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pbsCoat.py
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Sat, May 4, 07:06

pbsCoat.py
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#!/usr/bin/env python
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
from BlackDynamite import *
import os
import stat
import subprocess
import re
import socket
admissible_params = {"walltime": str,
"email": str,
"nproc": int,
"pbs_option": [str],
"module": [str],
"mpiprocs": int,
"ncpus": int,
"cwd": bool}
default_params = {"walltime": "48:00:00",
"cwd": True}
help = {"walltime": "Specify the wall time for the runs",
"email": "Specify the email to notify",
"nproc": "Force the number of processors and update the run",
"pbs_option": "Allow to provide additional PBS options",
"module": "List of module to load",
"ncpus": "Number of cpus per nodes",
"mpiprocs": "Number of mpi processus per nodes",
"cwd": "Run by default in the run folder"}
def launch(run, params):
_exec = run.getExecFile()
head = \
"""#!/bin/bash
#PBS -l walltime={0}
""".format(params["walltime"])
if ("email" in params):
head += "#PBS -m abe\n"
head += "#PBS -M {0}\n".format(params["email"])
pbs_head_name = "#PBS -N {0}_{1}\n".format(run["run_name"], run.id)
head += pbs_head_name
run["state"] = "PBS submit"
if ("nproc" in params):
run["nproc"] = params["nproc"]
nproc = run["nproc"]
if ("mpiprocs" in params or "npcus" in params):
args = []
if "ncpus" in params:
npernode = params["ncpus"]
args.append("ncpus={0}".format(npernode))
if "mpiprocs" in params:
npernode = min(params["mpiprocs"], nproc)
args.append("mpiprocs={0}".format(npernode))
select = max(1, nproc/npernode)
args.insert(0, "#PBS -l select={0}".format(select))
select_str = ":".join(args)
print select_str
head += select_str + "\n"
else:
head += "#PBS -l nodes=" + str(nproc) + "\n"
if ("pbs_option" in params):
for i in params["pbs_option"]:
head += "#PBS {0}\n".format(i)
if ("module" in params):
for i in params["module"]:
head += "module load {0}\n".format(i)
run.update()
head += """
export BLACKDYNAMITE_HOST=__BLACKDYNAMITE__dbhost__
export BLACKDYNAMITE_SCHEMA=__BLACKDYNAMITE__study__
export BLACKDYNAMITE_STUDY=__BLACKDYNAMITE__study__
export BLACKDYNAMITE_RUN_ID=__BLACKDYNAMITE__run_id__
export BLACKDYNAMITE_USER=""" + params["user"] + """
on_kill()
{
updateRuns.py --updates \"state = PBS killed\" --truerun
exit 0
}
on_stop()
{
updateRuns.py --updates \"state = PBS stopped\" --truerun
exit 0
}
# Execute function on_die() receiving TERM signal
#
trap on_stop SIGUSR1
trap on_stop SIGTERM
trap on_kill SIGUSR2
trap on_kill SIGKILL
"""
if (params["cwd"]):
head += """
cd __BLACKDYNAMITE__run_path__
"""
_exec["file"] = run.replaceBlackDynamiteVariables(head) + _exec["file"]
f = open(_exec["filename"], 'w')
f.write(_exec["file"])
f.close()
# os.chmod(_exec["filename"], stat.S_IRWXU)
print("execute qsub ./" + _exec["filename"])
print("in dir ")
subprocess.call("pwd")
if params["truerun"] is True:
ret = subprocess.call("qsub " + _exec["filename"], shell=True)

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