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Fixing unnecessary use of network storage to write log file data #28

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Fixing unnecessary use of network storage to write log file data #28

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2 changes: 1 addition & 1 deletion hercules/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
#container is running linux
#-> make sure it's PosixPath when run from windows
HEXBUG_DIR_CONTAINER = PosixPath('/') / 'tmp'
OUTPUT_DIR_CONTAINER = PosixPath('/') / 'home'
OUTPUT_DIR_CONTAINER = PosixPath('/') / 'home'
LOCUST_CONFIG_NAME_P2 = 'LocustPhase2Template.json'
KASS_CONFIG_NAME_P2 = 'Project8Phase2_electrons.xml'
LOCUST_CONFIG_NAME_P3 = 'LocustPhase3Template.json'
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2 changes: 1 addition & 1 deletion hercules/hexbug
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Submodule hexbug updated from 373cec to ec881e
27 changes: 21 additions & 6 deletions hercules/simulation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -342,6 +342,8 @@ def __init__(self, working_dir, direct=True):
"""

AbstractKassLocustP3.__init__(self, working_dir, direct)

self._tmp_dir = Path('/tmp', self._working_dir.parts[-1])

def __call__(self, config_list):
"""This method overrides :meth:`AbstractKassLocustP3.__call__`.
Expand Down Expand Up @@ -373,7 +375,8 @@ def _submit_job(self):
job_limit = '--max-jobs ' + CONFIG.job_limit
job_memory = '--mem-per-cpu ' + CONFIG.job_memory +'m'
job_timelimit = '-t ' + CONFIG.job_timelimit
job_status = '--status-dir ' + str(self._working_dir)
#job_status = '--status-dir ' + str(self._working_dir)
job_status = '--suppress-stats-file'
job_output = '--output /dev/null'

cmd = _char_concatenate(' ', module, dsq, job_file, job_partition,
Expand All @@ -389,6 +392,8 @@ def _add_job(self, sim_config: SimConfig):

output_dir = self._working_dir / sim_config.sim_name
output_dir.mkdir(parents=True, exist_ok=True)

tmp_output_dir = self._tmp_dir / sim_config.sim_name

locust_file = output_dir / LOCUST_CONFIG_NAME
kass_file = output_dir / KASS_CONFIG_NAME
Expand All @@ -398,33 +403,43 @@ def _add_job(self, sim_config: SimConfig):
sim_config.to_json(config_dump)

self._gen_locust_script(output_dir)
cmd = self._assemble_command(output_dir)
cmd = self._assemble_command(output_dir, tmp_output_dir)

with open(self._joblist, 'a+') as out_file:
out_file.write(cmd)

def _assemble_command(self, output_dir):
def _assemble_command(self, output_dir, tmp_output_dir):
#Assemble the singularity command that runs the KassLocust simulation
#in the p8compute singularity container

create_log_dir = f'mkdir -p {str(tmp_output_dir)}'

singularity_exec = 'singularity exec --no-home'
share_output_dir = _gen_shared_dir_string_singularity(output_dir,
OUTPUT_DIR_CONTAINER)
share_hexbug_dir = _gen_shared_dir_string_singularity(HEXBUG_DIR,
HEXBUG_DIR_CONTAINER)

container = str(self._singularity)
run_script = str(OUTPUT_DIR_CONTAINER/self._command_script_name)

log = '>' + str(output_dir) + '/run_singularity.out'
err = '2>' + str(output_dir) + '/run_singularity.err'
#log = '>' + str(output_dir) + '/run_singularity.out'
#err = '2>' + str(output_dir) + '/run_singularity.err'
log = '>' + str(tmp_output_dir) + '/run_singularity.out'
err = '2>' + str(tmp_output_dir) + '/run_singularity.err'

singularity_cmd = _char_concatenate(' ', singularity_exec, share_output_dir,
share_hexbug_dir, container,
run_script, log, err)

check_failure = "if [ $? -gt 1 ];then scontrol requeue $SLURM_JOB_ID;fi;"

mv_log_file = f"mv {str(tmp_output_dir)}/run_singularity.out {str(output_dir)}"
mv_err_file = f"mv {str(tmp_output_dir)}/run_singularity.err {str(output_dir)}"
mv_files = mv_log_file + ';' + mv_err_file

final_command = singularity_cmd + ';' + check_failure +'\n'
final_command = create_log_dir + ';' + singularity_cmd + ';' + mv_files + ';' + check_failure +'\n'
#final_command = create_log_dir + ';' + singularity_cmd + ';' + check_failure +'\n'

return final_command

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