New Software Stack Available on Scholar

December 18, 2019 – January 31, 2020
Scholar
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To expand the list of supported software on Scholar and to provide software updates at a faster pace, Research Computing is adopting a new software automation framework (Spack) that will replace our existing software stack. Applications built with Spack will be deployed on Scholar during the scheduled maintenance on Dec 18-19, 2019.

We have tried to keep the list of applications and their respective versions similar to the old applications. However, in some cases, the application names and minor versions may have changed. If you find that your code stopped working with the new modules, please find the correct applications and versions using the "module spider" command and update your scripts.

What you need to do

  • For a large majority of users, no action will be required. When you run "module load" commands, your environment will be automatically configured to use the new software stack.
  • If you are copying code from other RCAC clusters, please make sure the modules and their respective versions are available on Scholar.
  • If you previously compiled some applications on Scholar, it is recommended to recompile them.
  • Due to changes in scheduler (from Torque to Slurm), any application built with OpenMPI must be recompiled.

Bioinformatics

Due to the complexity of Bioinformatics software collection and its dependency on old RCAC software, these applications will NOT use the new software stack. When you load the bioinformatics module, your environment will be automatically configured to use bioinformatics packages and their dependency modules. You may notice duplicate messages while loading the bioinformatics module -- this is expected.

Highlights

  • Some applications and libraries (HDF5, NetCDF, CDO, NCO, ncview, etc.) which were previously combined under a single umbrella module (netcdf) have been separated into individual modules.
  • Embedded gmp, mpc, and mpfr libraries have been separated from GCC into their own modules. They will be automatically loaded when you load the gcc module.
  • The lapack module has been renamed as netlib-lapack. If your application requires LAPACK, you can also use the openblas module and link with "-lopenblas" flag.
  • The default OpenMPI version has changed from 2.1.6 to 2.1.5.
  • The default Anaconda version has changed from 5.1.0-py27 to 5.1.0-py36.
  • NO modification has been done to R/Rstudio and associated applications.

Originally posted: December 13, 2019  3:51pm