def setUp(self):
temp_output_filename = self.temp_output_filename = os.path.realpath('.') + '/temp.out'
self.pbs_script_filename = os.path.realpath('.') + '/test.pbs'
dump_to_file(self.pbs_script_filename,
pbs.generic_script("""
echo "Hello, World!" > %(temp_output_filename)s
sleep 1
""" % locals()))
def run_command_here(script_file_name, command, input_file_name=None, output_file_name=None, err_output_file_name=None, job_name='submit_command',
verbose=True, numcpu=None, mem=None, pmem=None, time=False, numnodes=None, queue=None, walltime=None,
disable_mpi=False):
"""Create a pbs script executing the given in the cwd command with given stdin and stderr/out files."""
pwd = os.getcwd()
if input_file_name:
redirect_input = '< %s ' % input_file_name
else:
redirect_input = ''
if time:
command = 'time ' + command
output_file_name = output_file_name or '/dev/null'
if err_output_file_name is None:
if output_file_name is not None:
err_output_file_name = output_file_name + '.err'
else:
err_output_file_name = '/dev/null'
if verbose:
processor_verbose = """echo --------------------------------------
echo + Running on host `hostname`
echo + Time is `date`
[ ${PBS_NODEFILE:-nonode} != "nonode" ] && echo + This job runs on the following processors: `cat ${PBS_NODEFILE}`
echo --------------------------------------
""" % locals()
else:
processor_verbose = ""
additional_configuration_lines = []
additional_configuration = '\n'.join(additional_configuration_lines)
if disable_mpi:
module_file = disable_mpi_module.__file__
if module_file[-1] == 'c':
module_file = module_file[:-1]
disable_mpi = 'python ' + module_file
else:
disable_mpi = ''
with open(script_file_name, 'w') as script_file:
script = pbs.generic_script("""
working_directory=%(pwd)s
if [ ! -d ${working_directory} ]; then
echo "Can not execute, working directory does not exist: ${working_directory}"
exit 1
fi
cd ${working_directory}
%(processor_verbose)s
%(disable_mpi)s
%(command)s %(redirect_input)s
""" % locals(),
numnodes=numnodes,
numcpu=numcpu,
queue=queue,
walltime=walltime,
mem=mem, pmem=pmem,
job_name=job_name)
script_file.write(script)
