Hi, the OpenMM code is still under review. You can download it using git fetch https://gerrit.gromacs.org/gromacs refs/changes/83/1283/14 && git checkout FETCH_HEAD You can check https://gerrit.gromacs.org/#/c/1283/ for the latest version of it (as of time of writing the above line gives you the latest).
Roland On Wed, Aug 29, 2012 at 10:37 AM, jesmin jahan <shraba...@gmail.com> wrote: > 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. > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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