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Changelog and Known Issues for OS Upgrade

Module changes

As part of the operating system upgrade, the module naming scheme has been revised so it is no longer necessary to load a "gateway" set of modules before accessing other software. However, this means that nearly every module name has changed to show the dependencies it uses.

To handle this transition, use the module spider command to find the new name of modules you are currently using, e.g.,

1
module spider Python

However, there are some specific module changes that are not clear from the output of module spider:

  • For Python and R, consider using bundles instead of the plain module names. These include many helpful pre-installed packages (use the module spider <insert-bundle-name> command for specifics):
    • For Python, we recommend either Scipy-Bundle and/or Python-bundle-PyPI
    • For R, we recommend either R-bundle-CRAN and/or R-bundle-Bioconductor
  • The PGI module has been replaced by NVHPC (installation still in progress). This is due to NVIDIA's rebranding of PGI.
  • The LiftOver software is provided by the UCSC_Tools module.

Changelog

Known issues

Below are issues that ICER is aware of and is taking steps to resolve. If you find an issue that is not on this page, please contact us with the subject line "OS Upgrade 2024"

  • The powertools module is available, but the tools within have not been checked for compatibility with the new operating system. Many work already, but others will need modifications. If one of the tools you need is not working, please request that we update it using the contact form to help us prioritize our updates.
  • OpenMPI/4.1.5-GCCcore-12.3.0 has issues when allocating at least 15 tasks to one node, and exactly one task to another. Until we can track down the source of this error, we recommend submitting SLURM scripts specifying --ntasks-per-node instead of just --ntasks so that tasks are spread equally between requested nodes.