# -*-Python-*-
# Created by grierson at 09 Jun 2018 18:08
"""
This script submits a SLURM job
"""
if SERVER(root['SETTINGS']['REMOTE_SETUP']['serverPicker']) == 'iris':
partition = 'preemptable'
elif SERVER(root['SETTINGS']['REMOTE_SETUP']['serverPicker']) == 'portal':
partition = 'sque'
else:
printe('SLURM partition not defined for chosen server')
OMFITx.End()
# The SLURM batch submission script
slurm_script = '''#!/bin/bash
#SBATCH -J ex
#SBATCH -o batch.out
#SBATCH -e batch.err
#SBATCH -t 0:01:00
#SBATCH -n 1
#SBATCH --mem=10M
#SBATCH -p {}
sleep 3
chmod +x ex.sh
./ex.sh
exit 0
'''.format(
partition
)
# The code to run.
ex = '''
#!/bin/bash
echo 'hello world std_out'
>&2 echo 'hello world std_err'
sleep 20
pwd > pwd.txt
exit 0
'''
# Make the code we want to run an executable script in a file
ex_sh = OMFITascii('ex.sh', fromString=ex)
OMFITx.executable(
root,
inputs=[ex_sh],
outputs=['pwd.txt'],
std_out='batch.out',
std_err='batch.err',
script=(slurm_script, 'slurm_script.sh'),
executable='sbatch %s',
queued=True,
)
root['OUTPUTS'].setdefault('SLURM', OMFITtree())
# Load the output of the job into OMFIT
root['OUTPUTS']['SLURM']['pwd'] = OMFITascii('./pwd.txt')
