I am trying to run a protein-ligand MD simulation using slurm script on the HPC system. But I am getting the following error (screenshot attached). Any suggestion to solve this error would be highly appreciated. Thanks!
"MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.
No executable was specified on the mpirun command line.
Aborting."
It already told you what the problem is:
No executable was specified on the mpirun command line.
Aborting.
This means you have not told mpirun what to run.
If you ask for help with something like that you will have to show us your SLURM bash job script otherwise no one will be able to help you with that.
I think the error you mentioned comes from the last line.
mpirun -np $SLURM_NTASK | tee log_gmx
this only makes sense if the left side of the pipe operator is a valid mpirun statement which it is not.
And the line above where the mpirun command would run gromacs probably throws an error that is just above your output that you shared here.
For one the -cpi option needs to be followed by a path to an .cpt file, so I guess there lies your error.
But also your last line is weird, what would you like to accomplish here ?
Run gromacs and print the output into a log file ?
(Assuming a standard slurm configuration the ouptut of your mdrun would be written into a slurm-.out file anyways)
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