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kpfm_sim_task_db.py
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kpfm_sim_task_db.py
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# coding: utf-8
import sqlite3
from kpfm_sim_tasks import Descend_tip_task, Tune_bias_task
eps = 1.0e-13
# Class for storing information on separate KPFM simulation tasks to a
# database. Simulation tasks can be planned and fetched for execution
# in a batch job later.
class Task_control_db(object):
def __init__(self, filename):
print("Initializing task database")
self.db_filename = filename
try:
self.db_con = self.open_db()
self.create_tables()
except sqlite3.Error as e:
print("An error occurred:", e.args[0])
finally:
self.close_db()
def __del__(self):
print("Closing task database connection and deleting database object.")
self.close_db()
def __enter__(self):
self.db_con = self.open_db()
self.db_con.row_factory = sqlite3.Row
self.db_con.text_factory = str
def __exit__(self, exc_type, exc_value, traceback):
self.close_db()
if exc_type is None:
return True
else:
return False
def open_db(self):
con = sqlite3.connect(self.db_filename, detect_types = sqlite3.PARSE_DECLTYPES)
return con
def close_db(self):
if self.db_con:
self.db_con.close()
def create_tables(self):
sqlite3.register_adapter(bool, int)
sqlite3.register_converter("BOOLEAN", lambda v: bool(int(v)))
cur = self.db_con.cursor()
cur.execute("CREATE TABLE IF NOT EXISTS active_tasks(id INTEGER PRIMARY KEY, "
"slurm_id INTEGER, type TEXT, state TEXT, x REAL, y REAL, s REAL, "
"V REAL, param_start REAL, param_end REAL, param_step REAL, "
"result_db TEXT, global_res_db TEXT)")
cur.execute("CREATE TABLE IF NOT EXISTS completed_tasks(id INTEGER PRIMARY KEY, "
"type TEXT, x REAL, y REAL, s REAL, V REAL, "
"param_start REAL, param_end REAL, param_step REAL)")
self.db_con.commit()
def write_task(self, task):
cur = self.db_con.cursor()
cur.execute("INSERT INTO active_tasks(slurm_id, type, state, x, y, s, "
"V, param_start, param_end, param_step, result_db, global_res_db) "
"VALUES(?,?,?,?,?,?,?,?,?,?,?,?)",
task.get_db_record())
self.db_con.commit()
def write_task_data(self, task_id, slurm_id, slurm_output_path = None,
cp2k_output_fn = None, cp2k_restart_fn = None,
wf_filename = None):
cur = self.db_con.cursor()
if slurm_output_path is not None:
slurm_output = self._read_file_if_exists(slurm_output_path)
else:
slurm_output = None
if cp2k_output_fn is not None:
cp2k_output = self._read_file_if_exists(cp2k_output_fn)
else:
cp2k_output = None
if cp2k_restart_fn is not None:
cp2k_restart = self._read_file_if_exists(cp2k_restart_fn)
else:
cp2k_restart = None
if wf_filename is not None:
wf_data = self._read_file_if_exists(wf_filename, is_binary=True)
else:
wf_data = None
cur.execute("INSERT INTO task_data VALUES(?,?,?,?,?,?)",
(task_id, slurm_id, slurm_output,
cp2k_output, cp2k_restart, wf_data))
self.db_con.commit()
print("Wrote task data to database.")
def move_task_to_completed(self, task_id):
cur = self.db_con.cursor()
cur.execute("SELECT type, x, y, s, V, param_start, param_end, param_step "
"FROM active_tasks WHERE id=?", (task_id,))
row = cur.fetchone()
if row is not None:
cur.execute("INSERT INTO completed_tasks(type, x, y, s, "
"param_start, param_end, param_step) "
"VALUES(?,?,?,?,?,?,?)",
(row["type"], row["x"], row["y"], row["s"], row["param_start"],
row["param_end"], row["param_step"]))
cur.execute("DELETE FROM active_tasks WHERE id=?",
(task_id,))
self.db_con.commit()
def update_task_state(self, task_id, new_state):
cur = self.db_con.cursor()
cur.execute("UPDATE active_tasks SET state=? WHERE id=?",
(new_state, task_id))
self.db_con.commit()
def update_task_slurm_id(self, task_id, new_slurm_id):
cur = self.db_con.cursor()
cur.execute("UPDATE active_tasks SET slurm_id=? WHERE id=?",
(new_slurm_id, task_id))
self.db_con.commit()
def update_task(self, task_id, task):
cur = self.db_con.cursor()
db_update = task.get_db_update()
db_update.append(task_id)
cur.execute("UPDATE active_tasks "
"SET state=?, x=?, y=?, s=?, V=? "
"WHERE id=?",
db_update)
self.db_con.commit()
def fetch_active_task_id(self, type_constraint=None, state_constraint=None):
cur = self.db_con.cursor()
if type_constraint is not None:
if state_constraint is not None:
cur.execute("SELECT id FROM active_tasks "
"WHERE type=? AND state=?",
(type_constraint, state_constraint))
else:
cur.execute("SELECT id FROM active_tasks "
"WHERE type=?",
(type_constraint,))
else:
if state_constraint is not None:
cur.execute("SELECT id FROM active_tasks "
"WHERE state=?",
(state_constraint,))
else:
cur.execute("SELECT id FROM active_tasks")
row = cur.fetchone()
if row is not None:
return row[0]
else:
return None
def reserve_active_task(self, type_constraint=None, state_constraint=None):
cur = self.db_con.cursor()
cur.execute("BEGIN EXCLUSIVE")
task_id = self.fetch_active_task_id(type_constraint, state_constraint)
if task_id is not None:
task = self.extract_task(task_id)
self.update_task_state(task_id, "reserved")
return task_id, task
else:
self.db_con.commit()
return None, None
def extract_task(self, task_id):
cur = self.db_con.cursor()
cur.execute("SELECT * FROM active_tasks WHERE id=?",
(task_id,))
row = cur.fetchone()
if row is not None:
if row["type"] == "descend_tip":
return Descend_tip_task(row["x"], row["y"], row["s"], row["V"],
row["param_start"], row["param_end"],
row["param_step"], row["result_db"],
row["global_res_db"], row["state"],
row["slurm_id"])
elif row["type"] == "tune_bias":
return Tune_bias_task(row["x"], row["y"], row["s"], row["V"],
row["param_start"], row["param_end"],
row["param_step"], row["result_db"],
row["global_res_db"], row["state"],
row["slurm_id"])
else:
return None
else:
return None
def extract_restart_files(self, task_id, cp2k_output_fn, cp2k_restart_fn, wf_filename):
cur = self.db_con.cursor()
restart_file_exists = False
cur.execute("SELECT cp2k_output, cp2k_restart, cp2k_wf_data "
"FROM task_data WHERE task_id=?",
(task_id,))
row = cur.fetchone()
if row is not None:
if row["cp2k_output"] is not None:
with open(cp2k_output_fn, 'w') as cp2k_output_file:
cp2k_output_file.write(row["cp2k_output"])
if row["cp2k_restart"] is not None:
with open(cp2k_restart_fn, 'w') as cp2k_restart_file:
cp2k_restart_file.write(row["cp2k_restart"])
restart_file_exists = True
if row["cp2k_wf_data"] is not None:
with open(wf_filename, 'wb') as cp2k_wf_file:
cp2k_wf_file.write(row["cp2k_wf_data"])
self.db_con.commit()
cur.execute("DELETE FROM task_data WHERE task_id=?",
(task_id,))
self.db_con.commit()
return restart_file_exists
def extract_output(self, task_id):
cur = self.db_con.cursor()
cur.execute("SELECT cp2k_output "
"FROM task_data WHERE task_id=?",
(task_id,))
row = cur.fetchone()
return row[0]
def _read_file_if_exists(self, filename, is_binary=False):
try:
if not is_binary:
with open(filename, 'r') as in_file:
contents = in_file.read()
else:
with open(filename, 'rb') as in_file:
contents = in_file.read()
return contents
except IOError:
return None