Move to AlmaLinux

In December 2020, Red Hat announced that development of CentOS, a free-of-cost downstream fork of the commercial Red Hat Enterprise Linux (RHEL), would be discontinued. As such, we will move to AlmaLinux, a community-supported, production-grade enterprise operating system that is binary-compatible with RHEL. This page covers the planned upgrade and testing of AlmaLinux on submit.

How we plan to upgrade submit

Because it is hard to predict how an operating system upgrade will affect everyone’s work, we will upgrade the system in stages and encourage users to test their workflows on AlmaLinux. For now, the submit system uses CentOS 7 with AlmaLinux machines available only through slurm using a test partition. For the future upgrades, the submit machines will get upgraded with announcements in the submit-users email group. Update: the default submit.mit.edu ssh address now points to AlmaLinux 9. A small number of Centos7 nodes are still available at submit-test.mit.edu for the time being.

Work on CentOS 7

The easiest way to start working is to start an interactive session with ssh

ssh <username>@submit-test.mit.edu

You can also gain access through slurm with salloc.

salloc --partition=submit-centos07

You can also run a slurm job with the following submit script.

#!/bin/bash
#
#SBATCH --job-name=test_centos7
#SBATCH --output=res.txt
#
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100
#SBATCH --partition=submit-centos07

<your script goes here>

Portability of conda on Alma Linux 9

Migrating a conda environment from CentOS 7 to AlmaLinux 9 can typically be done with ease, thanks to conda’s general portability between different operating systems.

Note: Conda is in general portable between operating systems, but for compiled code, you may need to recompile. When moving environments that include compiled code, you may encounter compatibility issues related to the underlying system libraries or compilers. This can manifest as unexpected behavior or even runtime errors. In such cases, the solution is often to recompile the code within the new operating system.

Will CentOS still be available

If your workflow is constrained to CentOS, submit will provide a centrally available singularity of CentOS7.9. You can test this singularity below.

singularity shell /cvmfs/cvmfs.cmsaf.mit.edu/submit/work/submit/submit-software/centos/centos7p9

Here is the recommended command to use centos 7 singularity

singularity shell --bind /cvmfs:/cvmfs --bind /work/submit:/work/submit --bind /data/submit:/data/submit  /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-el7:latest

You can add any additionally binding (with whatever you are using). Then use “bash” command to load your personal bash setup.

If you need something specific besides this singularity, please email us at submit-help@mit.edu

Feedback on AlmaLinux

If you run into any issues while running on the AlmaLinux testing partition, please report them to the submit team at submit-help@mit.edu

Additionally, please report any differences that you see between the base CentOS system and the AlmaLinux testing partitions.