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

[Åke Sandgren]

Is that build using openmpi?

We've seen cases when gromacs built with openmpi hangs repeatedly, while
the same build using intelmpi works.

We still haven't figured out why.

On 01/25/2018 06:39 PM, Searle Duay wrote:
> 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!
> 

-- 
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: ake at hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se