/usr/lib/python2.7/dist-packages/dolfin_utils/pjobs/sge.py is in python-dolfin 1.3.0+dfsg-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 | #!/usr/bin/env python
# Copyright (C) 2011 Johan Hake
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# DOLFIN 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
# Template for script sent to qsub
template = """#!/bin/sh
# Your job name
#$ -N %(jobname)s
# Resources
#$ -l %(resources)s
# enter the job-directory
cd %(workdir)s
# Use current working directory
#$ -cwd
# Join stdout and stderr
#$ -j y
# Execute in current environment
%(environment)s
# Set queue
#$ -q %(queue)s
# Set your number of processors here.
# Requests mpich environment although we actually are using openmpi
#$ -pe %(PE)s %(np)d
# add /usr/local/bin in path
PATH=$PATH:/usr/local/bin
# Run job through bash shell
#$ -S /bin/bash
# setup environment
%(paths)s
%(setup)s
%(job)s
"""
def job_script(job, jobname, nodes, ppn, walltime, mem, vmem, workdir, \
email, paths, setup, keep_environment, queue, parallel_environment):
"""
Generate a sge specific job script
"""
# Set default queue
queue = queue or "all.q"
# Check environment
if not parallel_environment:
raise RuntimeError("expected proper values for 'parallel_environment'. "\
"Check available environments using: qconf -spl")
# Set resources
resources="cpu=%d:00:00"%walltime
if mem:
mem = mem.replace("b", "").upper()
resources += ",mem_free=" + mem
if vmem:
vmem = vmem.replace("b", "").upper()
resources += ",h_vmem=" + vmem
# Issue warnings on not supported arguments
if email:
print "Warning: 'email' is not supported for the 'sge' backend"
args = dict(jobname=jobname,
resources=resources,
environment="#$ -V" if keep_environment else "# No",
queue=queue,
PE=parallel_environment,
np = nodes*ppn, # FIXME: Is this the correct way to set this?
workdir=workdir,
paths=paths,
setup=setup,
job=job)
return template % args
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