Operating System Updates¶

Overview¶

In early 2025, the Puma cluster was updated to a newer operating system called Rocky Linux 9. Ocelote has remained on the older OS called CentOS 7. Ocelote will be decommissioned on August 17^th, 2026 so it is now necessary for users to migrate their workflows to Puma to continue using HPC. Below is a summary of the main points of relevance to users:

System Software

The versions and locations of system software on Puma are different than Ocelote. Any software compiled on CentOS 7 will most likely need to be recompiled on Rocky 9 for use on Puma.

Module Availability

The module system on Puma is now distinct from Ocelote. While many modules available on the older OS are still available on Puma, some are not available at all, and some have changed version. Check available modules/versions on your cluster of choice. Significant changes include:

• The default compiler updated from GCC 8 (module gnu8) to GCC 13 (module gnu13).
• The default MPI distribution updated from OpenMPI 3 (module openmpi3) to OpenMPI 5 (module openmpi5).

Environment Compatibility

Software environments/libraries for programs like Python and R that were built on CentOS 7 may not function properly on Rocky 9. Users may need to rebuild custom environments on Puma to ensure compatibility.

Contrib Space Noninteroperable

Users who utilize the /contrib space should note that this space on Puma is now distinct from the space on Ocelote.

Adapting existing analyses.¶

Researchers may currently use cluster resources in a number of ways. Here are general guidelines for adapting to the new environment:

Users of Open OnDemand

Open OnDemand users should generally be able to continue usage unchanged. However, users of RStudio should see the R section below.

Users of software modules

Users who load analysis software with the module load command will generally be able to continue their analyses unchanged. All commonly used software modules are available on Puma, sometimes with version updates or changes.

Users of Conda environments

We recommend switching to Mamba going forward. However, many Conda users should be able to continue using their existing environments, although in some cases may need to recreate them.

Users of Python

Users who run pure Python code, with or without the use of virtual environments will likely be able to continue their analyses unchanged. The same versions of Python are available on Puma9.

Users of R

• The primary challenge for R users will be to create new libraries for the more recent operating system. R packages installed under the old CentOS 7 operating system may not function under the new Rocky 9 systems, and vice versa.
• R users should create new R libraries for Puma. See the Creating a Custom Library and Switching Between Custom Libraries sections on our R documentation page for details.

Users who compile code themselves

In many cases user-compiled software will need to be recompiled to run on Puma.

Intel compiled software¶

• On the previous system, a number of software modules were provided for use in compiling software using the Intel compiler, e.g., modules hdf5-intel, netcdf-intel, etc.
• On the new system, you should first load the Intel software module with module swap gnu13 intel. After loading the Intel module, you can load the Intel specific modules without the -intel specifier, i.e., as hdf5, netcdf, etc.