Differences

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--- slurm_scripts [2020/01/29 18:59] – root
+++ slurm_scripts [2025/10/15 19:51] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====Slurm Commands and Scripts====
-Basic torque/slurm commands are:
+Basic slurm commands are:
 <csv>
-torque,                     slurm, use
+slurm, use
-qsub,                       sbatch         ,       submit <job file>
+sbatch         ,       submit <job file>
-qsub -I   ,                  srun            ,      submit interactive job
+srun            ,      submit interactive job
-qstat  ,                     squeue           ,     list all queued jobs
+squeue           ,     list all queued jobs
-qstat -u rfeynman  ,         squeue -u rfeynman  ,  list queued jobs for user rfeynman
+squeue -u rfeynman  ,  list queued jobs for user rfeynman
-qdel        ,                scancel       ,        cancel <job#>
+scancel       ,        cancel <job#>
-shownodes -l -n;qstat -q ,   sinfo         ,        node status;list of queues
+sinfo         ,        node status;list of queues
 </csv>
-A basic slurm script looks like:
+A Torque compatibility layer also offers some torque commands such as ''qstat'' and ''qsub''.  A basic script in ''slurm'' looks like:
 <code>
 #!/bin/bash
@@ Line 25: / Line 26: @@
 mpirun -np $SLURM_NTASKS -machinefile /scratch/${SLURM_JOB_ID}/machinefile_${SLURM_JOB_ID} ./mympiexe -inputfile MA4um.mph -outputfile MA4um-output.mph
 </code>
-and a little more complicated with file moving in and out of a scratch area:
+and a more complex script with file moving looks like:
 <code>
-pinnacle-l1:$ cat script.slurm
 #!/bin/bash
 #SBATCH --job-name=espresso
@@ Line 40: / Line 43: @@
 cp *.in *UPF /scratch/$SLURM_JOB_ID
 cd /scratch/$SLURM_JOB_ID
-mpirun -ppn 16 -hostfile /scratch/${SLURM_JOB_ID}/machinefile_${SLURM_JOB_ID} -genv OMP_NUM_THREADS 4 -genv MKL_NUM_THREADS 4 /share/apps/espresso/qe-6.1-intel-mkl-impi/bin/pw.x -npools 1 <ausurf.in
+mpirun -ppn 16 -hostfile /scratch/${SLURM_JOB_ID}/machinefile_${SLURM_JOB_ID} -genv OMP_NUM_THREADS 2 \ /share/apps/espresso/qe-6.1-intel-mkl-impi/bin/pw.x -npools 1 <ausurf.in
 mv ausurf.log *mix* *wfc* *igk* $SLURM_SUBMIT_DIR/
 pinnacle-l1:$
 </code>
+See also [ https://www.marquette.edu/high-performance-computing/pbs-to-slurm.php ] [ https://hpc.nih.gov/docs/pbs2slurm.html
+ ]
+We have a conversion script **/share/apps/bin/pbs2slurm.sh** which should do 95% of the script conversion from old PBS scripts to SLURM scripts. Please report errors by the script so we can improve it. Normally it should be in your path and
+<code>
+pbs2slurm.sh <pbs-script-name>
+</code>
+will generate the conversion to stdout, thus save with
+<code>
+pbs2slurm.sh demoscriptpbs.sh > demoscriptslurm.sh
+</code>
+==Notes:==
+Leading hash-bang /bin/sh or /bin/bash or /bin/tcsh is optional in torque, required in slurm, pbs2slurm.sh inserts it if not present\\
+Slurm date formats with days are "2-00:00:00" not "2:00:00:00" like Torque.  If invalid sbatch will use the partition default and srun will kick the job back.\\
+Slurm unlike Torque does not autogenerate an MPI machinefile/hostfile, so the job creates
+<code>/scratch/${SLURM_JOB_ID}/machinefile_${SLURM_JOB_ID}</code>
+The generated machinefile differs from torque machinefile in that it has 1 entry per host instead of ''ncores'' entry per host.
+Slurm does define a variable with the total number of cores ''$SLURM_NTASKS'', good for most MPI jobs that use every core.