2. Updates with OS changes

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

Rocky Linux 9.6 updates

Important

HPC3 operating system is Rocky Linux 9.6 (as of July 29, 2025).
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:

  • Some modules were removed because they cannot be built on a new system as the underlying requirements are no longer satisfied.

  • Some modules were removed because they were unused. Where possible, a newer version is available.

For user compiled or installed software

  1. User compiled and installed software will need to be recompiled and reinstalled. 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/mamaba 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 8.10 and on the current Rocky Linux 9.6 operating systems:

Total

Rocky Linux 8.10

Rocky Linux 9.6

Comment

Installed

330

310

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 2.3 Software changes

Module name

Comments

Removed modules

bcftools/1.10.2

Cannot build, use newer version

bustools/0.40.0

Unused, use newer version

canu/2.0

Unused

charm/6.10.1/gcc.11.2.0

Unused

charm/6.10.1/gcc.11.2.0-openmpi.5.0.1

Unused

charm/7.0.0/gcc.11.2.0

Unused

cuda/10.1.243

Not supported on Rocky 9, use newer version

gatk/4.1.9.0

Security vulnerability, use newer version

gromacs/2021.2/gcc.8.4.0-cuda.10.1.243.openmpi.4.0.3

Unused

gromacs/2022.1/gcc.8.4.0-openmpi.4.1.2

Unused

intel/2020u1

This Intel compiler deoends on a shared library that is unavailable on Rocky 9.

The following affected modules are removed:

  • mpich/3.4/intel.2020u1

  • openmpi/4.0.3/intel.2020u1

  • hdf5/1.10.5/intel.2020u1

  • ioapi/3.2/intel.2020u1

  • netcdf-c/4.7.0/intel.2020u1 (including dependent netcdf-f version 4.5.2)

Use modules with newer intel compier where available

ioapi/3.2/gcc.11.2.0

Unused

petsc/3.20.1/gcc.11.2.0

petsc/3.20.1/gcc.11.2.0-cuda.11.7.1

Unused

Unused

protobuf/3.11.4

protobuf/3.19.4

Unused

Unused

salmon/1.2.1

Cannot build, use newer version

tensorflow/2.0.0

Cannot build, use newer version

tensorRT/6.0.1.5

Cannot build, use newer version

tk/8.6.12

Unused. Functionality is provided by tcl/8.6.12

Updated modules

CUDA 10 compiled modules:

  • gromacs/2020.4/gcc.8.4.0-cuda.10.1.243

  • gromacs/2021.2/gcc.8.4.0-cuda.10.1.243

  • gromacs/2021.2/gcc.8.4.0-cuda.10.1.243.openmpi.4.0.3

  • namd/2.14b2/gcc.8.4.0-cuda.10.1.243

Replaced by CUDA 11 compiled modules:

  • gromacs/2020.4/gcc.8.4.0-cuda.11.7.1

  • gromacs/2021.2/gcc.8.4.0-cuda.11.7.1

  • gromacs/2021.2/gcc.8.4.0-cuda.11.7.1.openmpi.4.0.3

  • namd/2.14b2/gcc.8.4.0-cuda.11.7.1

gcc/<any version>

No longer provides go. To use go please load module go/1.22.3

gcc/system

System default compiler is updated to version 11.5.0.

Modules compiled with system compiler:

  • openmpi/4.1.1/gcc.system

  • ucx/1.8.0/gcc.system

  • ucx/1.12.0/gcc.system

  • ucx/1.15.0/gcc.system

  • fftw/3.3.8/gcc.system

  • hdf5/1.10.5/gcc.system

  • hdf5/1.13.1/gcc.system

  • hdf5/1.13.1/gcc.system-openmpi.4.1.1

openmpi/4.1.1/gcc.system

System default openmpi compiled with gcc 11.5.0

gdal/3.1.0

gdal/3.4.1

gdal/3.6.2

Replaced by gdal/3.1.0/gcc.8.4.0

Replaced by gdal/3.4.1/gcc.11.2.0

Replaced by gdal/3.6.2/gcc.11.2.0

geos/3.8.1

geos/3.10.2

geos/3.11.1

Replaced by geos/3.8.1/gcc.8.4.0

Replaced by geos/3.10.2/gcc.11.2.0

Replaced by geos/3.11.1/gcc.11.2.0

intel-tbb/2021.5.0

Replaced by intel-tbb/2021.11

mpich/4.0/gcc.11.2.0

Replaced by mpich/4.0/gcc.system

proj/6.3.2

proj/9.0.0

proj/9.1.1

Replaced by proj/6.3.2/gcc.8.4.0

Replaced by proj/9.0.0/gcc.11.2.0

Replaced by proj/9.1.1/gcc.11.2.0

sqlite3/3.32.3

sqlite3/3.38.2

sqlite3/3.41.0

Replaced by sqlite3/3.32.3/gcc.8.4.0

Replaced by sqlite3/3.38.2/gcc.11.2.0

Replaced by sqlite3/3.41.0/gcc.11.2.0

R/4.1.2

R/4.2.2

Seurat and leiden libraries cannot be built. Use newer R if you need these specific packages.

R/4.3.3

R/4.4.2

Updated packages:

  • Seurat to version 5.3.0

  • SeuratObject to version 5.0.2

  • replace leiden by leidenbase

New modules

gatk/4.6.2.0

Added

hdf5/1.14.1/gcc.11.2.0-openmpi.5.0.1

Added

intel/2025.1.0

Added

intel-tbb/2022.1

Added (subset of Intel 2025 compiler)