[gmx-users] Simulation freezes but the job keeps on running

[Searle Duay]

Good day!

I am running a 10 ns peptide-membrane simulation using GPUs from PSC
Bridges. The simulation starts properly, but it does not end on the time
that the simulation will end, as estimated by the software. The job is
still running and the simulation seems frozen because no simulation time is
added even after an hour of the job running.

I have submitted the following SLURM code:

#!/bin/bash
#SBATCH -J k80_1n_4g
#SBATCH -o %j.out
#SBATCH -N 1
#SBATCH -n 28
#SBATCH --ntasks-per-node=28
#SBATCH -p GPU
#SBATCH --gres=gpu:k80:4
#SBATCH -t 48:00:00
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=searle.duay at uconn.edu

set echo
set -x

module load gromacs/2016_gpu

echo SLURM_NPROCS= $SLURM_NPROCS

cd $SCRATCH/prot_umbrella/gromacs/conv

mpirun -np $SLURM_NPROCS gmx_mpi mdrun -deffnm umbrella8 -pf
pullf-umbrella8.xvg -px pullx-umbrella8.xvg -v -ntomp 2

exit

I am not sure if the error is from the hardware or from my simulation
setup. I have already ran similar simulations (I just varied the number of
nodes that I am using, but same system), and some of them are successful.
There are just some which seems to freeze in the middle of the run.

Thank you!

-- 
Searle Aichelle S. Duay
Ph.D. Student
Chemistry Department, University of Connecticut
searle.duay at uconn.edu