cp2k/2023.2 can produce huge output containing MKL messages
On all clusters the cp2k executables from module cp2k/2023.2 can produce huge output files due to many many repeating errors from MKL, e.g.:
Cardinal
Some MKL environment variables have incorrect paths
MKL module files define some helper environment variables with incorrect paths. This can yield link time errors. All three clusters are affected. We are working to correct the module files. A workaround for users is to redefine the environment variable with the correct path; this requires some computational maturity. We recommend users contact oschelp@osc.edu for assistance. An example error from Cardinal with module intel-oneapi-mkl/2023.2.0 that defined environment variable MKL_LIBS_INT64 follows:
STAR error bgzf_open: Assertion failed
You may encounter errors that look similar to these when running STAR 2.7.10b:
STAR: bgzf.c:158: bgzf_open: Assertion `compressBound(0xff00) < 0x10000' failed.
Cause
It seems to be related to this issue: https://github.com/alexdobin/STAR/issues/2063
STAR bundles an older version of HTSlib which is incompatible with zlib-ng, a library we build STAR with
Workaround
Use star/2.7.11b
OSC will remove Jupyter MATLAB Kernel
OSC will remove the default MATLAB Jupyter Kernel on Tuesday, May 20th, 2025. To create your own Jupyter MATLAB Kernel please follow the documentation on the MATLAB Page
OpenMPI 4 and NVHPC MPI Compatibility Issues with SLURM HWLOC
A pure MPI application using mpirun or mpiexec with more ranks than the number of NUMA nodes may encounter an error similar to the following:
BWA 0.7.17 vulnerability
Cardinal hosted a version of bwa that had an unpatched vulnerability, 0.7.17.
This version has been removed from Cardinal in favor of 0.7.18
LS-DYNA mpp-dyna Cardinal: Remote access error on mlx5_0:1, RDMA_READ
You may encounter the following error while running mpp-dyna jobs with multiple nodes:
Ansys OMP: System error #22: Invalid argument
You may encounter the following error while running Ansys on Cardinal:
OMP: Error #100: Fatal system error detected. OMP: System error #22: Invalid argument forrtl: error (76): Abort trap signal
Workaround
Set the environment variable KMP_AFFINITY=disabled before running Ansys
Abaqus Parallel Job Failure with PMPI Due to Out-of-Memory (OOM) Error
You may encounter the following error while running an Abaqus parallel job with PMPI:
Handling full-node MPI warnings with MVAPICH 3.0
When running a full-node MPI job with MVAPICH 3.0 , you may encounter the following warning message:
