{"id":523,"date":"2018-06-19T11:05:32","date_gmt":"2018-06-19T10:05:32","guid":{"rendered":"https:\/\/portal.supercomputing.wales\/?page_id=523"},"modified":"2018-06-19T11:09:20","modified_gmt":"2018-06-19T10:09:20","slug":"pbs-pro-to-slurm-very-quick-reference","status":"publish","type":"page","link":"https:\/\/portal.supercomputing.wales\/index.php\/index\/slurm\/pbs-pro-to-slurm-very-quick-reference\/","title":{"rendered":"PBS Pro to Slurm Very Quick Reference"},"content":{"rendered":"

Commands<\/h3>\n\n\n\n\n\t\n\n\t\n\t\n\t\n\t\n\t\n\t\n\t
PBS<\/th>Slurm<\/th>Description<\/th>\n<\/tr>\n<\/thead>\n
qsub script_file<\/td>sbatch script_file<\/td>Submit a job from script_file<\/td>\n<\/tr>\n
qsub -I<\/td>salloc [options]<\/td>Request an interactive job<\/td>\n<\/tr>\n
qdel 123<\/td>scancel 123<\/td>Cancel job 123<\/td>\n<\/tr>\n
qstat -u [username]<\/td>squeue<\/td>List user's pending and running jobs<\/td>\n<\/tr>\n
qstat -f 123
\n
\nqstat -fx 123<\/td>		scontrol show job 123<\/td>Show job details
\n
\n-x in PBS to show finished job<\/td>\n<\/tr>\n
qstat queue_name<\/td>sinfo
\n
\nsinfo -s<\/td>		Cluster status with partition (queue) list
\n
\nWith '-s' a summarised partition list, which is shorter and simpler to interpret. <\/td>\n<\/tr>\n
<\/td><\/td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n

Job Specification<\/h3>\n\n\n\n\n\t\n\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t
PBS<\/th>Slurm<\/th>Description<\/th>\n<\/tr>\n<\/thead>\n
#QSUB<\/td>#SBATCH<\/td>Scheduler directive<\/td>\n<\/tr>\n
-q queue_name<\/td>-p queue_name<\/td>Queue to 'queue_name'<\/td>\n<\/tr>\n
-l select=4:ncpus=16
\n
\n(request 4 nodes and request that each node has the property of 16 cpus)<\/td>		-n 64<\/td>Processor count of 64<\/td>\n<\/tr>\n
-l walltime=h:mm:ss<\/td>-t [minutes]
\nor
\n-t [days-hh:mm:ss]<\/td>		Max wall run time<\/td>\n<\/tr>\n
-o file_name<\/td>-o file_name<\/td>STDOUT output file<\/td>\n<\/tr>\n
-e file_name<\/td>-e file_name<\/td>STDERR output file<\/td>\n<\/tr>\n
-N job_name<\/td>--job-name=job_name<\/td>Job name<\/td>\n<\/tr>\n
-l place=excl<\/td>--exclusive<\/td>Exclusive node usage for this job - i.e. no other jobs on same nodes<\/td>\n<\/tr>\n
-l mem=1gb<\/td>--mem-per-cpu=128M
\nor
\n--mem-per-cpu=1G<\/td>		Memory requirement<\/td>\n<\/tr>\n
-l nodes=x:ppn=16<\/td>--tasks-per-node=16<\/td>Processes per node<\/td>\n<\/tr>\n
-P proj_code<\/td>--account=proj_code<\/td>Project account to charge job to<\/td>\n<\/tr>\n
-t 1-10<\/td>--array=array_spec<\/td>Job array declaration<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n

Job Environment Variables<\/h3>\n\n\n\n\n\t\n\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t
PBS<\/th>Slurm<\/th>Description<\/th>\n<\/tr>\n<\/thead>\n
$PBS_JOBID<\/td>$SLURM_JOBID<\/td>Job ID<\/td>\n<\/tr>\n
$PBS_O_WORKDIR<\/td>$SLURM_SUBMIT_DIR<\/td>Submit directory<\/td>\n<\/tr>\n
<\/td>$SLURM_ARRAY_JOB_ID<\/td>Job Array Parent<\/td>\n<\/tr>\n
$PBS_ARRAYID<\/td>$SLURM_ARRAY_TASK_ID<\/td>Job Array Index<\/td>\n<\/tr>\n
$PBS_O_HOST<\/td>$SLURM_SUBMIT_HOST<\/td>Submission Host<\/td>\n<\/tr>\n
$PBS_NODEFILE<\/td>$SLURM_JOB_NODELIST<\/td>Allocated compute nodes<\/td>\n<\/tr>\n
<\/td>$SLURM_NTASKS
\n(mpirun can automatically pick this up from Slurm, it does not need to be specified)<\/td>		Number of processors allocated<\/td>\n<\/tr>\n
$PBS_QUEUE<\/td>$SLURM_JOB_PARTITION<\/td>Queue job is running in<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n

 <\/p>\n

Much more detail available in the Slurm documentation.<\/p>\n","protected":false},"excerpt":{"rendered":"

Commands Job Specification Job Environment Variables   Much more detail available in the Slurm documentation.<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":33,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-nosidebar.php","meta":{"_lmt_disableupdate":"","_lmt_disable":"","footnotes":""},"class_list":["post-523","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/portal.supercomputing.wales\/index.php\/wp-json\/wp\/v2\/pages\/523","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/portal.supercomputing.wales\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/portal.supercomputing.wales\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/portal.supercomputing.wales\/index.php\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/portal.supercomputing.wales\/index.php\/wp-json\/wp\/v2\/comments?post=523"}],"version-history":[{"count":3,"href":"https:\/\/portal.supercomputing.wales\/index.php\/wp-json\/wp\/v2\/pages\/523\/revisions"}],"predecessor-version":[{"id":527,"href":"https:\/\/portal.supercomputing.wales\/index.php\/wp-json\/wp\/v2\/pages\/523\/revisions\/527"}],"up":[{"embeddable":true,"href":"https:\/\/portal.supercomputing.wales\/index.php\/wp-json\/wp\/v2\/pages\/33"}],"wp:attachment":[{"href":"https:\/\/portal.supercomputing.wales\/index.php\/wp-json\/wp\/v2\/media?parent=523"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}