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_...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
