Running a Rocky8 apptainer image on Rocky9

If you absolutely need to still use the Rocky 8 software stack after the OS upgrade to Rocky 9, you can use it with Apptainer (formerly singularity).

We have an apptainer image with Rocky 8 and the same environment as the compute nodes. In addition, you can access the Rocky 8 modules from within the container. The image is stored at /cluster/software/containers/rocky8.sif.

You can execute this image and/or copy it, but you cannot modify it in its original location.

NOTE: It works with the majority of software modules, but some may fail due to OS dependencies which are not longer compatible between the OS and the container.

Run apptainer with Rocky 8

To get a bash shell on a Rocky 8 environment, you can run:

[fox ~]$ apptainer run --nv /cluster/software/containers/rocky8.sif
Apptainer>

or

[fox ~]$ apptainer exec --nv /cluster/software/containers/rocky8.sif /bin/bash
Apptainer>

NOTE: The command apptainer shell is also an option. However it does not allow you to access modules.

Load modules

You can still load modules that were available on Rocky 8 from inside the Apptainer container:

[fox ~]$ apptainer run --nv /cluster/software/containers/rocky8.sif
Apptainer> module avail
Apptainer> module load GCC/11.3.0
Apptainer> module list

Currently Loaded Modules:
  1) GCCcore/11.3.0   2) zlib/1.2.12-GCCcore-11.3.0   3) binutils/2.38-GCCcore-11.3.0   4) GCC/11.3.0

Note that the modules are from the Rocky 8 environment:

Apptainer> module display matlab/R2022b-fasrc01
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
   /cluster/software/rhel8/easybuild/modules/all/GCC/11.3.0.lua:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
help([[
Description
===========
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
 as well as libraries for these languages (libstdc++, libgcj,...).


More information
================
 - Homepage: https://gcc.gnu.org/
]])
whatis("Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
 as well as libraries for these languages (libstdc++, libgcj,...).")
whatis("Homepage: https://gcc.gnu.org/")
whatis("URL: https://gcc.gnu.org/")
conflict("GCC")
setenv("EBROOTGCC","/cluster/software/rhel8/easybuild/software/GCCcore/11.3.0")
setenv("EBVERSIONGCC","11.3.0")
setenv("EBDEVELGCC","/cluster/software/rhel8/easybuild/software/GCC/11.3.0/easybuild/GCC-11.3.0-easybuild-devel")

Submit slurm jobs

If you need to submit a job rather than getting to a shell, you have to do the following steps in the appropriate order:

  1. launch the apptainer image
  2. load modules
  3. (optional) compile code
  4. execute code

If you try to load modules before launching the image, it will try to load modules from the Rocky 9 host system.

To ensure that steps 2-4 are run within the apptainer container, they are place between END (see slurm batch script below).

NOTE: You cannot submit slurm jobs from inside the container, but you can submit a slurm job that will execute the container.

Example with a simple hello_world.f90 fortran code:

program hello
  print *, 'Hello, World!'
end program hello

Slurm batch script run_apptainer_rocky8.sh:

#!/bin/bash
#SBATCH --account=MyProject
#SBATCH --job-name=rocky8
#SBATCH --time=00:10:00
#SBATCH --mem-per-cpu=2G
#SBATCH --ntasks=1

# start a bash shell inside apptainer image
apptainer run --nv /cluster/software/containers/rocky8.sif <<END

# load modules
module load GCC/11.3.0
module list

# compile code
gfortran hello_world.f90 -o hello.exe

# execute code
./hello.exe
END

To ensure that the commands are run within the apptainer container, they are placed between END.

To submit the slurm batch script:

sbatch run_apptainer_rocky8.sh

Another option have a bash script with steps 2-4 and then use apptainer run to execute the script. For example, script_inside_container.sh:

#!/bin/bash

# load modules
module load GCC/11.3.0
module list

# compile code
gfortran hello_world.f90 -o hello.exe

# execute code
./hello.exe

And the slurm batch script run_apptainer_rocky8.sh becomes:

#!/bin/bash
#SBATCH --account=MyProject
#SBATCH --job-name=rocky8
#SBATCH --time=00:10:00
#SBATCH --mem-per-cpu=2G
#SBATCH --ntasks=1

# start a bash shell inside apptainer image
apptainer run --nv /cluster/software/containers/rocky8.sif script_inside_container.sh

You can submit a batch job with:

sbatch run_apptainer_rocky8.sh

CC Attribution: This page is maintained by the University of Oslo IT FFU-BT group. It has either been modified from, or is a derivative of, "Running Singularity image with CentOS 7 on Rocky 8" by FASRC under CC-BY-NC-SA-4.0.