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

There are two queues (partitions in Slurm terminology) named:
- CPUs being the default
- GPUs to be selected via -p GPUs for jobs which involve a GPU
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.
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.

... 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

Ana provided an example script to be submitted via sbatch.

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.