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torque_slurm_scripts [2020/01/29 19:13] – roottorque_slurm_scripts [2025/10/15 19:51] (current) – external edit 127.0.0.1
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-====PBS and Slurm Commands and Scripts==== +====Slurm Commands and Scripts==== 
-Basic torque/slurm commands are:+Basic slurm commands are:
 <csv> <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> </csv>
  
-A basic script in ''torque'' and ''slurm'' looks like: +A basic script in ''slurm'' looks like:
-<code> +
-#PBS -N mpi +
-#PBS -j oe +
-#PBS -o zzz.$PBS_JOBID +
-#PBS -l nodes=2:ppn=32,walltime=06:00:00 +
-#PBS -q q06h32c +
-cd $PBS_O_WORKDIR +
-NP=$(wc<$PBS_NODEFILE) +
-module purge +
-module load intel/18.0.1 impi/18.0.1 mkl/18.0.1 +
-mpirun -np $NP -machinefile $PBS_NODEFILE ./mympiexe -inputfile MA4um.mph -outputfile MA4um-output.mph +
-</code>+
  
 <code> <code>
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 mpirun -np $SLURM_NTASKS -machinefile /scratch/${SLURM_JOB_ID}/machinefile_${SLURM_JOB_ID} ./mympiexe -inputfile MA4um.mph -outputfile MA4um-output.mph mpirun -np $SLURM_NTASKS -machinefile /scratch/${SLURM_JOB_ID}/machinefile_${SLURM_JOB_ID} ./mympiexe -inputfile MA4um.mph -outputfile MA4um-output.mph
 </code> </code>
 +
 and a more complex script with file moving looks like: and a more complex script with file moving looks like:
-<code> + 
-#PBS -N espresso +
-#PBS -j oe +
-#PBS -o zzz.$PBS_JOBID +
-#PBS -l nodes=4:ppn=32,walltime=00:00:10 +
-#PBS -q q06h32c +
-module purge +
-module load intel/14.0.3 mkl/14.0.3 fftw/3.3.6 impi/5.1.2 +
-cd $PBS_O_WORKDIR +
-cp *.in *UPF /scratch/$PBS_JOBID +
-cd /scratch/$PBS_JOBID +
-sort -u $PBS_NODEFILE >hostfile +
-mpirun -ppn 16 -hostfile hostfile -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 +
-mv ausurf.log *mix* *wfc* *igk* $PBS_O_WORKDIR/ +
-</code>+
 <code> <code>
 #!/bin/bash #!/bin/bash
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 See also [ https://hprc.tamu.edu/wiki/TAMU_Supercomputing_Facility:HPRC:Batch_Translation ] [ https://slurm.schedmd.com/rosetta.pdf ] [ https://www.sdsc.edu/~hocks/FG/PBS.slurm.html ] See also [ https://hprc.tamu.edu/wiki/TAMU_Supercomputing_Facility:HPRC:Batch_Translation ] [ https://slurm.schedmd.com/rosetta.pdf ] [ https://www.sdsc.edu/~hocks/FG/PBS.slurm.html ]
  
-We have a conversion script **/share/apps/bin/pbs2slurm.sh** which should do 95% of the script conversion. Please report errors by the script so we can improve it. Normally it should be in your path and+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> <code>
 pbs2slurm.sh <pbs-script-name> pbs2slurm.sh <pbs-script-name>
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 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\\ 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 does not autogenerate an MPI machinefile/hostfile, so we makek+Slurm does not autogenerate an MPI machinefile/hostfile, so the job creates
 <code>/scratch/${SLURM_JOB_ID}/machinefile_${SLURM_JOB_ID}</code> <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. 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 ''$SLURM_NTASKS'', good for most MPI jobs.+Slurm does define a variable with the total number of cores ''$SLURM_NTASKS'', good for most MPI jobs that use every core.
  
torque_slurm_scripts.1580325225.txt.gz · Last modified: (external edit)