On Thu, Aug 30, 2012 at 1:06 AM, Roland Schulz <rol...@utk.edu> wrote: > Hi, > > the OpenMM code is still under review. You can download it using
I guess you meant OpenMP. As far as I know, the OpenMM build has not been tested much. > git fetch https://gerrit.gromacs.org/gromacs refs/changes/83/1283/14 && git > checkout FETCH_HEAD I've been advising people to get the nbnxn_hybrid_acc branch until the merge happens (which has the advantage of not having to check which one is the latest patch set. However, I just noticed that the last patches pushed to gerrit have not been pushed there. I'll push up the changes asap. -- Szilárd > 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 -- 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