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My slurm job tends to terminate and restart while mdrun is trying to write the *.gro file at the end, in HPC cluster. I could see from the *.err file that everything is fine until wait time is 0 s and my session hangs up and after sometime the job restarts.
I think it’s an issue with mpirun having communication issues, but now sure.
So what am i missing and how can i correct it?
My mpi-run script for 5 nodes * 28 cores
mpirun -np 140 gmx_mpi mdrun -deffnm nvt_g_dm_ -v -s nvt_g_dm_.tpr