From 0ff9f81cb1b5c3f9dab61b281a3bbabc91a90400 Mon Sep 17 00:00:00 2001
From: Cristian Lalescu <Cristian.Lalescu@ds.mpg.de>
Date: Wed, 19 Sep 2018 16:25:23 +0200
Subject: [PATCH] fix job script for SGE
I messed up the nprocesses/nthreads parameter
---
bfps/_code.py | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/bfps/_code.py b/bfps/_code.py
index fe7c35ab..fed603e3 100644
--- a/bfps/_code.py
+++ b/bfps/_code.py
@@ -271,7 +271,7 @@ class _code(_base):
qsub_script_name = 'run_' + suffix + '.sh'
self.write_sge_file(
file_name = os.path.join(self.work_dir, qsub_script_name),
- nprocesses = nb_processes*nb_threads_per_process,
+ nprocesses = nb_processes,
name_of_run = suffix,
command_atoms = command_atoms[5:],
hours = hours,
@@ -590,14 +590,15 @@ class _code(_base):
envprocs))
script_file.write('echo "got $NSLOTS slots."\n')
script_file.write('echo "Start time is `date`"\n')
- script_file.write('mpiexec -machinefile $TMPDIR/machines ' +
- '-genv OMP_NUM_THREADS={0} '.format(nb_threads_per_process) +
- '-genv OMP_PLACES=cores ' +
- '-genv LD_LIBRARY_PATH ' +
- '"' +
+ script_file.write('mpiexec \\\n' +
+ '\t-machinefile $TMPDIR/machines \\\n' +
+ '\t-genv OMP_NUM_THREADS={0} \\\n'.format(nb_threads_per_process) +
+ '\t-genv OMP_PLACES=cores \\\n' +
+ '\t-genv LD_LIBRARY_PATH \\\n' +
+ '\t"' +
':'.join([bfps.lib_dir] + bfps.install_info['library_dirs']) +
- '" ' +
- '-n {0} {1}\n'.format(nprocesses, ' '.join(command_atoms)))
+ '" \\\n' +
+ '\t-n {0} \\\n\t{1}\n'.format(nprocesses, ' '.join(command_atoms)))
script_file.write('echo "End time is `date`"\n')
script_file.write('exit 0\n')
script_file.close()
--
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