[gmx-users] reg GPU Mdrun Error

[Mark Abraham]

See http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Pinning_threads_to_physical_cores

On Sat, Sep 7, 2013 at 2:06 PM, vidhya sankar <scvsankar_agr at yahoo.com> wrote:
> respected  mark sir  ,
>                  Thank you fro your previous reply
>
> When i run the production Mdrun  I have got the following error
>
>
> job is terminating with segmentation fault error
>
> Back Off! I just backed up CNTPEPRSOLIONSfullplumedGPUtest2.log to ./#CNTPEPRSOLIONSfullplumedGPUtest2.log.5#
>
> Reading file CNTPEPRSOLIONSfullGPUtest2.tpr, VERSION 4.6.1 (single precision)
> Using 3 MPI threads
> Using 5 OpenMP threads per tMPI thread
>
> 3 GPUs detected:
>   #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC:  no, stat: compatible
>   #1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC:  no, stat: compatible
>   #2: NVIDIA Tesla K20m, compute cap.: 3.5, ECC:  no, stat: compatible
>
> 3 GPUs auto-selected for this run: #0, #1, #2
>
>
> NOTE: The number of threads is not equal to the number of (logical) cores
>       and the -pin option is set to auto: will not pin thread to cores.
>       This can lead to significant performance degradation.
>       Consider using -pin on (and -pinoffset in case you run multiple jobs).
>
>
> Back Off! I just backed up CNTPEPRSOLIONSfullplumedGPUtest2.trr to ./#CNTPEPRSOLIONSfullplumedGPUtest2.trr.5#
>
> Back Off! I just backed up CNTPEPRSOLIONSfullplumedGPUtest2.edr to ./#CNTPEPRSOLIONSfullplumedGPUtest2.edr.5#
>
> WARNING: This run will generate roughly 27348 Mb of data
>
> starting mdrun 'C225N99O45 in water'
> 10000000 steps,  20000.0 ps.
> Segmentation fault (core dumped)
>
> What is the meaning of the note ?
>
> How to Give the command  to run? i gave as follows
>
> mdrun -s CNTPEPRSOLIONSfullplumed.tpr   -plumed plumed1.dat     -nb  gpu    -v  -deffnm  CNTPEPRSOLIONSfull    -cpt 2
>
>
>
> Thanks in Advance
> --
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