Topola cluster update
We are planning on updating the OS and the entire application stack of the Topola cluster in the near future. As these updates may break your existing workflows, please familiarize yourself with the information below to minimize any disruptions.
Date
The rolling updates will commence on December 18th. This means that individual compute nodes will be updated after completing jobs. From your point of view, Topola should remain available, although it is unspecified whether you will be allocated old or new nodes for the duration of the update process.
Effects
The compute node OS will be upgraded to Rocky9. The updates also affect all installed applications. Depending on your workflow, this may have different consequences:
Users exclusively using applications loaded via modules
If your workflows consist purely of loading an application module and running it with an input file, your workflow should remain unaffected. Only the version of your application may change (to a newer one). Please refer to the list of maintained applications below. If the software that you are using is missing, please let us know at pomoc@icm.edu.pl. Please also note that if the software you are using maintains some manner of cache in your home directory, you may need to refresh that cache. In particular, if you are using Conda to manage Python packages in virtual environments, you'll likely need to delete the $HOME/.conda directory and reinstall the packages.
Users building their own software
Any previously built software will cease to work and will need to be recompiled using the new compilers and libraries. Please verify that the required software has been listed below.
We are happy to announce that the new application stack has mostly been installed using Spack - the supercomputer package manager. The global Spack instance is available in /apps/spack/current. We highly recommend that you use a private spack instance and chain it against the global one. Spack greatly helps with managing the complexity of you builds. More on spack chaining: https://spack.readthedocs.io/en/latest/chain.html
List of maintained applications
abinit 10.0.9 amber-tools 24 ansys 2024.2 cp2k 2024. dalton 2020.0 dftbplus 23.1 elk 8.3.22 elpa 2023.11 fftw 3.3.10 gaussian X gcc 13.2 grads 2.2.3 hdf5 1.14 kokkos 4.2.1 libxc 6.2.2 mathematica X matlab 2024b metis 5.1.0 netlib-scalapack 2.2.0 nwchem 7.2.3 openblas 0.3.26 openjdk 11.0.20 openmpi 5.0.3 openmx 3.9 orca 5.0.3 quantum espresso 7.3.1 r 4.4.0 siesta 5.2.0 subread 2.0.6 bedtools 2.31.1 netcdf-c 4.9.2 netcdf-fortran 4.6.1 parmetis 4.0.3 samtools 1.19.2 trilinos 15.1.1 vasp X wannier90 3.1.0