A partial-node MPI job failed to start using Intel MPI mpiexec
A partial-node MPI job may fail to start using mpiexec from intelmpi/2019.3 and intelmpi/2019.7 with error messages like
OpenMPI job stopped at 'There are not enough slots available in the system to satisfy the slots'
Users would encounter a MPI job failed with openmpi/3.1.0-hpcx on Owens and Pitzer. The job would stop with the error like "There are not enough slots available in the system to satisfy the slots". Please switch to openmpi/3.1.4-hpcx. The buggy version openmpi/3.1.0-hpcx will be removed on August 18 2020.
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Resolved: We removed openmpi/3.1.0-hpcx on August 18 2020.
Unable to unload Intel software stack
Users may experience unable to unload Intel software stack via module rm intel after switching between intel and ohter compilers. This is a known issue with current versions of Lmod on Pitzer and Ruby. The issue will be fixed by upgrading Lmod during system-wide downtime May 19th.
cuda-gdb segmentation fault on startup
The CUDA debugger, cuda-gdb, can raise a segmentation fault immediately upon execution. A workaround before executing cuda-gdb is to unload the xalt module, e.g.:
module unload xalt
This issue affects most cuda modules on Pitzer and Owens.
Error 'libim_client.so: undefined reference to uuid@' with MVAPICH2 in Conda environment
Users may encoutner an error like 'libim_client.so: undefined reference to `uuid_unparse@UUID_1.0' while compiling MPI applications with mvapich2 in some Conda enivronments. We found pre-installed libuuid package from Conda conflicting with system libuuid libraries. The affected Conda packages are python/2.7-conda5.2, python/3.6-conda5.2 and python/3.7-2019.10.
Incorrect MPI launcher and compiler wrappers with Conda environments python/2.7-conda5.2 and python/3.6-conda5.2
Users may encounter under-performing MPI jobs or failures of compiling MPI applications if you are using Conda from system. We found pre-installed mpich2 package in some Conda environments overrides default MPI path. The affected Conda packages are python/2.7-conda5.2 and python/3.6-conda5.2. If users experience these issues, please re-load MPI module, e.g. module load mvapich2/2.3.2 after setting up your Conda environment.
Ansys DesignModeler with hardware acceleration
Ansys DesignModeler with hardware acceleration is not working.
With Ansys version greater than 19.1, DesignModeler is working with software rendering mode, but it is very slow.
Large MPI job startup hang with mvapich2/2.3 and mvapich2/2.3.1
We have found that large MPI jobs may hang at startup with mvapich2/2.3 and mvapich/2.3.1 (on any compiler dependency) due to a known bug that has been fixed in release 2.3.2. If users experience this issue, please switch to mvapich2/2.3.2.
Error when downloading SRA data on computing nodes
NCBI blocks any connection from computing nodes because they are behind firewalls. Thus OSC users cannot use SRA tools to download data "on-the-fly" at runtime on computing nodes, e.g. 'fastq-dump -X 5 SRR390728'. OSC users must download SRA data on login using the command 'prefetch' before any sequence analysis. Please see the section 'Download SRA Data' in the SRA Toolkit software page for more detail.
BWA Software Security Vulnerability
Due to a recent software vulnerability discovered in bwa versions 0.7.17 and 0.7.13, it is highly recommended to immediately stop using these versions and instead use bwa/0.7.17-r1198 which contains a patch to mitigate this vulnerability.