def submit_single(self, group_name):
cmd = """#!/bin/bash
#SBATCH --job-name={job_name}
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=5000
#SBATCH --output={log}/{group_name}.log
#SBATCH --error={err}/{group_name}.log
#SBATCH --account=pi-lgrandi
#SBATCH --partition={partition}
#SBATCH --qos={qos}
export PATH=/project/lgrandi/anaconda3/bin:$PATH
export PROCESSING_DIR={tmp}
cd {cwd}
source activate {conda_env}
python {script} {indir} {outdir} {log}/{group_name}_id_list.txt
rm -rf ${{PROCESSING_DIR}}
"""
y = cmd.format(
job_name='submit{:02}'.format(self.id),
group_name=group_name,
log=os.path.join(self.log),
err=os.path.join(self.log),
tmp=os.path.join(os.getcwd(), 'tmp'),
cwd=os.getcwd(),
partition=self.config['MIDWAYSUBMIT']['partition'],
qos=self.config['MIDWAYSUBMIT']['qos'],
conda_env=self.config['BASICS']['conda_env'],
indir=self.config['PROCESSING']['input'],
outdir=os.path.join(self.head_directory,
self.config['BASICS']['name']),
script=self.config['MIDWAYSUBMIT']['script'],
)
submit_job(y)
self.y = y
self.id += 1
'commissioning',
'pmttrip','trip','_pmttrip',
'source_opening',
],
)
datasets= hax.cuts.selection(datasets, datasets['source__type']=='none', 'Source in place')
datasets= hax.cuts.selection(datasets, datasets['location'] != '', 'Processed data available')
run_numbers = datasets['number'].values
dataset_names = datasets['name']
print('Total of %d datasets' % len(run_numbers))
def check_queue():
command='squeue -u jpienaar --partition=%s| wc -l' %queue_name
var=subprocess.Popen(command, stdout=subprocess.PIPE, shell=True)
(var, err)=var.communicate()
var=int(str(var, 'utf-8'))
return var
#For every run, make and submit the script
for dataset in dataset_names[8000::]:# in run_numbers[:1]:
while check_queue()>30:
print("Jobs in queue: ", check_queue())
time.sleep(60)
y = x.format(run=dataset, queue=queue_name)
submit_job(y)
# Check your jobs with: 'squeue -u <username>'
# Check number of submitted jobs with 'squeue -u <username> | wc -l' (is off by +2 btw)