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 |
|
However, there are some specific module changes that are not clear from the output of module spider
:
- For
Python
andR
, consider using bundles instead of the plain module names. These include many helpful pre-installed packages (use themodule spider <insert-bundle-name>
command for specifics):- For
Python
, we recommend eitherScipy-Bundle
and/orPython-bundle-PyPI
- For
R
, we recommend eitherR-bundle-CRAN
and/orR-bundle-Bioconductor
- For
- The
PGI
module has been replaced byNVHPC
(installation still in progress). This is due to NVIDIA's rebranding of PGI. - The
LiftOver
software is provided by theUCSC_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.