3. Software and modules updates

This page lists specific software and modules changes that are a result of the Operating System update.

Please see Environment modules to learn how to use software modules, including how to to see the most recent software versions and availability.

3.1. General Info

  • Important

    HPC3 operating system is Rocky Linux 8.8 (as of July 25, 2023).
    All installed software is compiled specifically for this OS.

  • The intel and mkl modules provide access to a number of Intel Math Kernel Libraries including LAPACK, SCALAPACK, BLAS and threading options. The MKL libraries can be linked with Intel or GNU compilers. If you are compiling software yourself and are using intel or mkl modules please see Intel MKL Documentaion and Intel MKL Link Advisory to help you figure out how to use variables set by them.

  • docker is not available per security vulnerability. Use singularity instead.

  • sudo and su are not available to regular users per security vulnerability.

  • screen command is not available, use tmux.

  • Operating system provides default compiler gcc 8.5.0 and openmpi 4.1.1 which are available via modules:

    Package

    Module

    gcc 8.5.0

    gcc.system

    openmpi 4.1.1

    openmpi/4.1.1/gcc.system

3.2. Rocky Linux 8.8 updates

Operating System:
HPC3 operating system is Rocky Linux 8.8 (as of July 25, 2023).
All installed software is compiled specifically for this OS.

For user compiled or installed software:

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

  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 some have changed with the new OS.

  3. If you installed any packages with anaconda or miniconda, it is possible you will need to reinstall them. 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.

Summary of changes

The following table summarizes the modules availability on the previous Rocky Linux 8.6 and on the current Rocky Linux 8.8 operating systems:

Total

Rocky Linux 8.6

Rocky Linux 8.8

Comment

Installed

333

330

active modules

Removed

24

unused

New

21

latest available version

Detailed Changes

Please use the table below to find out changes in modules availability for Rocky Linux 8.8. See notes after the table for a few specific cases.

Removed modules

Added modules

bamtools/2.5.1

awscli/2.11.21

bracken/2.6.0

bowtie2/2.5.1

gromacs/2020.4/gcc.8.4.0-cuda.10.1.243.openmpi.4.0.3

cellranger-arc/2.0.2

gromacs/2020.4/gcc.8.4.0-cuda.10.1.243.openmpi.4.0.3.plumed.2.6.1

charm/6.10.1/gcc.8.4.0-openmpi.4.0.3

gromacs/2020.4/gcc.8.4.0-openmpi.4.0.3

cudasdk/22.9

icu/65.1

gdal/3.6.2

igv/2.8.9

geos/3.11.1

jsoncpp/1.9.4

go/1.20.4

julia/1.5.1

hdf5/1.13.1/cudasdk.22.9

kraken2/2.1.1

hdf5/1.14.1/gcc.11.2.0

mdtraj/1.9.3

hdf5/1.14.1/gcc.11.2.0-openmpi.4.1.2

mdtraj/1.9.7

OpenBLAS/0.3.21

meme/5.2.0

proj/9.1.1

midas/1.3.2

qe/7.1/gcc.11.2.0-openmpi.4.1.2

minimap2/2.17

R/4.2.2

mummer/4.0.0

rstudio/2022.12.0.353

pilon/1.23

singularity/3.11.3

plumed/2.6.1/gcc.8.4.0-openmpi.4.0.3

sqlite3/3.41.0

racon/1.4.13

sra-tools/3.0.0

rMATS/4.1.0

vasp/6.3.2/cudasdk.22.9

sas/94M7

vasp/6.3.2/gcc.11.2.0

sra-tools/2.10.9

sra-tools/2.11.3

unicycler/0.4.8

Notes

  • sra-tools tools prior to v.3 do not handle writing temp files to a separate directory and are removed as they cause issues. Please see SRA toolkit fasterq-dump for explanation how to use this toolkit with currently available version.

  • Python 2.7 has reached the end of life and is no longer supported. It is installed but the outcome of any program can not be predicted. If you have any python code that is still using python 2 convert your code to Python 3. Test your application with the -W default command-line option to see any deprecation warnings and follow online guides (google) for porting Python 2 to Python 3.

  • Cufflinks does not work under Rocky Linux 8. Use a singularity container build with cufflinks compiled for CentOS 7. The image /dfs8/singularity-images/cufflinks.simg is build with singularity/3.7.2. Example of usage:

    [user@login-x:~]$ module load singularity/3.7.2
[user@login-x:~]$ singularity exec \
                     /dfs8/singularity-images/cufflinks.simg cuffdiff arg1 ... argN

  • If you are using an older container built with singulariy 3.4.1, and it fails with an error that looks like

    FATAL: container creation failed: mount /proc/

    Please try adding option -B to your singularity command and use the latest singularity module:

    [user@login-x:~]$ module load singularity/3.9.4
[user@login-x:~]$ singularity exec \
                     -B /dfs8/singularity_containers/rcic/bashrc:/etc/bashrc \
                     /dfs3a/singularity_containers/contName.simg binaryName