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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).

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

Infiniband and file system performance

We found that the infiniband connections are not always stable, and may be underperforming. Similarly, the GPFS file systems (home, project and scratch) are not performing as expected. Reading/writing large files performs as expected, but reading/writing many small files is slower than expected. Among other things, this can affect the time it takes to start a binary, run commands, etc.

We are looking into both issues. 

Allocating multiple GPU nodes

Normally, batch scripts like

#!/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.

#!/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.


myquota command not available

The myquota command, used to check the disk quota on the system, is not available on Snellius at the moment. We are currently working to port it to the new system. 

Missing software packages

A number of software packages of the 2021 environment and system tools, are still being installed and it might take a few days to become available (status as of 28/10/21):

  • 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
  • PyTorch-1.9.0
  • RELION-3.1.0
  • RStudio-Server-1.4.1717
  • swak4foam
  • Trilinos-13.0.1
  • TurboVNC-2.2.6
  • VirtualGL-2.6.90
  • ncview-2.1.7
  • gedit
  • nedit
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