node. bianca_private_remote_desktop-->|must also use|bianca_private_terminal ``` - ## Extra material ### Overview diff --git a/docs/getting_started/login_dardel.md b/docs/getting_started/login_dardel.md index 079ccabb4..e1d758d90 100644 --- a/docs/getting_started/login_dardel.md +++ b/docs/getting_started/login_dardel.md @@ -86,12 +86,10 @@ Create SSH key and add it to the PDC Login Portal. - Create the password less SSH key in a Linux terminal (e.g. from Rackham): - ```bash module load darsync ``` - ```bash darsync sshkey ``` @@ -137,4 +135,3 @@ where `[username]` is your PDC username, for example `ssh -X sven@dardel.pdc.kth The `-X` is for so-called [X forwarding](../software/ssh_x_forwarding.md). It allows you to view graphical things, such as viewing plots or running graphical programs - diff --git a/docs/getting_started/login_rackham.md b/docs/getting_started/login_rackham.md index f7ecdcb97..496b0e01f 100644 --- a/docs/getting_started/login_rackham.md +++ b/docs/getting_started/login_rackham.md @@ -31,7 +31,6 @@ Here we describe how to log in to [Rackham](../cluster_guides/rackham.md) - Below you find how to log in - Further down we present other procedures to reach Rackham, depending on your planned work. - ## Log in with a terminal, omitting support for graphics === "Mac" @@ -83,12 +82,9 @@ Here we describe how to log in to [Rackham](../cluster_guides/rackham.md) - [Git bash](https://gitforwindows.org/) - - !!! info "Working on Rackham" - Now we present alternatives to work on Rackham - ## Alternative ways to log in and work !!! info "Login procedure" @@ -135,8 +131,6 @@ Here we describe how to log in to [Rackham](../cluster_guides/rackham.md) - *ThinLinc application* - - ## Terminals (see above) ## Terminal with X11 server and light graphics @@ -202,8 +196,6 @@ Here we describe how to log in to [Rackham](../cluster_guides/rackham.md) ![Caption](./img/mobax_start.jpg) - - !!! note "X-forwarding from the command line (generally)" [X forwarding](../software/ssh_x_forwarding.md) allows @@ -220,8 +212,6 @@ Here we describe how to log in to [Rackham](../cluster_guides/rackham.md) - Alternatively, use `-z` to put e.g. gedit to sleep and type "`bg`" to make last process in background. - - ???+ question "Test log in to **Rackham**, using your terminal" - First try: @@ -251,7 +241,7 @@ This gives you a desktop environment, as if you were working on your own compute You can do so: - [via the web](#remote-desktop-via-the-web) -- [via a ThinLinc client](#remote-desktop-via-a-ThinLinc-client) +- [via a ThinLinc client](#remote-desktop-via-a-thinlinc-client) ### Remote desktop via the web @@ -273,19 +263,17 @@ Use the ThinLinc client from [https://www.cendio.com/thinlinc/download](https:// - Mac is UNIX and very Linux-like - Windows requires WSL (Windows subsystem for Linux) - ??? question "For windows users who wants to get started with WSL (not covered here)" - Install WSL (Windows Subsystem for Linux) - - https://docs.microsoft.com/en-us/windows/wsl/install-win10 (Links to an external site.) + - (Links to an external site.) - Don’t forget to update to wsl2 - Install a distribution or a ssh (secure shell) program - Distribution such as ubuntu or - (recommended) a ssh program such as MobaXTerm - - https://mobaxterm.mobatek.net/ (Links to an external site.) + - (Links to an external site.) - sftp frame makes it easy to move, upload and download files. - You may want to check this webpage as well! - - https://hackmd.io/@pmitev/Linux4WinUsers (Links to an external site.) - + - (Links to an external site.) ## Visual Studio Code (not covered here) @@ -296,9 +284,7 @@ Use the ThinLinc client from [https://www.cendio.com/thinlinc/download](https:// - Integrate you cluster work with *code development* - [SSH-remote from VS Code](https://code.visualstudio.com/docs/remote/remote-overview) - [Remote development using Visual Studio Code on Alvis cluster](https://www.c3se.chalmers.se/documentation/remote-vscode/) - - Similar to Rackham. Just change login details! - - + - Similar to Rackham. Just change login details! !!! abstract "keypoints" - When you log in from your local computer you will always arrive at a login node with limited resources. @@ -311,4 +297,3 @@ Use the ThinLinc client from [https://www.cendio.com/thinlinc/download](https:// - Best integrated systems - Visual Studio Code has several extensions (remote, SCP, programming IDE:s) - Windows: MobaXterm is somewhat easier to use. - diff --git a/docs/getting_started/login_snowy.md b/docs/getting_started/login_snowy.md index 705b3fd9e..2038800e9 100644 --- a/docs/getting_started/login_snowy.md +++ b/docs/getting_started/login_snowy.md @@ -18,7 +18,6 @@ After logging in, one can - [Start a batch job using Snowy resources](../cluster_guides/slurm.md) - [Start an interactive job](../cluster_guides/start_interactive_node_on_snowy.md) - ```mermaid graph TB diff --git a/docs/getting_started/project.md b/docs/getting_started/project.md index a3ba36d2b..e1f4a9318 100644 --- a/docs/getting_started/project.md +++ b/docs/getting_started/project.md @@ -7,9 +7,9 @@ To use [UPPMAX](../cluster_guides/uppmax.md) resources, one needs: This page is about UPPMAX projects: - * [View your existing UPPMAX projects](#view-your-uppmax-projects) - * [Type of UPPMAX projects](#type-of-uppmax-projects) - * [Apply to an UPPMAX project](#apply-to-an-uppmax-project) +- [View your existing UPPMAX projects](#view-your-uppmax-projects) +- [Type of UPPMAX projects](#type-of-uppmax-projects) +- [Apply to an UPPMAX project](#apply-to-an-uppmax-project) ## View your UPPMAX projects diff --git a/docs/hardware/clusters/rackham.md b/docs/hardware/clusters/rackham.md index 6f65be6bd..64c3edbf3 100644 --- a/docs/hardware/clusters/rackham.md +++ b/docs/hardware/clusters/rackham.md @@ -5,8 +5,6 @@ | 4 | 2x Xeon E5-2630 V4 2.2 GHz (turbo 3.1 GHz) | 20 (2 x 10) | 1TB | 3/4TB | N/A | ? | | | 4 | 2x Xeon E5-2630 V4 2.2 GHz (turbo 3.1 GHz) | 20 (2 x 10) | 256GB | 3/4TB | Nvidia Quatro K2200 | rackham1-rackham3 | Login nodes | - - The Rackham cluster was introduced in February 2017. Rackham is a NAISS resource and is estimated to be in production until first of January 2023. The major features of Rackham and its storage system Crex is found below. For more diff --git a/docs/hardware/clusters/snowy.md b/docs/hardware/clusters/snowy.md index c592f79e1..c42400275 100644 --- a/docs/hardware/clusters/snowy.md +++ b/docs/hardware/clusters/snowy.md @@ -8,7 +8,6 @@ | 1 | 2x Xeon E5-2660 2.2 GHz | 80 (10 x 8) | 4TB | 3/4TB | N/A | s229 | | | 1 | 2x Xeon E5-2660 2.2 GHz | 16 (2 x 8) | 256GB | 3/4TB | Tesla T4 | s138 | | - ## CPU ## GPU diff --git a/docs/hardware/overview.md b/docs/hardware/overview.md index 33b839cdf..ac3104f6d 100644 --- a/docs/hardware/overview.md +++ b/docs/hardware/overview.md @@ -4,12 +4,11 @@ at UPPMAX as well as their storage systems. UPPMAX is part of the [National Academic Infrastructure for Supercomputing in Sweden (NAISS)](https://www.naiss.se/) and as such - | |Rackham|Snowy|Bianca|UPPMAX Cloud| |-------|-----|------|---|---| |**Purpose**|General-purpose|General-purpose|Sensitive data|IaaS |**Reserved for**|NAISS projects|Uppsala researchers and course projects|NAISS-SENS projects|NAISS and local projects | -|** Nodes (Intel)**|486+144|228+
50 N vidia T4 GPUs|272 +
4 nodes á 2
NVIDIA A100 GPUs| 40 +
20 A2 and 4 T4 Nvidia GPUs | +|**Nodes (Intel)**|486+144|228+
50 N vidia T4 GPUs|272 +
4 nodes á 2
NVIDIA A100 GPUs| 40 +
20 A2 and 4 T4 Nvidia GPUs | |**Cores per node**|20/16|16|16/64| 16 |**Memory per node**|128GB|128GB|128GB |128/256GB | |**Fat nodes**|256GB & 1TB| 256, 512 GB & 4TB| 256 & 512GB|N/A diff --git a/docs/hardware/storage/lutra.md b/docs/hardware/storage/lutra.md index 0193f5678..0bafd29bb 100644 --- a/docs/hardware/storage/lutra.md +++ b/docs/hardware/storage/lutra.md @@ -6,4 +6,4 @@ SEK/TB/year, for a commitment of four years and a minimum 50TB. The design and filesystem choice makes Lutra very scalable, cost efficient while retaining moderate read/write performance. Lutra is connected to Rackham and Snowy for general availability. If you are interested in this type of storage please -contact support@uppmax.uu.se. +contact . diff --git a/docs/index.md b/docs/index.md index b0652daca..080f4da33 100644 --- a/docs/index.md +++ b/docs/index.md @@ -10,10 +10,8 @@ template: home.html
- # Welcome to the UPPMAX documentation -
[Apply for a project](getting_started/project_apply.md){ .md-button .md-button--primary } @@ -27,5 +25,4 @@ template: home.html

- diff --git a/docs/software/allinea-ddt.md b/docs/software/allinea-ddt.md index 691e3a3a1..e1f466178 100644 --- a/docs/software/allinea-ddt.md +++ b/docs/software/allinea-ddt.md @@ -23,26 +23,16 @@ Start an interactive job with multiple cores (e.g. "interactive -p core -n 20 -A Debugging MPI programs: To be able to debug MPI program select MPI option as well as the "Submit to Queue" option, and then click on "Change" to select submission script configuration for Rackham and provide the job specific options. - - System> select "Auto-Detect" for "MPI/UPC Implementation" and tick "Create Root and Workers group automatically". - - Job Submission> Browse and select "/sw/comp/ddt/7.0/templates/rackham-core.qtf" in the filed "Submission template file:". Make sure that "Quick Restart" is also ticked. This will allow you to restart your program without cancelling the allocated time and allocating it again. (There is also a rackham-node.qtf in the same directory as the rackham-core.qtf configuration, this will allow you to submit the node and devcore partitions as well.) - - "Edit Queue Submission Parameters..." to specify Partition, Project and requested time. Failing to provide project number will cause failures in the submission process. - - On the main configuration window the button "Run" will change to "Submit". Click on this button to submit your debugging session to the queue manager. If you enable "Memory debugging", click the "Details" button and tick "Preload the memory debugging library" and select "C/Fortran threads" in the "Language:" field. Read the manual for more detail on the other options in this panel. - - Useful links Allinea DDT home page diff --git a/docs/software/beast2.md b/docs/software/beast2.md index 988f05a95..dd2f10fb2 100644 --- a/docs/software/beast2.md +++ b/docs/software/beast2.md @@ -79,7 +79,6 @@ or use a script. View the UPPMAX documentation ['How to start an interactive node on Rackham'](../cluster_guides/start_interactive_node_on_rackham). - On an interactive node, run BEAST2 on the saved BEAST2 model: ``` @@ -96,8 +95,8 @@ module load bioinfo-tools beast2/2.7.4 beast beast2_setup.xml ``` - * In line 2, replace `uppmax2023-2-25` with [your UPPMAX project](../getting_started/project.md). - * In line 3, you may want to replace `beast2/2.7.4` with your favorite BEAST2 version +* In line 2, replace `uppmax2023-2-25` with [your UPPMAX project](../getting_started/project.md). +* In line 3, you may want to replace `beast2/2.7.4` with your favorite BEAST2 version Then run this script using `sbatch run_beast2.sh`. @@ -243,7 +242,7 @@ beast -beagle_info ### BEAUti gives `BadAlloc` - * Platform(s): MacOS +* Platform(s): MacOS This problem seems to be related to not having a proper X server installed. In this case, [SSH X forwarding](ssh_x_forwarding.md) works to the extent @@ -285,10 +284,10 @@ A solution may be to [use the remote desktop via the web](../getting_started/log ## Optimize performance - * [BEAST2 performance suggestions](https://www.beast2.org/performance-suggestions/index.html) - * [BEAST2 and BEAGLE](https://www.beast2.org/beagle-beast-2-in-cluster/index.html) +* [BEAST2 performance suggestions](https://www.beast2.org/performance-suggestions/index.html) +* [BEAST2 and BEAGLE](https://www.beast2.org/beagle-beast-2-in-cluster/index.html) ## Links - * [DensiTree GitHub repository](https://github.com/rbouckaert/DensiTree) - * [CIPRES: cyberinfrastructure for phylogenetics research](https://www.phylo.org/) +* [DensiTree GitHub repository](https://github.com/rbouckaert/DensiTree) +* [CIPRES: cyberinfrastructure for phylogenetics research](https://www.phylo.org/) diff --git a/docs/software/cram.md b/docs/software/cram.md index ef910ba87..2c71aaf1d 100644 --- a/docs/software/cram.md +++ b/docs/software/cram.md @@ -1,7 +1,8 @@ # Using CRAM to compress BAM files ## Introduction -### Biological data is being produced at a higher rate each day, and it is a challenge to store it all somewhere. + +### Biological data is being produced at a higher rate each day, and it is a challenge to store it all somewhere The bioinformatics community is trying to keep up with the growing data amounts, and new file formats is part of this evolution. The BAM format was a huge success due to its ability to compress aligned reads by ~50-80% of their original size, but even that is not sustainable in the long run. @@ -44,24 +45,25 @@ Illumina 8-binning scheme: [Illumina's white paper on the matter](../files/c_557912-l_1-k_whitepaper_datacompression.pdf) ## Compression rate + So, how much compression are we talking about here? Here are the results of a test with a 1.9 GB BAM file (7.4 GB SAM format). CRAM COMPRESSION RATE -File format |File size (GB) +File format |File size (GB) ------------|-------------- -SAM |7.4 -BAM |1.9 -CRAM lossless| 1.4 -CRAM 8 bins| 0.8 -CRAM no quality scores| 0.26 +SAM |7.4 +BAM |1.9 +CRAM lossless| 1.4 +CRAM 8 bins| 0.8 +CRAM no quality scores| 0.26 ![Graph showing the content of the above table](../img/c_557912-l_1-k_cram_compression.png) - - ## Examples + ### Lossless compression of a BAM file + Lossless compression means that the BAM file will be identical before and after compression/decompression The downside of this is that the produced CRAM file will be larger since if has to save each and every quality score. To make a lossless compression, use the following command (can also be written as a single line by removing the backslashes): $ module load bioinfo-tools cramtools @@ -98,9 +100,11 @@ If you had NM or MD tags in your original BAM file, you have to specify that the and/or --calculate-nm-tag ``` + to the command. ### Lossy compression of a BAM file + The motivation to use a lossy compression is that the compression ratio will be much larger, i.e. the cram file will be much smaller. The best compression ratio is reached, naturally, when the quality scores are removed all together. This does have an impact on future analysis such as SNP calling, so the trick is, as usual, to find a good balance. Illumina has started with a practice called binning. That means that instead of having 40 unique quality scores, you put similar values into bins. Illumina thought 8 bins would get the job done, and that is what CRAM recommends. See this page's introduction for more details about the bins. diff --git a/docs/software/directly-from-IG/img/README.md b/docs/software/directly-from-IG/img/README.md index 32b8888af..0b371079f 100644 --- a/docs/software/directly-from-IG/img/README.md +++ b/docs/software/directly-from-IG/img/README.md @@ -1,2 +1 @@ -# Put related images here! - +# Put related images here diff --git a/docs/software/doc.md b/docs/software/doc.md index c31734262..e824dcb7b 100644 --- a/docs/software/doc.md +++ b/docs/software/doc.md @@ -1,2 +1 @@ # Software-specific documentation - diff --git a/docs/software/eog.md b/docs/software/eog.md index 8ce56d1e9..281ac3d15 100644 --- a/docs/software/eog.md +++ b/docs/software/eog.md @@ -2,7 +2,6 @@ ![Example use of eog](./img/eog.png) - `eog` is a tool to view images on an UPPMAX cluster. To be able to see the images, @@ -11,7 +10,6 @@ or [login to a remote desktop](../getting_started/login.md) Usage: - ``` eog [filename] ``` diff --git a/docs/software/games_us.md b/docs/software/games_us.md index 8a9dd1784..a6b3a327c 100644 --- a/docs/software/games_us.md +++ b/docs/software/games_us.md @@ -5,10 +5,13 @@ GAMESS-US versions 20170930 is installed on Rackham. Newer versions can be insta ## Running GAMESS Load the module using + ```bash module load gamess/20170930 ``` + Below is an example submit script for Rackham, running on 40 cores (2 nodes with 20 cores each). It is essential to specify the project name: + ```slurm #!/bin/bash -l #SBATCH -J jobname @@ -22,14 +25,17 @@ rungms gms >gms.out ``` ## Memory specification + GAMESS uses two kinds of memory: replicated memory and distributed memory. Both kinds of memory should be given in the $SYSTEM specification. Replicated memory is specified using the MWORDS keyword and distributed memory with the MEMDDI keyword. It is very important that you understand the uses of these keywords. Check the GAMESS documentation for further information. If your job requires 16MW (mega-words) of replicated memory and 800MW of distributed memory, as in the example below, the memory requirements per CPU core varies as 16+800/N where N is the number of cores. Each word is 8 bytes of memory, why the amount of memory per core is (16+800/N)*8. The amount of memory per node depends on the number of cores per node. Rackham has 20 cores per node, most nodes have 128 GB of memory, but 30 nodes have 512 GB and 4 nodes at 1 TB. ## Communication + For intra-node communication shared memory is used. For inter-node communication MPI is used which uses the Infiniband interconnect. ## Citing GAMESS papers + It is essential that you read the GAMESS manual thoroughly to properly reference the papers specified in the instructions. All publications using GAMESS should cite at least the following paper: ```bibtex @@ -43,4 +49,5 @@ pages={1347}, year=1993, comment={The GAMESS program}} ``` -If you need to obtain GAMESS yourself, please visit the GAMESS website for further instructions. \ No newline at end of file + +If you need to obtain GAMESS yourself, please visit the GAMESS website for further instructions. diff --git a/docs/software/gaussian.md b/docs/software/gaussian.md index 9e63595b2..0a62b58c0 100644 --- a/docs/software/gaussian.md +++ b/docs/software/gaussian.md @@ -3,14 +3,17 @@ > A short guide on how to run g09 on UPPMAX. ## Access to Gaussian 09 + Gaussian 09 is available at UPPMAX. Uppsala University has an university license for all employees. If you want to be able to run g09 email [support@uppmax.uu.se](mailto:support@uppmax.uu.se) and ask to be added to the g09 group. ## Running g09 + In order to run g09 you must first set up the correct environment. You do this with: `module load gaussian/g09.d01` ### Running single core jobs in SLURM + Here is an example of a submit script for SLURM: ```slurm @@ -44,6 +47,7 @@ F 1 1.0 ``` ## Scratch space + The g09 module sets the environment `GAUSS_SCRDIR` to `/scratch/$SLURM_JOBID` in slurm. These directories are removed after the job is finished. If you want to set `GAUSS_SCRDIR`, you must do it after module load `gaussian/g09.a02` in your script. @@ -55,6 +59,7 @@ If you think you will use a large amount of scratch space, you might want to set ``` #P MP2 aug-cc-pVTZ SCF=Tight maxdisk=170GB ``` + or you can put something like: ```bash @@ -66,9 +71,11 @@ sed -i '/^#/ s/$/ maxdisk='$MAXDISK'/'; inputfile in your scriptfile. This will set **maxdisk** to the currently available size of the /scratch disk on the node you will run on. Read more on maxdisk in the [online manual](https://gaussian.com/maxdisk/). ## Running g09 in parallel + Gaussian can be run in parallel on a single node using shared memory. This is the input file for the slurm example below: The `dimer4.inp` input: + ``` %Mem=3800MB %NProcShared=4 @@ -93,6 +100,7 @@ methanol dimer MP2 ``` ### Running g09 in parallel in slurm + This can be done by asking for CPUs on the same **node** using the parallel node environments and telling Gaussian to use several CPUs using the `NProcShared` link 0 command. An example submit-script: @@ -118,9 +126,11 @@ _PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda._ The reason for specifying `OMP_NUM_THREADS=1` is to not use the parts of OpenMP in the Gaussian code, but to use Gaussians own threads. ## Running g09 in parallel with linda + In order to run g09 in parallel over several nodes we have acquired Linda TCP. ### Running g09 in parallel with linda in slurm + This can be done by asking for CPUs on the same **node** using the parallel node environments and telling Gaussian to use several CPUs using the `NProcLinda` and `NProcShared` link 0 command. An example submit-script: @@ -180,23 +190,25 @@ Please benchmark your own inputs as the speedup depends heavily on the method an In some cases Gaussian cannot use all the cpus you ask for. This is indicated in the output with lines looking like this: -_ PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda._ +_PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda._ ## Number of CPUs on the shared memory nodes + Use the information below as a guide to how many CPUs to request for your calculation: -### On Rackham: +### On Rackham - 272 nodes with two 10-core CPUs and 128GB memory - 32 nodes with two 10-core CPUs and 256GB memory -### On Milou: +### On Milou - 174 nodes with two 8-core CPUs and 128GB memory - 17 nodes with two 8-core CPUs and 256GB memory - 17 nodes with two 8-core CPUs and 512GB memory -### Note on chk-files: +### Note on chk-files + You may experience difficulties if you mix different versions (g09 and g03) or revisions of gaussian. If you use a checkpoint file (.chk file) from an older revision (say g03 e.01), in a new calculation with revision a.02, g09 may not run properly. We recommend using the same revision if you want to restart a calculation or reuse an older checkpoint file. diff --git a/docs/software/gromacs.md b/docs/software/gromacs.md index ea914a5a5..b50e49127 100644 --- a/docs/software/gromacs.md +++ b/docs/software/gromacs.md @@ -4,14 +4,12 @@ This page describes how to run the GROMACS molecular dynamics software on UPPMAX Have a look on this page as well - [best practices](https://docs.bioexcel.eu/gromacs_bpg/en/master/cookbook/cookbook.html) running GROMAC on HPC. - - Selected setups for benchmarking on HPC2N as [examples](https://github.com/hpc2n/CourseEfficientMD/tree/main/benchmark/GROMACS). ## Loading the gromac module ``` bash -$ module load gromacs/2021.1.th +module load gromacs/2021.1.th ``` ## SBATCH script @@ -52,11 +50,12 @@ $MPIRUN $GMX mdrun $ntmpi -ntomp $ntomp -s MEM.tpr -nsteps 10000 -resethway ``` ## How important is to select appropriate options -Here is a simple benchmark ran on single interactive node with 20CPUs using the MEM example from this benchmark https://www.mpibpc.mpg.de/grubmueller/bench. + +Here is a simple benchmark ran on single interactive node with 20CPUs using the MEM example from this benchmark . ``` bash -$ module load gromacs/2021.1.th -$ mpirun -np XX gmx_mpi mdrun -ntomp YY -s MEM.tpr -nsteps 10000 -resethway +module load gromacs/2021.1.th +mpirun -np XX gmx_mpi mdrun -ntomp YY -s MEM.tpr -nsteps 10000 -resethway ``` where XX * YY = 20 @@ -96,20 +95,24 @@ Notice how bad is the last run According to this short test, this particular setup runs best on single Rackham node with `$ mpirun -np 10 gmx_mpi mdrun -ntomp 2 -s MEM.tpr -nsteps 10000 -resethway` (lines 8-10) - ## Running older versions of gromacs -### Versions 4.5.1 to 5.0.4: +### Versions 4.5.1 to 5.0.4 + The gromacs tools have been compiled serially. The mdrun program has also been compiled in parallel using MPI. The name of the parallel binary is mdrun_mpi. Run the parallelized program using: + ``` bash mpirun -np XXX mdrun_mpi ``` + ... where XXX is the number of cores to run the program on. ### Version 5.1.1 + The binary is gmx_mpi and (e.g.) the mdrun command is issued like this: + ``` bash mpirun -np XXX gmx_mpi mdrun ``` diff --git a/docs/software/ides.md b/docs/software/ides.md index d98fd59bb..6164a367c 100644 --- a/docs/software/ides.md +++ b/docs/software/ides.md @@ -17,7 +17,7 @@ language (e.g. RStudio) and some allow multiple programming languages. How to use an IDE depends on the UPPMAX cluster you want to use: - * [IDEs on Bianca](../cluster_guides/ides_on_bianca.md) - * [IDEs on Rackham](../cluster_guides/ides_on_rackham.md) +* [IDEs on Bianca](../cluster_guides/ides_on_bianca.md) +* [IDEs on Rackham](../cluster_guides/ides_on_rackham.md) In general, using an IDE is easiest on Rackham and hardest on Bianca. diff --git a/docs/software/igv.md b/docs/software/igv.md index 5f7d1550b..e8ea07b70 100644 --- a/docs/software/igv.md +++ b/docs/software/igv.md @@ -20,6 +20,7 @@ ssh -X sven@rackham.uppmax.uu.se - MacOS users: the built-in [SSH client](../software/ssh_client.md) `ssh` does need [XQuartz](https://www.xquartz.org/) installed too ## Step 2: Reserve a node using "interactive" + Since genomic sequences require lots of memory, it is not suitable to run IGV on one of the login nodes. That would slow down the response times for all other users on the same login node.. Instead, reserve a node that you will have all by yourself. This command will reserve a whole node for 12 hours, the maximum amount of interactive time you can get and still receive a high priority for your job (feel free to change that if you want to). @@ -27,6 +28,7 @@ Instead, reserve a node that you will have all by yourself. This command will re ```console interactive -A [UPPMAX project id] -p node -t 12:00:00 ``` + For example: ```console @@ -40,6 +42,7 @@ interactive -A snic2017-7-274 -M snowy -p node -t\ 12:00:00 ``` ## Step 3: Load the IGV module + When your job has been started, type the following command to load the IGV module: ```console @@ -47,9 +50,11 @@ module load bioinfo-tools IGV ``` ## Step 4: Start IGV + To start IGV, type the following: ```console igv-node ``` + That's it, now IGV should be loaded and ready to go. For more information about how to use IGV, please visit [IGV's user guide](https://igv.org/doc/desktop/). diff --git a/docs/software/jobstats.md b/docs/software/jobstats.md index c2cc89418..1d24bd9af 100644 --- a/docs/software/jobstats.md +++ b/docs/software/jobstats.md @@ -9,11 +9,11 @@ for jobs submitted to the [Slurm](../cluster_guides/slurm.md) job queue. At this page, it is described: - * [`jobstats --plot`](#jobstats--plot): How to use is `jobstats --plot` to see resource use in a graphical plot - * [Efficient use](#efficient-use): How to use your resources efficiently - * [Examples](#example): Examples of ineffective resource use plots - * Other `jobstats` functionality - * Using `jobstats --help` +* [`jobstats --plot`](#jobstats--plot): How to use is `jobstats --plot` to see resource use in a graphical plot +* [Efficient use](#efficient-use): How to use your resources efficiently +* [Examples](#example): Examples of ineffective resource use plots +* Other `jobstats` functionality + * Using `jobstats --help` ## `jobstats --plot` @@ -41,10 +41,10 @@ Use any image viewer, e.g. [eog](eog.md) to see it. Each plot shows: - * detailed information in the title. - * CPU usage in blue - * current memory usage in solid black - * overall memory usage in dotted black (if available) +* detailed information in the title. +* CPU usage in blue +* current memory usage in solid black +* overall memory usage in dotted black (if available) ## Interpreting a plot @@ -52,12 +52,12 @@ For example, in this plot: ![jobstats showing a single-node job](./img/jobstats_c_555912-l_1-k_milou-b2010042-douglas-8769275_with_border.png) - * the title shows the detailed info. `milou` is the name of a former UPPMAX cluster. - * CPU usage in blue, which is around 1000%, which is the equivalent of 10 cores +* the title shows the detailed info. `milou` is the name of a former UPPMAX cluster. +* CPU usage in blue, which is around 1000%, which is the equivalent of 10 cores being used 100% - * current memory usage in solid black, which is around 20 GB (left-side vertical +* current memory usage in solid black, which is around 20 GB (left-side vertical axis) or a little bit less than 1 core (right-side vertical axis) - * overall memory usage in dotted black, which is around 340 GB (left-side vertical +* overall memory usage in dotted black, which is around 340 GB (left-side vertical axis) or a little bit less than 11 cores (right-side vertical axis) For jobs running on multiple nodes, plots have multiple columns: @@ -68,15 +68,15 @@ Some plots shows suggestions in red: Text in plot |Description ----------------------------------------------------|--------------------------------------------------------------------------------- -`nodes_overbooked : nodes booked : nodes used: ` |More nodes were booked than used +`nodes_overbooked : nodes booked : nodes used:` |More nodes were booked than used `overbooked : % used` |The maximum percentage of booked cores and/or memory that was used (if < 80%) `!!half_overbooked` |No more than one-half of both cores and memory of a node was used; consider booking half a node instead. `!!severely_overbooked` |No more than one-quarter of both cores and memory of a node was used, examine your job requirements closely. `!!swap_used` |Swap storage was used at any point within the job run `node_type_overbooked : type booked : type used:` |A fat node was requested that was larger than was needed. This flag may be produced spuriously if SLURM ran the job on a fat node when a fat node was not requested by the user. -`cores_overbooked : cores booked : cores used: ` |More cores were booked than used (if < 80%) -`mem_overbooked : GB booked : GB used: ` |More memory was available than was used (if < 25% and more than one core). -`core_mem_overbooked : GB in used cores : GB used: `|Less memory was used than was available in the cores that were used (if < 50%). +`cores_overbooked : cores booked : cores used:` |More cores were booked than used (if < 80%) +`mem_overbooked : GB booked : GB used:` |More memory was available than was used (if < 25% and more than one core). +`core_mem_overbooked : GB in used cores : GB used:`|Less memory was used than was available in the cores that were used (if < 50%). In this example plot, however, the setup is considered good enough. @@ -235,9 +235,9 @@ This has an effect. This is around 8 cores (800%), as with that amount of cores: -- half of the time, there is 1 out of 7 cores booked, +* half of the time, there is 1 out of 7 cores booked, that is 6 too much -- half of the time, there is 7 out of 13 cores booked, +* half of the time, there is 7 out of 13 cores booked, that is 6 too little This is not an exact algorithm and all numbers from 2 to 9 cores @@ -264,9 +264,9 @@ This has an impact on the runtime speed. This is around 6 cores (600%), as with that amount of cores: -- most of the time, there is 6 out of 6 cores booked, +* most of the time, there is 6 out of 6 cores booked, that is 0 too much -- only rarely, there is a little spike up or a bigger spike down +* only rarely, there is a little spike up or a bigger spike down There are no signs of anything slowing them down, as the line is very even. @@ -588,17 +588,16 @@ jobstats --help Version: 2023-11-16 ``` - ## Modes of `jobstats` discovery There are five modes for discovery, depending on what the user provides on the command line: -- (1) discovery by job number for a completed job; -- (2) discovery by job number for a currently running job; -- (3) discovery by node and job number, for a completed or running job; -- (4) discovery by project -- (5) discovery via information provided on stdin. +* (1) discovery by job number for a completed job; +* (2) discovery by job number for a currently running job; +* (3) discovery by node and job number, for a completed or running job; +* (4) discovery by project +* (5) discovery via information provided on stdin. In the example command lines below, the -p/--plot option requests that plots of job resource usage are created. @@ -609,6 +608,7 @@ Discovery by job number for a completed job: ``` jobstats --plot jobid1 jobid2 jobid3 ``` + The job numbers valid on the cluster. [finishedjobinfo](finishedjobinfo.md) is used to determine further information for each job. diff --git a/docs/software/julia.md b/docs/software/julia.md index 3e0906aac..35e72ed90 100644 --- a/docs/software/julia.md +++ b/docs/software/julia.md @@ -1,6 +1,5 @@ # Julia user guide - ## Julia installations There is no system-installed Julia on the clusters. Therefore you need to load Julia with the module system. Different versions of Julia are available via the module system on Rackham, Snowy, and Bianca. Some installed packages are available via the module. @@ -30,17 +29,15 @@ Versions: To load a specific version of Julia into your environment, type e.g. ```console -$ module load julia/1.6.7_LTS +module load julia/1.6.7_LTS ``` - ​Doing: ```console -$ module load julia +module load julia ``` - will give you the default version (1.9.3), often the latest version. A good and important suggestion is that you always specify a certain version. This is to be able to reproduce your work, a very important key in research! @@ -48,20 +45,17 @@ A good and important suggestion is that you always specify a certain version. Th You can run a julia script in the shell by: ```console -$ julia example_script.jl +julia example_script.jl ``` - After loading the appropriate modules for Julia, you will have access to the read-eval-print-loop (REPL) command line by typing julia. ```console -$ julia +julia ``` - You will get a prompt like this: - ```julia-repl julia> ``` @@ -108,13 +102,12 @@ A variable referring to the last computed value, automatically set at the intera ​ - Exit with or 'exit()'. - !!! seealso More detailed information about the modes in Julia can be found here: - ## Introduction + Julia is according to : - Fast @@ -129,6 +122,7 @@ Julia is according to : [Julia discussions](https://discourse.julialang.org/) ## Packages + Some packages are pre-installed. That means that they are available also on **Bianca**. These include: - "BenchmarkTools" @@ -159,6 +153,7 @@ To use module functions, use import Module to import the module, and Module.fn(x Alternatively, using Module will import all exported Module functions into the current namespace. ### Use centrally installed packages the first time + You may have to build the package the first time you run it. Julia will in such case ask you to do so. Then: ```julia-repl @@ -168,9 +163,11 @@ julia> Pkg.build() ``` ## How to install personal packages + You may ignore the pre-installed packages. They are there mainly for Bianca users, but may help you to relieving some disk space! If you ignore you can jump over the ### Check if packages are installed centrally + To make sure that the package is not already installed, type in Julia: ```julia @@ -178,55 +175,61 @@ julia> using Pkg julia> Pkg.activate(DEPOT_PATH[2]*"/environments/v1.8"); #change version accordingly julia> Pkg.status() ``` + To go back to your own personal packages: ```julia-repl julia> Pkg.activate(DEPOT_PATH[1]*"/environments/v1.8"); julia> Pkg.status() ``` + You can load (using/import) ANY package from both lotcal and central installation irrespective to which environment you activate. However, the setup is that your package is prioritized if there are similar names. ### Start an installation locally + To install personal packages, start to be sure that you are in your local environment. You type within Julia: ```julia-repl Pkg.activate(DEPOT_PATH[1]*"/environmentts/v1.8"); Pkg.add("") ``` + This will install under the path ~/.julia/packages/. Then you can load it by just doing "using/import ". ```julia-repl using ``` -You can also activate a "package prompt" in julia with ']': +You can also activate a "package prompt" in julia with ']': ```julia-repl (@v1.8) pkg> add ``` + For installing specific versions specify with @. After adding you may be asked to precompile or build. Do so according to instruction given on the screen. Otherwise, first time importing or using the package, Julia may start a precompilation that will take a few seconds up to several minutes. Exit with : - ```julia-repl julia> ``` ### Own packages on Bianca + You can use make an installation on Rackham and then use the wharf to copy it over to your ~/.julia/ directory. -Otherwise, send an email to support@uppmax.uu.se and we'll help you. +Otherwise, send an email to and we'll help you. ## Running IJulia from Jupyter notebook + Like for python it is possible to run a Julia in a notebook, i.e. in a web interface with possibility of inline figures and debugging. An easy way to do this is to load the python module as well. In shell: ```console -$ module load julia/1.8.5 -$ module load python/3.10.8 -$ julia +module load julia/1.8.5 +module load python/3.10.8 +julia ``` In Julia: @@ -244,9 +247,11 @@ If not, you may have to build IJulia the first time with Pkg.build(“IJulia”) This builds the package also locally before starting the notebook. If not done, Jupyter will not find the julia kernel of that version. With notebook(dir="", detached=true) the notebook will not be killed when you exit your REPL julia session in the terminal. ## How to run parallel jobs + There are several packages available for Julia that let you run parallel jobs. Some of them are only able to run on one node, while others try to leverage several machines. You'll find an introduction here. ### Run interactively on compute node + Always run parallel only on the compute nodes. This is an example with 4 cores on Rackham ```console @@ -254,18 +259,17 @@ $ interactive -A -n 4 -t 3:00:00 Running interactively at UPPMAX ``` - Slurm user guide ### Threading + Threading divides up your work among a number of cores within a node. The threads share their memory. Below is an example from within Julia. First, in the shell type: ```console -$ export JULIA_NUM_THREADS=4 -$ julia +export JULIA_NUM_THREADS=4 +julia ``` - in Julia: using Base.Threads @@ -275,8 +279,8 @@ nthreads() a[i] = Threads.threadid() end - ### Distributed computing + Distributed processing uses individual processes with individual memory, that communicate with each other. In this case, data movement and communication is explicit. Julia supports various forms of distributed computing. @@ -288,10 +292,11 @@ If choosing between distributed and MPI, distributed is easier to program, where For more detailed info please confer the manual for distributed computing and julia MPI. #### Master-Worker model + We need to launch Julia with ```console -$ julia -p 4 +julia -p 4 ``` then inside Julia you can check @@ -345,49 +350,49 @@ julia hello_world_distributed.jl ​Put job in queue: ```console -$ sbatch job_distributed.slurm +sbatch job_distributed.slurm ``` - #### Interactive example ```console -$ salloc -A -p node -N 1 -n 10 -t 1:0:0 -$ julia hello_world_distributed.jl +salloc -A -p node -N 1 -n 10 -t 1:0:0 +julia hello_world_distributed.jl ``` - ### MPI + The Threaded and Distributed packages are included in the Base installation. However, in order to use MPI with Julia you will need to follow the next steps (only the first time): - Load the tool chain which contains a MPI library For julia/1.6.3 and earlier: ```console -$ module load gcc/9.3.0 openmpi/3.1.5 +module load gcc/9.3.0 openmpi/3.1.5 ``` For julia/1.6.7_LTS & 1.7.2: ```console -$ module load gcc/10.3.0 openmpi/3.1.6 +module load gcc/10.3.0 openmpi/3.1.6 ``` For julia/1.8.5: ```console -$ module load gcc/11.3.0 openmpi/4.1.3 +module load gcc/11.3.0 openmpi/4.1.3 ``` - - Load Julia + ```console -$ ml julia/1.8.5 # or other +ml julia/1.8.5 # or other ``` - Start Julia on the command line + ```console -$ julia +julia ``` - Change to ``package mode`` and add the ``MPI`` package @@ -416,8 +421,8 @@ MPI.Finalize() You can execute your code as in an interactive session with several cores (at least 3 in this case): ```console -$ module load gcc/11.3.0 openmpi/4.1.3 -$ mpiexecjl -np 3 julia juliaMPI.jl +module load gcc/11.3.0 openmpi/4.1.3 +mpiexecjl -np 3 julia juliaMPI.jl ``` A batch script, job_MPI.slurm, should include a "module load gcc/XXX openmpi/XXX" @@ -439,14 +444,17 @@ module load gcc/11.3.0 openmpi/4.1.3 export PATH=~/.julia/bin:$PATH mpiexecjl -n 20 julia juliaMPI.jl ``` + - Run with ```console -$ sbatch job_MPI.slurm +sbatch job_MPI.slurm ``` + See the MPI.jl examples for more input! ### GPU + Example Julia script, juliaCUDA.jl: using CUDA, Test @@ -478,24 +486,28 @@ julia juliaCUDA.jl ``` - Put job in queue: + ```console -$ sbatch juliaGPU.slurm +sbatch juliaGPU.slurm ``` #### Interactive session with GPU + On Snowy, getting 1 cpu and 1 gpu: ```console -$ interactive -A -n 1 -M snowy --gres=gpu:1 -t 3:00:00 +interactive -A -n 1 -M snowy --gres=gpu:1 -t 3:00:00 ``` + On Bianca, getting 2 cpu:s and 1 gpu: ```console -$ interactive -A -n 2 -C gpu --gres=gpu:1 -t 01:10:00 +interactive -A -n 2 -C gpu --gres=gpu:1 -t 01:10:00 ``` - wait until session is started + ```console -$ julia/1.7.2 -$ julia/1.8.5 (Default) +julia/1.7.2 +julia/1.8.5 (Default) ``` diff --git a/docs/software/jupyter.md b/docs/software/jupyter.md index 857cea9ab..f41bb35e2 100644 --- a/docs/software/jupyter.md +++ b/docs/software/jupyter.md @@ -23,20 +23,21 @@ Jupyter is an [IDE](../software/ides.md) specialized for [the Python programming Start a notebook like this: ```bash -$ module load python/ -$ jupyter-notebook +module load python/ +jupyter-notebook ``` + or jupyter lab: ``` bash -$ jupyter-lab +jupyter-lab ``` A local Firefox session (not a internet web page!) should start with the Jupyter notebook/lab interface. - If not, make Jupyter work in background, start Firefox and paste the address. -- `` `` +- ```` - ``bg`` - ``firefox &`` @@ -52,9 +53,9 @@ If you decide to use the ``--system-site-packages`` configuration you will get ` However, you won't find your locally installed packages from that jupyter session. To solve this, reinstall jupyter within the virtual environment by force (option ``-I``): ```bash -$ pip install -I jupyter +pip install -I jupyter ``` + and run it as above. Be sure to start the kernel with the virtual environment name, like "project A", and not "Python 3 (ipykernel)". - diff --git a/docs/software/matlab.md b/docs/software/matlab.md index c43c52c06..1f76d9bab 100644 --- a/docs/software/matlab.md +++ b/docs/software/matlab.md @@ -7,7 +7,7 @@ MATLAB can be started only if you load the matlab module first. Most of availabl Doing: ```console -$ module load matlab +module load matlab ``` will give you the latest version. @@ -15,54 +15,52 @@ will give you the latest version. If you need a different version, check the availability by: ```console -$ module avail matlab +module avail matlab ``` To get started with MATLAB do (for instance): ```console -$ module load matlab/R2023a -$ matlab & +module load matlab/R2023a +matlab & ``` That will start a matlab session with the common GUI. Use "&" to have MATLAB in background making terminal still active for other work. - A good and important suggestion is that you always specify a certain version. This is to be able to reproduce your work, a very important key in research! ### First time, since May 13 2024 - If you use MATLAB after May 13 2024, of any version, you have to do the following step to be able to use the full features of running parallel jobs. - - only needs to be called once per version of MATLAB. - - Note, however, that on Bianca this has to be done separately. + - only needs to be called once per version of MATLAB. + - Note, however, that on Bianca this has to be done separately. - After logging into the cluster, configure MATLAB to run parallel jobs on the cluster by calling the shell script configCluster.sh. ```console -$ module load matlab -$ configCluster.sh # Note: no '-A' +module load matlab +configCluster.sh # Note: no '-A' ``` - This will run a short configuration job in an interactive session, closing itself when done. - Jobs will now default to the cluster rather than submit to the local machine. - ## Introduction Using MATLAB on the cluster enables you to utilize high performance facilities like: - [Parallel computing](https://se.mathworks.com/help/parallel-computing/getting-started-with-parallel-computing-toolbox.html?s_tid=CRUX_lftnav) - - Parallel for-loops - - Evaluate functions in the background + - Parallel for-loops + - Evaluate functions in the background - [Big data processing](https://se.mathworks.com/help/parallel-computing/big-data-processing.html?s_tid=CRUX_lftnav) - - Analyze big data sets in parallel + - Analyze big data sets in parallel - [Batch Processing](https://se.mathworks.com/help/parallel-computing/batch-processing.html?s_tid=CRUX_lftnav) - - Offload execution of functions to run in the background + - Offload execution of functions to run in the background - [GPU computing](https://se.mathworks.com/help/parallel-computing/gpu-computing.html?s_tid=CRUX_lftnav) (Available on Bianca and Snowy) - - Accelerate your code by running it on a GPU + - Accelerate your code by running it on a GPU - Machine & Deep learning - - [Statistics and Machine Learning](https://se.mathworks.com/help/stats/index.html) - - [Deep Learning](https://se.mathworks.com/help/deeplearning/index.html) + - [Statistics and Machine Learning](https://se.mathworks.com/help/stats/index.html) + - [Deep Learning](https://se.mathworks.com/help/deeplearning/index.html) [See MathWork's complete user guide](https://se.mathworks.com/help/parallel-computing/index.html?s_tid=CRUX_lftnav) @@ -70,25 +68,26 @@ Some online tutorials and courses: - [Parallel computing](https://se.mathworks.com/solutions/parallel-computing.html) - Machine Learning - - [Machine learning article](https://se.mathworks.com/solutions/machine-learning.html) - - [Machine learning tutorial](https://matlabacademy.mathworks.com/details/machine-learning-onramp/machinelearning) + - [Machine learning article](https://se.mathworks.com/solutions/machine-learning.html) + - [Machine learning tutorial](https://matlabacademy.mathworks.com/details/machine-learning-onramp/machinelearning) - Deep Learning - - [Deep learning article](https://se.mathworks.com/solutions/deep-learning.html) - - [Deep learning tutorial](https://matlabacademy.mathworks.com/details/deep-learning-onramp/deeplearning) + - [Deep learning article](https://se.mathworks.com/solutions/deep-learning.html) + - [Deep learning tutorial](https://matlabacademy.mathworks.com/details/deep-learning-onramp/deeplearning) ## Running MATLAB + ### Graphical user interface To start MATLAB with its usual graphical interface, start it with: ```console -$ matlab +matlab ``` If you will use significant resources, like processor or RAM, you should start an interactive session on a calculation node. Use at least 2 cores (-n 2), when running interactive. Otherwise MATLAB may not start. You can use several cores if you will do some parallel calculations (see parallel section below). Example: ```console -$ interactive -A -p core -n 2 -t 1:0:0 +interactive -A -p core -n 2 -t 1:0:0 ``` This example starts a session with 2 cores for a wall time of 1 hour. @@ -98,7 +97,7 @@ This example starts a session with 2 cores for a wall time of 1 hour. For simple calculations it is possible to start just a command shell in your terminal: ```console -$ matlab -nodisplay +matlab -nodisplay ``` Exit with 'exit'. @@ -108,13 +107,13 @@ Run script from terminal or bash script In order to run a script directly from terminal: ```console -$ matlab -batch "run('')" | tail -n +2 +matlab -batch "run('')" | tail -n +2 ``` List all ways to run/start MATLAB: ```console -$ matlab -h +matlab -h ``` ### Thinlinc @@ -132,19 +131,18 @@ You may want to confer our UPPMAX [ThinLinc user guide](http://docs.uppmax.uu.se ### First time, since May 13 2024 - If you use MATLAB after May 13 2024, of any version, you have to do the following step to be able to use the full features of running parallel jobs. - - only needs to be called once per version of MATLAB. - - Note, however, that on Bianca this has to be done separately. + - only needs to be called once per version of MATLAB. + - Note, however, that on Bianca this has to be done separately. - After logging into the cluster, configure MATLAB to run parallel jobs on the cluster by calling the shell script configCluster.sh. ```console -$ module load matlab -$ configCluster.sh # Note: no '-A' +module load matlab +configCluster.sh # Note: no '-A' ``` - This will run a short configuration job in an interactive session, closing itself when done. - Jobs will now default to the cluster rather than submit to the local machine. - ### Two MATLAB commands Two commands in MATLAB are important to make your code parallel: @@ -157,7 +155,7 @@ Two commands in MATLAB are important to make your code parallel: First, start an interactive session on a calculation node with, for instance 8 cores by: ```console -$ interactive -A -p core -n 8 -t 3:00:00 +interactive -A -p core -n 8 -t 3:00:00 ``` In MATLAB open a parallel pool of 8 local workers: @@ -208,6 +206,7 @@ With MATLAB you can e.g. submit jobs directly to our job queue scheduler, withou end t = toc(t0); ``` + and the second, little longer, saved in ``parallel_example_hvy.m``: ```matlab @@ -223,6 +222,7 @@ and the second, little longer, saved in ``parallel_example_hvy.m``: end end ``` + Begin by running the command ```matlab @@ -245,6 +245,7 @@ in Matlab Command Window to choose a cluster configuration. Matlab will set up a >> job.wait >> job.fetchOutputs{:}" ``` + Follow them. These inform you what is needed in your script or in command line to run in parallel on the cluster. The line "c.batch(@parallel_example, 1, {90, 5}, 'pool', 19)" can be understood as put the function "parallel_example" to the batch queue. The arguments to batch are: ```matlab @@ -286,13 +287,13 @@ Running MATLAB with GPU is, as of now, only possible on the Snowy and Bianca clu Start an interactive session with at least 2 cores (otherwise MATLAB may not start). On Snowy, getting (for instance) 2 cpu:s (-n 2) and 1 gpu: ```console -$ interactive -A -n 2 -M snowy --gres=gpu:1 -t 3:00:00 +interactive -A -n 2 -M snowy --gres=gpu:1 -t 3:00:00 ``` On Bianca, getting 3 cpu:s and 1 gpu: ```console -$ interactive -A -n 3 -C gpu --gres=gpu:1 -t 01:10:00 +interactive -A -n 3 -C gpu --gres=gpu:1 -t 01:10:00 ``` Note that wall time "-t" should be set to more than one hour to not automatically put job in "devel" or "devcore" queue, which is not allowed for gpu jobs. Also check the GPU quide for Snowy at Using the GPU nodes on Snowy. @@ -344,10 +345,11 @@ Batch script example with 2 nodes (Rackham), matlab_submit.sh. module load matlab/R2020b &> /dev/null srun -N 2 -n 40 matlab -batch "run('')" ``` + Run with ```console -$ sbatch matlab_submit.sh +sbatch matlab_submit.sh ``` ## Common problems @@ -357,18 +359,19 @@ Sometimes things do not work out. As a first step, try with removing local files: ```console -$ rm -rf ~/.matlab +rm -rf ~/.matlab ``` If the graphics is slow, try: ```console -$ vglrun matlab -nosoftwareopengl +vglrun matlab -nosoftwareopengl ``` + Unfortunately this only works from login nodes. You may want to run MATLAB on a single thread. This makes it work: ```console -$ matlab -singleCompThread +matlab -singleCompThread ``` diff --git a/docs/software/metontiime.md b/docs/software/metontiime.md index 8c36bb43b..f8e5367ca 100644 --- a/docs/software/metontiime.md +++ b/docs/software/metontiime.md @@ -11,4 +11,4 @@ It is not installed as a module. ## Links - * [MetONTIIME GitHub repository](https://github.com/MaestSi/MetONTIIME) +* [MetONTIIME GitHub repository](https://github.com/MaestSi/MetONTIIME) diff --git a/docs/software/nvidia-deep-learning-frameworks.md b/docs/software/nvidia-deep-learning-frameworks.md index 60efd8747..912b22d56 100644 --- a/docs/software/nvidia-deep-learning-frameworks.md +++ b/docs/software/nvidia-deep-learning-frameworks.md @@ -5,10 +5,13 @@ Here is how easy one can use an NVIDIA [environment](https://docs.nvidia.com/dee ![web screenshot](./img/pytorch-nvidia.png) First - pull the container (6.5GB). + ```bash singularity pull docker://nvcr.io/nvidia/pytorch:22.03-py3 ``` + Get an interactive shell. + ```bash singularity shell --nv ~/external_1TB/tmp/pytorch_22.03-py3.sif @@ -34,7 +37,9 @@ True >>> torch.zeros(1).to('cuda') tensor([0.], device='cuda:0') ``` + From the container shell, check what else is available... + ```bash Singularity> nvcc -V nvcc: NVIDIA (R) Cuda compiler driver @@ -60,7 +65,9 @@ Singularity> jupyter-lab [I 13:35:46.616 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). ... ``` + You can use this container to add more packages. + ```singularity Bootstrap: docker From: nvcr.io/nvidia/pytorch:22.03-py3 @@ -68,6 +75,7 @@ From: nvcr.io/nvidia/pytorch:22.03-py3 ``` Just keep in mind that "upgrading" the build-in torch package might install a package that is compatible with less GPU architectures and it might not work anymore on your hardware. + ```bash Singularity> python3 -c "import torch; print(torch.__version__); print(torch.cuda.is_available()); print(torch.cuda.get_arch_list()); torch.zeros(1).to('cuda')" @@ -76,4 +84,4 @@ True ['sm_37', 'sm_50', 'sm_60', 'sm_70'] NVIDIA A100-PCIE-40GB with CUDA capability sm_80 is not compatible with the current PyTorch installation. The current PyTorch install supports CUDA capabilities sm_37 sm_50 sm_60 sm_70. -``` \ No newline at end of file +``` diff --git a/docs/software/openmolcas.md b/docs/software/openmolcas.md index 762663242..11a7aebd7 100644 --- a/docs/software/openmolcas.md +++ b/docs/software/openmolcas.md @@ -3,41 +3,53 @@ > How to run the program MOLCAS on UPPMAX ## Information + MOLCAS is an ab initio computational chemistry program. Focus in the program is placed on methods for calculating general electronic structures in molecular systems in both ground and excited states. MOLCAS is, in particular, designed to study the potential surfaces of excited states This guide will help you get started running MOLCAS on UPPMAX. More detailed information on how to use Molcas can be found on the [official website](https://molcas.org/). ## Licensing + A valid license key is required to run Molcas on UPPMAX. The licence key should be kept in a directory named .Molcas under the home directory. Molcas is currently free of charge for academic researchers active in the Nordic countries. You can get hold of a license by following [these instructions](https://www.molcas.org/order.html). ## Versions installed at UPPMAX + At UPPMAX the following versions are installed: - 8.0 (serial) - 7.8 (serial) + ## Modules needed to run MOLCAS + In order to run MOLCAS you must first load the MOLCAS module. You can see all available versions of MOLCAS installed at UPPMAX with: ```bash module avail molcas ``` + Load a MOLCAS module with, eg: ```bash module load molcas/7.8.082 ``` + ## How to run MOLCAS interactively + If you would like to do tests or short runs, we recommend using the interactive command: + ```bash interactive -A your_project_name ``` + This will reserve a node for you to do your test on. Note that you must provide the name of an active project in order to run on UPPMAX resources. After a short wait you will get access to the node. Then you can run MOLCAS by: + ```bash module load molcas/7.8.082 molcas -f test000.input ``` + The `test000.input` looks like: ``` @@ -82,9 +94,11 @@ Ras2 &CASPT2 ``` + See the [SLURM user guide](../cluster_guides/slurm.md) for more information on the interactive command. Don't forget to exit your interactive job when you have finished your calculation. Exiting will free the resource for others to use. ## Batch scripts for slurm + It's possible to run MOLCAS in the batch queue. Here is an example running MOLCAS on one core: ```sbatch @@ -102,9 +116,11 @@ export MOLCASMEM=2000 molcas -f test000.input ``` + Again you'll have to provide your project name. If the script is called `test000.job` you can submit it to the batch queue with: + ```bash sbatch test000.job ``` diff --git a/docs/software/overview.md b/docs/software/overview.md index 9eecc3980..e80c6efda 100644 --- a/docs/software/overview.md +++ b/docs/software/overview.md @@ -20,14 +20,14 @@ and accessible via the module system. You can always install software in your home on any UPPMAX system. If there are many users who would like to request the same software, it can be installed by UPPMAX application or system experts. -Please send such requests to support@uppmax.uu.se. +Please send such requests to . ## Reach the Bioinformatics tools - Before you can list available bioinformatics tools you need to issue the command: ``` -$ module load bioinfo-tools +module load bioinfo-tools ``` - When you list available modules with ``module avail`` after this, you will see that the bioinformatics tools are now also available in the listing. diff --git a/docs/software/perl.md b/docs/software/perl.md index be08e6987..497972f3d 100644 --- a/docs/software/perl.md +++ b/docs/software/perl.md @@ -2,6012 +2,6011 @@ A number of modules/packages are available by default with all Perl versions. This is a list of modules for perl/5.26.2 available by loading the module perl_modules/5.26.2. For previous Perl versions 5.18.4 and 5.24.1 (available through the software module system as perl/5.18.4 and perl/5.24.1), many more Perl modules are available by loading the software module perl_modules/5.18.4 or perl_modules/5.24.1. A complete list of the Perl modules available in perl_modules/5.26.2 module is as follows: - ```console Perl Module Search on perl_modules/5.26.2/rackham -Module name Version -$pkg 2.019 -Acme::Damn 0.08 -Algorithm::C3 0.10 -Algorithm::Combinatorics 0.27 -Algorithm::Diff 1.1903 -Algorithm::FastPermute 0.999 -Algorithm::Loops 1.032 -Algorithm::Munkres 0.08 -Algorithm::Permute 0.16 -aliased 0.34 -Apache::Htpasswd 1.9 -Apache::LogFormat::Compiler 0.35 -Apache::SOAP 1.27 -App::Ack 2.24 -App::Ack::ConfigDefault unknown -App::Ack::ConfigFinder unknown -App::Ack::ConfigLoader unknown -App::Ack::Filter unknown -App::Ack::Filter::Collection unknown -App::Ack::Filter::Default unknown -App::Ack::Filter::Extension unknown -App::Ack::Filter::ExtensionGroup unknown -App::Ack::Filter::FirstLineMatch unknown -App::Ack::Filter::Inverse unknown -App::Ack::Filter::Is unknown -App::Ack::Filter::IsGroup unknown -App::Ack::Filter::IsPath unknown -App::Ack::Filter::IsPathGroup unknown -App::Ack::Filter::Match unknown -App::Ack::Filter::MatchGroup unknown -App::Ack::Resource unknown -App::Ack::Resources unknown -App::Cmd 0.331 -App::Cmd::ArgProcessor 0.331 -App::Cmd::Command 0.331 -App::Cmd::Command::commands 0.331 -App::Cmd::Command::help 0.331 -App::Cmd::Command::version 0.331 -App::Cmd::Plugin 0.331 -App::Cmd::Setup 0.331 -App::Cmd::Simple 0.331 -App::Cmd::Subdispatch 0.331 -App::Cmd::Subdispatch::DashedStyle 0.331 -App::Cmd::Tester 0.331 -App::Cmd::Tester::CaptureExternal 0.331 -App::cpanminus 1.7044 -App::cpanminus::fatscript 1.7044 -App::FatPacker 0.010007 -App::FatPacker::Trace unknown -App::Nopaste 1.012 -App::Nopaste::Command 1.012 -App::Nopaste::Service 1.012 -App::Nopaste::Service::Codepeek 1.012 -App::Nopaste::Service::Debian 1.012 -App::Nopaste::Service::Gist 1.012 -App::Nopaste::Service::GitLab 1.012 -App::Nopaste::Service::Mojopaste 1.012 -App::Nopaste::Service::PastebinCom 1.012 -App::Nopaste::Service::Pastie 1.012 -App::Nopaste::Service::Shadowcat 1.012 -App::Nopaste::Service::Snitch 1.012 -App::Nopaste::Service::ssh 1.012 -App::Nopaste::Service::Ubuntu 1.012 -App::perlbrew 0.84 -App::Pinto 0.14 -App::Pinto::Command 0.14 -App::Pinto::Command::add 0.14 -App::Pinto::Command::clean 0.14 -App::Pinto::Command::copy 0.14 -App::Pinto::Command::default 0.14 -App::Pinto::Command::delete 0.14 -App::Pinto::Command::diff 0.14 -App::Pinto::Command::help 0.14 -App::Pinto::Command::init 0.14 -App::Pinto::Command::install 0.14 -App::Pinto::Command::kill 0.14 -App::Pinto::Command::list 0.14 -App::Pinto::Command::lock 0.14 -App::Pinto::Command::log 0.14 -App::Pinto::Command::look 0.14 -App::Pinto::Command::manual 0.14 -App::Pinto::Command::merge 0.14 -App::Pinto::Command::migrate 0.14 -App::Pinto::Command::new 0.14 -App::Pinto::Command::nop 0.14 -App::Pinto::Command::pin 0.14 -App::Pinto::Command::props 0.14 -App::Pinto::Command::pull 0.14 -App::Pinto::Command::register 0.14 -App::Pinto::Command::rename 0.14 -App::Pinto::Command::reset 0.14 -App::Pinto::Command::revert 0.14 -App::Pinto::Command::roots 0.14 -App::Pinto::Command::stacks 0.14 -App::Pinto::Command::statistics 0.14 -App::Pinto::Command::thanks 0.14 -App::Pinto::Command::unlock 0.14 -App::Pinto::Command::unpin 0.14 -App::Pinto::Command::unregister 0.14 -App::Pinto::Command::update 0.14 -App::Pinto::Command::verify 0.14 -App::Prove 3.42 -App::Prove::State 3.42 -App::Prove::State::Result 3.42 -App::Prove::State::Result::Test 3.42 -AppConfig 1.71 -AppConfig::Args 1.71 -AppConfig::CGI 1.71 -AppConfig::File 1.71 -AppConfig::Getopt 1.71 -AppConfig::State 1.71 -AppConfig::Sys 1.71 -Archive::Any::Create 0.03 -Archive::Any::Create::Tar unknown -Archive::Any::Create::Zip unknown -Archive::Extract 0.80 -Archive::Zip 1.60 -Archive::Zip::Archive 1.60 -Archive::Zip::BufferedFileHandle 1.60 -Archive::Zip::DirectoryMember 1.60 -Archive::Zip::FileMember 1.60 -Archive::Zip::Member 1.60 -Archive::Zip::MemberRead 1.60 -Archive::Zip::MockFileHandle 1.60 -Archive::Zip::NewFileMember 1.60 -Archive::Zip::StringMember 1.60 -Archive::Zip::Tree 1.60 -Archive::Zip::ZipFileMember 1.60 -Array::Compare 3.0.1 -Array::Unique 0.08 -Array::Utils 0.5 -asa 1.03 -Astro::FITS::Header 3.04 -Astro::FITS::Header::AST 3.01 -Astro::FITS::Header::CFITSIO 3.02 -Astro::FITS::Header::GSD 3.01 -Astro::FITS::Header::Item 3.02 -Astro::FITS::Header::NDF 3.02 -Authen::SASL 2.16 -Authen::SASL::CRAM_MD5 2.14 -Authen::SASL::EXTERNAL 2.14 -Authen::SASL::Perl 2.14 -Authen::SASL::Perl::ANONYMOUS 2.14 -Authen::SASL::Perl::CRAM_MD5 2.14 -Authen::SASL::Perl::DIGEST_MD5 2.14 -Authen::SASL::Perl::EXTERNAL 2.14 -Authen::SASL::Perl::GSSAPI 0.05 -Authen::SASL::Perl::LOGIN 2.14 -Authen::SASL::Perl::PLAIN 2.14 -Authen::Simple 0.5 -Authen::Simple::Adapter unknown -Authen::Simple::Apache unknown -Authen::Simple::Log unknown -Authen::Simple::Passwd 0.6 -Authen::Simple::Password unknown -autobox unknown -autobox::universal unknown -B::Hooks::EndOfScope 0.24 -B::Hooks::EndOfScope::PP 0.24 -B::Hooks::EndOfScope::XS 0.24 -B::Hooks::OP::Check 0.22 -B::Hooks::OP::Check::Install::Files unknown -B::Hooks::OP::PPAddr 0.06 -B::Hooks::OP::PPAddr::Install::Files unknown -B::Keywords 1.18 -B::Utils 0.27 -B::Utils::Install::Files unknown -B::Utils::OP 0.27 -bareword::filehandles 0.006 -Bit::Vector 7.4 -Bit::Vector::Overload 7.4 -Bit::Vector::String 7.4 -boolean 0.46 -Browser::Open 0.04 -Bundle::DBD::mysql 4.046 -Bundle::DBI 12.008696 -Bundle::Object::InsideOut 4.04 -C::StructType unknown -C::Type unknown -C::Var unknown -Cache::BaseCache unknown -Cache::BaseCacheTester unknown -Cache::Cache 1.08 -Cache::CacheMetaData unknown -Cache::CacheSizer unknown -Cache::CacheTester unknown -Cache::CacheUtils unknown -Cache::FileBackend unknown -Cache::FileCache unknown -Cache::LRU 0.04 -Cache::MemoryBackend unknown -Cache::MemoryCache unknown -Cache::NullCache unknown -Cache::Object unknown -Cache::SharedMemoryBackend unknown -Cache::SharedMemoryCache unknown -Cache::SizeAwareCache unknown -Cache::SizeAwareCacheTester unknown -Cache::SizeAwareFileCache unknown -Cache::SizeAwareMemoryCache unknown -Cache::SizeAwareSharedMemoryCache unknown -Capture::Tiny 0.48 -Carp::Always 0.13 -Carp::Assert 0.21 -Carp::Assert::More 1.16 -Carp::Clan 6.06 -Carp::REPL 0.18 -Carton unknown -Carton::Builder unknown -Carton::CLI unknown -Carton::CPANfile unknown -Carton::Dependency unknown -Carton::Dist unknown -Carton::Dist::Core unknown -Carton::Environment unknown -Carton::Error unknown -Carton::Index unknown -Carton::Mirror unknown -Carton::Package unknown -Carton::Packer unknown -Carton::Snapshot unknown -Carton::Snapshot::Emitter unknown -Carton::Snapshot::Parser unknown -Carton::Tree unknown -Carton::Util unknown -Catalyst 5.90118 -Catalyst::Action unknown -Catalyst::Action::Deserialize 1.21 -Catalyst::Action::Deserialize::Callback 1.21 -Catalyst::Action::Deserialize::JSON 1.21 -Catalyst::Action::Deserialize::JSON::XS 1.21 -Catalyst::Action::Deserialize::View 1.21 -Catalyst::Action::Deserialize::XML::Simple 1.21 -Catalyst::Action::Deserialize::YAML 1.21 -Catalyst::Action::DeserializeMultiPart 1.21 -Catalyst::Action::RenderView 0.16 -Catalyst::Action::REST 1.21 -Catalyst::Action::REST::ForBrowsers 1.21 -Catalyst::Action::Role::ACL 0.07 -Catalyst::Action::Serialize 1.21 -Catalyst::Action::Serialize::Callback 1.21 -Catalyst::Action::Serialize::JSON 1.21 -Catalyst::Action::Serialize::JSON::XS 1.21 -Catalyst::Action::Serialize::JSONP 1.21 -Catalyst::Action::Serialize::View 1.21 -Catalyst::Action::Serialize::XML::Simple 1.21 -Catalyst::Action::Serialize::YAML 1.21 -Catalyst::Action::Serialize::YAML::HTML 1.21 -Catalyst::Action::SerializeBase 1.21 -Catalyst::ActionChain unknown -Catalyst::ActionContainer unknown -Catalyst::ActionRole::ACL 0.07 -Catalyst::ActionRole::ConsumesContent unknown -Catalyst::ActionRole::HTTPMethods unknown -Catalyst::ActionRole::NeedsLogin unknown -Catalyst::ActionRole::QueryMatching unknown -Catalyst::ActionRole::Scheme unknown -Catalyst::Authentication::Credential::HTTP 1.018 -Catalyst::Authentication::Credential::NoPassword unknown -Catalyst::Authentication::Credential::Password unknown -Catalyst::Authentication::Credential::Remote unknown -Catalyst::Authentication::Realm unknown -Catalyst::Authentication::Realm::Compatibility unknown -Catalyst::Authentication::Realm::Progressive unknown -Catalyst::Authentication::Realm::SimpleDB unknown -Catalyst::Authentication::Store::DBIx::Class 0.1506 -Catalyst::Authentication::Store::DBIx::Class::User unknown -Catalyst::Authentication::Store::Minimal unknown -Catalyst::Authentication::Store::Null unknown -Catalyst::Authentication::User unknown -Catalyst::Authentication::User::Hash unknown -Catalyst::Base unknown -Catalyst::ClassData unknown -Catalyst::Component unknown -Catalyst::Component::ApplicationAttribute unknown -Catalyst::Component::ContextClosure unknown -Catalyst::Component::InstancePerContext 0.001001 -Catalyst::Controller unknown -Catalyst::Controller::ActionRole 0.17 -Catalyst::Controller::REST 1.21 -Catalyst::Devel 1.39 -Catalyst::Dispatcher unknown -Catalyst::DispatchType unknown -Catalyst::DispatchType::Chained unknown -Catalyst::DispatchType::Default unknown -Catalyst::DispatchType::Index unknown -Catalyst::DispatchType::Path unknown -Catalyst::Engine unknown -Catalyst::EngineLoader unknown -Catalyst::Exception unknown -Catalyst::Exception::Basic unknown -Catalyst::Exception::Detach unknown -Catalyst::Exception::Go unknown -Catalyst::Exception::Interface unknown -Catalyst::Helper 1.39 -Catalyst::Helper::Model::Adaptor unknown -Catalyst::Helper::Model::DBIC::Schema 0.65 -Catalyst::Helper::Model::Factory unknown -Catalyst::Helper::Model::Factory::PerRequest unknown -Catalyst::Helper::View::Email 0.36 -Catalyst::Helper::View::Email::Template 0.36 -Catalyst::Helper::View::TT 0.44 -Catalyst::Helper::View::TTSite 0.44 -Catalyst::Log unknown -Catalyst::Manual 5.9009 -Catalyst::Middleware::Stash unknown -Catalyst::Model unknown -Catalyst::Model::Adaptor 0.10 -Catalyst::Model::Adaptor::Base unknown -Catalyst::Model::DBIC::Schema 0.65 -Catalyst::Model::Factory 0.10 -Catalyst::Model::Factory::PerRequest 0.10 -Catalyst::Plugin::Authentication 0.10023 -Catalyst::Plugin::Authentication::Credential::Password unknown -Catalyst::Plugin::Authentication::Store::Minimal unknown -Catalyst::Plugin::Authentication::User unknown -Catalyst::Plugin::Authentication::User::Hash unknown -Catalyst::Plugin::ConfigLoader 0.34 -Catalyst::Plugin::I18N 0.10 -Catalyst::Plugin::Session 0.40 -Catalyst::Plugin::Session::State unknown -Catalyst::Plugin::Session::State::Cookie 0.17 -Catalyst::Plugin::Session::Store unknown -Catalyst::Plugin::Session::Store::DBIC 0.14 -Catalyst::Plugin::Session::Store::DBIC::Delegate unknown -Catalyst::Plugin::Session::Store::Delegate 0.06 -Catalyst::Plugin::Session::Store::Dummy unknown -Catalyst::Plugin::Session::Store::File 0.18 -Catalyst::Plugin::Session::Test::Store 123 -Catalyst::Plugin::StackTrace 0.12 -Catalyst::Plugin::Static::Simple 0.36 -Catalyst::Plugin::Unicode::Encoding 5.90118 -Catalyst::Request unknown -Catalyst::Request::PartData unknown -Catalyst::Request::REST 1.21 -Catalyst::Request::REST::ForBrowsers 1.21 -Catalyst::Request::Upload unknown -Catalyst::Response unknown -Catalyst::Response::Writer unknown -Catalyst::Restarter unknown -Catalyst::Restarter::Forking unknown -Catalyst::Restarter::Win32 unknown -Catalyst::Runtime 5.90118 -Catalyst::Script::CGI unknown -Catalyst::Script::Create unknown -Catalyst::Script::FastCGI unknown -Catalyst::Script::Server unknown -Catalyst::Script::Test unknown -Catalyst::ScriptRole unknown -Catalyst::ScriptRunner unknown -Catalyst::Stats unknown -Catalyst::Test unknown -Catalyst::TraitFor::Model::DBIC::Schema::Caching unknown -Catalyst::TraitFor::Model::DBIC::Schema::PerRequestSchema unknown -Catalyst::TraitFor::Model::DBIC::Schema::Replicated unknown -Catalyst::TraitFor::Model::DBIC::Schema::SchemaProxy unknown -Catalyst::TraitFor::Request::REST 1.21 -Catalyst::TraitFor::Request::REST::ForBrowsers 1.21 -Catalyst::Utils unknown -Catalyst::View unknown -Catalyst::View::Email 0.36 -Catalyst::View::Email::Template 0.36 -Catalyst::View::TT 0.44 -CatalystX::Component::Traits 0.19 -CatalystX::InjectComponent 0.025 -CatalystX::LeakChecker 0.06 -CatalystX::Profile 0.02 -CatalystX::Profile::Controller::ControlProfiling 0.02 -CatalystX::REPL 0.04 -CatalystX::SimpleLogin 0.20 -CatalystX::SimpleLogin::Controller::Login unknown -CatalystX::SimpleLogin::Form::Login unknown -CatalystX::SimpleLogin::Form::LoginOpenID unknown -CatalystX::SimpleLogin::TraitFor::Controller::Login::Logout unknown -CatalystX::SimpleLogin::TraitFor::Controller::Login::OpenID unknown -CatalystX::SimpleLogin::TraitFor::Controller::Login::RenderAsTTTemplate unknown -CatalystX::SimpleLogin::TraitFor::Controller::Login::WithRedirect unknown -CGI 4.38 -CGI::Carp 4.38 -CGI::Cookie 4.38 -CGI::File::Temp 4.38 -CGI::FormBuilder 3.10 -CGI::FormBuilder::Field 3.10 -CGI::FormBuilder::Field::button 3.10 -CGI::FormBuilder::Field::checkbox 3.10 -CGI::FormBuilder::Field::date 3.10 -CGI::FormBuilder::Field::datetime 3.10 -CGI::FormBuilder::Field::datetime_local 3.10 -CGI::FormBuilder::Field::email 3.10 -CGI::FormBuilder::Field::file 3.10 -CGI::FormBuilder::Field::hidden 3.10 -CGI::FormBuilder::Field::image 3.10 -CGI::FormBuilder::Field::number 3.10 -CGI::FormBuilder::Field::password 3.10 -CGI::FormBuilder::Field::radio 3.10 -CGI::FormBuilder::Field::select 3.10 -CGI::FormBuilder::Field::static 3.10 -CGI::FormBuilder::Field::submit 3.10 -CGI::FormBuilder::Field::text 3.10 -CGI::FormBuilder::Field::textarea 3.10 -CGI::FormBuilder::Field::time 3.10 -CGI::FormBuilder::Field::url 3.10 -CGI::FormBuilder::Messages 3.10 -CGI::FormBuilder::Messages::base 3.10 -CGI::FormBuilder::Messages::default 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Messages::locale 3.10 -CGI::FormBuilder::Multi 3.10 -CGI::FormBuilder::Source 3.10 -CGI::FormBuilder::Source::File 3.10 -CGI::FormBuilder::Source::Perl 0.01 -CGI::FormBuilder::Template 3.10 -CGI::FormBuilder::Template::Builtin 3.10 -CGI::FormBuilder::Template::CGI_SSI 3.10 -CGI::FormBuilder::Template::Div 3.10 -CGI::FormBuilder::Template::Fast 3.10 -CGI::FormBuilder::Template::HTML 3.10 -CGI::FormBuilder::Template::Text 3.10 -CGI::FormBuilder::Template::TT2 3.10 -CGI::FormBuilder::Test 3.10 -CGI::FormBuilder::Util 3.10 -CGI::HTML::Functions unknown -CGI::Pretty 4.38 -CGI::Push 4.38 -CGI::Simple 1.15 -CGI::Simple::Cookie 1.15 -CGI::Simple::Standard 1.15 -CGI::Simple::Util 1.15 -CGI::Struct 1.21 -CGI::Util 4.38 -CHI 0.60 -CHI::CacheObject 0.60 -CHI::Constants 0.60 -CHI::Driver 0.60 -CHI::Driver::Base::CacheContainer 0.60 -CHI::Driver::CacheCache 0.60 -CHI::Driver::FastMmap 0.60 -CHI::Driver::File 0.60 -CHI::Driver::Memory 0.60 -CHI::Driver::Metacache 0.60 -CHI::Driver::Null 0.60 -CHI::Driver::RawMemory 0.60 -CHI::Driver::Role::HasSubcaches 0.60 -CHI::Driver::Role::IsSizeAware 0.60 -CHI::Driver::Role::IsSubcache 0.60 -CHI::Driver::Role::Universal 0.60 -CHI::Serializer::JSON 0.60 -CHI::Serializer::Storable 0.60 -CHI::Stats 0.60 -CHI::t::Bugs 0.60 -CHI::t::Config 0.60 -CHI::t::Constants 0.60 -CHI::t::Driver 0.60 -CHI::t::Driver::CacheCache 0.60 -CHI::t::Driver::FastMmap 0.60 -CHI::t::Driver::File 0.60 -CHI::t::Driver::File::DepthZero 0.60 -CHI::t::Driver::Memory 0.60 -CHI::t::Driver::NonMoose 0.60 -CHI::t::Driver::RawMemory 0.60 -CHI::t::Driver::Subcache 0.60 -CHI::t::Driver::Subcache::l1_cache 0.60 -CHI::t::Driver::Subcache::mirror_cache 0.60 -CHI::t::GetError 0.60 -CHI::t::Initialize 0.60 -CHI::t::Null 0.60 -CHI::t::RequiredModules 0.60 -CHI::t::Sanity 0.60 -CHI::t::SetError 0.60 -CHI::t::Subcache 0.60 -CHI::t::Subclass 0.60 -CHI::t::Util 0.60 -CHI::Test 0.60 -CHI::Test::Class 0.60 -CHI::Test::Driver::NonMoose 0.60 -CHI::Test::Driver::Readonly 0.60 -CHI::Test::Driver::Role::CheckKeyValidity 0.60 -CHI::Test::Driver::Writeonly 0.60 -CHI::Test::Util 0.60 -CHI::Types 0.60 -CHI::Util 0.60 -Class::Accessor 0.51 -Class::Accessor::Chained 0.01 -Class::Accessor::Chained::Fast unknown -Class::Accessor::Fast 0.51 -Class::Accessor::Faster 0.51 -Class::Accessor::Grouped 0.10014 -Class::Accessor::Lite 0.08 -Class::AutoClass 1.56 -Class::AutoClass::Root 1 -Class::C3 0.34 -Class::C3::Adopt::NEXT 0.14 -Class::C3::Componentised 1.001002 -Class::C3::Componentised::ApplyHooks unknown -Class::Data::Inheritable 0.08 -Class::Factory::Util 1.7 -Class::Inspector 1.32 -Class::Inspector::Functions 1.32 -Class::Load 0.25 -Class::Load::PP 0.25 -Class::Load::XS 0.10 -Class::Method::Modifiers 2.12 -Class::MethodMaker 2.24 -Class::MethodMaker::array unknown -Class::MethodMaker::Constants unknown -Class::MethodMaker::Engine 2.24 -Class::MethodMaker::hash unknown -Class::MethodMaker::OptExt unknown -Class::MethodMaker::scalar unknown -Class::MethodMaker::V1Compat unknown -Class::MOP 2.2011 -Class::MOP::Attribute 2.2011 -Class::MOP::Class 2.2011 -Class::MOP::Class::Immutable::Trait 2.2011 -Class::MOP::Deprecated 2.2011 -Class::MOP::Instance 2.2011 -Class::MOP::Method 2.2011 -Class::MOP::Method::Accessor 2.2011 -Class::MOP::Method::Constructor 2.2011 -Class::MOP::Method::Generated 2.2011 -Class::MOP::Method::Inlined 2.2011 -Class::MOP::Method::Meta 2.2011 -Class::MOP::Method::Wrapped 2.2011 -Class::MOP::MiniTrait 2.2011 -Class::MOP::Mixin 2.2011 -Class::MOP::Mixin::AttributeCore 2.2011 -Class::MOP::Mixin::HasAttributes 2.2011 -Class::MOP::Mixin::HasMethods 2.2011 -Class::MOP::Mixin::HasOverloads 2.2011 -Class::MOP::Module 2.2011 -Class::MOP::Object 2.2011 -Class::MOP::Overload 2.2011 -Class::MOP::Package 2.2011 -Class::Singleton 1.5 -Class::Tiny 1.006 -Class::Trigger 0.14 -Class::Unload 0.11 -Class::XSAccessor 1.19 -Class::XSAccessor::Array 1.19 -Clipboard 0.13 -Clipboard::MacPasteboard unknown -Clipboard::Win32 unknown -Clipboard::Xclip unknown -Clone 0.39 -Clone::Choose 0.010 -Clone::PP 1.07 -Commandable 0.01 -Commandable::Invocation 0.01 -common::sense 3.74 -Compress::Bzip2 2.26 -Compress::Raw::Bzip2 2.081 -Compress::Raw::Zlib 2.081 -Config::Any 0.32 -Config::Any::Base unknown -Config::Any::General unknown -Config::Any::INI unknown -Config::Any::JSON unknown -Config::Any::Perl unknown -Config::Any::XML unknown -Config::Any::YAML unknown -Config::General 2.63 -Config::General::Extended 2.07 -Config::General::Interpolated 2.15 -Config::INI 0.025 -Config::INI::Reader 0.025 -Config::INI::Writer 0.025 -Config::MVP 2.200011 -Config::MVP::Assembler 2.200011 -Config::MVP::Assembler::WithBundles 2.200011 -Config::MVP::Error 2.200011 -Config::MVP::Reader 2.200011 -Config::MVP::Reader::Findable 2.200011 -Config::MVP::Reader::Findable::ByExtension 2.200011 -Config::MVP::Reader::Finder 2.200011 -Config::MVP::Reader::Hash 2.200011 -Config::MVP::Reader::INI 2.101463 -Config::MVP::Section 2.200011 -Config::MVP::Sequence 2.200011 -Config::Tiny 2.23 -constant::boolean 0.02 -Context::Preserve 0.03 -Contextual::Return 0.004014 -Contextual::Return::Failure unknown -Convert::Binary::C 0.78 -Convert::Binary::C::Cached 0.78 -Convert::BinHex 1.125 -Convert::Color 0.11 -Convert::Color::CMY 0.11 -Convert::Color::CMYK 0.11 -Convert::Color::HSL 0.11 -Convert::Color::HSV 0.11 -Convert::Color::RGB 0.11 -Convert::Color::RGB16 0.11 -Convert::Color::RGB8 0.11 -Convert::Color::VGA 0.11 -Convert::Color::X11 0.11 -Convert::Color::XTerm 0.05 -Convert::UU 0.5201 -Cookie::Baker 0.09 -CPAN::Changes 0.400002 -CPAN::Changes::Group unknown -CPAN::Changes::Release unknown -CPAN::Checksums 2.12 -CPAN::Common::Index 0.010 -CPAN::Common::Index::LocalPackage 0.010 -CPAN::Common::Index::MetaDB 0.010 -CPAN::Common::Index::Mirror 0.010 -CPAN::Common::Index::Mux::Ordered 0.010 -CPAN::DistnameInfo 0.12 -CPAN::Meta::Check 0.014 -CPAN::Mini 1.111016 -CPAN::Mini::App 1.111016 -CPAN::Perl::Releases 3.68 -CPAN::Uploader 0.103013 -Cpanel::JSON::XS 4.04 -Cpanel::JSON::XS::Type unknown -Crypt::Blowfish 2.14 -Crypt::CBC 2.33 -Crypt::PasswdMD5 1.40 -Crypt::Random::Seed 0.03 -Crypt::Random::TESHA2 0.01 -Crypt::Random::TESHA2::Config 0.01 -Crypt::RC4 2.02 -CSS::Tiny 1.20 -curry 1.001000 -curry::weak unknown -Curses::Window 1.36 -Cwd 3.74 -Cwd::Guard 0.05 -Dancer 1.3400 -Dancer2 0.206000 -Dancer2::CLI 0.206000 -Dancer2::CLI::Command::gen 0.206000 -Dancer2::CLI::Command::version 0.206000 -Dancer2::Core 0.206000 -Dancer2::Core::App 0.206000 -Dancer2::Core::Cookie 0.206000 -Dancer2::Core::Dispatcher 0.206000 -Dancer2::Core::DSL 0.206000 -Dancer2::Core::Error 0.206000 -Dancer2::Core::Factory 0.206000 -Dancer2::Core::Hook 0.206000 -Dancer2::Core::HTTP 0.206000 -Dancer2::Core::MIME 0.206000 -Dancer2::Core::Request 0.206000 -Dancer2::Core::Request::Upload 0.206000 -Dancer2::Core::Response 0.206000 -Dancer2::Core::Response::Delayed 0.206000 -Dancer2::Core::Role::ConfigReader 0.206000 -Dancer2::Core::Role::DSL 0.206000 -Dancer2::Core::Role::Engine 0.206000 -Dancer2::Core::Role::Handler 0.206000 -Dancer2::Core::Role::HasLocation 0.206000 -Dancer2::Core::Role::Hookable 0.206000 -Dancer2::Core::Role::Logger 0.206000 -Dancer2::Core::Role::Serializer 0.206000 -Dancer2::Core::Role::SessionFactory 0.206000 -Dancer2::Core::Role::SessionFactory::File 0.206000 -Dancer2::Core::Role::StandardResponses 0.206000 -Dancer2::Core::Role::Template 0.206000 -Dancer2::Core::Route 0.206000 -Dancer2::Core::Runner 0.206000 -Dancer2::Core::Session 0.206000 -Dancer2::Core::Time 0.206000 -Dancer2::Core::Types 0.206000 -Dancer2::FileUtils 0.206000 -Dancer2::Handler::AutoPage 0.206000 -Dancer2::Handler::File 0.206000 -Dancer2::Logger::Capture 0.206000 -Dancer2::Logger::Capture::Trap 0.206000 -Dancer2::Logger::Console 0.206000 -Dancer2::Logger::Diag 0.206000 -Dancer2::Logger::File 0.206000 -Dancer2::Logger::LogReport 1.27 -Dancer2::Logger::Note 0.206000 -Dancer2::Logger::Null 0.206000 -Dancer2::Plugin 0.206000 -Dancer2::Plugin::LogReport 1.27 -Dancer2::Plugin::LogReport::Message 1.27 -Dancer2::Serializer::Dumper 0.206000 -Dancer2::Serializer::JSON 0.206000 -Dancer2::Serializer::Mutable 0.206000 -Dancer2::Serializer::YAML 0.206000 -Dancer2::Session::Simple 0.206000 -Dancer2::Session::YAML 0.206000 -Dancer2::Template::Implementation::ForkedTiny 0.206000 -Dancer2::Template::Simple 0.206000 -Dancer2::Template::TemplateToolkit 0.206000 -Dancer2::Template::Tiny 0.206000 -Dancer2::Test 0.206000 -Dancer::App 1.3400 -Dancer::Config 1.3400 -Dancer::Config::Object 1.3400 -Dancer::Continuation 1.3400 -Dancer::Continuation::Halted 1.3400 -Dancer::Continuation::Route 1.3400 -Dancer::Continuation::Route::ErrorSent 1.3400 -Dancer::Continuation::Route::FileSent 1.3400 -Dancer::Continuation::Route::Forwarded 1.3400 -Dancer::Continuation::Route::Passed 1.3400 -Dancer::Continuation::Route::Templated 1.3400 -Dancer::Cookie 1.3400 -Dancer::Cookies 1.3400 -Dancer::Deprecation 1.3400 -Dancer::Engine 1.3400 -Dancer::Error 1.3400 -Dancer::Exception 1.3400 -Dancer::Exception::Base 1.3400 -Dancer::Factory::Hook 1.3400 -Dancer::FileUtils 1.3400 -Dancer::GetOpt 1.3400 -Dancer::Handler 1.3400 -Dancer::Handler::Debug 1.3400 -Dancer::Handler::PSGI 1.3400 -Dancer::Handler::Standalone 1.3400 -Dancer::Hook 1.3400 -Dancer::Hook::Properties 1.3400 -Dancer::HTTP 1.3400 -Dancer::Logger 1.3400 -Dancer::Logger::Abstract 1.3400 -Dancer::Logger::Capture 1.3400 -Dancer::Logger::Capture::Trap 1.3400 -Dancer::Logger::Console 1.3400 -Dancer::Logger::Diag 1.3400 -Dancer::Logger::File 1.3400 -Dancer::Logger::LogReport 1.27 -Dancer::Logger::Note 1.3400 -Dancer::Logger::Null 1.3400 -Dancer::MIME 1.3400 -Dancer::ModuleLoader 1.3400 -Dancer::Object 1.3400 -Dancer::Object::Singleton 1.3400 -Dancer::Plugin 1.3400 -Dancer::Plugin::Ajax 1.3400 -Dancer::Renderer 1.3400 -Dancer::Request 1.3400 -Dancer::Request::Upload 1.3400 -Dancer::Response 1.3400 -Dancer::Route 1.3400 -Dancer::Route::Cache 1.3400 -Dancer::Route::Registry 1.3400 -Dancer::Serializer 1.3400 -Dancer::Serializer::Abstract 1.3400 -Dancer::Serializer::Dumper 1.3400 -Dancer::Serializer::JSON 1.3400 -Dancer::Serializer::JSONP 1.3400 -Dancer::Serializer::Mutable 1.3400 -Dancer::Serializer::XML 1.3400 -Dancer::Serializer::YAML 1.3400 -Dancer::Session 1.3400 -Dancer::Session::Abstract 1.3400 -Dancer::Session::Simple 1.3400 -Dancer::Session::YAML 1.3400 -Dancer::SharedData 1.3400 -Dancer::Template 1.3400 -Dancer::Template::Abstract 1.3400 -Dancer::Template::Simple 1.3400 -Dancer::Template::TemplateToolkit 1.3400 -Dancer::Test 1.3400 -Dancer::Timer 1.3400 -Data::Clone 0.004 -Data::Compare 1.25 -Data::Compare::Plugins::Scalar::Properties 1 -Data::Dump 1.23 -Data::Dump::FilterContext unknown -Data::Dump::Filtered unknown -Data::Dump::Streamer 2.40 -Data::Dump::Streamer::_::StringPrinter 0.1 -Data::Dump::Trace 0.02 -Data::Dumper::Again 0.01 -Data::Dumper::Concise 2.023 -Data::Dumper::Concise::Sugar 2.023 -Data::Dumper::Perltidy 0.03 -Data::Grove 0.08 -Data::Grove::Parent 0.08 -Data::Grove::Visitor 0.08 -Data::Munge 0.097 -Data::OptList 0.110 -Data::Page 2.02 -Data::Paginator 0.08 -Data::Paginator::Types 0.08 -Data::Perl 0.002009 -Data::Perl::Bool 0.002009 -Data::Perl::Bool::MooseLike 0.001008 -Data::Perl::Code 0.002009 -Data::Perl::Collection::Array 0.002009 -Data::Perl::Collection::Array::MooseLike 0.001008 -Data::Perl::Collection::Hash 0.002009 -Data::Perl::Collection::Hash::MooseLike 0.001008 -Data::Perl::Counter 0.002009 -Data::Perl::Number 0.002009 -Data::Perl::Number::MooseLike 0.001008 -Data::Perl::Role::Bool 0.002009 -Data::Perl::Role::Code 0.002009 -Data::Perl::Role::Collection::Array 0.002009 -Data::Perl::Role::Collection::Hash 0.002009 -Data::Perl::Role::Counter 0.002009 -Data::Perl::Role::Number 0.002009 -Data::Perl::Role::String 0.002009 -Data::Perl::String 0.002009 -Data::Perl::String::MooseLike 0.001008 -Data::PowerSet 0.05 -Data::Printer 0.40 -Data::Printer::Filter unknown -Data::Printer::Filter::DateTime unknown -Data::Printer::Filter::DB unknown -Data::Printer::Filter::Digest unknown -Data::Section 0.200007 -Data::Stag 0.14 -Data::Stag::Arr2HTML 0.14 -Data::Stag::Base 0.14 -Data::Stag::BaseGenerator unknown -Data::Stag::ChainHandler 0.14 -Data::Stag::DTDWriter 0.14 -Data::Stag::GraphHandler 0.14 -Data::Stag::HashDB 0.14 -Data::Stag::IndentParser 0.14 -Data::Stag::IndentWriter 0.14 -Data::Stag::ITextParser 0.14 -Data::Stag::ITextWriter 0.14 -Data::Stag::JSONWriter 0.14 -Data::Stag::null 0.14 -Data::Stag::PerlWriter 0.14 -Data::Stag::PodParser 0.14 -Data::Stag::SAX2Stag 0.14 -Data::Stag::Simple 0.14 -Data::Stag::StagDB 0.14 -Data::Stag::StagI unknown -Data::Stag::StagImpl 0.14 -Data::Stag::SxprParser 0.14 -Data::Stag::SxprWriter 0.14 -Data::Stag::Util 0.14 -Data::Stag::Writer 0.14 -Data::Stag::XMLParser 0.14 -Data::Stag::XMLWriter 0.14 -Data::Stag::XSLHandler unknown -Data::Stag::XSLTHandler unknown -Data::UUID 1.221 -Data::Validate::Domain 0.14 -Data::Validate::IP 0.27 -Data::Validate::URI 0.07 -Data::Visitor 0.30 -Data::Visitor::Callback 0.30 -Date::Format 2.24 -Date::Language 1.10 -Date::Language::Afar 0.99 -Date::Language::Amharic 1.00 -Date::Language::Austrian 1.01 -Date::Language::Brazilian 1.01 -Date::Language::Bulgarian 1.01 -Date::Language::Chinese 1.00 -Date::Language::Chinese_GB 1.01 -Date::Language::Czech 1.01 -Date::Language::Danish 1.01 -Date::Language::Dutch 1.02 -Date::Language::English 1.01 -Date::Language::Finnish 1.01 -Date::Language::French 1.04 -Date::Language::Gedeo 0.99 -Date::Language::German 1.02 -Date::Language::Greek 1.00 -Date::Language::Hungarian 1.01 -Date::Language::Icelandic 1.01 -Date::Language::Italian 1.01 -Date::Language::Norwegian 1.01 -Date::Language::Oromo 0.99 -Date::Language::Romanian 1.01 -Date::Language::Russian 1.01 -Date::Language::Russian_cp1251 1.01 -Date::Language::Russian_koi8r 1.01 -Date::Language::Sidama 0.99 -Date::Language::Somali 0.99 -Date::Language::Spanish 1.00 -Date::Language::Swedish 1.01 -Date::Language::Tigrinya 1.00 -Date::Language::TigrinyaEritrean 1.00 -Date::Language::TigrinyaEthiopian 1.00 -Date::Language::Turkish 1.0 -Date::Parse 2.30 -Date::Tiny 1.07 -DateTime 1.49 -DateTime::Astro 1.03 -DateTime::Astro unknown -DateTime::Astro unknown -DateTime::Calendar::Chinese 1.00 -DateTime::Calendar::Japanese::Era 0.08003 -DateTime::Duration 1.49 -DateTime::Event::Chinese 1.00 -DateTime::Event::ICal 0.13 -DateTime::Event::SolarTerm unknown -DateTime::Format::Builder 0.81 -DateTime::Format::Builder::Parser 0.81 -DateTime::Format::Builder::Parser::Dispatch 0.81 -DateTime::Format::Builder::Parser::generic 0.81 -DateTime::Format::Builder::Parser::Quick 0.81 -DateTime::Format::Builder::Parser::Regex 0.81 -DateTime::Format::Builder::Parser::Strptime 0.81 -DateTime::Format::DateParse 0.05 -DateTime::Format::Duration 1.04 -DateTime::Format::Epoch 0.16 -DateTime::Format::Epoch::ActiveDirectory 0.13 -DateTime::Format::Epoch::DotNet 0.13 -DateTime::Format::Epoch::JD 0.13 -DateTime::Format::Epoch::Lilian 0.13 -DateTime::Format::Epoch::MacOS 0.13 -DateTime::Format::Epoch::MJD 0.13 -DateTime::Format::Epoch::NTP 0.14 -DateTime::Format::Epoch::RataDie 0.13 -DateTime::Format::Epoch::RJD 0.13 -DateTime::Format::Epoch::TAI64 0.13 -DateTime::Format::Epoch::TJD 0.13 -DateTime::Format::Epoch::Unix 0.13 -DateTime::Format::Flexible 0.30 -DateTime::Format::Flexible::lang unknown -DateTime::Format::Flexible::lang::de unknown -DateTime::Format::Flexible::lang::en unknown -DateTime::Format::Flexible::lang::es unknown -DateTime::Format::ICal 0.09 -DateTime::Format::Mail 0.403 -DateTime::Format::Natural 1.05 -DateTime::Format::Natural::Calc 1.41 -DateTime::Format::Natural::Compat 0.07 -DateTime::Format::Natural::Duration 0.06 -DateTime::Format::Natural::Duration::Checks 0.04 -DateTime::Format::Natural::Expand 0.03 -DateTime::Format::Natural::Extract 0.11 -DateTime::Format::Natural::Formatted 0.07 -DateTime::Format::Natural::Helpers 0.06 -DateTime::Format::Natural::Lang::Base 1.08 -DateTime::Format::Natural::Lang::EN 1.62 -DateTime::Format::Natural::Rewrite 0.06 -DateTime::Format::Natural::Test 0.10 -DateTime::Format::Natural::Utils 0.05 -DateTime::Format::Natural::Wrappers 0.03 -DateTime::Format::Strptime 1.75 -DateTime::Format::Strptime::Types 1.75 -DateTime::Format::W3CDTF 0.07 -DateTime::Helpers 1.49 -DateTime::Infinite 1.49 -DateTime::LeapSecond 1.49 -DateTime::Locale 1.22 -DateTime::Locale::Base 1.22 -DateTime::Locale::Catalog 1.22 -DateTime::Locale::Data 1.22 -DateTime::Locale::FromData 1.22 -DateTime::Locale::Util 1.22 -DateTime::PP 1.49 -DateTime::PPExtra 1.49 -DateTime::Set 0.3900 -DateTime::Set::ICal 0.19 -DateTime::Span unknown -DateTime::SpanSet unknown -DateTime::TimeZone 2.19 -DateTime::TimeZone::Africa::Abidjan 2.19 -DateTime::TimeZone::Africa::Accra 2.19 -DateTime::TimeZone::Africa::Algiers 2.19 -DateTime::TimeZone::Africa::Bissau 2.19 -DateTime::TimeZone::Africa::Cairo 2.19 -DateTime::TimeZone::Africa::Casablanca 2.19 -DateTime::TimeZone::Africa::Ceuta 2.19 -DateTime::TimeZone::Africa::El_Aaiun 2.19 -DateTime::TimeZone::Africa::Johannesburg 2.19 -DateTime::TimeZone::Africa::Juba 2.19 -DateTime::TimeZone::Africa::Khartoum 2.19 -DateTime::TimeZone::Africa::Lagos 2.19 -DateTime::TimeZone::Africa::Maputo 2.19 -DateTime::TimeZone::Africa::Monrovia 2.19 -DateTime::TimeZone::Africa::Nairobi 2.19 -DateTime::TimeZone::Africa::Ndjamena 2.19 -DateTime::TimeZone::Africa::Sao_Tome 2.19 -DateTime::TimeZone::Africa::Tripoli 2.19 -DateTime::TimeZone::Africa::Tunis 2.19 -DateTime::TimeZone::Africa::Windhoek 2.19 -DateTime::TimeZone::America::Adak 2.19 -DateTime::TimeZone::America::Anchorage 2.19 -DateTime::TimeZone::America::Araguaina 2.19 -DateTime::TimeZone::America::Argentina::Buenos_Aires 2.19 -DateTime::TimeZone::America::Argentina::Catamarca 2.19 -DateTime::TimeZone::America::Argentina::Cordoba 2.19 -DateTime::TimeZone::America::Argentina::Jujuy 2.19 -DateTime::TimeZone::America::Argentina::La_Rioja 2.19 -DateTime::TimeZone::America::Argentina::Mendoza 2.19 -DateTime::TimeZone::America::Argentina::Rio_Gallegos 2.19 -DateTime::TimeZone::America::Argentina::Salta 2.19 -DateTime::TimeZone::America::Argentina::San_Juan 2.19 -DateTime::TimeZone::America::Argentina::San_Luis 2.19 -DateTime::TimeZone::America::Argentina::Tucuman 2.19 -DateTime::TimeZone::America::Argentina::Ushuaia 2.19 -DateTime::TimeZone::America::Asuncion 2.19 -DateTime::TimeZone::America::Atikokan 2.19 -DateTime::TimeZone::America::Bahia 2.19 -DateTime::TimeZone::America::Bahia_Banderas 2.19 -DateTime::TimeZone::America::Barbados 2.19 -DateTime::TimeZone::America::Belem 2.19 -DateTime::TimeZone::America::Belize 2.19 -DateTime::TimeZone::America::Blanc_Sablon 2.19 -DateTime::TimeZone::America::Boa_Vista 2.19 -DateTime::TimeZone::America::Bogota 2.19 -DateTime::TimeZone::America::Boise 2.19 -DateTime::TimeZone::America::Cambridge_Bay 2.19 -DateTime::TimeZone::America::Campo_Grande 2.19 -DateTime::TimeZone::America::Cancun 2.19 -DateTime::TimeZone::America::Caracas 2.19 -DateTime::TimeZone::America::Cayenne 2.19 -DateTime::TimeZone::America::Chicago 2.19 -DateTime::TimeZone::America::Chihuahua 2.19 -DateTime::TimeZone::America::Costa_Rica 2.19 -DateTime::TimeZone::America::Creston 2.19 -DateTime::TimeZone::America::Cuiaba 2.19 -DateTime::TimeZone::America::Curacao 2.19 -DateTime::TimeZone::America::Danmarkshavn 2.19 -DateTime::TimeZone::America::Dawson 2.19 -DateTime::TimeZone::America::Dawson_Creek 2.19 -DateTime::TimeZone::America::Denver 2.19 -DateTime::TimeZone::America::Detroit 2.19 -DateTime::TimeZone::America::Edmonton 2.19 -DateTime::TimeZone::America::Eirunepe 2.19 -DateTime::TimeZone::America::El_Salvador 2.19 -DateTime::TimeZone::America::Fort_Nelson 2.19 -DateTime::TimeZone::America::Fortaleza 2.19 -DateTime::TimeZone::America::Glace_Bay 2.19 -DateTime::TimeZone::America::Godthab 2.19 -DateTime::TimeZone::America::Goose_Bay 2.19 -DateTime::TimeZone::America::Grand_Turk 2.19 -DateTime::TimeZone::America::Guatemala 2.19 -DateTime::TimeZone::America::Guayaquil 2.19 -DateTime::TimeZone::America::Guyana 2.19 -DateTime::TimeZone::America::Halifax 2.19 -DateTime::TimeZone::America::Havana 2.19 -DateTime::TimeZone::America::Hermosillo 2.19 -DateTime::TimeZone::America::Indiana::Indianapolis 2.19 -DateTime::TimeZone::America::Indiana::Knox 2.19 -DateTime::TimeZone::America::Indiana::Marengo 2.19 -DateTime::TimeZone::America::Indiana::Petersburg 2.19 -DateTime::TimeZone::America::Indiana::Tell_City 2.19 -DateTime::TimeZone::America::Indiana::Vevay 2.19 -DateTime::TimeZone::America::Indiana::Vincennes 2.19 -DateTime::TimeZone::America::Indiana::Winamac 2.19 -DateTime::TimeZone::America::Inuvik 2.19 -DateTime::TimeZone::America::Iqaluit 2.19 -DateTime::TimeZone::America::Jamaica 2.19 -DateTime::TimeZone::America::Juneau 2.19 -DateTime::TimeZone::America::Kentucky::Louisville 2.19 -DateTime::TimeZone::America::Kentucky::Monticello 2.19 -DateTime::TimeZone::America::La_Paz 2.19 -DateTime::TimeZone::America::Lima 2.19 -DateTime::TimeZone::America::Los_Angeles 2.19 -DateTime::TimeZone::America::Maceio 2.19 -DateTime::TimeZone::America::Managua 2.19 -DateTime::TimeZone::America::Manaus 2.19 -DateTime::TimeZone::America::Martinique 2.19 -DateTime::TimeZone::America::Matamoros 2.19 -DateTime::TimeZone::America::Mazatlan 2.19 -DateTime::TimeZone::America::Menominee 2.19 -DateTime::TimeZone::America::Merida 2.19 -DateTime::TimeZone::America::Metlakatla 2.19 -DateTime::TimeZone::America::Mexico_City 2.19 -DateTime::TimeZone::America::Miquelon 2.19 -DateTime::TimeZone::America::Moncton 2.19 -DateTime::TimeZone::America::Monterrey 2.19 -DateTime::TimeZone::America::Montevideo 2.19 -DateTime::TimeZone::America::Nassau 2.19 -DateTime::TimeZone::America::New_York 2.19 -DateTime::TimeZone::America::Nipigon 2.19 -DateTime::TimeZone::America::Nome 2.19 -DateTime::TimeZone::America::Noronha 2.19 -DateTime::TimeZone::America::North_Dakota::Beulah 2.19 -DateTime::TimeZone::America::North_Dakota::Center 2.19 -DateTime::TimeZone::America::North_Dakota::New_Salem 2.19 -DateTime::TimeZone::America::Ojinaga 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-Font::TTF::Kern::ClassArray unknown -Font::TTF::Kern::CompactClassArray unknown -Font::TTF::Kern::OrderedList unknown -Font::TTF::Kern::StateTable unknown -Font::TTF::Kern::Subtable unknown -Font::TTF::Loca unknown -Font::TTF::LTSH unknown -Font::TTF::Maxp unknown -Font::TTF::Mort unknown -Font::TTF::Mort::Chain unknown -Font::TTF::Mort::Contextual unknown -Font::TTF::Mort::Insertion unknown -Font::TTF::Mort::Ligature unknown -Font::TTF::Mort::Noncontextual unknown -Font::TTF::Mort::Rearrangement unknown -Font::TTF::Mort::Subtable unknown -Font::TTF::Name 1.1 -Font::TTF::OldCmap unknown -Font::TTF::OldMort unknown -Font::TTF::OS_2 unknown -Font::TTF::OTTags unknown -Font::TTF::PCLT unknown -Font::TTF::Post 0.01 -Font::TTF::Prep 0.0001 -Font::TTF::Prop unknown -Font::TTF::PSNames unknown -Font::TTF::Segarr 0.0001 -Font::TTF::Silf unknown -Font::TTF::Sill unknown -Font::TTF::Table 0.0001 -Font::TTF::Ttc 0.0001 -Font::TTF::Ttopen unknown -Font::TTF::Utils 0.0001 -Font::TTF::Vhea unknown 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-HTML::FormHandler::Field::Compound 0.40068 -HTML::FormHandler::Field::Date 0.40068 -HTML::FormHandler::Field::DateMDY 0.40068 -HTML::FormHandler::Field::DateTime 0.40068 -HTML::FormHandler::Field::Display 0.40068 -HTML::FormHandler::Field::Duration 0.40068 -HTML::FormHandler::Field::Email 0.40068 -HTML::FormHandler::Field::File 0.40068 -HTML::FormHandler::Field::Float 0.40068 -HTML::FormHandler::Field::Hidden 0.40068 -HTML::FormHandler::Field::Hour 0.40068 -HTML::FormHandler::Field::Integer 0.40068 -HTML::FormHandler::Field::IntRange 0.40068 -HTML::FormHandler::Field::Minute 0.40068 -HTML::FormHandler::Field::Money 0.40068 -HTML::FormHandler::Field::Month 0.40068 -HTML::FormHandler::Field::MonthDay 0.40068 -HTML::FormHandler::Field::MonthName 0.40068 -HTML::FormHandler::Field::Multiple 0.40068 -HTML::FormHandler::Field::Nested 0.40068 -HTML::FormHandler::Field::NonEditable 0.40068 -HTML::FormHandler::Field::NoValue 0.40068 -HTML::FormHandler::Field::Password 0.40068 -HTML::FormHandler::Field::PasswordConf 0.40068 -HTML::FormHandler::Field::PosInteger 0.40068 -HTML::FormHandler::Field::PrimaryKey 0.40068 -HTML::FormHandler::Field::Repeatable 0.40068 -HTML::FormHandler::Field::RequestToken 0.40068 -HTML::FormHandler::Field::Reset 0.40068 -HTML::FormHandler::Field::Result 0.40068 -HTML::FormHandler::Field::RmElement 0.40068 -HTML::FormHandler::Field::Role::RequestToken 0.40068 -HTML::FormHandler::Field::Second 0.40068 -HTML::FormHandler::Field::Select 0.40068 -HTML::FormHandler::Field::SelectCSV 0.40068 -HTML::FormHandler::Field::Submit 0.40068 -HTML::FormHandler::Field::Text 0.40068 -HTML::FormHandler::Field::TextArea 0.40068 -HTML::FormHandler::Field::TextCSV 0.40068 -HTML::FormHandler::Field::Upload 0.40068 -HTML::FormHandler::Field::Weekday 0.40068 -HTML::FormHandler::Field::Year 0.40068 -HTML::FormHandler::Fields 0.40068 -HTML::FormHandler::Foo 0.40068 -HTML::FormHandler::I18N 0.40068 -HTML::FormHandler::I18N::ar_kw 0.40068 -HTML::FormHandler::I18N::bg_bg 0.40068 -HTML::FormHandler::I18N::ca_es 0.40068 -HTML::FormHandler::I18N::cs_cz 0.40068 -HTML::FormHandler::I18N::de_de 0.40068 -HTML::FormHandler::I18N::en_us 0.40068 -HTML::FormHandler::I18N::es_es 0.40068 -HTML::FormHandler::I18N::hu_hu 0.40068 -HTML::FormHandler::I18N::it_it 0.40068 -HTML::FormHandler::I18N::ja_jp 0.40068 -HTML::FormHandler::I18N::pt_br 0.40068 -HTML::FormHandler::I18N::ru_ru 0.40068 -HTML::FormHandler::I18N::sv_se 0.40068 -HTML::FormHandler::I18N::tr_tr 0.40068 -HTML::FormHandler::I18N::ua_ua 0.40068 -HTML::FormHandler::InitResult 0.40068 -HTML::FormHandler::Merge 0.40068 -HTML::FormHandler::Model 0.40068 -HTML::FormHandler::Model::Object 0.40068 -HTML::FormHandler::Moose 0.40068 -HTML::FormHandler::Moose::Role 0.40068 -HTML::FormHandler::Page 0.40068 -HTML::FormHandler::Page::Simple 0.40068 -HTML::FormHandler::Pages 0.40068 -HTML::FormHandler::Render::RepeatableJs 0.40068 -HTML::FormHandler::Render::Simple 0.40068 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-HTML::FormHandler::Widget::Field::HorizCheckboxGroup 0.40068 -HTML::FormHandler::Widget::Field::NoRender 0.40068 -HTML::FormHandler::Widget::Field::Password 0.40068 -HTML::FormHandler::Widget::Field::RadioGroup 0.40068 -HTML::FormHandler::Widget::Field::Repeatable 0.40068 -HTML::FormHandler::Widget::Field::Reset 0.40068 -HTML::FormHandler::Widget::Field::Role::HTMLAttributes 0.40068 -HTML::FormHandler::Widget::Field::Role::SelectedOption 0.40068 -HTML::FormHandler::Widget::Field::Select 0.40068 -HTML::FormHandler::Widget::Field::Span 0.40068 -HTML::FormHandler::Widget::Field::Submit 0.40068 -HTML::FormHandler::Widget::Field::Text 0.40068 -HTML::FormHandler::Widget::Field::Textarea 0.40068 -HTML::FormHandler::Widget::Field::Upload 0.40068 -HTML::FormHandler::Widget::Form::Role::HTMLAttributes 0.40068 -HTML::FormHandler::Widget::Form::Simple 0.40068 -HTML::FormHandler::Widget::Form::Table 0.40068 -HTML::FormHandler::Widget::Theme::Bootstrap 0.40068 -HTML::FormHandler::Widget::Theme::Bootstrap3 0.40068 -HTML::FormHandler::Widget::Theme::BootstrapFormMessages 0.40068 -HTML::FormHandler::Widget::Wrapper::Base 0.40068 -HTML::FormHandler::Widget::Wrapper::Bootstrap 0.40068 -HTML::FormHandler::Widget::Wrapper::Bootstrap3 0.40068 -HTML::FormHandler::Widget::Wrapper::Fieldset 0.40068 -HTML::FormHandler::Widget::Wrapper::None 0.40068 -HTML::FormHandler::Widget::Wrapper::Simple 0.40068 -HTML::FormHandler::Widget::Wrapper::SimpleInline 0.40068 -HTML::FormHandler::Widget::Wrapper::Table 0.40068 -HTML::FormHandler::Widget::Wrapper::TableInline 0.40068 -HTML::FormHandler::Wizard 0.40068 -HTML::HeadParser 3.71 -HTML::LinkExtor 3.69 -HTML::Parse 5.07 -HTML::Parser 3.72 -HTML::Perlinfo 1.69 -HTML::Perlinfo::Apache unknown -HTML::Perlinfo::Base unknown -HTML::Perlinfo::Common unknown -HTML::Perlinfo::General unknown -HTML::Perlinfo::Loaded 1.02 -HTML::Perlinfo::Modules 1.19 -HTML::PullParser 3.57 -HTML::TableExtract 2.15 -HTML::Tagset 3.20 -HTML::TokeParser 3.69 -HTML::Tree 5.07 -HTML::TreeBuilder 5.07 -HTTP::Body 1.22 -HTTP::Body::MultiPart 1.22 -HTTP::Body::OctetStream 1.22 -HTTP::Body::UrlEncoded 1.22 -HTTP::Body::XForms 1.22 -HTTP::Body::XFormsMultipart 1.22 -HTTP::Config 6.18 -HTTP::CookieJar 0.008 -HTTP::CookieJar::LWP 0.008 -HTTP::Cookies 6.04 -HTTP::Cookies::Microsoft 6.04 -HTTP::Cookies::Netscape 6.04 -HTTP::Daemon 6.01 -HTTP::Date 6.02 -HTTP::Entity::Parser 0.21 -HTTP::Entity::Parser::JSON unknown -HTTP::Entity::Parser::MultiPart unknown -HTTP::Entity::Parser::OctetStream unknown -HTTP::Entity::Parser::UrlEncoded unknown -HTTP::Headers 6.18 -HTTP::Headers::Auth 6.18 -HTTP::Headers::ETag 6.18 -HTTP::Headers::Fast 0.21 -HTTP::Headers::Util 6.18 -HTTP::Message 6.18 -HTTP::Message::PSGI unknown -HTTP::MultiPartParser 0.02 -HTTP::Negotiate 6.01 -HTTP::Parser::XS 0.17 -HTTP::Parser::XS::PP unknown -HTTP::Request 6.18 -HTTP::Request::AsCGI 1.2 -HTTP::Request::Common 6.18 -HTTP::Response 6.18 -HTTP::Server::PSGI unknown -HTTP::Server::PSGI::Net::Server::PreFork unknown -HTTP::Server::Simple 0.52 -HTTP::Server::Simple::CGI unknown -HTTP::Server::Simple::CGI::Environment unknown -HTTP::Server::Simple::PSGI 0.16 -HTTP::Status 6.18 -HTTP::Thin 0.006 -HTTP::Tinyish 0.14 -HTTP::Tinyish::Base unknown -HTTP::Tinyish::Curl unknown -HTTP::Tinyish::HTTPTiny unknown -HTTP::Tinyish::LWP unknown -HTTP::Tinyish::Wget unknown -HTTP::XSCookies 0.000021 -Image::PNG 0.23 -Image::PNG::Const 0.45 -Image::PNG::Container 0.23 -Image::PNG::Libpng 0.45 -Image::PNG::Util unknown -Import::Into 1.002005 -Importer 0.025 -inc::Module::Install 1.19 -inc::Module::Install::DSL 1.19 -indirect 0.38 -Inline 0.80 -Inline::C 0.78 -Inline::C::Parser unknown -Inline::C::Parser::Pegex unknown -Inline::C::Parser::Pegex::AST unknown -Inline::C::Parser::Pegex::Grammar unknown -Inline::C::Parser::RecDescent unknown -Inline::C::Parser::RegExp unknown -Inline::denter unknown -Inline::Foo 0.80 -Inline::MakeMaker 0.80 -Inline::MakePdlppInstallable unknown -Inline::Pdlpp 0.4 -IO::All 0.87 -IO::All::Base unknown -IO::All::DBM unknown -IO::All::Dir unknown -IO::All::File unknown -IO::All::Filesys unknown -IO::All::Link unknown -IO::All::MLDBM unknown -IO::All::Pipe unknown -IO::All::Socket unknown -IO::All::STDIO unknown -IO::All::String unknown -IO::All::Temp unknown -IO::Async 0.72 -IO::Async::Channel 0.72 -IO::Async::Debug 0.72 -IO::Async::File 0.72 -IO::Async::FileStream 0.72 -IO::Async::Function 0.72 -IO::Async::Future 0.72 -IO::Async::Handle 0.72 -IO::Async::Internals::ChildManager 0.72 -IO::Async::Listener 0.72 -IO::Async::Loop 0.72 -IO::Async::Loop::Poll 0.72 -IO::Async::Loop::Select 0.72 -IO::Async::LoopTests 0.72 -IO::Async::Notifier 0.72 -IO::Async::OS 0.72 -IO::Async::OS::cygwin 0.72 -IO::Async::OS::linux 0.72 -IO::Async::OS::MSWin32 0.72 -IO::Async::PID 0.72 -IO::Async::Process 0.72 -IO::Async::Protocol 0.72 -IO::Async::Protocol::LineStream 0.72 -IO::Async::Protocol::Stream 0.72 -IO::Async::Resolver 0.72 -IO::Async::Routine 0.72 -IO::Async::Signal 0.72 -IO::Async::Socket 0.72 -IO::Async::Stream 0.72 -IO::Async::Test 0.72 -IO::Async::Timer 0.72 -IO::Async::Timer::Absolute 0.72 -IO::Async::Timer::Countdown 0.72 -IO::Async::Timer::Periodic 0.72 -IO::AtomicFile 2.111 -IO::CaptureOutput 1.1104 -IO::HTML 1.001 -IO::InnerFile 2.111 -IO::Interactive 1.022 -IO::Lines 2.111 -IO::Pipely 0.005 -IO::Prompt 0.997004 -IO::Pty 1.12 -IO::Scalar 2.111 -IO::ScalarArray 2.111 -IO::SessionData 1.03 -IO::SessionSet unknown -IO::Socket::SSL 2.058 -IO::Socket::SSL::Intercept 2.056 -IO::Socket::SSL::PublicSuffix unknown -IO::Socket::SSL::Utils 2.014 -IO::Socket::Timeout 0.32 -IO::String 1.08 -IO::Stringy 2.111 -IO::TieCombine 1.005 -IO::TieCombine::Handle 1.005 -IO::TieCombine::Scalar 1.005 -IO::Tty 1.12 -IO::Tty::Constant unknown -IO::Wrap 2.111 -IO::WrapTie 2.111 -IPC::Run 20180523.0 -IPC::Run3 0.048 -IPC::Run3::ProfArrayBuffer 0.048 -IPC::Run3::ProfLogger 0.048 -IPC::Run3::ProfLogReader 0.048 -IPC::Run3::ProfPP 0.048 -IPC::Run3::ProfReporter 0.048 -IPC::Run::Debug 20180523.0 -IPC::Run::IO 20180523.0 -IPC::Run::Timer 20180523.0 -IPC::Run::Win32Helper 20180523.0 -IPC::Run::Win32IO 20180523.0 -IPC::Run::Win32Pump 20180523.0 -IPC::ShareLite 0.17 -IPC::System::Simple 1.25 -JSON 2.97001 -JSON::Any 1.39 -JSON::MaybeXS 1.004000 -Lexical::Persistence 1.020 -lib::core::only unknown -Lingua::EN::FindNumber 1.32 -Lingua::EN::Inflect 1.903 -Lingua::EN::Inflect::Number 1.12 -Lingua::EN::Inflect::Phrase 0.20 -Lingua::EN::Number::IsOrdinal 0.05 -Lingua::EN::Tagger 0.29 -Lingua::EN::Words2Nums unknown -Lingua::GL::Stemmer 0.02 -Lingua::PT::Stemmer 0.02 -Lingua::Stem 0.84 -Lingua::Stem::AutoLoader 1.02 -Lingua::Stem::Da 1.01 -Lingua::Stem::De 1.01 -Lingua::Stem::En 2.16 -Lingua::Stem::EnBroken 2.13 -Lingua::Stem::Fr 0.02 -Lingua::Stem::Gl 1.02 -Lingua::Stem::It 0.02 -Lingua::Stem::No 1.01 -Lingua::Stem::Pt 1.01 -Lingua::Stem::Ru 0.04 -Lingua::Stem::Snowball::Da 1.01 -Lingua::Stem::Snowball::No 1.2 -Lingua::Stem::Snowball::Se 1.2 -Lingua::Stem::Sv 1.01 -List::AllUtils 0.14 -List::MoreUtils 0.428 -List::MoreUtils::PP 0.428 -List::MoreUtils::XS 0.428 -List::SomeUtils 0.56 -List::SomeUtils::PP 0.56 -List::SomeUtils::XS 0.58 -List::Util 1.50 -List::Util::XS 1.50 -List::UtilsBy 0.11 -local::lib 2.000024 -Locale::Maketext::Extract 1.00 -Locale::Maketext::Extract::Plugin::Base 1.00 -Locale::Maketext::Extract::Plugin::FormFu 1.00 -Locale::Maketext::Extract::Plugin::Generic 1.00 -Locale::Maketext::Extract::Plugin::Haml 1.00 -Locale::Maketext::Extract::Plugin::Mason 1.00 -Locale::Maketext::Extract::Plugin::Perl 1.00 -Locale::Maketext::Extract::Plugin::PPI 1.00 -Locale::Maketext::Extract::Plugin::TextTemplate 1.00 -Locale::Maketext::Extract::Plugin::TT2 1.00 -Locale::Maketext::Extract::Plugin::YAML 1.00 -Locale::Maketext::Extract::Run 1.00 -Locale::Maketext::Lexicon 1.00 -Locale::Maketext::Lexicon::Auto 1.00 -Locale::Maketext::Lexicon::Gettext 1.00 -Locale::Maketext::Lexicon::Msgcat 1.00 -Locale::Maketext::Lexicon::Tie 1.00 -Log::Any 1.706 -Log::Any::Adapter 1.706 -Log::Any::Adapter::Base 1.706 -Log::Any::Adapter::File 1.706 -Log::Any::Adapter::Null 1.706 -Log::Any::Adapter::Stderr 1.706 -Log::Any::Adapter::Stdout 1.706 -Log::Any::Adapter::Syslog 1.706 -Log::Any::Adapter::Test 1.706 -Log::Any::Adapter::Util 1.706 -Log::Any::Manager 1.706 -Log::Any::Proxy 1.706 -Log::Any::Proxy::Null 1.706 -Log::Any::Proxy::Test 1.706 -Log::Any::Test 1.706 -Log::Contextual 0.008001 -Log::Contextual::Easy::Default 0.008001 -Log::Contextual::Easy::Package 0.008001 -Log::Contextual::Role::Router 0.008001 -Log::Contextual::Role::Router::HasLogger 0.008001 -Log::Contextual::Role::Router::SetLogger 0.008001 -Log::Contextual::Role::Router::WithLogger 0.008001 -Log::Contextual::Router 0.008001 -Log::Contextual::SimpleLogger 0.008001 -Log::Contextual::TeeLogger 0.008001 -Log::Contextual::WarnLogger 0.008001 -Log::Dispatch 2.67 -Log::Dispatch::ApacheLog 2.67 -Log::Dispatch::Array 1.003 -Log::Dispatch::Base 2.67 -Log::Dispatch::Code 2.67 -Log::Dispatch::Config 1.04 -Log::Dispatch::Configurator 1.00 -Log::Dispatch::Configurator::AppConfig 1.00 -Log::Dispatch::Email 2.67 -Log::Dispatch::Email::MailSend 2.67 -Log::Dispatch::Email::MailSender 2.67 -Log::Dispatch::Email::MailSendmail 2.67 -Log::Dispatch::Email::MIMELite 2.67 -Log::Dispatch::File 2.67 -Log::Dispatch::File::Locked 2.67 -Log::Dispatch::Handle 2.67 -Log::Dispatch::Null 2.67 -Log::Dispatch::Output 2.67 -Log::Dispatch::Screen 2.67 -Log::Dispatch::Syslog 2.67 -Log::Dispatch::Types 2.67 -Log::Dispatch::Vars 2.67 -Log::Dispatchouli 2.016 -Log::Dispatchouli::Global 2.016 -Log::Dispatchouli::Proxy 2.016 -Log::Log4perl 1.49 -Log::Log4perl::Appender unknown -Log::Log4perl::Appender::Buffer unknown -Log::Log4perl::Appender::DBI unknown -Log::Log4perl::Appender::File unknown -Log::Log4perl::Appender::Limit unknown -Log::Log4perl::Appender::RRDs unknown -Log::Log4perl::Appender::Screen unknown -Log::Log4perl::Appender::ScreenColoredLevels unknown -Log::Log4perl::Appender::Socket unknown -Log::Log4perl::Appender::String unknown -Log::Log4perl::Appender::Synchronized unknown -Log::Log4perl::Appender::TestArrayBuffer unknown -Log::Log4perl::Appender::TestBuffer unknown -Log::Log4perl::Appender::TestFileCreeper unknown -Log::Log4perl::Catalyst unknown -Log::Log4perl::Config unknown -Log::Log4perl::Config::BaseConfigurator unknown -Log::Log4perl::Config::DOMConfigurator 0.03 -Log::Log4perl::Config::PropertyConfigurator unknown -Log::Log4perl::Config::Watch unknown -Log::Log4perl::DateFormat unknown -Log::Log4perl::Filter unknown -Log::Log4perl::Filter::Boolean unknown -Log::Log4perl::Filter::LevelMatch unknown -Log::Log4perl::Filter::LevelRange unknown -Log::Log4perl::Filter::MDC unknown -Log::Log4perl::Filter::StringMatch unknown -Log::Log4perl::InternalDebug unknown -Log::Log4perl::JavaMap unknown -Log::Log4perl::JavaMap::ConsoleAppender unknown -Log::Log4perl::JavaMap::FileAppender unknown -Log::Log4perl::JavaMap::JDBCAppender unknown -Log::Log4perl::JavaMap::NTEventLogAppender unknown -Log::Log4perl::JavaMap::RollingFileAppender unknown -Log::Log4perl::JavaMap::SyslogAppender unknown -Log::Log4perl::JavaMap::TestBuffer unknown -Log::Log4perl::Layout unknown -Log::Log4perl::Layout::NoopLayout unknown -Log::Log4perl::Layout::PatternLayout unknown -Log::Log4perl::Layout::PatternLayout::Multiline unknown -Log::Log4perl::Layout::SimpleLayout unknown -Log::Log4perl::Level unknown -Log::Log4perl::Logger unknown -Log::Log4perl::MDC unknown -Log::Log4perl::NDC unknown -Log::Log4perl::Resurrector unknown -Log::Log4perl::Util unknown -Log::Log4perl::Util::Semaphore unknown -Log::Log4perl::Util::TimeTracker unknown -Log::Message 0.08 -Log::Message::Config 0.08 -Log::Message::Handlers 0.08 -Log::Message::Item 0.08 -Log::Message::Simple 0.10 -Log::Report 1.27 -Log::Report::DBIC::Profiler 1.27 -Log::Report::Die 1.27 -Log::Report::Dispatcher 1.27 -Log::Report::Dispatcher::Callback 1.27 -Log::Report::Dispatcher::File 1.27 -Log::Report::Dispatcher::Log4perl 1.27 -Log::Report::Dispatcher::LogDispatch 1.27 -Log::Report::Dispatcher::Perl 1.27 -Log::Report::Dispatcher::Syslog 1.27 -Log::Report::Dispatcher::Try 1.27 -Log::Report::Domain 1.27 -Log::Report::Exception 1.27 -Log::Report::Message 1.27 -Log::Report::Minimal 1.06 -Log::Report::Minimal::Domain 1.06 -Log::Report::Optional 1.06 -Log::Report::Translator 1.27 -Log::Report::Util 1.06 -Logger::Simple 2.0 -LWP 6.35 -LWP::Authen::Basic 6.35 -LWP::Authen::Digest 6.35 -LWP::Authen::Ntlm 6.35 -LWP::ConnCache 6.35 -LWP::Debug 6.35 -LWP::Debug unknown -LWP::Debug::TraceHTTP 6.35 -LWP::DebugFile 6.35 -LWP::MediaTypes 6.02 -LWP::MemberMixin 6.35 -LWP::Protocol 6.35 -LWP::Protocol::cpan 6.35 -LWP::Protocol::data 6.35 -LWP::Protocol::file 6.35 -LWP::Protocol::ftp 6.35 -LWP::Protocol::gopher 6.35 -LWP::Protocol::http 6.35 -LWP::Protocol::https 6.07 -LWP::Protocol::loopback 6.35 -LWP::Protocol::mailto 6.35 -LWP::Protocol::nntp 6.35 -LWP::Protocol::nogo 6.35 -LWP::RobotUA 6.35 -LWP::Simple 6.35 -LWP::UserAgent 6.35 -Mail::Address 2.20 -Mail::Cap 2.20 -Mail::Field 2.20 -Mail::Field::AddrList 2.20 -Mail::Field::Date 2.20 -Mail::Field::Generic 2.20 -Mail::Filter 2.20 -Mail::Header 2.20 -Mail::Internet 2.20 -Mail::Mailer 2.20 -Mail::Mailer::qmail 2.20 -Mail::Mailer::rfc822 2.20 -Mail::Mailer::sendmail 2.20 -Mail::Mailer::smtp 2.20 -Mail::Mailer::smtps 2.20 -Mail::Mailer::testfile 2.20 -Mail::Send 2.20 -Mail::Util 2.20 -MailTools 2.20 -Math::Bezier 0.01 -Math::BigFloat 1.999813 -Math::BigInt 1.999813 -Math::BigInt::Calc 1.999813 -Math::BigInt::CalcEmu 1.999813 -Math::BigInt::Lib 1.999813 -Math::CDF 0.1 -Math::Cephes 0.5305 -Math::Cephes::Complex 0.5305 -Math::Cephes::Fraction 0.5305 -Math::Cephes::Matrix 0.5305 -Math::Cephes::Polynomial 0.5305 -Math::Combinatorics 0.09 -Math::Counting 0.1305 -Math::Derivative 1.01 -Math::GSL::Linalg::SVD 0.0.2 -Math::MatrixReal 2.13 -Math::Prime::Util 0.70 -Math::Prime::Util::ChaCha 0.70 -Math::Prime::Util::ECAffinePoint 0.70 -Math::Prime::Util::ECProjectivePoint 0.70 -Math::Prime::Util::Entropy 0.70 -Math::Prime::Util::GMP 0.50 -Math::Prime::Util::MemFree 0.70 -Math::Prime::Util::PP 0.70 -Math::Prime::Util::PPFE unknown -Math::Prime::Util::PrimalityProving 0.70 -Math::Prime::Util::PrimeArray 0.70 -Math::Prime::Util::PrimeIterator 0.70 -Math::Prime::Util::RandomPrimes 0.70 -Math::Prime::Util::ZetaBigFloat 0.70 -Math::Random 0.72 -Math::Random::ISAAC 1.004 -Math::Random::ISAAC::PP 1.004 -Math::Random::MT::Auto 6.22 -Math::Random::MT::Auto::Range 6.22 -Math::Round 0.07 -Math::Spline 0.02 -Math::Utils 1.12 -Math::VecStat 0.08 -Memoize::ExpireLRU 0.56 -Menlo 1.9019 -Menlo::Builder::Static unknown -Menlo::CLI::Compat 1.9022 -Menlo::Dependency unknown -Menlo::Index::MetaCPAN unknown -Menlo::Index::MetaDB 1.9019 -Menlo::Index::Mirror unknown -Menlo::Legacy 1.9022 -Menlo::Util unknown -Meta::Builder 0.003 -Meta::Builder::Base unknown -Meta::Builder::Util unknown -metaclass 2.2011 -Method::Generate::Accessor unknown -Method::Generate::BuildAll unknown -Method::Generate::Constructor unknown -Method::Generate::DemolishAll unknown -Method::Inliner unknown -MIME::Charset 1.012.2 -MIME::Charset::_Compat 1.003.1 -MIME::Charset::UTF 1.010 -MIME::Type 2.17 -MIME::Types 2.17 -Mixin::Linewise 0.108 -Mixin::Linewise::Readers 0.108 -Mixin::Linewise::Writers 0.108 -Mock::Config 0.03 -Modern::Perl 1.20180701 -Module::AutoInstall 1.19 -Module::Build 0.4224 -Module::Build::Base 0.4224 -Module::Build::Compat 0.4224 -Module::Build::Config 0.4224 -Module::Build::ConfigData unknown -Module::Build::Cookbook 0.4224 -Module::Build::Dumper 0.4224 -Module::Build::Notes 0.4224 -Module::Build::Platform::aix 0.4224 -Module::Build::Platform::cygwin 0.4224 -Module::Build::Platform::darwin 0.4224 -Module::Build::Platform::Default 0.4224 -Module::Build::Platform::MacOS 0.4224 -Module::Build::Platform::os2 0.4224 -Module::Build::Platform::Unix 0.4224 -Module::Build::Platform::VMS 0.4224 -Module::Build::Platform::VOS 0.4224 -Module::Build::Platform::Windows 0.4224 -Module::Build::PodParser 0.4224 -Module::Build::PPMMaker 0.4224 -Module::Build::Tiny 0.039 -Module::Build::XSUtil 0.19 -Module::Compile 0.37 -Module::Compile::Opt unknown -Module::CPANfile 1.1004 -Module::CPANfile::Environment unknown -Module::CPANfile::Prereq unknown -Module::CPANfile::Prereqs unknown -Module::CPANfile::Requirement unknown -Module::Faker 0.020 -Module::Faker::Appendix 0.020 -Module::Faker::Dist 0.020 -Module::Faker::File 0.020 -Module::Faker::Heavy 0.020 -Module::Faker::Module 0.020 -Module::Faker::Package 0.020 -Module::Find 0.13 -Module::Implementation 0.09 -Module::Install 1.19 -Module::Install::Admin 1.19 -Module::Install::Admin::Bundle 1.19 -Module::Install::Admin::Compiler 1.19 -Module::Install::Admin::Find 1.19 -Module::Install::Admin::Include 1.19 -Module::Install::Admin::Makefile 1.19 -Module::Install::Admin::Manifest 1.19 -Module::Install::Admin::Metadata 1.19 -Module::Install::Admin::ScanDeps 1.19 -Module::Install::Admin::WriteAll 1.19 -Module::Install::AutoInstall 1.19 -Module::Install::Base 1.19 -Module::Install::Bundle 1.19 -Module::Install::Can 1.19 -Module::Install::Catalyst unknown -Module::Install::Compiler 1.19 -Module::Install::Deprecated 1.19 -Module::Install::DSL 1.19 -Module::Install::External 1.19 -Module::Install::Fetch 1.19 -Module::Install::Include 1.19 -Module::Install::Inline 1.19 -Module::Install::Makefile 1.19 -Module::Install::MakeMaker 1.19 -Module::Install::Metadata 1.19 -Module::Install::PAR 1.19 -Module::Install::Run 1.19 -Module::Install::Scripts 1.19 -Module::Install::Share 1.19 -Module::Install::Win32 1.19 -Module::Install::With 1.19 -Module::Install::WriteAll 1.19 -Module::Optimize unknown -Module::Path 0.19 -Module::Pluggable 5.2 -Module::Pluggable::Object 5.2 -Module::Runtime 0.016 -Module::Runtime::Conflicts 0.003 -Module::ScanDeps 1.24 -Module::ScanDeps::Cache unknown -Module::Util 1.09 -Mojo unknown -Mojo::Asset unknown -Mojo::Asset::File unknown -Mojo::Asset::Memory unknown -Mojo::Base unknown -Mojo::ByteStream unknown -Mojo::Cache unknown -Mojo::Collection unknown -Mojo::Content unknown -Mojo::Content::MultiPart unknown -Mojo::Content::Single unknown -Mojo::Cookie unknown -Mojo::Cookie::Request unknown -Mojo::Cookie::Response unknown -Mojo::Date unknown -Mojo::DOM unknown -Mojo::DOM::CSS unknown -Mojo::DOM::HTML unknown -Mojo::EventEmitter unknown -Mojo::Exception unknown -Mojo::File unknown -Mojo::Headers unknown -Mojo::HelloWorld unknown -Mojo::Home unknown -Mojo::IOLoop unknown -Mojo::IOLoop::Client unknown -Mojo::IOLoop::Delay unknown -Mojo::IOLoop::Server unknown -Mojo::IOLoop::Stream unknown -Mojo::IOLoop::Stream::HTTPClient unknown -Mojo::IOLoop::Stream::HTTPServer unknown -Mojo::IOLoop::Stream::WebSocketClient unknown -Mojo::IOLoop::Stream::WebSocketServer unknown -Mojo::IOLoop::Subprocess unknown -Mojo::IOLoop::TLS unknown -Mojo::JSON unknown -Mojo::JSON::Pointer unknown -Mojo::Loader unknown -Mojo::Log unknown -Mojo::Message unknown -Mojo::Message::Request unknown -Mojo::Message::Response unknown -Mojo::Parameters unknown -Mojo::Path unknown -Mojo::Promise unknown -Mojo::Reactor unknown -Mojo::Reactor::EV unknown -Mojo::Reactor::Poll unknown -Mojo::Server unknown -Mojo::Server::CGI unknown -Mojo::Server::Daemon unknown -Mojo::Server::Hypnotoad unknown -Mojo::Server::Morbo unknown -Mojo::Server::Morbo::Backend unknown -Mojo::Server::Morbo::Backend::Poll unknown -Mojo::Server::Prefork unknown -Mojo::Server::PSGI unknown -Mojo::Template unknown -Mojo::Transaction unknown -Mojo::Transaction::HTTP unknown -Mojo::Transaction::WebSocket unknown -Mojo::Upload unknown -Mojo::URL unknown -Mojo::UserAgent unknown -Mojo::UserAgent::CookieJar unknown -Mojo::UserAgent::Proxy unknown -Mojo::UserAgent::Server unknown -Mojo::UserAgent::Transactor unknown -Mojo::Util unknown -Mojo::WebSocket unknown -Mojolicious 7.88 -Mojolicious::Command unknown -Mojolicious::Command::cgi unknown -Mojolicious::Command::cpanify unknown -Mojolicious::Command::daemon unknown -Mojolicious::Command::eval unknown -Mojolicious::Command::generate unknown -Mojolicious::Command::generate::app unknown -Mojolicious::Command::generate::lite_app unknown -Mojolicious::Command::generate::makefile unknown -Mojolicious::Command::generate::plugin 0.01 -Mojolicious::Command::get unknown -Mojolicious::Command::inflate unknown -Mojolicious::Command::prefork unknown -Mojolicious::Command::psgi unknown -Mojolicious::Command::routes unknown -Mojolicious::Command::test unknown -Mojolicious::Command::version unknown -Mojolicious::Commands unknown -Mojolicious::Controller unknown -Mojolicious::Lite unknown -Mojolicious::Plugin unknown -Mojolicious::Plugin::Config unknown -Mojolicious::Plugin::DefaultHelpers unknown 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unknown -XML::XPathEngine::NodeSet unknown -XML::XPathEngine::Number unknown -XML::XPathEngine::Root unknown -XML::XPathEngine::Step 1.0 -XML::XPathEngine::Variable unknown -XS unknown -YAML 1.26 -YAML::Any 1.26 -YAML::Dumper unknown -YAML::Dumper::Base unknown -YAML::Error unknown -YAML::LibYAML 0.72 -YAML::Loader unknown -YAML::Loader::Base unknown -YAML::Marshall unknown -YAML::Mo unknown -YAML::Node unknown -YAML::Tag unknown -YAML::Tiny 1.73 -YAML::Types unknown -YAML::XS 0.72 -YAML::XS::LibYAML unknown +Module name Version +$pkg 2.019 +Acme::Damn 0.08 +Algorithm::C3 0.10 +Algorithm::Combinatorics 0.27 +Algorithm::Diff 1.1903 +Algorithm::FastPermute 0.999 +Algorithm::Loops 1.032 +Algorithm::Munkres 0.08 +Algorithm::Permute 0.16 +aliased 0.34 +Apache::Htpasswd 1.9 +Apache::LogFormat::Compiler 0.35 +Apache::SOAP 1.27 +App::Ack 2.24 +App::Ack::ConfigDefault unknown +App::Ack::ConfigFinder unknown +App::Ack::ConfigLoader unknown +App::Ack::Filter unknown +App::Ack::Filter::Collection unknown +App::Ack::Filter::Default unknown +App::Ack::Filter::Extension unknown +App::Ack::Filter::ExtensionGroup unknown +App::Ack::Filter::FirstLineMatch unknown +App::Ack::Filter::Inverse unknown +App::Ack::Filter::Is unknown +App::Ack::Filter::IsGroup unknown +App::Ack::Filter::IsPath unknown +App::Ack::Filter::IsPathGroup unknown +App::Ack::Filter::Match unknown +App::Ack::Filter::MatchGroup unknown +App::Ack::Resource unknown +App::Ack::Resources unknown +App::Cmd 0.331 +App::Cmd::ArgProcessor 0.331 +App::Cmd::Command 0.331 +App::Cmd::Command::commands 0.331 +App::Cmd::Command::help 0.331 +App::Cmd::Command::version 0.331 +App::Cmd::Plugin 0.331 +App::Cmd::Setup 0.331 +App::Cmd::Simple 0.331 +App::Cmd::Subdispatch 0.331 +App::Cmd::Subdispatch::DashedStyle 0.331 +App::Cmd::Tester 0.331 +App::Cmd::Tester::CaptureExternal 0.331 +App::cpanminus 1.7044 +App::cpanminus::fatscript 1.7044 +App::FatPacker 0.010007 +App::FatPacker::Trace unknown +App::Nopaste 1.012 +App::Nopaste::Command 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2.14 +Authen::SASL::Perl::PLAIN 2.14 +Authen::Simple 0.5 +Authen::Simple::Adapter unknown +Authen::Simple::Apache unknown +Authen::Simple::Log unknown +Authen::Simple::Passwd 0.6 +Authen::Simple::Password unknown +autobox unknown +autobox::universal unknown +B::Hooks::EndOfScope 0.24 +B::Hooks::EndOfScope::PP 0.24 +B::Hooks::EndOfScope::XS 0.24 +B::Hooks::OP::Check 0.22 +B::Hooks::OP::Check::Install::Files unknown +B::Hooks::OP::PPAddr 0.06 +B::Hooks::OP::PPAddr::Install::Files unknown +B::Keywords 1.18 +B::Utils 0.27 +B::Utils::Install::Files unknown +B::Utils::OP 0.27 +bareword::filehandles 0.006 +Bit::Vector 7.4 +Bit::Vector::Overload 7.4 +Bit::Vector::String 7.4 +boolean 0.46 +Browser::Open 0.04 +Bundle::DBD::mysql 4.046 +Bundle::DBI 12.008696 +Bundle::Object::InsideOut 4.04 +C::StructType unknown +C::Type unknown +C::Var unknown +Cache::BaseCache unknown +Cache::BaseCacheTester unknown +Cache::Cache 1.08 +Cache::CacheMetaData unknown +Cache::CacheSizer unknown +Cache::CacheTester unknown +Cache::CacheUtils unknown +Cache::FileBackend unknown +Cache::FileCache unknown +Cache::LRU 0.04 +Cache::MemoryBackend unknown +Cache::MemoryCache unknown +Cache::NullCache unknown +Cache::Object unknown +Cache::SharedMemoryBackend unknown +Cache::SharedMemoryCache unknown +Cache::SizeAwareCache unknown +Cache::SizeAwareCacheTester unknown +Cache::SizeAwareFileCache unknown +Cache::SizeAwareMemoryCache unknown +Cache::SizeAwareSharedMemoryCache unknown +Capture::Tiny 0.48 +Carp::Always 0.13 +Carp::Assert 0.21 +Carp::Assert::More 1.16 +Carp::Clan 6.06 +Carp::REPL 0.18 +Carton unknown +Carton::Builder unknown +Carton::CLI unknown +Carton::CPANfile unknown +Carton::Dependency unknown +Carton::Dist unknown +Carton::Dist::Core unknown +Carton::Environment unknown +Carton::Error unknown +Carton::Index unknown +Carton::Mirror unknown +Carton::Package unknown +Carton::Packer unknown +Carton::Snapshot unknown +Carton::Snapshot::Emitter unknown +Carton::Snapshot::Parser unknown 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unknown +Catalyst::Helper::Model::Factory::PerRequest unknown +Catalyst::Helper::View::Email 0.36 +Catalyst::Helper::View::Email::Template 0.36 +Catalyst::Helper::View::TT 0.44 +Catalyst::Helper::View::TTSite 0.44 +Catalyst::Log unknown +Catalyst::Manual 5.9009 +Catalyst::Middleware::Stash unknown +Catalyst::Model unknown +Catalyst::Model::Adaptor 0.10 +Catalyst::Model::Adaptor::Base unknown +Catalyst::Model::DBIC::Schema 0.65 +Catalyst::Model::Factory 0.10 +Catalyst::Model::Factory::PerRequest 0.10 +Catalyst::Plugin::Authentication 0.10023 +Catalyst::Plugin::Authentication::Credential::Password unknown +Catalyst::Plugin::Authentication::Store::Minimal unknown +Catalyst::Plugin::Authentication::User unknown +Catalyst::Plugin::Authentication::User::Hash unknown +Catalyst::Plugin::ConfigLoader 0.34 +Catalyst::Plugin::I18N 0.10 +Catalyst::Plugin::Session 0.40 +Catalyst::Plugin::Session::State unknown +Catalyst::Plugin::Session::State::Cookie 0.17 +Catalyst::Plugin::Session::Store unknown 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unknown +Catalyst::Stats unknown +Catalyst::Test unknown +Catalyst::TraitFor::Model::DBIC::Schema::Caching unknown +Catalyst::TraitFor::Model::DBIC::Schema::PerRequestSchema unknown +Catalyst::TraitFor::Model::DBIC::Schema::Replicated unknown +Catalyst::TraitFor::Model::DBIC::Schema::SchemaProxy unknown +Catalyst::TraitFor::Request::REST 1.21 +Catalyst::TraitFor::Request::REST::ForBrowsers 1.21 +Catalyst::Utils unknown +Catalyst::View unknown +Catalyst::View::Email 0.36 +Catalyst::View::Email::Template 0.36 +Catalyst::View::TT 0.44 +CatalystX::Component::Traits 0.19 +CatalystX::InjectComponent 0.025 +CatalystX::LeakChecker 0.06 +CatalystX::Profile 0.02 +CatalystX::Profile::Controller::ControlProfiling 0.02 +CatalystX::REPL 0.04 +CatalystX::SimpleLogin 0.20 +CatalystX::SimpleLogin::Controller::Login unknown +CatalystX::SimpleLogin::Form::Login unknown +CatalystX::SimpleLogin::Form::LoginOpenID unknown +CatalystX::SimpleLogin::TraitFor::Controller::Login::Logout unknown 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unknown +Class::MethodMaker::scalar unknown +Class::MethodMaker::V1Compat unknown +Class::MOP 2.2011 +Class::MOP::Attribute 2.2011 +Class::MOP::Class 2.2011 +Class::MOP::Class::Immutable::Trait 2.2011 +Class::MOP::Deprecated 2.2011 +Class::MOP::Instance 2.2011 +Class::MOP::Method 2.2011 +Class::MOP::Method::Accessor 2.2011 +Class::MOP::Method::Constructor 2.2011 +Class::MOP::Method::Generated 2.2011 +Class::MOP::Method::Inlined 2.2011 +Class::MOP::Method::Meta 2.2011 +Class::MOP::Method::Wrapped 2.2011 +Class::MOP::MiniTrait 2.2011 +Class::MOP::Mixin 2.2011 +Class::MOP::Mixin::AttributeCore 2.2011 +Class::MOP::Mixin::HasAttributes 2.2011 +Class::MOP::Mixin::HasMethods 2.2011 +Class::MOP::Mixin::HasOverloads 2.2011 +Class::MOP::Module 2.2011 +Class::MOP::Object 2.2011 +Class::MOP::Overload 2.2011 +Class::MOP::Package 2.2011 +Class::Singleton 1.5 +Class::Tiny 1.006 +Class::Trigger 0.14 +Class::Unload 0.11 +Class::XSAccessor 1.19 +Class::XSAccessor::Array 1.19 +Clipboard 0.13 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0.000115 +Test2::Util::Table 0.000115 +Test2::Util::Table::Cell 0.000115 +Test2::Util::Table::LineBreak 0.000115 +Test2::Util::Term 0.000115 +Test2::Util::Times 0.000115 +Test2::Util::Trace 1.302138 +Test2::V0 0.000115 +Test2::Workflow 0.000115 +Test2::Workflow::BlockBase 0.000115 +Test2::Workflow::Build 0.000115 +Test2::Workflow::Runner 0.000115 +Test2::Workflow::Task 0.000115 +Test2::Workflow::Task::Action 0.000115 +Test2::Workflow::Task::Group 0.000115 +Test::Assert 0.0504 +Test::Base 0.89 +Test::Base::Filter unknown +Test::Builder 1.302138 +Test::Builder::Formatter 1.302138 +Test::Builder::IO::Scalar 2.114 +Test::Builder::Module 1.302138 +Test::Builder::Tester 1.302138 +Test::Builder::Tester::Color 1.302138 +Test::Builder::TodoDiag 1.302138 +Test::Class 0.50 +Test::Class::Load 0.50 +Test::Class::MethodInfo 0.50 +Test::Class::Moose 0.92 +Test::Class::Moose::AttributeRegistry 0.92 +Test::Class::Moose::CLI 0.92 +Test::Class::Moose::Config 0.92 +Test::Class::Moose::Deprecated 0.92 +Test::Class::Moose::Executor::Parallel 0.92 +Test::Class::Moose::Executor::Sequential 0.92 +Test::Class::Moose::Load 0.92 +Test::Class::Moose::Report 0.92 +Test::Class::Moose::Report::Class 0.92 +Test::Class::Moose::Report::Instance 0.92 +Test::Class::Moose::Report::Method 0.92 +Test::Class::Moose::Report::Time 0.92 +Test::Class::Moose::Role 0.92 +Test::Class::Moose::Role::AutoUse 0.92 +Test::Class::Moose::Role::CLI 0.92 +Test::Class::Moose::Role::Executor 0.92 +Test::Class::Moose::Role::HasTimeReport 0.92 +Test::Class::Moose::Role::ParameterizedInstances 0.92 +Test::Class::Moose::Role::Reporting 0.92 +Test::Class::Moose::Runner 0.92 +Test::Class::Moose::Tutorial 0.92 +Test::Class::Moose::Util 0.92 +Test::CleanNamespaces 0.23 +Test::CPAN::Changes 0.400002 +Test::CPAN::Meta 0.25 +Test::CPAN::Meta::Version 0.25 +Test::Deep 1.128 +Test::Deep::All unknown +Test::Deep::Any unknown +Test::Deep::Array unknown +Test::Deep::ArrayEach unknown +Test::Deep::ArrayElementsOnly unknown +Test::Deep::ArrayLength unknown +Test::Deep::ArrayLengthOnly unknown +Test::Deep::Blessed unknown +Test::Deep::Boolean unknown +Test::Deep::Cache unknown +Test::Deep::Cache::Simple unknown +Test::Deep::Class unknown +Test::Deep::Cmp unknown +Test::Deep::Code unknown +Test::Deep::Hash unknown +Test::Deep::HashEach unknown +Test::Deep::HashElements unknown +Test::Deep::HashKeys unknown +Test::Deep::HashKeysOnly unknown +Test::Deep::Ignore unknown +Test::Deep::Isa unknown +Test::Deep::JSON 0.05 +Test::Deep::ListMethods unknown +Test::Deep::Methods unknown +Test::Deep::MM unknown +Test::Deep::None unknown +Test::Deep::NoTest unknown +Test::Deep::Number unknown +Test::Deep::Obj unknown +Test::Deep::Ref unknown +Test::Deep::RefType unknown +Test::Deep::Regexp unknown +Test::Deep::RegexpMatches unknown +Test::Deep::RegexpOnly unknown +Test::Deep::RegexpRef unknown +Test::Deep::RegexpRefOnly unknown +Test::Deep::RegexpVersion unknown +Test::Deep::ScalarRef unknown +Test::Deep::ScalarRefOnly unknown +Test::Deep::Set unknown +Test::Deep::Shallow unknown +Test::Deep::Stack unknown +Test::Deep::String unknown +Test::Deep::Type 0.008 +Test::Differences 0.64 +Test::EOL 2.00 +Test::Exception 0.43 +Test::Expect 0.34 +Test::FailWarnings 0.008 +Test::Fatal 0.014 +Test::File 1.443 +Test::File::ShareDir 1.001002 +Test::File::ShareDir::Dist 1.001002 +Test::File::ShareDir::Module 1.001002 +Test::File::ShareDir::Object::Dist 1.001002 +Test::File::ShareDir::Object::Inc 1.001002 +Test::File::ShareDir::Object::Module 1.001002 +Test::File::ShareDir::TempDirObject 1.001002 +Test::File::ShareDir::Utils 1.001002 +Test::Fork 0.02 +Test::Future 0.38 +Test::Harness 3.42 +Test::Identity 0.01 +Test::JSON 0.11 +Test::LeakTrace 0.16 +Test::LeakTrace::Script unknown +Test::LongString 0.17 +Test::LWP::UserAgent 0.033 +Test::Memory::Cycle 1.06 +Test::Mock::HTTP::Request 0.01 +Test::Mock::HTTP::Response 0.01 +Test::Mock::LWP 0.08 +Test::Mock::LWP::UserAgent 0.01 +Test::MockModule 0.15 +Test::MockObject 1.20180705 +Test::MockObject::Extends 1.20180705 +Test::MockTime 0.17 +Test::Mojo unknown +Test::Moose 2.2011 +Test::MooseX::Daemonize 0.21 +Test::More 1.302138 +Test::More::UTF8 0.05 +Test::Most 0.35 +Test::Most::Exception 0.35 +Test::Needs 0.002005 +Test::NoWarnings 1.04 +Test::NoWarnings::Warning 1.04 +Test::Number::Delta 1.06 +Test::Object 0.08 +Test::Object::Test 0.08 +Test::Output 1.031 +Test::Perl::Critic::Policy 1.132 +Test::Pod 1.52 +Test::Pod::Content unknown +Test::Pod::Coverage 1.10 +Test::RDF::Trine::Store 1.019 +Test::Refcount 0.08 +Test::Requires 0.10 +Test::RequiresInternet 0.05 +Test::SharedFork 0.35 +Test::SharedFork::Array unknown +Test::SharedFork::Scalar unknown +Test::SharedFork::Store unknown +Test::Simple 1.302138 +Test::Spec 0.54 +Test::Spec::Context unknown +Test::Spec::Example unknown +Test::Spec::Mocks unknown +Test::Spec::SharedHash unknown +Test::Spec::TodoExample unknown +Test::Specio 0.42 +Test::SQL::Translator 1.59 +Test::SubCalls 1.10 +Test::TCP 2.19 +Test::TCP::CheckPort unknown +Test::TempDir::Tiny 0.018 +Test::Tester 1.302138 +Test::Tester::Capture 1.302138 +Test::Tester::CaptureRunner 1.302138 +Test::Tester::Delegate 1.302138 +Test::Time 0.06 +Test::Toolbox 0.4 +Test::Trap unknown +Test::Trap::Builder unknown +Test::Trap::Builder::PerlIO unknown +Test::Trap::Builder::SystemSafe unknown +Test::Trap::Builder::TempFile unknown +Test::TypeTiny 1.002002 +Test::Unit::Lite 0.1202 +Test::use::ok 1.302138 +Test::utf8 1.01 +Test::Warn 0.36 +Test::Warnings 0.026 +Test::Without::Module 0.20 +Test::WWW::Mechanize 1.50 +Test::WWW::Mechanize::Catalyst 0.60 +Test::WWW::Mechanize::PSGI 0.38 +Test::WWW::Selenium 1.36 +Test::YAML 1.07 +Text::Aligner 0.13 +Text::Autoformat 1.74 +Text::Autoformat::Hang 1.74 +Text::Autoformat::NullHang 1.74 +Text::CSV 1.95 +Text::CSV_PP 1.95 +Text::CSV_XS 1.36 +Text::Diff 1.45 +Text::Diff::Config 1.44 +Text::Diff::Table 1.44 +Text::Format 0.61 +Text::German 0.06 +Text::German::Adjektiv unknown +Text::German::Ausnahme unknown +Text::German::Cache unknown +Text::German::Endung unknown +Text::German::Regel unknown +Text::German::Util unknown +Text::German::Verb unknown +Text::German::Vorsilbe unknown +Text::Glob 0.11 +Text::LineFold 2016.00702 +Text::Reform 1.20 +Text::SimpleTable 2.05 +Text::Table 1.133 +Text::Template 1.53 +Text::Template::Preprocess 1.53 +Text::Unidecode 1.30 +Text::VisualWidth::PP 0.05 +threads::shared::array 0.36 +threads::shared::handle 0.36 +threads::shared::hash 0.36 +threads::shared::scalar 0.36 +Throwable 0.200013 +Throwable::Error 0.200013 +Tie::Handle::Offset 0.004 +Tie::Handle::SkipHeader 0.004 +Tie::Hash::MultiValue 1.05 +Tie::IxHash 1.23 +Tie::ToObject 0.03 +Tie::Watch 1.302 +Time::CTime 2011.0505 +Time::DaysInMonth 99.1117 +Time::Duration 1.20 +Time::Duration::Parse 0.14 +Time::HiRes 1.9758 +Time::JulianDay 2011.0505 +Time::ParseDate 2015.103 +Time::Piece 1.3204 +Time::Seconds 1.3204 +Time::Timezone 2015.0925 +Time::Tiny 1.08 +Time::Zone 2.24 +Tk 804.034 +Tk::Adjuster 4.008 +Tk::After 4.008 +Tk::Animation 4.008 +Tk::Balloon 4.012 +Tk::Bitmap 4.004 +Tk::BrowseEntry 4.015 +Tk::Button 4.010 +Tk::Canvas 4.013 +Tk::Checkbutton 4.006 +Tk::Clipboard 4.009 +Tk::CmdLine 4.007 +Tk::ColorDialog 4.014 +Tk::ColorEditor 4.014 +Tk::ColorSelect 4.014 +Tk::Compound 4.004 +Tk::Config 804.034 +Tk::Configure 4.009 +Tk::Derived 4.011 +Tk::Dialog 4.005 +Tk::DialogBox 4.016 +Tk::Dirlist 4.004 +Tk::DirTree 4.022 +Tk::DragDrop 4.015 +Tk::DragDrop::Common 4.005 +Tk::DragDrop::Local 4.004 +Tk::DragDrop::Rect 4.012 +Tk::DragDrop::SunConst 4.004 +Tk::DragDrop::SunDrop 4.006 +Tk::DragDrop::SunSite 4.007 +Tk::DragDrop::XDNDDrop 4.007 +Tk::DragDrop::XDNDSite 4.007 +Tk::DropSite 4.008 +Tk::DummyEncode 4.007 +Tk::English 4.006 +Tk::Entry 4.018 +Tk::ErrorDialog 4.007 +Tk::Event 4.035 +Tk::Event::IO 4.009 +Tk::FBox 4.018 +Tk::FileSelect 4.018 +Tk::FloatEntry 4.004 +Tk::Font 4.004 +Tk::Frame 4.010 +Tk::HList 4.015 +Tk::IconList 4.007 +Tk::Image 4.011 +Tk::InputO 4.004 +Tk::install 4.004 +Tk::IO 4.006 +Tk::ItemStyle 4.004 +Tk::JPEG 4.003 +Tk::Label 4.006 +Tk::LabeledEntryLabeledRadiobutton 4.004 +Tk::Labelframe 4.003 +Tk::LabEntry 4.006 +Tk::LabFrame 4.010 +Tk::LabRadiobutton 4.004 +Tk::Listbox 4.015 +Tk::MainWindow 4.015 +Tk::MakeDepend 4.015 +Tk::Menu 4.023 +Tk::Menu::Item 4.005 +Tk::Menubar 4.006 +Tk::Menubutton 4.005 +Tk::Message 4.006 +Tk::MMtry 4.009 +Tk::MMutil 4.026 +Tk::MsgBox 4.002 +Tk::Mwm 4.004 +Tk::NBFrame 4.004 +Tk::NoteBook 4.009 +Tk::Optionmenu 4.014 +Tk::Pane 4.007 +Tk::Panedwindow 4.004 +Tk::Photo 4.006 +Tk::Pixmap 4.004 +Tk::PNG 4.004 +Tk::Pretty 4.006 +Tk::ProgressBar 4.015 +Tk::Radiobutton 4.006 +Tk::Region 4.006 +Tk::Reindex 4.006 +Tk::ReindexedROText 4.004 +Tk::ReindexedText 4.004 +Tk::ROText 4.010 +Tk::Scale 4.004 +Tk::Scrollbar 4.010 +Tk::Spinbox 4.007 +Tk::Stats 4.004 +Tk::Submethods 4.005 +Tk::Table 4.016 +Tk::Text 4.024 +Tk::Text::Tag 4.004 +Tk::TextEdit 4.004 +Tk::TextList 4.006 +Tk::TextUndo 4.015 +Tk::Tiler 4.012 +Tk::TixGrid 4.010 +Tk::TList 4.006 +Tk::Toplevel 4.006 +Tk::Trace 4.009 +Tk::Tree 4.72 +Tk::Widget 4.036 +Tk::widgets 4.005 +Tk::WinPhoto 4.005 +Tk::Wm 4.015 +Tk::X 4.005 +Tk::X11Font 4.007 +Tk::Xlib 4.004 +Tk::Xrm 4.005 +Tree::DAG_Node 1.31 +Tree::Simple 1.33 +Tree::Simple::Visitor 1.33 +Tree::Simple::Visitor::BreadthFirstTraversal 0.15 +Tree::Simple::Visitor::CreateDirectoryTree 0.15 +Tree::Simple::Visitor::FindByNodeValue 0.15 +Tree::Simple::Visitor::FindByPath 0.15 +Tree::Simple::Visitor::FindByUID 0.15 +Tree::Simple::Visitor::FromNestedArray 0.15 +Tree::Simple::Visitor::FromNestedHash 0.15 +Tree::Simple::Visitor::GetAllDescendents 0.15 +Tree::Simple::Visitor::LoadClassHierarchy 0.15 +Tree::Simple::Visitor::LoadDirectoryTree 0.15 +Tree::Simple::Visitor::PathToRoot 0.15 +Tree::Simple::Visitor::PostOrderTraversal 0.15 +Tree::Simple::Visitor::PreOrderTraversal 0.15 +Tree::Simple::Visitor::Sort 0.15 +Tree::Simple::Visitor::ToNestedArray 0.15 +Tree::Simple::Visitor::ToNestedHash 0.15 +Tree::Simple::Visitor::VariableDepthClone 0.15 +Tree::Simple::VisitorFactory 0.15 +Try::Tiny 0.30 +TryCatch 1.003002 +Type::Coercion 1.002002 +Type::Coercion::FromMoose 1.002002 +Type::Coercion::Union 1.002002 +Type::Library 1.002002 +Type::Params 1.002002 +Type::Parser 1.002002 +Type::Registry 1.002002 +Type::Tiny 1.002002 +Type::Tiny::_HalfOp 1.002002 +Type::Tiny::Class 1.002002 +Type::Tiny::Duck 1.002002 +Type::Tiny::Enum 1.002002 +Type::Tiny::Intersection 1.002002 +Type::Tiny::Role 1.002002 +Type::Tiny::Union 1.002002 +Type::Utils 1.002002 +Types::Common::Numeric 1.002002 +Types::Common::String 1.002002 +Types::Serialiser 1.0 +Types::Standard 1.002002 +Types::Standard::ArrayRef 1.002002 +Types::Standard::CycleTuple 1.002002 +Types::Standard::Dict 1.002002 +Types::Standard::HashRef 1.002002 +Types::Standard::Map 1.002002 +Types::Standard::ScalarRef 1.002002 +Types::Standard::Tuple 1.002002 +Types::TypeTiny 1.002002 +Unicode::CharName 0.00 +Unicode::EastAsianWidth 1.33 +Unicode::EastAsianWidth::Detect 0.03 +Unicode::GCString 2013.10 +Unicode::LineBreak 2018.003 +Unicode::LineBreak unknown +Unicode::Map 0.112 +Unicode::Map8 0.13 +Unicode::String 2.10 +UNIVERSAL::can 1.20140328 +UNIVERSAL::isa 1.20171012 +UNIVERSAL::require 0.18 +URI 1.74 +URI::_foreign 1.74 +URI::_generic 1.74 +URI::_idna 1.74 +URI::_ldap 1.74 +URI::_login 1.74 +URI::_punycode 1.74 +URI::_query 1.74 +URI::_segment 1.74 +URI::_server 1.74 +URI::_userpass 1.74 +URI::data 1.74 +URI::Escape 3.31 +URI::file 4.21 +URI::file::Base 1.74 +URI::file::FAT 1.74 +URI::file::Mac 1.74 +URI::file::OS2 1.74 +URI::file::QNX 1.74 +URI::file::Unix 1.74 +URI::file::Win32 1.74 +URI::Find 20160806 +URI::Find::Schemeless 20160806 +URI::ftp 1.74 +URI::gopher 1.74 +URI::Heuristic 4.20 +URI::http 1.74 +URI::https 1.74 +URI::IRI 1.74 +URI::ldap 1.74 +URI::ldapi 1.74 +URI::ldaps 1.74 +URI::mailto 1.74 +URI::mms 1.74 +URI::news 1.74 +URI::nntp 1.74 +URI::pop 1.74 +URI::QueryParam 1.74 +URI::rlogin 1.74 +URI::rsync 1.74 +URI::rtsp 1.74 +URI::rtspu 1.74 +URI::sftp 1.74 +URI::sip 1.74 +URI::sips 1.74 +URI::snews 1.74 +URI::Split 1.74 +URI::ssh 1.74 +URI::telnet 1.74 +URI::tn3270 1.74 +URI::URL 5.04 +URI::urn 1.74 +URI::urn::isbn 1.74 +URI::urn::oid 1.74 +URI::WithBase 2.20 +URI::ws 0.03 +URI::wss 0.03 +UUID::Tiny 1.04 +Variable::Magic 0.62 +Want 0.29 +WidgetDemo 4.012 +Win32::ShellQuote 0.003001 +WWW::Form::UrlEncoded 0.24 +WWW::Form::UrlEncoded::PP unknown +WWW::Mechanize 1.88 +WWW::Mechanize::Image 1.88 +WWW::Mechanize::Link 1.88 +WWW::Mechanize::TreeBuilder 1.20000 +WWW::Pastebin::PastebinCom::Create 1.003 +WWW::RobotRules 6.02 +WWW::RobotRules::AnyDBM_File 6.00 +WWW::Selenium 1.36 +WWW::Selenium::Util 1.36 +XML::Atom 0.42 +XML::Atom::Base unknown +XML::Atom::Category unknown +XML::Atom::Client unknown +XML::Atom::Content unknown +XML::Atom::Entry unknown +XML::Atom::ErrorHandler unknown +XML::Atom::Feed unknown +XML::Atom::Link unknown +XML::Atom::Person unknown +XML::Atom::Server unknown +XML::Atom::Thing unknown +XML::Atom::Util unknown +XML::CommonNS 0.06 +XML::Compile 1.60 +XML::Compile::Iterator 1.60 +XML::Compile::Schema 1.60 +XML::Compile::Schema::BuiltInFacets 1.60 +XML::Compile::Schema::BuiltInTypes 1.60 +XML::Compile::Schema::Instance 1.60 +XML::Compile::Schema::NameSpaces 1.60 +XML::Compile::Schema::Specs 1.60 +XML::Compile::Tester 0.91 +XML::Compile::Translate 1.60 +XML::Compile::Translate::Reader 1.60 +XML::Compile::Translate::Template 1.60 +XML::Compile::Translate::Writer 1.60 +XML::Compile::Util 1.60 +XML::DOM 1.46 +XML::DOM::DOMException unknown +XML::DOM::NamedNodeMap unknown +XML::DOM::NodeList unknown +XML::DOM::PerlSAX unknown +XML::DOM::XPath 0.14 +XML::ESISParser 0.08 +XML::Filter::BufferText 1.01 +XML::Generator::PerlData 0.95 +XML::Handler::BuildDOM unknown +XML::Handler::CanonXMLWriter 0.08 +XML::Handler::Sample unknown +XML::Handler::Subs 0.08 +XML::Handler::XMLWriter 0.08 +XML::LibXML 2.0132 +XML::LibXML::AttributeHash 2.0132 +XML::LibXML::Boolean 2.0132 +XML::LibXML::Common 2.0132 +XML::LibXML::Devel 2.0132 +XML::LibXML::ErrNo 2.0132 +XML::LibXML::Error 2.0132 +XML::LibXML::Literal 2.0132 +XML::LibXML::NodeList 2.0132 +XML::LibXML::Number 2.0132 +XML::LibXML::Reader 2.0132 +XML::LibXML::SAX 2.0132 +XML::LibXML::SAX::Builder 2.0132 +XML::LibXML::SAX::Generator 2.0132 +XML::LibXML::SAX::Parser 2.0132 +XML::LibXML::Simple 0.99 +XML::LibXML::XPathContext 2.0132 +XML::LibXSLT 1.96 +XML::Namespace 0.02 +XML::NamespaceFactory 1.02 +XML::NamespaceSupport 1.12 +XML::Parser 2.44 +XML::Parser::Expat 2.44 +XML::Parser::Lite 0.721 +XML::Parser::PerlSAX 0.08 +XML::Parser::Style::Debug unknown +XML::Parser::Style::Objects unknown +XML::Parser::Style::Stream unknown +XML::Parser::Style::Subs unknown +XML::Parser::Style::Tree unknown +XML::PatAct::ACTION unknown +XML::PatAct::Amsterdam 0.08 +XML::PatAct::MatchName 0.08 +XML::PatAct::PATTERN unknown +XML::PatAct::ToObjects 0.08 +XML::Perl2SAX 0.08 +XML::RegExp 0.04 +XML::RSS 1.60 +XML::RSS::Private::Output::Base 1.60 +XML::RSS::Private::Output::Roles::ImageDims 1.60 +XML::RSS::Private::Output::Roles::ModulesElems 1.60 +XML::RSS::Private::Output::V0_9 1.60 +XML::RSS::Private::Output::V0_91 1.60 +XML::RSS::Private::Output::V1_0 1.60 +XML::RSS::Private::Output::V2_0 1.60 +XML::SAX 1.00 +XML::SAX2Perl 0.08 +XML::SAX::Base 1.09 +XML::SAX::DocumentLocator unknown +XML::SAX::Exception 1.09 +XML::SAX::Expat 0.51 +XML::SAX::ParserFactory 1.01 +XML::SAX::PurePerl 1.00 +XML::SAX::PurePerl unknown +XML::SAX::PurePerl unknown +XML::SAX::PurePerl unknown +XML::SAX::PurePerl unknown +XML::SAX::PurePerl unknown +XML::SAX::PurePerl unknown +XML::SAX::PurePerl::DebugHandler unknown +XML::SAX::PurePerl::Exception unknown +XML::SAX::PurePerl::Productions unknown +XML::SAX::PurePerl::Reader unknown +XML::SAX::PurePerl::Reader unknown +XML::SAX::PurePerl::Reader unknown +XML::SAX::PurePerl::Reader::Stream unknown +XML::SAX::PurePerl::Reader::String unknown +XML::SAX::PurePerl::Reader::URI unknown +XML::SAX::Writer 0.57 +XML::SAX::Writer::XML 0.57 +XML::Simple 2.25 +XML::Twig 3.52 +XML::Twig::XPath 0.02 +XML::Writer 0.625 +XML::XPath 1.42 +XML::XPath::Boolean 1.42 +XML::XPath::Builder 1.42 +XML::XPath::Expr 1.42 +XML::XPath::Function 1.42 +XML::XPath::Literal 1.42 +XML::XPath::LocationPath 1.42 +XML::XPath::Node 1.42 +XML::XPath::Node::Attribute 1.42 +XML::XPath::Node::Comment 1.42 +XML::XPath::Node::Element 1.42 +XML::XPath::Node::Namespace 1.42 +XML::XPath::Node::PI 1.42 +XML::XPath::Node::Text 1.42 +XML::XPath::NodeSet 1.42 +XML::XPath::Number 1.42 +XML::XPath::Parser 1.42 +XML::XPath::PerlSAX 1.42 +XML::XPath::Root 1.42 +XML::XPath::Step 1.42 +XML::XPath::Variable 1.42 +XML::XPath::XMLParser 1.42 +XML::XPathEngine 0.14 +XML::XPathEngine::Boolean unknown +XML::XPathEngine::Expr unknown +XML::XPathEngine::Function unknown +XML::XPathEngine::Literal unknown +XML::XPathEngine::LocationPath unknown +XML::XPathEngine::NodeSet unknown +XML::XPathEngine::Number unknown +XML::XPathEngine::Root unknown +XML::XPathEngine::Step 1.0 +XML::XPathEngine::Variable unknown +XS unknown +YAML 1.26 +YAML::Any 1.26 +YAML::Dumper unknown +YAML::Dumper::Base unknown +YAML::Error unknown +YAML::LibYAML 0.72 +YAML::Loader unknown +YAML::Loader::Base unknown +YAML::Marshall unknown +YAML::Mo unknown +YAML::Node unknown +YAML::Tag unknown +YAML::Tiny 1.73 +YAML::Types unknown +YAML::XS 0.72 +YAML::XS::LibYAML unknown -Include path (INC) directories Searched Number of Modules -/sw/comp/perl_modules/5.26.2/rackham/lib/perl5/5.26.2/x86_64-linux-thread-multi yes 0 -/sw/comp/perl_modules/5.26.2/rackham/lib/perl5/5.26.2 yes 0 -/sw/comp/perl_modules/5.26.2/rackham/lib/perl5/x86_64-linux-thread-multi yes 1055 -/sw/comp/perl_modules/5.26.2/rackham/lib/perl5 yes 5989 -/sw/comp/perl/5.26.2/rackham/lib/5.26.2/x86_64-linux-thread-multi no unknown -/sw/comp/perl/5.26.2/rackham/lib/5.26.2 no unknown -/sw/comp/perl/5.26.2/rackham/lib no unknown -/sw/comp/perl/5.26.2/rackham/lib/site_perl/5.26.2/x86_64-linux-thread-multi no unknown -/sw/comp/perl/5.26.2/rackham/lib/site_perl/5.26.2 no unknown +Include path (INC) directories Searched Number of Modules +/sw/comp/perl_modules/5.26.2/rackham/lib/perl5/5.26.2/x86_64-linux-thread-multi yes 0 +/sw/comp/perl_modules/5.26.2/rackham/lib/perl5/5.26.2 yes 0 +/sw/comp/perl_modules/5.26.2/rackham/lib/perl5/x86_64-linux-thread-multi yes 1055 +/sw/comp/perl_modules/5.26.2/rackham/lib/perl5 yes 5989 +/sw/comp/perl/5.26.2/rackham/lib/5.26.2/x86_64-linux-thread-multi no unknown +/sw/comp/perl/5.26.2/rackham/lib/5.26.2 no unknown +/sw/comp/perl/5.26.2/rackham/lib no unknown +/sw/comp/perl/5.26.2/rackham/lib/site_perl/5.26.2/x86_64-linux-thread-multi no unknown +/sw/comp/perl/5.26.2/rackham/lib/site_perl/5.26.2 no unknown -Total modules 5989 +Total modules 5989 ``` diff --git a/docs/software/python.md b/docs/software/python.md index 0489516a7..68bd5cc5f 100644 --- a/docs/software/python.md +++ b/docs/software/python.md @@ -11,7 +11,6 @@ Then, we show how to [load Python](#loading-python) and to [load Python packages](#loading-python-packages) after which you can [run Python](#running-python). - Finally, you can find [UPPMAX Python-related courses](#uppmax-python-related-courses) and these more advanced topics: @@ -226,7 +225,6 @@ which allows any user to run complex tools from a terminal or script. For example, the following Python code imports the functionality of the `pandas` library: - ```python import pandas ``` @@ -477,12 +475,13 @@ Python programming [here](python_programming.md) You can run a Python script in the shell by: ```console -$ python example_script.py +python example_script.py ``` + or, if you loaded a `python3` module: ```console -$ python3 example_script.py +python3 example_script.py ``` ### Use Python in an interactive session @@ -490,13 +489,13 @@ $ python3 example_script.py You start a python session by typing: ```console -$ python +python ``` or ```console -$ python3 +python3 ``` The python prompt looks like this: @@ -504,6 +503,7 @@ The python prompt looks like this: ```python >>> ``` + Exit with ``, `quit()` or `exit()`. ## Programming in Python @@ -537,14 +537,12 @@ is described [here](python_parallel_jobs.md). ## References - * [Kuhlman, 2009] Kuhlman, Dave. A python book: Beginning python, advanced python, and python exercises. Lutz: Dave Kuhlman, 2009. +- [Kuhlman, 2009] Kuhlman, Dave. A python book: Beginning python, advanced python, and python exercises. Lutz: Dave Kuhlman, 2009. ## Links -* [Official Python documentation](https://docs.python.org/3/) -* [Python forum](https://www.python.org/community/forums/) -* [Free online book: 'How to Think Like a Computer Scientist'](https://openbookproject.net/thinkcs/python/english3e/index.html) -* [UPPMAX TensorFlow guide](tensorflow.md) -* [UPPMAX PyTorch guide](pytorch.md) - - +- [Official Python documentation](https://docs.python.org/3/) +- [Python forum](https://www.python.org/community/forums/) +- [Free online book: 'How to Think Like a Computer Scientist'](https://openbookproject.net/thinkcs/python/english3e/index.html) +- [UPPMAX TensorFlow guide](tensorflow.md) +- [UPPMAX PyTorch guide](pytorch.md) diff --git a/docs/software/python_install_packages.md b/docs/software/python_install_packages.md index 81b4eae5c..fda75b3f6 100644 --- a/docs/software/python_install_packages.md +++ b/docs/software/python_install_packages.md @@ -13,6 +13,7 @@ You may want to [check if a package is already installed](#check-if-a-package-is [The Python package installers are compared](#comparison-between-conda-and-pypi) after which each is discussed: + - **PyPI** using [`pip`](#pip) - **Conda** using [`conda`](#conda) @@ -45,11 +46,11 @@ Does it work? Then it is there! ## Comparison between Conda and PyPI -* **PyPI** (`pip`) is traditionally for Python-only packages but it is no problem to +- **PyPI** (`pip`) is traditionally for Python-only packages but it is no problem to also distribute packages written in other languages as long as they provide a Python interface. -* **Conda** (`conda`) is more general and while it contains many Python packages and +- **Conda** (`conda`) is more general and while it contains many Python packages and packages with a Python interface, it is often used to also distribute packages which do not contain any Python (e.g. C or C++ packages). @@ -136,19 +137,19 @@ If that is the case for the package you need, this is how you do it: - Pick a location for your installation (change below to fit - I am installing under a project storage) - - ``mkdir /proj///mypythonpackages`` - - ``cd /proj///mypythonpackages`` + - ``mkdir /proj///mypythonpackages`` + - ``cd /proj///mypythonpackages`` - Load Python + (on Kebnekaise) site-installed prerequisites (SciPy-bundle, matplotlib, etc.) - Install any remaining prerequisites. Remember to activate your Virtualenv if installing with pip! - Download Python package, place it in your chosen installation dir, then untar/unzip it - cd into the source directory of the Python package - - Run ``python setup.py build`` - - Then install with: ``python setup.py install --prefix=`` + - Run ``python setup.py build`` + - Then install with: ``python setup.py install --prefix=`` - Add the path to $HOME/.bash_profile (note that it will differ by Python version): - - ``export PYTHONPATH=$PYTHONPATH:/lib/python3.11/site-packages`` + - ``export PYTHONPATH=$PYTHONPATH:/lib/python3.11/site-packages`` You can use it as normal inside Python (remember to load dependent modules as well as activate virtual environment if it depends on some packages you installed with pip): ``import `` diff --git a/docs/software/python_parallel_jobs.md b/docs/software/python_parallel_jobs.md index 661ac7c8a..524061508 100644 --- a/docs/software/python_parallel_jobs.md +++ b/docs/software/python_parallel_jobs.md @@ -29,9 +29,8 @@ There are several packages available for Python that let you run parallel jobs. Threading divides up your work among a number of cores within a node. The threads shares its memory. -- Multi-threading documentation -- Examples - +* Multi-threading documentation +* Examples The designers of the Python language made the choice that only one thread in a process can run actual Python code by using the so-called global interpreter lock (GIL). This means that approaches that may work in other languages (C, C++, Fortran), may not work in Python without being a bit careful. At first glance, this is bad for parallelism. But it’s not all bad!: @@ -162,24 +161,25 @@ python distributed.py ``` ### MPI + Presently you have to install your own mpi4py. You will need to activate paths to the MPI libraries. Therefore follow these steps. 1. If you use python 3.10.8: ``` -$ module load gcc/12.2.0 openmpi/4.1.4 +module load gcc/12.2.0 openmpi/4.1.4 ``` Otherwise: ``` -$ module load gcc/9.3.0 openmpi/3.1.5 +module load gcc/9.3.0 openmpi/3.1.5 ``` 2. pip install locally or in an virtual environment ``` -$ pip install --user mpi4py +pip install --user mpi4py ``` Remember that you will also have to load the the openmpi module before running mpi4py code, so that the MPI header files can be found (e.g. with the command "module load gcc/X.X.X openmpi/X.X.X"). Because of how MPI works, we need to explicitly write our code into a file, pythonMPI.py: @@ -228,7 +228,6 @@ if rank == 0: You can execute your code the normal way as - ``` mpirun -n 3 python pythonMPI.py ``` diff --git a/docs/software/python_programming.md b/docs/software/python_programming.md index 05b3ed71a..ad58bbfaa 100644 --- a/docs/software/python_programming.md +++ b/docs/software/python_programming.md @@ -65,6 +65,7 @@ python3 example_script.py ``` Some features of this approach are: + - this is a simple way to write code: it is the same as writing any text file. - you get no help while writing code - you can only run the script from start to finish, i.e. you cannot @@ -337,10 +338,8 @@ Some features are: ## Links -* [Official Python documentation](https://docs.python.org/3/) -* [Python forum](https://www.python.org/community/forums/) -* [Free online book: 'How to Think Like a Computer Scientist'](https://openbookproject.net/thinkcs/python/english3e/index.html) -* [UPPMAX TensorFlow guide](tensorflow.md) -* [UPPMAX PyTorch guide](pytorch.md) - - +- [Official Python documentation](https://docs.python.org/3/) +- [Python forum](https://www.python.org/community/forums/) +- [Free online book: 'How to Think Like a Computer Scientist'](https://openbookproject.net/thinkcs/python/english3e/index.html) +- [UPPMAX TensorFlow guide](tensorflow.md) +- [UPPMAX PyTorch guide](pytorch.md) diff --git a/docs/software/python_pyenv.md b/docs/software/python_pyenv.md index 9e4cf501c..88dd405fb 100644 --- a/docs/software/python_pyenv.md +++ b/docs/software/python_pyenv.md @@ -43,7 +43,6 @@ Python 3.3 or any other version. ### Install packages in your selected python version - 1. Set python version with ```pyenv global ``` @@ -55,6 +54,7 @@ Python 3.3 or any other version. ``` Example: + ``` pip install mechanize ``` diff --git a/docs/software/python_venv.md b/docs/software/python_venv.md index d4ce2c18d..dc9952d62 100644 --- a/docs/software/python_venv.md +++ b/docs/software/python_venv.md @@ -23,6 +23,7 @@ for example, from scratch, which is not recommended. Here we discuss the recommended way to create a virtual environment, which has these steps: + 1. Load a Python module or a modules with Python packages 1. Create the virtual environment @@ -145,8 +146,6 @@ to work with it again. ## Export and import a virtual environment - - ### Export To export the Python packages used in your virtual environment, do: @@ -179,7 +178,6 @@ using the conventional name for such a file. Note that `[more Python packages]` is a placeholder for many more Python packages. - ### Import ``` diff --git a/docs/software/python_virtual_environments.md b/docs/software/python_virtual_environments.md index d50694fb8..dcf18f1c5 100644 --- a/docs/software/python_virtual_environments.md +++ b/docs/software/python_virtual_environments.md @@ -53,4 +53,3 @@ for example, from scratch. However, there are more efficient ways, such as by re-using already installed Python packages. How to do so, can be found on the page about your specific virtual environment manager. - diff --git a/docs/software/pytorch.md b/docs/software/pytorch.md index 2238fe33f..0647a10a9 100644 --- a/docs/software/pytorch.md +++ b/docs/software/pytorch.md @@ -1,2 +1 @@ # PyTorch - diff --git a/docs/software/r.md b/docs/software/r.md index 114fd358a..495630dd0 100644 --- a/docs/software/r.md +++ b/docs/software/r.md @@ -13,7 +13,6 @@ Here we discuss: - [R software development](#r-software-development) - [How to install personal packages](#how-to-install-personal-packages) - ```mermaid flowchart TD @@ -201,6 +200,7 @@ Note that R_packages/4.3.1 contains 23475 packages, nearly all packages availabl ## What R packages are in the omnibus `R_packages` modules? ### R_PACKAGES/4.1.1 + As of 2021-11-11 there are a total of 21659 R packages installed. A total of 21740 packages are available in CRAN and BioConductor. 18022 CRAN packages are installed, out of 18348 available. 3382 BioConductor-specific packages are installed, out of 3392 available. 255 other R packages are installed. These are not in CRAN/BioConductor, and instead are hosted on github or elsewhere. These R packages are available as part of the R_packages/4.1.1 module as installed on rackham, bianca and snowy, which requires and loads the R/4.1.1 module. When the R_packages/4.1.1 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). @@ -209,6 +209,7 @@ Note that R_packages/4.3.1 contains 23475 packages, nearly all packages availabl - See module help R_packages/4.1.1 for more information. ### R_PACKAGES/4.0.4 + As of 2021-04-16 there are a total of 20663 CRAN and BioConductor packages installed, out of 20751 packages available. 17354 CRAN packages are installed, out of 17428 available. 3309 BioConductor-specific packages are installed, out of 3323 available. These R packages are available as part of the R_packages/4.0.4 module as installed on rackham, bianca and snowy, which requires and loads the R/4.0.4 module. When the R_packages/4.0.4 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). @@ -217,6 +218,7 @@ Note that R_packages/4.3.1 contains 23475 packages, nearly all packages availabl - See module help R_packages/4.0.4 for more information. ### R_PACKAGES/4.0.0 + As of 2021-02-24 there are a total of 18652 CRAN and BioConductor packages installed, out of 20422 packages available. 14839 CRAN packages are installed, out of 17165 available. 3217 BioConductor-specific packages are installed, out of 3257 available. These R packages are available as part of the R_packages/4.0.0 module as installed on rackham, bianca and snowy, which requires and loads the R/4.0.0 module. When the R_packages/4.0.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). @@ -224,21 +226,25 @@ Note that R_packages/4.3.1 contains 23475 packages, nearly all packages availabl See module help R_packages/4.0.0 for more information. ### R_PACKAGES/3.6.1 + As of 2019-09-18 there are a total of 17657 packages available in this module. This includes 14579 CRAN packages installed, out of 14913 available; and 3054 BioConductor-specific packages installed, out of 3079 available. These R packages are available as part of the R_packages/3.6.1 module as installed on rackham, bianca and snowy, which requires and loads the R/3.6.1 module. When the R_packages/3.6.1 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). See module help R_packages/3.6.1 for more information. ### R_PACKAGES/3.6.0 + As of 2019-05-14 there are a total of 17257 packages available. This includes 13769 CRAN packages installed, out of 14178 available; and 3031 BioConductor-specific packages installed, out of 3079 available. These R packages are available as part of the R_packages/3.6.0 module as installed on rackham, bianca and snowy, which requires and loads the R/3.6.0 module. When the R_packages/3.6.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). See module help R_packages/3.6.0 for more information. ### R_PACKAGES/3.5.2 + As of 2019-02-08 there are a total of 16642 packages available. This includes 13355 CRAN packages installed, out of 13683 available; and 2933 BioConductor-specific packages installed, out of 2959 available. These R packages are available as part of the R_packages/3.5.2 module as installed on rackham, bianca and snowy, which requires and loads the R/3.5.2 module. When the R_packages/3.5.2 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). See module help R_packages/3.5.2 for more information. ### R_PACKAGES/3.5.0 + With its 3.5.0 version, R_packages now attempts to install all available R packages from both CRAN and BioConductor. As of 2018-06-26 there are a total of 14532 packages available. This includes 11734 CRAN packages installed, out of 12867 available; and 2798 BioConductor-specific packages installed, out of 2843 available. These R packages are available as part of the R_packages/3.5.0 module as installed on rackham, bianca and snowy, which requires and loads the R/3.5.0 module. When the R_packages/3.5.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). @@ -246,18 +252,23 @@ With its 3.5.0 version, R_packages now attempts to install all available R packa See module help R_packages/3.5.0 for more information. ### R_packages/3.4.3 + A large number of R packages are available as part of the R_packages/3.4.3 module as installed on rackham and bianca, which requires and loads the R/3.4.3 module. When the R_packages/3.4.3 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). ### R_packages/3.4.0 + A large number of R packages are available as part of the R_packages/3.4.0 module, which requires and loads the R/3.4.0 module. When the R_packages/3.4.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). ### R_packages/3.3.2 + A large number of R packages are available as part of the R_packages/3.3.2 module, which requires and loads the R/3.3.2 module. When the R_packages/3.3.2 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these packages will be available via library(package-name). ### R_packages/3.3.1 + A large number of R packages are available as part of the R_packages/3.3.1 module, which requires and loads the R/3.3.1 module. When the R_packages/3.3.1 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these should be available via library(package-name). ### R_packages/3.3.0 + A large number of R packages are available as part of the R_packages/3.3.0 module, which requires and loads the R/3.3.0 module. When the R_packages/3.3.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these should be available via library(package-name). ## Learning R @@ -265,6 +276,7 @@ See module help R_packages/3.5.0 for more information. ### Starter R courses [The Carpentries](https://carpentries.org/) teaches basic lab skills for research computing, such as: + - [Programming with R](swcarpentry.github.io/r-novice-inflammation/) - [R for reproducible scientific analysis](https://swcarpentry.github.io/r-novice-gapminder) @@ -273,6 +285,7 @@ See module help R_packages/3.5.0 for more information. [CodeRefinery](https://coderefinery.org) develops and maintains training material on software best practices for researchers that already write code. Their material addresses all academic disciplines and tries to be as programming language-independent as possible: + - [CodeRefinery lessons](https://coderefinery.org/lessons/) Aalto Scientific Computing: @@ -294,4 +307,3 @@ Aalto Scientific Computing: - [Official R documentation](https://cran.r-project.org/manuals.html) - [CRAN homepage](https://cran.r-project.org) - [CRAN mirrors](https://cran.r-project.org/mirrors.html) - diff --git a/docs/software/rclone.md b/docs/software/rclone.md index 1cf2e44bf..22bf34c37 100644 --- a/docs/software/rclone.md +++ b/docs/software/rclone.md @@ -116,7 +116,6 @@ Rclone is one of the recommended ways to connect to Swestore. If you see the Swestore folder structure above, Rclone works fine. - ## Links - [The Rclone homepage](https://rclone.org/) diff --git a/docs/software/rsync.md b/docs/software/rsync.md index 0f47f3c3b..4397a5bdc 100644 --- a/docs/software/rsync.md +++ b/docs/software/rsync.md @@ -9,8 +9,8 @@ such as is ideal for making a backup. At this page, we use the word 'copy', although `rsync` by default does a one-way synchronize: if the data is already there, it will do nothing. - * [Using `rsync` on Bianca](../cluster_guides/rsync_on_bianca.md) - * [Using `rsync` on Rackham](../cluster_guides/rsync_on_rackham.md) +* [Using `rsync` on Bianca](../cluster_guides/rsync_on_bianca.md) +* [Using `rsync` on Rackham](../cluster_guides/rsync_on_rackham.md) ## Copy a folder from local to Rackham diff --git a/docs/software/sftp.md b/docs/software/sftp.md index ad842c464..cca7f8d32 100644 --- a/docs/software/sftp.md +++ b/docs/software/sftp.md @@ -1,6 +1,7 @@ # SFTP ## 1. Getting Help + Once, you in the sftp prompt, check the available commands by typing ‘?‘ or ‘help‘ at command prompt. This will print out a list of the available commands and give a short description of them. We'll cover the most common ones in this guide. ``` @@ -13,6 +14,7 @@ cd path Change remote directory to 'path' ``` ## 2. Check Present Working Directory + The command ‘lpwd‘ is used to check the Local present working directory, whereas ‘pwd‘ command is used to check Remote working directory. ``` @@ -25,19 +27,23 @@ pwd – print the current directory on the ftp server ``` ## 3. Listing Files + Listing files and directories in local as well as remote system. On Remote + ``` sftp> ls ``` On Local + ``` sftp> lls ``` ## 4. Upload File + Put single or multiple files in remote system. ``` @@ -47,6 +53,7 @@ sftp> put local.profile Uploading local.profile to /tecmint/local.profile ## 5. Upload Multiple Files + Putting multiple files on remote system. ``` @@ -56,11 +63,13 @@ sftp> mput *.xls Another alternative to uploading many files is to tar and/or compress the files to a single file before uploading. The file transfer will stop in between every file, so the more file you have to upload the more stops it will make. This can have a dramatic impact on transfer speed if there are 1000s of files that you want to transfer. Running tar and/or zip on the files before transferring them will package all the files into a single file, so there will be no stops at all during the transfer. ## 6. Download Files + Getting single or multiple files in local system. ``` sftp> get SettlementReport_1-10th.xls ``` + Fetching /tecmint/SettlementReport_1-10th.xls to SettlementReport_1-10th.xls Get multiple files on a local system. ``` @@ -70,19 +79,23 @@ sftp> mget *.xls Note: As we can see by default the get command downloads the file to the local system with the same name. We can download remote file and store it with a different name by specifying the name at the end. (This applies only while downloading single file). ## 7. Switching Directories + Switching from one directory to another directory in local and remote locations. On Remote + ``` sftp> cd test ``` On Local + ``` sftp> lcd Documents ``` ## 8. Create Directories + Creating new directories on remote and local locations. ``` @@ -91,6 +104,7 @@ sftp> lmkdir Documents ``` ## 9. Remove Directory or File + Remove directory or file in remote system. ``` @@ -101,6 +115,7 @@ sftp> rmdir sub1 Note: To remove/delete any directory from remote location, the directory must be empty. ## 10. Exit sFTP Shell + The ‘!‘ (exclamation mark) command drops us in local shell from where we can execute Linux commands. Type ‘exit‘ command where we can see sftp> prompt return. ``` diff --git a/docs/software/ssh.md b/docs/software/ssh.md index ea172dbdd..a80ee5b9d 100644 --- a/docs/software/ssh.md +++ b/docs/software/ssh.md @@ -70,7 +70,6 @@ ServerAliveInterval 120 #======================================= ``` - Now ``` @@ -90,4 +89,4 @@ sftp ... ## Links - * [SSH Tips by Pavlin Mitev](https://hackmd.io/@pmitev/SSH_tips) +- [SSH Tips by Pavlin Mitev](https://hackmd.io/@pmitev/SSH_tips) diff --git a/docs/software/ssh_client.md b/docs/software/ssh_client.md index 3645a1740..a7458ea76 100644 --- a/docs/software/ssh_client.md +++ b/docs/software/ssh_client.md @@ -26,4 +26,4 @@ MobaXterm is an SSH client that is easy to use and install for Windows. When MobaXterm is started, start a terminal to run `ssh`. The usage of `ssh` is described at the UPPMAX page on `ssh` [here](ssh.md). - * [MobaXterm homepage](https://mobaxterm.mobatek.net/) +- [MobaXterm homepage](https://mobaxterm.mobatek.net/) diff --git a/docs/software/ssh_key_use.md b/docs/software/ssh_key_use.md index 5d78152ed..4b1b47e80 100644 --- a/docs/software/ssh_key_use.md +++ b/docs/software/ssh_key_use.md @@ -2,6 +2,6 @@ Here we show how to create and use an [SSH](ssh.md) key pair for use with our clusters: - - [Create and use an SSH key pair for Bianca](ssh_key_use_bianca.md) - - [Create and use an SSH key pair for Dardel](ssh_key_use_dardel.md) - - [Create and use an SSH key pair for Rackham](ssh_key_use_rackham.md) +- [Create and use an SSH key pair for Bianca](ssh_key_use_bianca.md) +- [Create and use an SSH key pair for Dardel](ssh_key_use_dardel.md) +- [Create and use an SSH key pair for Rackham](ssh_key_use_rackham.md) diff --git a/docs/software/ssh_key_use_dardel.md b/docs/software/ssh_key_use_dardel.md index bb093dc25..75c2837e3 100644 --- a/docs/software/ssh_key_use_dardel.md +++ b/docs/software/ssh_key_use_dardel.md @@ -89,7 +89,6 @@ The key will now be created and you can add it to the PDC Login Portal. +----[SHA256]-----+ ``` - ## 2. How to add an SSH key to the PDC Login Portal To add an SSH key to the PDC login portal, one needs to: diff --git a/docs/software/tensorflow.md b/docs/software/tensorflow.md index e66e1bc9f..b14bc8fbe 100644 --- a/docs/software/tensorflow.md +++ b/docs/software/tensorflow.md @@ -51,7 +51,6 @@ for example, `python_ML_packages/3.11.8-cpu`. TensorFlow as a Python package for GPU that works on [Bianca](../cluster_guides/bianca.md) and [Snowy](../cluster_guides/snowy.md). - It is part of the `python_ML_packages/[version]-gpu` [modules](../cluster_guides/modules.md), where `[version]` is a version, for example, `python_ML_packages/3.9.5-gpu` @@ -63,16 +62,15 @@ If you want to work interactively and test things, first allocate resources as s **On Snowy** ```console -$ interactive -A -n 2 -M snowy --gres=gpu:1 -t 1:00:01 +interactive -A -n 2 -M snowy --gres=gpu:1 -t 1:00:01 ``` **On Bianca** ```console -$ interactive -A -n 1 -C gpu --gres=gpu:1 -t 01:10:00 +interactive -A -n 1 -C gpu --gres=gpu:1 -t 01:10:00 ``` - ???- question "How to test TensorFlow as a Python package for GPU?" Load the module to get access to the library: diff --git a/docs/software/text_editors.md b/docs/software/text_editors.md index c44e2a4e5..249f245b7 100644 --- a/docs/software/text_editors.md +++ b/docs/software/text_editors.md @@ -63,9 +63,9 @@ vi Then: - - 1. Insert mode (type like normal text editor. Press ``i`` for insert mode) - - 2. Command mode (give commands to the editor to get things done . Press `` for command mode) - - Cheat sheet: [https://coderwall.com/p/adv71w/basic-vim-commands-for-getting-started](https://coderwall.com/p/adv71w/basic-vim-commands-for-getting-started) +- 1. Insert mode (type like normal text editor. Press ``i`` for insert mode) +- 2. Command mode (give commands to the editor to get things done . Press `` for command mode) +- Cheat sheet: [https://coderwall.com/p/adv71w/basic-vim-commands-for-getting-started](https://coderwall.com/p/adv71w/basic-vim-commands-for-getting-started) ### emacs @@ -79,11 +79,11 @@ emacs Then: - - Cheat sheet: [https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf](https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf) - - (C = ``) +- Cheat sheet: [https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf](https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf) + - (C = ``) - also With GUI - - ``emacs –nw`` - - keeps you in terminal window. + - ``emacs –nw`` + - keeps you in terminal window. ## Simple graphical editors diff --git a/docs/software/tkinter.md b/docs/software/tkinter.md index f897cb753..7d8e8326c 100644 --- a/docs/software/tkinter.md +++ b/docs/software/tkinter.md @@ -59,5 +59,4 @@ That is, this solution should work: ## Links - * [Wikipedia page on Tkinter](https://en.wikipedia.org/wiki/Tkinter) - +* [Wikipedia page on Tkinter](https://en.wikipedia.org/wiki/Tkinter) diff --git a/docs/software/tracer.md b/docs/software/tracer.md index db7dbf437..590cad8ae 100644 --- a/docs/software/tracer.md +++ b/docs/software/tracer.md @@ -69,4 +69,4 @@ java -jar lib/tracer.jar ## Links - * [Tracer GitHub repository](https://github.com/beast-dev/tracer) +* [Tracer GitHub repository](https://github.com/beast-dev/tracer) diff --git a/docs/software/vscode.md b/docs/software/vscode.md index 017545b7f..0ada68145 100644 --- a/docs/software/vscode.md +++ b/docs/software/vscode.md @@ -15,5 +15,3 @@ Cluster | Works/fails |Documentation page [Rackham](../cluster_guides/rackham.md) | Works |[VSCode on Rackham](../cluster_guides/vscode_on_rackham.md) - [1] Use [VSCodium on Bianca](../cluster_guides/vscodium_on_bianca.md) instead - - diff --git a/docs/software/vscodium.md b/docs/software/vscodium.md index cb133367e..82a3880d4 100644 --- a/docs/software/vscodium.md +++ b/docs/software/vscodium.md @@ -15,5 +15,3 @@ Cluster | Works/fails |Documentation page [Rackham](../cluster_guides/rackham.md) | Fails [1] |[VSCodium on Rackham](../cluster_guides/vscodium_on_rackham.md) - [1] Use [VSCode on Rackham](../cluster_guides/vscode_on_rackham.md) instead - - diff --git a/docs/software/whisper.md b/docs/software/whisper.md index 26db9ca79..793e0e04d 100644 --- a/docs/software/whisper.md +++ b/docs/software/whisper.md @@ -9,7 +9,6 @@ Snowy and Bianca. To load the Whisper module, run the following command: - ```bash module load Whisper/0.5.1 ``` diff --git a/docs/software/wrf.md b/docs/software/wrf.md index 4221af1ea..c7b10775f 100644 --- a/docs/software/wrf.md +++ b/docs/software/wrf.md @@ -12,11 +12,11 @@ - WRF is installed as modules for version 4.1.3 and compiled with INTEL and parallelized for distributed memory (dmpar) or hybrid shared and distributed memory (sm+dm). These are available as: - - WRF/4.1.3-dmpar default as WRF/4.1.3 - - WRF/4.1.3-dm+sm + - WRF/4.1.3-dmpar default as WRF/4.1.3 + - WRF/4.1.3-dm+sm - WPS is installed as version 4.1 and available as: - - WPS/4.1 + - WPS/4.1 - There are WPS_GEOG data available. - Set the path in namelist.wps to: @@ -28,12 +28,13 @@ - It may not work for a large domain. If so, either modify TBL file or use in inner domains only. - To analyse the WRF output on the cluster you can use Vapor, NCL (module called as NCL-graphics) or wrf-python (module called as wrf-python). For details on how, please confer the web pages below: - - [wrf-python](https://wrf-python.readthedocs.io/en/latest/), - - [Vapor](https://www.vapor.ucar.edu/) or - - [NCL](https://www.ncl.ucar.edu/Document/Pivot_to_Python/september_2019_update.shtml) - - is not updated anymore and the developers recommend [GeoCAT](https://geocat.ucar.edu/) which serves as an umbrella over wrf-python, among others. + - [wrf-python](https://wrf-python.readthedocs.io/en/latest/), + - [Vapor](https://www.vapor.ucar.edu/) or + - [NCL](https://www.ncl.ucar.edu/Document/Pivot_to_Python/september_2019_update.shtml) + - is not updated anymore and the developers recommend [GeoCAT](https://geocat.ucar.edu/) which serves as an umbrella over wrf-python, among others. # Get started + - This section assumes that you are already familiar in running WRF. If not, please check the [tutorial](https://www2.mmm.ucar.edu/wrf/OnLineTutorial/index.php), where you can at least omit the first 5 buttons and go directly to the last button, or depending on your needs, also check the “Static geography data” and “Real-time data”. - When running WRF/WPS you would like your own settings for the model to run and not to interfere with other users. Therefore, you need to set up a local or project directory (e.g. 'WRF') and work from there like for a local installation. You also need some of the content from the central installation. Follow these steps: @@ -131,6 +132,7 @@ If you would like to change in the FORTRAN code for physics or just want the lat 1. ``tar zxvf `` ### Step 2: Configure and compile + - Create and set the environment in a ``SOURCEME`` file, see example below for a intel-dmpar build. - Loading module WRF sets most of the environment but some variables have different names in configure file. - Examples below assumes dmpar, but can be interchanged to dm+sm for hybrid build. @@ -154,6 +156,7 @@ export HDF5=$HDF5_DIR ``` - Then + ``` source SOURCEME ./configure @@ -184,6 +187,7 @@ NETCDFFPATH = $(NETCDFF) ``` Then: + ``` ./compile em_real ``` @@ -193,11 +197,15 @@ When you have made modification of the code and once configure.wrf is created, j ``` source SOURCEME ``` + and run: + ``` ./compile em_real ``` + ### Running + Batch script should include: ```bash diff --git a/docs/support.md b/docs/support.md index 5bf98e9aa..f09ed77ec 100644 --- a/docs/support.md +++ b/docs/support.md @@ -5,9 +5,7 @@ - Lost your password? You can [request a new password here](https://supr.naiss.se/login/). - Please contact UPPMAX support through the [Support Form](https://supr.naiss.se/support/). - - or by emailing support@uppmax.uu.se. We are available during normal office hours. + - or by emailing . We are available during normal office hours. - For Uppsala University Education, support is provided through the UU IT Servicedesk. [What should I think about when planning a course using UPPMAX resources](https://www.uu.se/en/centre/uppmax/get-started/create-account-and-apply-for-project/apply-for-projects/course/planning-a-course) - - diff --git a/scripts/fix_markdown_style_errors.sh b/scripts/fix_markdown_style_errors.sh index 4336008fd..1e9267788 100755 --- a/scripts/fix_markdown_style_errors.sh +++ b/scripts/fix_markdown_style_errors.sh @@ -19,6 +19,6 @@ if [[ "$PWD" =~ scripts$ ]]; then exit 42 fi -markdownlint '**/*.md' --ignore node_modules --fix +markdownlint --fix 'docs/**/*.md' --ignore node_modules # ./scripts/remove_trailing_spaces.sh