Version vom 14. Oktober 2021, 12:51 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.

sinfo displays the cluster's total load.
squeue shows running jobs.
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.
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.)
The assignment of cores can be non-trivial (cf. also task affinity), some rules:
- gromacs: Don't use its -pin options.

... installed (on the compute nodes)

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

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

(not all tested)

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

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.

@@ Zeile 3: / Zeile 3: @@
 = Login =
-External address is 134.91.59.31 (will change soon and then get a hostname), internal hostname is <code>stor2</code>.
+External Hostname is <code>a-cluster.physik.uni-due.de</code> (134.91.59.16), internal hostname is <code>stor2</code>.
 = Queueing system: [https://slurm.schedmd.com/documentation.html Slurm] =