comment in bash script processed by slurm
just add another # at the beginning. ##SBATCH –mail-user… This will not be processed by Slurm
hpc
mpirun – not enough slots available
Apparently oversubscribing can be attained using the “–oversubscribe” option with mpirun – did the trick for me with running torque/maui
Slurm: Why use srun inside sbatch?
The srun command is used to create job ‘steps’. First, it will bring better reporting of the resource usage ; the sstat command will provide real-time resource usage for processes that are started with srun, and each step (each call to srun) will be reported individually in the accounting. Second, it can be used to … Read more
Use slurm job id
You can do something like this: RES=$(sbatch simulation) && sbatch –dependency=afterok:${RES##* } postprocessing The RES variable will hold the result of the sbatch command, something like Submitted batch job 102045. The construct ${RES##* } isolates the last word (see more info here), in the current case the job id. The && part ensures you do … Read more
HPC cluster: select the number of CPUs and threads in SLURM sbatch
Depending on the parallelism you are using: distributed or shared memory –ntasks=# : Number of “tasks” (use with distributed parallelism). –ntasks-per-node=# : Number of “tasks” per node (use with distributed parallelism). –cpus-per-task=# : Number of CPUs allocated to each task (use with shared memory parallelism). From this question: if every node has 24 cores, is … Read more
MPICH vs OpenMPI
Purpose First, it is important to recognize how MPICH and Open-MPI are different, i.e. that they are designed to meet different needs. MPICH is supposed to be high-quality reference implementation of the latest MPI standard and the basis for derivative implementations to meet special purpose needs. Open-MPI targets the common case, both in terms of … Read more