You may encounter errors that look similar to these when running STAR 2.7.10b on Cardinal:
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 on Cardinal
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:
[c0054:22206:0:22206] ib_mlx5_log.c:179 Remote access error on mlx5_0:1/IB (synd 0x13 vend 0x88 hw_synd 0/0) [c0054:22206:0:22206] ib_mlx5_log.c:179 RC QP 0xef8 wqe[365]: RDMA_READ s-- [rva 0x32a5cb38 rkey 0x20000] [va 0x319d3bf0 len 10200 lkey 0x2e5f98] [rqpn 0xfb8 dlid=2285 sl=0 port=1 src_path_bits=0] forrtl: error (76): Abort trap signal
Unknown
mpp-dyna versions 11, 13, when running on 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:
When running a full-node MPI job with MVAPICH 3.0 , you may encounter the following warning message:
When running MPI+OpenMP hybrid code with the Intel Classic Compiler and MVAPICH 3.0, you may encounter the following warning message from hwloc:
Users may encounter the following errors when compiling a C++ program with GCC 13:
error: 'uint64_t' in namespace 'std' does not name a type
or
