From cf7b68b86e723294e933afe9bb76967cfb563fee Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Tue, 20 Jul 2021 14:37:58 +0100
Subject: [PATCH] Different sbatch options for finalize job
---
src/xfel_calibrate/calibrate.py | 18 ++++++++++++------
src/xfel_calibrate/settings.py | 3 +++
2 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/src/xfel_calibrate/calibrate.py b/src/xfel_calibrate/calibrate.py
index 2f9d86203..b20a40220 100755
--- a/src/xfel_calibrate/calibrate.py
+++ b/src/xfel_calibrate/calibrate.py
@@ -28,6 +28,7 @@ from .finalize import tex_escape
from .notebooks import notebooks
from .settings import (
default_report_path,
+ finalize_time_limit,
free_nodes_cmd,
launcher_command,
max_reserved,
@@ -621,15 +622,21 @@ def create_finalize_script(fmt_args, temp_path, job_list) -> str:
return f_name
-def run_finalize(fmt_args, temp_path, job_list, args, sequential=False):
+def run_finalize(fmt_args, temp_path, job_list, sequential=False):
finalize_script = create_finalize_script(fmt_args, temp_path, job_list)
cmd = []
if not sequential:
- cmd = get_launcher_command(args, temp_path)
- cmd.append(
- "--dependency=afterany:" + ":".join(str(j) for j in job_list)
- )
+ cmd = [
+ 'sbatch',
+ '--parsable',
+ '--requeue',
+ '--output', f'{temp_path}/slurm-%j.out',
+ '--job-name', 'xfel-cal-finalize',
+ '--time', finalize_time_limit,
+ '--partition', 'exfel',
+ "--dependency=afterany:" + ":".join(str(j) for j in job_list),
+ ]
print(" ".join(cmd))
cmd += [
@@ -1107,7 +1114,6 @@ def run():
fmt_args=fmt_args,
temp_path=run_tmp_path,
job_list=joblist,
- args=args,
sequential=sequential,
))
diff --git a/src/xfel_calibrate/settings.py b/src/xfel_calibrate/settings.py
index 0697bb580..989cd1022 100644
--- a/src/xfel_calibrate/settings.py
+++ b/src/xfel_calibrate/settings.py
@@ -26,3 +26,6 @@ max_reserved = 8
# is giving xcal priority by default.
reservation = ""
reservation_char = "darks"
+
+# Time limit for the finalize job (creates PDF report & moves files)
+finalize_time_limit = "30:00"
--
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