Thanks David and Szilárd. I am attaching a log file that I have got from my experiment. Please have a look. It says, gromacs version 4.6-dev I am using :-) VERSION 4.6-dev-20120820-87e5bcf (-: of Gromacs.
I have used the commands: git clone git://git.gromacs.org/gromacs.git cd gromacs git checkout --track -b release-4-6 origin/release-4-6 as written on the gromacs website. to download it and used cmake .. -DGMX_MPI=ON -DGMX_OPENMP=ON to configure it. Is it the case that later version of 4.6 has this feature? Please let me know. Thanks, Jesmin On Wed, Aug 29, 2012 at 4:27 AM, Szilárd Páll <szilard.p...@cbr.su.se> wrote: > On Wed, Aug 29, 2012 at 5:32 AM, jesmin jahan <shraba...@gmail.com> wrote: >> Dear All, >> >> I have installed gromacs VERSION 4.6-dev-20120820-87e5bcf with >> -DGMX_MPI=ON . I am assuming as OPENMP is default, it will be >> automatically installed. >> >> My Compiler is >> /opt/apps/intel11_1/mvapich2/1.6/bin/mpicc Intel icc (ICC) 11.1 20101201 >> >> And I am using OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi -s imd.tpr >> >> I was hopping this will run 16 processes each with 12 threads. >> However, in the log file I saw something like this: >> >> R E A L C Y C L E A N D T I M E A C C O U N T I N G >> >> Computing: Nodes Number G-Cycles Seconds % >> ----------------------------------------------------------------------- >> Domain decomp. 16 1 0.027 0.0 1.8 >> Comm. coord. 16 1 0.002 0.0 0.1 >> Neighbor search 16 1 0.113 0.1 7.7 >> Force 16 1 1.236 0.8 83.4 >> Wait + Comm. F 16 1 0.015 0.0 1.0 >> Update 16 1 0.005 0.0 0.4 >> Comm. energies 16 1 0.008 0.0 0.5 >> Rest 16 0.076 0.0 5.1 >> ----------------------------------------------------------------------- >> Total 16 1.481 0.9 100.0 >> ----------------------------------------------------------------------- >> >> >> Its not clear whether each of the 16 nodes runs 12 threads internally or not. > > No it's not. That out put is not from 4.6, you should have an extra > column with the number of threads. > > -- > Szilárd > > >> If anyone knows about this, please let me know. >> >> Thanks for help. >> >> Best Regards, >> Jesmin >> >> >> >> -- >> Jesmin Jahan Tithi >> PhD Student, CS >> Stony Brook University, NY-11790. >> -- >> 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 -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790.
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