A-Cluster
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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
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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 likealias 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 tompirun
, 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 prependingrtx2080:
orrtx3090:
to n. - Don't use background jobs (
&
), unless youwait
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 containmpirun
, otherwise you'd end up with n² busy cores.)- For an interactive shell with n reserved cores on a compute node:
srun --pty -c
nbash
- The assignment of cores can be non-trivial (cf. also task affinity), some rules:
- gromacs: Don't use its
-pin
options.
- gromacs: Don't use its
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
(providesparmed
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 yourMODULEPATH
), thenmodule avail
lists the available modules.