def __init__(self,
filename,
command,
job_name=None,
queue='fast',
walltime=None, # e.g. '24:00:00'
nodes=1,
ppn=1,
setups=None,
no_redirect=False):
filename = expand_path(filename)
self.filename = filename
pbslog=filename+'.pbslog'
logf = filename+'.log'
# don't put job name there at all if not sent
if job_name is not None:
jobstring = "#PBS -N %s" % job_name
else:
jobstring=""
if walltime is not None:
timestring = '#PBS -l walltime=' % walltime
else:
timestring = ''
if setups is not None:
if not isstring(setups):
setups = '\n'.join(setups)
else:
setups=""
script="""# vim: set ft=sh :
#PBS -S /bin/bash
#PBS -l nodes={nodes}:ppn={ppn}
#PBS -q {queue}
#PBS -j oe
#PBS -o {pbslog}
#PBS -m a
#PBS -V
#PBS -r n
#PBS -W umask=0022
{timestring}
{jobstring}
{setups}
logf="{logf}"
{command}"""
if not no_redirect:
command += ''' &> "$logf"'''
script += "\n"
script=script.format(nodes=nodes,
ppn=ppn,
queue=queue,
pbslog=pbslog,
timestring=timestring,
jobstring=jobstring,
setups=setups,
logf=logf,
command=command)
self.script=script
def __init__(self,
filename,
commands,
job_name=None,
queue='fast',
walltime=None, # e.g. '24:00:00',
nodes=1,
ppn=1,
setups=None,
buffer=False):
filename = expand_path(filename)
self.filename = filename
pbslog=filename+'.pbslog'
logf = filename+'.log'
# don't put job name there at all if not sent
if job_name is not None:
jobstring = "#PBS -N %s" % job_name
else:
jobstring=""
if walltime is not None:
timestring = '#PBS -l walltime=' % walltime
else:
timestring = ''
if setups is not None:
if not isstring(setups):
setups = '\n'.join(setups)
else:
setups=""
# now the python commands
if isinstance(commands, basestring):
commands = [commands]
commands = [c.strip() for c in commands]
commands = '\n'.join(commands)
if buffer:
ex='python'
else:
ex='python -u'
self.script="""
#PBS -S /bin/bash
#PBS -l nodes={nodes}:ppn={ppn}
#PBS -q {queue}
#PBS -j oe
#PBS -o {pbslog}
#PBS -m a
#PBS -V
#PBS -r n
#PBS -W umask=0022
{timestring}
{jobstring}
{setups}
logf="{logf}"
{ex} &> "$logf" <<EOF
{commands}
EOF
\n""".format(nodes=nodes,
ppn=ppn,
queue=queue,
pbslog=pbslog,
timestring=timestring,
jobstring=jobstring,
setups=setups,
logf=logf,
ex=ex,
commands=commands)
