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KU Community Cluster Operating System Upgrade

Date of Upgrade

Starting at 8:00 AM CST on January 15, 2025 and ending on 8:00 AM CST January 17, 2025, CRC will be upgrading the OS on the KU Community Cluster from CentOS 7 to Rocky 9.

This upgrade will involve updating the Operating System as well as the software packages made available to users. Previously compiled software will most likely not work on the new OS, and will need to be recompiled.

Minor or no changes

  • All user files will remain unchanged
  • Scheduler, partitions, time limits will stay the same
  • The majority of software modules previously available will remain available, sometimes with version changes

Signficant changes

  • Anaconda introduced licensing restrictions to their conda repo.
    • We have migrated our conda to miniforge which uses the conda-forge repo by default.
    • We recommend you reinstall any conda environments you have
  • The path /panfs/pfs.local will no longer be available. Replace with /kuhpc.
  • Significant changes to system software have occurred, the Standard Environment modules are now:
    • compiler/gcc/11.4 replaces compiler/gcc/8.3
    • openmpi/5.0 replaces openmpi/4.0
  • If you have software you compiled yourself, it will likely not not run on the new system, and will need to be recompiled
  • PGI compiler is now NVC (compiler/nvc/24). NVIDIA merged them in 2020
  • AMD CPUs and GPUs mixed into sixhour. Need to specify intel/amd or nvidia/amdgpu constraint if you wish to run on specific hardware
  • Older C6320 which have 24 cores will not have Infiniband hooked up. The ConnectX-3 card (56 Gb/s) is not supported by latest NVIDIA IB software.

Software

We installed the most used software from the KU Community Cluster. If you do not see the software that you need, please send a software request.

Anaconda License Restrictions

While Anaconda does state that the imposed licensing restrictions do not effect accredited universities, we are still taking precautions with this OS upgrade to move away from using the Anaconda channel. We suggest all users re-create their conda environments using the new conda/latest module which uses the conda-forge channel.

You should not notice any change in using the conda/latest module from the old one.

  • conda, the command, is the same
  • You can still use the bioconda channel
  • Your previous conda environments will still work with the new miniforge install, but we do recommend to recreate them