A-Cluster: Unterschied zwischen den Versionen

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(GROMACS: Ana's example)
(Queueing system: Slurm: doc-Links, squeue-alias, GPUs, bash auf Knoten)
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= Queueing system: [https://slurm.schedmd.com/documentation.html Slurm] =
 
= Queueing system: [https://slurm.schedmd.com/documentation.html Slurm] =
  
* <code>sinfo</code> displays the cluster's total load.
+
* <code>[https://slurm.schedmd.com/sinfo.html sinfo]</code> displays the cluster's total load.
* <code>squeue</code> shows running jobs.
+
* <code>[https://slurm.schedmd.com/squeue.html squeue]</code> shows running jobs. You can modify its output via the option <code>-o</code>. To make that permanent put something like <code>alias squeue='squeue -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R %C %o"'</code> into your <code>.bashrc</code>.
 
* Currently, there's just one ''partiton'': "a-cluster"
 
* Currently, there's just one ''partiton'': "a-cluster"
* In the most simple cases, jobs are submitted via <code>sbatch -n</code> ''n'' ''script-name''. The number ''n'' of CPUs is available within the script as <code>$SLURM_NTASKS</code>. It's not necessary to pass it on to <code>mpirun</code>, since the latter evaluates it on its own, anyway.
+
* In the most simple cases, jobs are submitted via <code>[https://slurm.schedmd.com/sbatch.html sbatch] -n</code> ''n'' ''script-name''. The number ''n'' of CPUs is available within the script as <code>$SLURM_NTASKS</code>. It's not necessary to pass it on to <code>mpirun</code>, since the latter evaluates it on its own, anyway.
 +
* To allocate GPUs as well, add <code>-G </code>''n'' or <code>--gpus=</code>''n'' with ''n'' ∈ {1,2}. You can specify the type as well by prepending <code>rtx2080:</code> or <code>rtx3090:</code> to ''n''.
 
* Don't use background jobs (<code>&</code>), unless you <code>wait</code> for them before the end of the script.
 
* Don't use background jobs (<code>&</code>), unless you <code>wait</code> for them before the end of the script.
* <code>srun</code> is intended for interactive jobs (stdin+stdout+stderr stay attached to the terminal) and its <code>-n</code> doesn't only reserve ''n'' cores but starts ''n'' jobs. (Those shouldn't contain <code>mpirun</code>, otherwise you'd end up with ''n''² busy cores.)
+
* <code>[https://slurm.schedmd.com/srun.html srun]</code> is intended for interactive jobs (stdin+stdout+stderr stay attached to the terminal) and its <code>-n</code> doesn't only reserve ''n'' cores but starts ''n'' jobs. (Those shouldn't contain <code>mpirun</code>, otherwise you'd end up with ''n''² busy cores.)
 +
* For an interactive shell with ''n'' reserved cores on a compute node: <code>srun --pty -c</code>''n''<code> bash</code>
 
* The assignment of cores can be non-trivial (cf. also [[Slurm/Task-Affinity|task affinity]]), some rules:
 
* The assignment of cores can be non-trivial (cf. also [[Slurm/Task-Affinity|task affinity]]), some rules:
 
** gromacs: '''Don't''' use its <code>-pin</code> options.
 
** gromacs: '''Don't''' use its <code>-pin</code> options.

Version vom 9. Dezember 2021, 15:48 Uhr

Linux cluster with currently 13 compute nodes (CPUs: 416 cores, GPUs: 8x RTX 2080 + 18x RTX 3090), purchased by Ana Vila Verde and Christopher Stein

Login

External Hostname is a-cluster.physik.uni-due.de (134.91.59.16), internal hostname is stor2.

Queueing system: Slurm

  • sinfo displays the cluster's total load.
  • squeue shows running jobs. You can modify its output via the option -o. To make that permanent put something like alias squeue='squeue -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R %C %o"' into your .bashrc.
  • Currently, there's just one partiton: "a-cluster"
  • In the most simple cases, jobs are submitted via sbatch -n n script-name. The number n of CPUs is available within the script as $SLURM_NTASKS. It's not necessary to pass it on to mpirun, since the latter evaluates it on its own, anyway.
  • To allocate GPUs as well, add -G n or --gpus=n with n ∈ {1,2}. You can specify the type as well by prepending rtx2080: or rtx3090: to n.
  • Don't use background jobs (&), unless you wait for them before the end of the script.
  • srun is intended for interactive jobs (stdin+stdout+stderr stay attached to the terminal) and its -n doesn't only reserve n cores but starts n jobs. (Those shouldn't contain mpirun, otherwise you'd end up with n² busy cores.)
  • For an interactive shell with n reserved cores on a compute node: srun --pty -cn bash
  • The assignment of cores can be non-trivial (cf. also task affinity), some rules:
    • gromacs: Don't use its -pin options.

Simulation Software

... installed (on the compute nodes)

The module system is not involved. Instead, scripts provided by the software set the environment.

AMBER

  • /usr/local/amber18
  • /usr/local/amber20 (provides parmed as well)

Script to source therein (assuming bash): amber.sh

GROMACS

(not all tested)

  • /usr/local/gromacs-2018.3
  • /usr/local/gromacs-2020.4
  • /usr/local/gromacs-3.3.4
  • /usr/local/gromacs-4.6.4
  • /usr/local/gromacs-5.0.1
  • /usr/local/gromacs-5.1.1

Script to source therein (assuming bash): bin/GMXRC.bash

Ana provided an example script to be submitted via sbatch.

Intel Compiler & Co.

  • is located in /opt/intel/oneapi
  • must be made available via module use /opt/intel/oneapi/modulefiles (unless you include /opt/intel/oneapi/modulefiles in your MODULEPATH), then module avail lists the available modules.