Hi,
I try to use a ParGenes, a program that allow its usage in hpc.
It is installed via conda.
When running it on a single thread, it works fine but very slowly (pargenes.py). So I tried the hpc version (pargenes-hpc.py).
It is specified that it needs MPI to be installed. What I did with ml GCC/13.2.0 OpenMPI/4.1.6
It get the following error message, related to git.
This is the error message for job # 37669149
[Error] [0:00:00] mpi-scheduler execution failed with error code 1
[Error] [0:00:00] Will now exit...
[Error] <class 'RuntimeError'> mpi-scheduler execution failed with error code 1
Writing report file in /home/christec/Clematis/Run3/Analyses/Tree/raxml_all/report.txt
When reporting the issue, please always send us this file.
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
I tried different combination of SBATCH header as its seems it is related to the multi-threading and I get another very similar error message :
This is the error message for the job # is 37669225
[Error] [0:00:28] mpi-scheduler execution failed with error code 134
[Error] [0:00:28] Will now exit...
[Error] <class 'RuntimeError'> mpi-scheduler execution failed with error code 134
Writing report file in /home/christec/Clematis/Run3/Analyses/Tree/raxml_all/report.txt
When reporting the issue, please always send us this file.
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
I would be grateful if you could help me with this issue.
Best regards,
Camille Christe