Arkansas High Performace Computing Center [hpcwiki]

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====Slurm Commands and Scripts====
Basic slurm commands are:
<csv>
slurm, use
sbatch         ,       submit <job file>
srun            ,      submit interactive job
squeue           ,     list all queued jobs
squeue -u rfeynman  ,  list queued jobs for user rfeynman
scancel       ,        cancel <job#>
sinfo         ,        node status;list of queues
</csv>

A Torque compatibility layer also offers some torque commands such as ''qstat'' and ''qsub''.  A basic script in ''slurm'' looks like:

<code>
#!/bin/bash
#SBATCH --job-name=mpi
#SBATCH --output=zzz.slurm
#SBATCH --partition comp06
#SBATCH --nodes=2
#SBATCH --tasks-per-node=32
#SBATCH --time=6:00:00
cd $SLURM_SUBMIT_DIR
module purge
module load intel/18.0.1 impi/18.0.1 mkl/18.0.1
mpirun -np $SLURM_NTASKS -machinefile /scratch/${SLURM_JOB_ID}/machinefile_${SLURM_JOB_ID} ./mympiexe -inputfile MA4um.mph -outputfile MA4um-output.mph
</code>

and a more complex script with file moving looks like:


<code>
#!/bin/bash
#SBATCH --job-name=espresso
#SBATCH --output=zzz.slurm
#SBATCH --nodes=4
#SBATCH --tasks-per-node=32
$SBATCH --time=00:00:10
#SBATCH --partition comp06
module purge
module load intel/14.0.3 mkl/14.0.3 fftw/3.3.6 impi/5.1.2
cd $SLURM_SUBMIT_DIR
cp *.in *UPF /scratch/$SLURM_JOB_ID
cd /scratch/$SLURM_JOB_ID
mpirun -ppn 16 -hostfile /scratch/${SLURM_JOB_ID}/machinefile_${SLURM_JOB_ID} -genv OMP_NUM_THREADS 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.
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