The next era for Apocrita is here¶

For much of the year we have been working on a major project to upgrade Apocrita to a new operating system, (Rocky Linux 9, hereafter known as Rocky 9). As part of the project, we have deployed a new package building tool to help us recompile all of the research applications to work on the new system.

The majority of the cluster has now been upgraded to Rocky 9. The remaining CentOS 7 nodes will be updated in due course.

Frequently asked questions when migrating from CentOS 7

Please see the FAQs section for commonly asked questions relating to the migration from CentOS 7 to Rocky 9.

Notice

This blog post will receive further updates during the migration phase.

How can I use the new system?¶

SSH into login.hpc.qmul.ac.uk following guidance on this page. To check what applications are available, you can run module avail on the login nodes.

We have also provisioned a new OnDemand server running Rocky 9. This server brings new functionality, and newer versions of applications (for example a newer RStudio).

Changes for conda users¶

Due to some recent anaconda licence changes, we now only provide the miniforge module for using conda environments. This works in the same way as anaconda and miniconda but does not use certain problematic anaconda repositories. Miniforge is the officially supported installation method for the faster Mamba libsolver and comes with the popular conda-forge channel pre-configured as its only channel, where most of the common conda packages are found.

We strongly advise not to use any existing conda environments on Rocky 9 that you created previously on CentOS 7. Instead, you should start with fresh environments. If you want to "migrate" old ones, export them as a YML file on a CentOS 7 node and then use that same YML file to re-create the environment again on a Rocky 9 node.

More detailed information can be found in this separate blog post.

Migration from CentOS 7 FAQs¶

Do I need to copy/move my data across from the CentOS 7 cluster?¶

No. All current storage systems (home directories, scratch and lab shares) are available on Rocky 9 using the same path as the CentOS 7 cluster, for example /data/home/$USER for home directories and /data/scratch/$USER for scratch. You will not need to copy or move your data when migrating to Rocky 9.

How can I use applications on the Rocky 9 cluster?¶

The modules built on Rocky 9 are similar to those in CentOS 7, providing a familiar environment for users transitioning between the two clusters. To view a list of all available modules, run module avail.

Note that we have only built newer versions of software on the Rocky 9 cluster, so you should check that the versions available are suitable for your research.

See the Using Modules page on our docs site for more information.

How can I resolve `GLIBC_2.17' not found` errors in Rocky 9?¶

GLIBC is an immovable core library of the Operating System. Software requiring version 2.17 of GLIBC (CentOS 7) will need to be rebuilt using the newer version of GLIBC present in Rocky 9.

You may also need to remove any local files written in your home directory before rebuilding the software. This includes, but is not limited to: ~/.cache, ~/.jupyter and~/.local.

Do I need to generate a new SSH key for the Rocky 9 cluster?¶

No. Even though we now recommend using ED25519 keys, we are still supporting existing 4096+ RSA keys.

See our SSH keys page on our docs site for more information.

How can I fix a `REMOTE HOST IDENTIFICATION HAS CHANGED!` login error?¶

This is shown because phase 2 of the cluster migration included changing the login.hpc.qmul.ac.uk address to point to the Rocky 9 login servers, which have a different host identification than the legacy CentOS 7 frontend nodes.

To fix this, you will need to remove the cached entry for login.hpc.qmul.ac.uk in your local ~/.ssh/known_hosts file by either manually removing it using a text editor, or by running the ssh-keygen -R login.hpc.qmul.ac.uk command. This is a one-off operation caused by the move from CentOS 7 to Rocky 9.

After removing the cached entry, simply log into the cluster again and accept the new host identification if prompted.

If you previously connected to login-test.hpc.qmul.ac.uk, during the migration phase, you will also need to remove this cached entry as that address no longer exists.

Photo by Chris Liverani on Unsplash.