2. Updates with OS changes

This page lists changes that are a result of the Operating System upgrade.

Rocky Linux 9.7 updates

Important

HPC3 operating system is Rocky Linux 9.7 (as of March 24, 2026).

All installed software is compiled specifically for this OS.

The operating system update involves many changes across the software stack. While we try to build all the previous software versions for the new OS, some builds are impossible. As a result:

For user compiled or installed software

1. If you compiled any software packages yourself using gcc, intel, openmpi modules and your compiled software no longer works as before you will have to recompile it anew.

2. Some commands, include files and libraries are available from system RPMs and do not require modules. If you compiled any software using such libraries/binaries you may need to recompile anew as many have changed.

3. User installed anaconda/miniconda/mamba environments will VERY LIKELY need to be reinstalled. In this case, please try to use the latest version of anaconda or miniconda modules that we provide. Please see Install with conda/mamba user guide that explains how to build and use conda environments on HPC3.

4. If you previously used a module that has been removed, you will need to use a newer version of it where available.

Summary of changes

Modules availability on the previous Rocky Linux 9.6 and on the current Rocky Linux 9.7 operating systems:

Total	Rocky Linux 9.6	Rocky Linux 9.7	Comment
Installed	310	360	active modules

Operating system provides default gcc and openmpi which are available via modules:

Version	Module
gcc 11.5.0	gcc/system
openmpi 4.1.1	openmpi/4.1.1/gcc.system

Software changes details

Table 2.4 Software changes

Module name	Comments
anaconda/2025.12	Added
boost/1.90.0/gcc.15.2.0	Added
clang/20.1.8	Added
cmake/4.2.3	Added
cuda/13.0.1	Added
eigen/5.0.1	Added
ffmpeg/8.0.1	Added
ffnvcodec/13.0.19.0	Added
fftw/3.3.10/gcc.15.2.0	Added
fftw/3.3.10/gcc.15.2.0-openmpi.5.0.9	Added
gcc/15.2.0	Added
gdal/3.12.1/gcc.15.2.0	Added
gdrcopy/2.5.1	Added
geos/3.14.1/gcc.15.2.0	Added
glpk/5.0/gcc.15.2.0	Added
gsl/2.8/gcc.15.2.0	Added
julia/1.12.4	Added
libgit2/1.8.5	Added
llvm/20.1.8	Added
mamba/26.1.0	Added
miniconda3/25.11.1	Added
mkl/2025.1.0	Added
OpenBLAS/0.3.31	Added
openmpi/5.0.9/gcc.15.2.0	Added
openmpi/5.0.9/gcc.15.2.0-cuda.13.0.1	Added
proj/9.7.1/gcc.15.2.0	Added
python/3.14.3	Added
qiime2/2025.10	Added
R/4.5.2	Added
sqlite3/3.51.0/gcc.15.2.0	Added
ucx/1.20.0	Added
ucx/1.20.0-cuda.13.0.1	Added