[Hpc-notice] ALL CLEAR: HPC software upgrade complete

[Casey Mc Laughlin]

Hi HPC & Spear users,

We have completed upgrading all HPC, Spear, and Login nodes to Alma8.6. We appreciate your patience during this upgrade.

Due to the large scope and the many moving parts of this project, we are still cleaning up some residual issues. Let us know<mailto:support at rcc.fsu.edu> if you experience any problems after the upgrade.

Most libraries are available, but we are working on lesser used ones. Please review the list and recommended workarounds below the signature line in this email. Our Apps specialists will be working through the list in the coming days. Please contact us<mailto:support at rcc.fsu.edu> if you need us to prioritize any package in that list.

Important notes:

  *   We upgraded the GNU GCC compiler from v8.3 to v8.5. If you use that compiler, your code will likely need to be recompiled for the new software stack. As with any software upgrade, shared libraries have changed; some have been removed in favor of newer alternatives, and some have new versions. Please let us know if you need help recompiling your code.
  *   OpenMPI is currently available only with the GNU v8.5.0 and Intel v21 compilers.
  *   We upgraded our CUDA libraries and installed both v11.8 and v12.1. Load the cuda/12.1 module to use the newer version.
  *   If you need a version of Python newer than v3.6.8, we recommend installing it in a Conda environment. You can install any version up to and including v3.12. Instructions or on our website<https://docs.rcc.fsu.edu/software/python/#using-newer-versions-of-python-on-the-hpc>.

For those of you who have outstanding software installation or upgrade requests, we appreciate your patience. In our triage process, we are prioritizing existing packages before attending to new software requests. This will be the case for the next few weeks.

If you have any questions or comments, please let us know: support at rcc.fsu.edu<mailto:support at rcc.fsu.edu>.

Best regards,
The RCC Team
________________________________

The following libraries and executables are not yet available. Please let us know<mailto:support at rcc.fsu.edu> if you need any of the following packages:

Package
Compilers
Workaround
GNU Compilers v4.8.5
-
Use 8.5.0 (default)
OpenMPI v4.1.3
All GNU and Intel
Use OpenMPI 4.1.0
MVAPICH2 v2.3.7
All GNU and Intel
Use MVAPICH2 2.3.5
NetCDF v4.7.0
All GNU and Intel
Use NetCDF 4.8.0
NetCDF-Fortran v4.4.5
All GNU and Intel
Use NetCDF-Fortran 4.5.3
RELION 3.13
GNU 8.5.0 + CUDA 11.8
Contact support at rcc.fsu.edu<mailto:support at rcc.fsu.edu>
bcl2fastq v2.20.0
GNU
Use a Conda<https://docs.rcc.fsu.edu/software/python/#using-newer-versions-of-python-on-the-hpc> environment:
conda install -c dranew bcl2fastq
blat v34
GNU
Use a Conda<https://docs.rcc.fsu.edu/software/conda/> environment:
conda install -c bioconda blat
Python >=3.6.8
-
Use a Conda<https://docs.rcc.fsu.edu/software/conda/> environment:
conda install python=3.10
HDF5 v1.12.2
All GNU and Intel
Use HDF5 1.12.0
NCL v6.6.2
Intel
Use a Conda<https://docs.rcc.fsu.edu/software/conda/> environment:
conda install -c conda-forge ncl

FreeFEM++ v4.7
GNU
Contact support at rcc.fsu.edu<mailto:support at rcc.fsu.edu>
bbftp-client v3.2.1
GNU
Contact support at rcc.fsu.edu<mailto:support at rcc.fsu.edu>

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