From 5b0304f0b5309ba74bdf4c1bba38c64cc25ce2e9 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Thu, 10 Sep 2020 10:46:49 +0100
Subject: [PATCH] Finalize script in Python
---
bin/slurm_calibrate.sh | 2 +-
xfel_calibrate/calibrate.py | 16 +++++++---------
2 files changed, 8 insertions(+), 10 deletions(-)
diff --git a/bin/slurm_calibrate.sh b/bin/slurm_calibrate.sh
index 12f574071..80d84603d 100755
--- a/bin/slurm_calibrate.sh
+++ b/bin/slurm_calibrate.sh
@@ -59,6 +59,6 @@ fi
if [ "${final}" == "FINAL" ]
then
- XFEL_CALIBRATE_PYTHON="${python_path}" ${finalize} $SLURM_JOB_ID
+ ${python_path} ${finalize} $SLURM_JOB_ID
fi
killall -9 cal_influx_feeder.sh || true
diff --git a/xfel_calibrate/calibrate.py b/xfel_calibrate/calibrate.py
index ad56618c7..a3395d75c 100755
--- a/xfel_calibrate/calibrate.py
+++ b/xfel_calibrate/calibrate.py
@@ -500,17 +500,15 @@ def create_finalize_script(fmt_args, temp_path, job_list):
"""
Create a finalize script to produce output report
:param fmt_args: Dictionary of fmt arguments
- :param temp_path: Path to temopary folder to run slurm job
+ :param temp_path: Path to temporary folder to run slurm job
:param job_list: List of slurm jobs
"""
tmpl = Template('''
- #!/bin/tcsh
- source /etc/profile.d/modules.sh
- module load texlive/2019
- echo 'Running finalize script'
- "${XFEL_CALIBRATE_PYTHON}" -c "from xfel_calibrate.finalize import finalize;
+ import sys
+ from xfel_calibrate.finalize import finalize
+
finalize(joblist={{joblist}},
- finaljob=$1,
+ finaljob=sys.argv[1],
run_path='{{run_path}}',
out_path='{{out_path}}',
project='{{project}}',
@@ -525,7 +523,7 @@ def create_finalize_script(fmt_args, temp_path, job_list):
''')
fmt_args['joblist'] = job_list
- f_name = os.path.join(temp_path, "finalize.sh")
+ f_name = os.path.join(temp_path, "finalize.py")
with open(f_name, "w") as finfile:
finfile.write(textwrap.dedent(tmpl.render(**fmt_args)))
@@ -658,7 +656,7 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
'"{}"'.format(args["detector"].upper()),
'"{}"'.format(args["type"].upper()),
"FINAL" if final_job else "NONFINAL",
- ". {}/finalize.sh".format(os.path.abspath(temp_path)),
+ "{}/finalize.py".format(os.path.abspath(temp_path)),
str(cluster_cores)]
output = check_output(srun_base).decode('utf8')
--
GitLab