A-Cluster

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, 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.

Scientific Software

... installed (on the compute nodes)

AMBER

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

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

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

GROMACS

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

Versions (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.

OpenMolcas

(compiled with Intel compiler and MKL)

Minimal example script to be sbatched:

 #!/bin/bash
 
 export MOLCAS=/usr/local/openmolcas
 export MOLCAS_WORKDIR=/tmp/$USER-$SLURM_JOB_NAME-$SLURM_JOB_ID
 mkdir $MOLCAS_WORKDIR
 export PATH=$PATH:$MOLCAS
 export LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/mkl/latest/lib/intel64
 export OMP_NUM_THREADS=${SLURM_NTASKS:-1}
 
 pymolcas the_input.inp
 
 # Emptying/removing $MOLCAS_WORKDIR in the end is reccomended.

If you want/need to use the module system instead of setting LD_LIBRARY_PATH manually:

 shopt -s expand_aliases
 source /etc/profile.d/modules.sh
 
 module use /opt/intel/oneapi/modulefiles
 module -s load compiler/latest
 module -s load mkl/latest

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.