def _writeJobScript(statement, job_memory, job_name, shellfile):
# disabled - problems with quoting
# tmpfile.write( '''echo 'statement=%s' >> %s\n''' %
# (shellquote(statement), shellfile) )
# module list outputs to stderr, so merge stderr and stdout
script = '''#!/bin/bash\n
echo "%(job_name)s : START -> ${0}" >> %(shellfile)s
set | sed 's/^/%(job_name)s : /' &>> %(shellfile)s
module list 2>&1 | sed 's/^/%(job_name)s: /' &>> %(shellfile)s
hostname | sed 's/^/%(job_name)s: /' &>> %(shellfile)s
cat /proc/meminfo | sed 's/^/%(job_name)s: /' &>> %(shellfile)s
echo "%(job_name)s : END -> ${0}" >> %(shellfile)s
''' % locals()
# restrict virtual memory
# Note that there are resources in SGE which could do this directly
# such as v_hmem.
# Note that limiting resident set sizes (RSS) with ulimit is not
# possible in newer kernels.
script += "ulimit -v %i\n" % IOTools.human2bytes(job_memory)
script += expandStatement(statement,
ignore_pipe_errors=ignore_pipe_errors)
script += "\n"
job_path = getTempFilename(dir=PARAMS["workingdir"])
with open(job_path, "w") as script_file:
script_file.write(script)
return(job_path)
def _writeJobScript(statement, job_memory, job_name, shellfile):
# disabled - problems with quoting
# tmpfile.write( '''echo 'statement=%s' >> %s\n''' %
# (shellquote(statement), shellfile) )
# module list outputs to stderr, so merge stderr and stdout
script = '''#!/bin/bash -e \n
echo "%(job_name)s : START -> ${0}" >> %(shellfile)s
set | sed 's/^/%(job_name)s : /' &>> %(shellfile)s
set +o errexit
module list 2>&1 | sed 's/^/%(job_name)s: /' &>> %(shellfile)s
set -o errexit
hostname | sed 's/^/%(job_name)s: /' &>> %(shellfile)s
cat /proc/meminfo | sed 's/^/%(job_name)s: /' &>> %(shellfile)s
echo "%(job_name)s : END -> ${0}" >> %(shellfile)s
''' % locals()
# restrict virtual memory
# Note that there are resources in SGE which could do this directly
# such as v_hmem.
# Note that limiting resident set sizes (RSS) with ulimit is not
# possible in newer kernels.
script += "ulimit -v %i\n" % IOTools.human2bytes(job_memory)
script += expandStatement(statement,
ignore_pipe_errors=ignore_pipe_errors)
script += "\n"
job_path = getTempFilename(dir=PARAMS["workingdir"])
with open(job_path, "w") as script_file:
script_file.write(script)
return (job_path)
def buildJobScript(statement, job_memory, job_name):
'''build job script from statement.
returns (name_of_script, stdout_path, stderr_path)
'''
tmpfile = getTempFile(dir=PARAMS["workingdir"])
# disabled: -l -O expand_aliases\n" )
tmpfile.write("#!/bin/bash\n")
tmpfile.write(
'echo "%s : START -> %s" >> %s\n' %
(job_name, tmpfile.name, shellfile))
# disabled - problems with quoting
# tmpfile.write( '''echo 'statement=%s' >> %s\n''' %
# (shellquote(statement), shellfile) )
tmpfile.write("set | sed 's/^/%s : /' &>> %s\n" %
(job_name, shellfile))
# module list outputs to stderr, so merge stderr and stdout
tmpfile.write("module list 2>&1 | sed 's/^/%s: /' &>> %s\n" %
(job_name, shellfile))
tmpfile.write("hostname | sed 's/^/%s: /' &>> %s\n" %
(job_name, shellfile))
tmpfile.write("cat /proc/meminfo | sed 's/^/%s: /' &>> %s\n" %
(job_name, shellfile))
tmpfile.write(
'echo "%s : END -> %s" >> %s\n' %
(job_name, tmpfile.name, shellfile))
# restrict virtual memory
# Note that there are resources in SGE which could do this directly
# such as v_hmem.
# Note that limiting resident set sizes (RSS) with ulimit is not
# possible in newer kernels.
tmpfile.write("ulimit -v %i\n" % IOTools.human2bytes(job_memory))
tmpfile.write(
expandStatement(
statement,
ignore_pipe_errors=ignore_pipe_errors) + "\n")
tmpfile.close()
job_path = os.path.abspath(tmpfile.name)
stdout_path = job_path + ".stdout"
stderr_path = job_path + ".stderr"
os.chmod(job_path, stat.S_IRWXG | stat.S_IRWXU)
return (job_path, stdout_path, stderr_path)
