[gmx-users] Simulation freezes but the job keeps on running
ake.sandgren at hpc2n.umu.se
Thu Jan 25 19:08:56 CET 2018
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:
> #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
> 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
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