A-Cluster: Unterschied zwischen den Versionen
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(→AMBER: +parmed) |
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* <code>/usr/local/amber18</code> | * <code>/usr/local/amber18</code> | ||
* <code>/usr/local/amber20</code> | * <code>/usr/local/amber20</code> (provides <code>parmed</code> as well) | ||
== GROMACS == | == GROMACS == |
Version vom 30. September 2021, 13:09 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 address is 134.91.59.31 (will change soon and then get a hostname), internal hostname is stor2
.
Queueing system: Slurm
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$SLURM_NTASKS
. It's not necessary to pass it on tompirun
, since the latter evaluates it on its own, anyway. srun
is intended for interactive jobs (stdin+stdout+stderr stay attached to the terminal) and its-n
doesn't only reserve n cores but starts n jobs. (Those shouldn't containmpirun
, otherwise you'd end up with n² busy cores.)- The assignment of cores can be non-trivial (cf. also task affinity), some rules:
- gromacs: Don't use its
-pin
options.
- gromacs: Don't use its
Simulation Software
... installed (on the compute nodes)
Since just one path has to be adjusted, the module system is not involved. Instead, activate the desired version in your job-script via:
export PATH=/usr/local/
version/bin:$PATH
AMBER
/usr/local/amber18
/usr/local/amber20
(providesparmed
as well)
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
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.