OS Update to RockyLinux8 

General Information

FastX

On RockyLinux8, only FastX 3 is installed.  Please visit the FastX page for information on accessing/installing FastX 3.  You will also note that the options for the terminals and desktops has changed (one example is the MATE desktop and terminal are no longer available).

Modules

We have started a new base module installation for RockyLinux8, which includes both the removal of modules for installations that do not run as well as a cleanup of old modules. If you do not find a module for the specific version of an application that you need, please let us know by sending a support request.

If any CHPC installed applications need rebuilt, please send a request to helpdesk@chpc.utah.edu and we will work on doing a new installation.

Compilers

The default GNU compiler that is shipped with RockyLinux8 is gcc/8.5.0. We build most of the applications with this compiler.

The modules for Intel software development tools have different name to reflect the branding change (oneAPI). The formerly  intel compiler is now intel-oneapi-compilers, Intel MPI, formerly impi is now intel-oneapi-mpi, and the MKL library, formerly mkl is now intel-oneapi-mkl. See our Intel oneAPI page for details.

The PGI compilers are now branded as a part of the Nvidia HPC Toolkit, under module nvhpc. The CentOS7 installed PGI compilers do not work on RockyLinux8. Due to nvhpc's requirements for supported CPU architecture, the latest version working on all CHPC clusters, lonepeak in particular, is 21.5. See our Compilers page for details.

MPI

MPI libraries have been updated to the latest versions, please use them as they provide better performance and SLURM scheduler support. Some but not all old CentOS 7 built MPIs work, for that reason, please, migrate to the new MPI versions. We have installed OpenMPI, MVAPICH2 and Intel MPI. MPICH currently does not run well on the InfiniBand, we will be looking into this once the InfiniBand clusters are installed, however we intend to de-emphasize MPICH, since it serves as a reference MPI implementation and has less performance optimizations. See our MPI page for details.

We highly recommend to re-build MPI software with the new compilers and MPIs. If your MPI applications that ran previously crash, please, rebuild them with one of the new compilers and MPIs before submitting a support request.

NOTE that the newer verions of intel-oneapi-mpi do not work on the Notchpeak AMD nodes. The latest version that does work is intel-oneapi-mpi/2021.1.1. This version is set to default and we recommend to use it instead of the newer versions. Some programs that we have built before discovering this problem were built with newer intel-oneapi-mpi. Should you run into issues running on the AMD nodes with intel-oneapi-mpi, please, let us know. 

Libraries

Commonly used libraries, including HDF5, NetCDF, FFTW, GSL, OpenBLAS and Boost have been freshly installed. See the Math Libraries and Data Libraries pages for details. Notably, the NetCDF Fortran library module name has changed from to netcdf-f to netcdf-fortran, and the Parallel NetCDF, pnetcdf pnetcdf, changed to parallel-netcdf. 

Python

RockyLinux8 does not provide the python command, use either python2, or python3. Sometimes the python command is necessary, e.g. when Python is called from a script or a program that is difficult to modify. For these reasons we are providing two modules, python/2.7.18, and python/3.6.8, which set the python command to python2, or python3,  respectively.

CHPC newly installed python 3.10.3 on RockyLinux8, which is the recommended Python 3 to use. User installed Anaconda distributions should also work. Older versions of Python such as 3.6.3 do not work.

R

The R build for RockyLinux8 is R version 4.1.3.  Note that the containerized R distributions also work (this includes the 4.1.2-basic, 4.1.2-bioconductor, and 4.1.2-geospatial). The R/4.1.1 and older CentOS7 builds of R do not run on RockyLinux8 systems.

End User Applications

Please take the time to test the current installation of any of your applications on the clusters running RockyLinux8. 

While CHPC staff has been doing testing, we do not have the time, inputs, nor the expertise to test all applications.  From the testing that we have completed, most of the CentOS7 installations have run without issue on RockyLinux8. Therefore most of the applications from CentOS7 have been retained.

There have been a few CentOS7 applications that do not work on RockyLinux8, and we have installed new versions of them. Some of these programs have been built manually and are located in /uufs/chpc.utah.edu/sys/installdir/r8 . Majority of new builds have been built with the Spack package manager, and can be found through Spack commands. Both the manual and Spack built programs can be seen also through the module commands, e.g. module avail or module spider , which is the preferred way.

If you have gone over the changes we detail above and still encounter problems with your application, please send a support request to helpdesk@chpc.utah.edu.