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As Snellius is a new system and was newly installed and configured some things might not be fully working yet and are still in the process of being set up. Here, we list the issues that are known to us and that you don't have to report to the Service Desk. Of course, if you encounter issues on Snellius not listed here then please let us know (through the Service Desk). |
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Resolved issues (updated 20-10-21 11:37)
Project spaces
Project space data should be complete and writeable as of October 20, 10:30. Please check your data.
Accounting not active in October
Your jobs will not get accounted against your budget in the month of October. Starting in November accounting will be fully active.
Remote visualization
The remote visualization stack is not available yet (status as of 18/10/21):
- The
remotevis
module is not present in the 2021 environment - GPU-based accelerated rendering, e.g. in ParaView, is not available yet
Allocating multiple GPU nodes
Normally, batch scripts like
Code Block |
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#!/bin/bash
#SBATCH -p gpu
#SBATCH -n 8
#SBATCH --ntasks-per-node=4
#SBATCH --gpus=8
#SBATCH -t 20:00
#SBATCH --exclusive
module load ...
srun <my_executable> |
Should get you an allocation with 2 GPU nodes, 8 gpus, and 4 MPI tasks per node. However, right now, there is an issue related to specifying an amount of GPUs larger than 4: jobs with the above SBATCH arguments that use OpenMPI and call srun or mpirun will hang.
Instead of specifying the total number of GPUs, please specify the number of GPUs per node, combined with the number of nodes instead. E.g.
Code Block |
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#!/bin/bash
#SBATCH -p gpu
#SBATCH -N 2
#SBATCH --ntasks-per-node=4
#SBATCH --gpus-per-node=4
#SBATCH -t 20:00
#SBATCH --exclusive
module load ...
srun <my_executable> |
This will give you the desired allocation with a total of 2 GPU nodes, 8 gpus, and 4 MPI tasks per node, and the srun (or mpirun) will not hang.
Missing software packages
A number of software packages of the 2021 environment is still being installed and might take a few days to become available (status as of 21/10/21):
- BLIS-3.0
- COMSOL-5.6.0.341
- Darshan-3.3.1
- DFlowFM
- EIGENSOFT-7.2.1
- Extrae-3.8.3
- FSL-6.0.4
- LAMMPS-29Oct2020
- MotionCor2-1.4.4
- PyTorch-1.9.0
- RELION-3.1.0
- RStudio-Server-1.4.1717
- Stata-16.1-MP
- swak4foam
Stopos-0.93
- Trilinos-13.0.1
- TurboVNC-2.2.6
- VirtualGL-2.6.90
- ncview-2.1.7