[gmx-users] gmx5.0.2 with GPU acceleration problem

[Szilárd Páll]

Hi Chungwen,

I run on Piz Daint on a regular basis and never had these issues. The
only reason for such a thing to happen is that some strange rank over
nodes distribution ends up leaving some nodes without PP rank.

Could you please post a log file (thread pastebin or something
similar) of the failing run?

BTW, you know that you are almost always better off running
OMP_NUM_THREADS<8 (and -N > 1)?

--
Szilárd


On Fri, Mar 27, 2015 at 12:09 PM, Wayne Liang <chungwen.liang at gmail.com> wrote:
> Dear Users,
>
> I have encountered a problem that mdrun always crashes with the following
> msg, when I run it on more than 32 nodes:
>
> Software inconsistency error:
>
> Limiting the number of GPUs to <1 doesn't make sense (detected 1, 0
> requested)!
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
>
> My submission script:
>
> #!/bin/bash -l
>
> #SBATCH --job-name test-gpu
>
> #SBATCH --nodes 32
>
> #SBATCH --cpus-per-task 8
>
> #SBATCH --ntasks-per-node 1
>
> #SBATCH --time 01:00:00
>
>
> GMX=/apps/daint/gromacs/5.0.2/gnu_482/bin
>
>
> cd $SLURM_SUBMIT_DIR/
>
> export OMP_NUM_THREADS=8
>
> aprun -n 32 -N 1 -d 8 $GMX/mdrun_mpi
>
> However, using option -nb cpu (bypass GPU acceleration), there is no any
> problem.
> I have searched online, including mailing list. There is not much
> information about it.
>
> Thanks very much for any response.
>
> Best,
>
> Chungwen
> --
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