We have observed that several applications built with MVAPICH2, including Quantum ESPRESSO 7.4.1, HDF5, and OpenFOAM, may experience poor performance on Cardinal. We suspect this issue could be related to the newer network devices or drivers. Since MVAPICH2 is no longer supported, we recommend switching to MVAPICH 3.0 or another MPI implementation to ensure continued performance and stability in your work.
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.:
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:
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.
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
Use star/2.7.11b
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
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:
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
You may encounter the following error while running mpp-dyna jobs with multiple nodes:
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
Set the environment variable KMP_AFFINITY=disabled before running Ansys
You may encounter the following error while running an Abaqus parallel job with PMPI:
