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Snellius Cluster Guide

Installation

  1. Connect via SSH. See instructions from SURF here.

  2. Set up your working environment. You have to load some modules and set up the environment variables prior to the installation. To facilitate this, we suggest that you copy the following lines into your ~/.bashrc file.

    module load 2024
module load MPICH/4.2.2-GCC-13.3.0
export LD_LIBRARY_PATH=""
module load netCDF-Fortran/4.6.1-gompi-2024a
export RAD_DIR="$HOME/SOCRATES/"
export FWL_DATA="$HOME/FWL_DATA/"
    You must then logout.

  3. When you login again, run module list and confirm that you have loaded the following modules.

    Currently Loaded Modules:
1) 2024                           11) libpciaccess/0.18.1-GCCcore-13.3.0  21) Szip/2.1.1-GCCcore-13.3.0
2) GCCcore/13.3.0                 12) hwloc/2.10.0-GCCcore-13.3.0         22) HDF5/1.14.5-gompi-2024a
3) zlib/1.3.1-GCCcore-13.3.0      13) OpenSSL/3                           23) cURL/8.7.1-GCCcore-13.3.0
4) binutils/2.42-GCCcore-13.3.0   14) libevent/2.1.12-GCCcore-13.3.0      24) gzip/1.13-GCCcore-13.3.0
5) GCC/13.3.0                     15) libfabric/1.21.0-GCCcore-13.3.0     25) lz4/1.9.4-GCCcore-13.3.0
6) numactl/2.0.18-GCCcore-13.3.0  16) PMIx/5.0.2-GCCcore-13.3.0           26) zstd/1.5.6-GCCcore-13.3.0
7) UCX/1.16.0-GCCcore-13.3.0      17) PRRTE/3.0.5-GCCcore-13.3.0          27) bzip2/1.0.8-GCCcore-13.3.0
8) MPICH/4.2.2-GCC-13.3.0         18) UCC/1.3.0-GCCcore-13.3.0            28) netCDF/4.9.2-gompi-2024a
9) XZ/5.4.5-GCCcore-13.3.0        19) OpenMPI/5.0.3-GCC-13.3.0            29) netCDF-Fortran/4.6.1-gompi-2024a
10) libxml2/2.12.7-GCCcore-13.3.0  20) gompi/2024a

  4. You can now follow the usual installation steps here.

Note that when logging into snellius.surf.nl, you will not always connect to the same computer. For example, sometimes your hostname might be int5 while other times it could be int6. This means that tmux sessions might suddenly appear to vanish, but in reality they are running on a different node. You can access a particular session (e.g. int5) by running ssh int5 once logged into Snellius.