GPC2 Upgrade Information

We have finished developing and testing our Ubuntu cluster nodes and are ready to begin migration of our production nodes to Ubuntu 24.04, allowing us to keep up with security updates and to be able to run current versions of the software that we depend on.

This will not be a seamless transition, however. We are making some changes that will require you to alter your submission scripts and workflows, although don't worry, our team will help you make the necessary changes.

We are planning on migrating in stages, with the gpc2_compute partition first, (06/03/25) to allow our condo node owners to test their workflows before we migrate their nodes. After that the rest of the partitions will be moved on a schedule that accommodates their current workflows and deadlines. Note that nodes moved to the new OS will be unavailable for the"low" partitions until the migration is completed.

The changes are generally in the use and versions of our modules. We currently have a large number of modules installed, with multiple versions of most of them. We won't be reinstalling all of these modules, but rather we will determine which need to be installed as modules, and will install the current version, rather than all previous versions. (For instance, GCC 14.2.0 will be available as a module, but not GCC 10.4.0, and the currently installed Matlab versions will be present on the new system as modules.)

Some software will be installed into the base OS rather than as a module (zsh, emacs and git for instance) and for other software we will suggest the use of Conda environments and/or Apptainer containers (if we have removed a module from our system, that means that we either installed it into the base OS, or found it available in the conda repositories.)

If you have automated loading of modules in your .bashrc file, then after the upgrade you will need to edit the file to reflect the modules that no longer exist, or which have new versions available. We have code available for you to use to make different options active depending on which Operating System you are logged into (Centos or Ubuntu), which may be necessary during the transition period when you may be submitting jobs to both Centos and Ubuntu nodes.

Below are the modules available for Ubuntu nodes. Contact us to request additional modules or versions.

Anaconda Information:

Previous installations of anaconda will still work, according to our tests so far, so there is no need to make changes right away unless you encounter issues.

A fresh installation of miniconda is available as the module "miniforge" (a customized version that uses conda-forge as the default repository.) It is faster than the old installs and it is suggested to migrate to it when your schedule allows. We are available to assist you if needed.

Connecting to the new nodes:

During the transition period, for jobs to be run on the gpu2_compute or testing partitions, please ssh to gpc2b.sas.upenn.edu and submit your job from there.

List of nodes that have been moved to Ubuntu, last updated 5/21/25: