GPyOpt Singuarlity Image

[MaryHadley]

Hi,

I've read the various docs about how to install GPyOpt, and I've had some trouble with all the methods, even checking out the package from Github. Ultimately, I would like to make a singularity image that has GPyOpt that I can pass on to others in my collaboration -- do you have instructions for creating such an image?

Thank you,
Mary

[apaleyes]

Hi. Unfortunately I've never even heard of "singularity image". Can you please elaborate what's that?

Also, can you share the issues you had install GPyOpt? It's just a Python package, so normally pip install gpyopt should work fine. If you could post what you have tried and what specific errors you've encountered, we might be able to help.

[ekalosak]

Hey fellow Bruno - I'm guessing, from what I've read on singularity, you might be looking for something like a Dockerfile that contains GPyOpt. This is going to be the same process as building a docker image with the GPyOpt package installed. As Andrei writes, you could do something like

FROM python3.8
RUN pip install gypopt
COPY myscript.py /
ENTRYPOINT python myscript.py

[MaryHadley]

Thanks for your quick and kind replies. The problem seems to be (when working on my mac, which only has python 2): pip install GPyOpt Collecting GPyOpt Collecting scipy>=0.16 (from GPyOpt) Using cached https://files.pythonhosted.org/packages/dc/7a/3de1700fb471a6f56353446b4b962a7e4a5baaf24e5e4dec2d91d5f500da/scipy-1.2.3-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Requirement already satisfied: numpy>=1.7 in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from GPyOpt) Collecting GPy>=1.8 (from GPyOpt) Using cached https://files.pythonhosted.org/packages/40/13/4112894b8ef87847b50a6d04acdab1366aafadf0a78e4207e65c33e82b8a/GPy-1.9.9-cp27-cp27m-macosx_10_7_x86_64.whl Requirement already satisfied: six in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from GPy>=1.8->GPyOpt) Collecting paramz>=0.9.0 (from GPy>=1.8->GPyOpt) Collecting decorator>=4.0.10 (from paramz>=0.9.0->GPy>=1.8->GPyOpt) Using cached https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl Installing collected packages: scipy, decorator, paramz, GPy, GPyOpt Found existing installation: scipy 0.13.0b1 DEPRECATION: Uninstalling a distutils installed project (scipy) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Uninstalling scipy-0.13.0b1: Exception: Traceback (most recent call last): File "/Library/Python/2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/Library/Python/2.7/site-packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/Library/Python/2.7/site-packages/pip/req/req_set.py", line 778, in install requirement.uninstall(auto_confirm=True) File "/Library/Python/2.7/site-packages/pip/req/req_install.py", line 754, in uninstall paths_to_remove.remove(auto_confirm) File "/Library/Python/2.7/site-packages/pip/req/req_uninstall.py", line 115, in remove renames(path, new_path) File "/Library/Python/2.7/site-packages/pip/utils/__init__.py", line 267, in renames shutil.move(old, new) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 325, in move copy2(src, real_dst) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 154, in copy2 copystat(src, dst) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 123, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 1] Operation not permitted: '/var/folders/f8/88v7l4yn5v577qwbhl_vbpgm0000gn/T/pip-UUQ8F5-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy-0.13.0b1-py2.7.egg-info' You are using pip version 9.0.3, however version 20.1.1 is available. *You should consider upgrading via the 'pip install --upgrade pip*' command. So I try that: pip install --upgrade pip pip install --upgrade pip Collecting pip Using cached https://files.pythonhosted.org/packages/43/84/23ed6a1796480a6f1a2d38f2802901d078266bda38388954d01d3f2e821d/pip-20.1.1-py2.py3-none-any.whl Installing collected packages: pip Found existing installation: pip 9.0.3 Uninstalling pip-9.0.3: Exception: Traceback (most recent call last): File "/Library/Python/2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/Library/Python/2.7/site-packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/Library/Python/2.7/site-packages/pip/req/req_set.py", line 778, in install requirement.uninstall(auto_confirm=True) File "/Library/Python/2.7/site-packages/pip/req/req_install.py", line 754, in uninstall paths_to_remove.remove(auto_confirm) File "/Library/Python/2.7/site-packages/pip/req/req_uninstall.py", line 115, in remove renames(path, new_path) File "/Library/Python/2.7/site-packages/pip/utils/__init__.py", line 267, in renames shutil.move(old, new) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 326, in move os.unlink(src) OSError: [Errno 13] Permission denied: '/Library/Python/2.7/site-packages/pip-9.0.3.dist-info/DESCRIPTION.rst' You are using pip version 9.0.3, however version 20.1.1 is available. *You should consider upgrading via the 'pip install --upgrade pip' command.* So looks like I may have 3 problems -- the fact that this pip installation of GPyOpt isn't working, the fact that pip install upgrade isn't working, and the fact that I don't have python3. I suppose, since my goal really is to make the docker image, that I could just try the commands you suggested in a docker file. I am a docker very newbie, so was trying to test things locally on my laptop first. Thank you, Mary

…

On Tue, Jun 30, 2020 at 6:40 PM Eric Kalosa-Kenyon ***@***.***> wrote: Hey fellow Bruno - I'm guessing, from what I've read on singularity, you might be looking for something like a Dockerfile that contains GPyOpt. This is going to be the same process as building a docker image with the GPyOpt package installed. As Andrei writes, you could do something like FROM python3.8 RUN pip install gypopt COPY myscript.py / ENTRYPOINT python myscript.py — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#325 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADRHPZK7ZGLSZX25A2D3USLRZJZXLANCNFSM4OMRUBQQ> .

[apaleyes]

What I see in the installation log is just a permission issue, nothing to do with gpyopt or python version. By default pip installs packages into system directory, which requires root access. Things you could do:

• sudo pip install gpyopt
• pip install gpyopt --user
• Create a virtual environment

[MaryHadley]

Thank you!

…

On Wed, Jul 1, 2020 at 11:40 AM Andrei Paleyes ***@***.***> wrote: What I see in the installation log is just a permission issue, nothing to do with gpyopt or python version. By default pip installs packages into system directory, which requires root access. Things you could do: - sudo pip install gpyopt - pip install gpyopt --user - Create a virtual environment <https://docs.python-guide.org/dev/virtualenvs/> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#325 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADRHPZL5NJTKEIT6M47JWOTRZNRETANCNFSM4OMRUBQQ> .

[ekalosak]

@MaryHadley when you figure this out, it would be great to have your Dockerfile (or a stripped down example) in the wiki: https://github.com/SheffieldML/GPyOpt/wiki