Roland, indeed the error was that I'have compilate mdrun-openmm which is not the native gpu.
now I've made mdrun via cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0 and obtain workable gromacs. My test system consist of calmodulin (charmm27) solvated in tip3p water. total size of the system: 67752 atoms. I have set below values on the mdp file as grompp told me nstlist = 20 cutoff-scheme = Verlet ; !not quite sure whai is this! vdwtype = cut-off Now on the mdrun output I have Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected to be used for this run: #0 does it mean that all 4 cores of my CPU + gpu are used at same time ? is there any other ways to increase performance ? ( e.g I'm not quite sure if open_mpi is used with that build because during compilation cmake asked me only about fftw3 libs). Is there any ways to monitor total performance ( e.g separate cpu and gpu usage ) ? Thanks for suggestions, James 2013/1/9 Roland Schulz <rol...@utk.edu>: > On Wed, Jan 9, 2013 at 3:17 AM, James Starlight <jmsstarli...@gmail.com>wrote: > >> As I understood that gromacs version already has included openMM so >> the installation of the external openMM sources is not needed, isnt it >> ? >> > > No the new build in GPU implementation and openMM are two different things. > The Gromacs-OpenMM interface isn't actively maintained and thus not > recommended. > > >> also I wounder to know what exactly CUDA version is needed ? For >> example I've tried lattest cuda-5.0 but with that version i've obtain >> error from mdrun-openmm that platform cuda was not detected (gromacs >> was compilated without any errors). >> > with the natived gpu implementation (GMX_GPU) cuda 5.0 works fine. > > >> by the way is it possible to compilate gromacs-4.6 agains other >> platgorm ( e.g openCL) ? I have no problems with the compatibility of >> the openCL and openMM. >> > GMX_GPU doesn't support openCL. > > Roland > > >> >> James >> >> 2013/1/9 Szilárd Páll <szilard.p...@cbr.su.se>: >> > On Tue, Jan 8, 2013 at 3:22 PM, James Starlight <jmsstarli...@gmail.com >> >wrote: >> > >> >> So could someone provide me more about gpu-accelerated MD implemented >> >> in the 4.6 gromacs ? Does it require openMM (what version is supported >> >> >> > >> > FYI, if nobody can, trust G: >> > http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration >> > http://lmgtfy.com/?q=gromacs+4.6+installation+instructions >> > >> > The wiki and mailing list contains quite extensive information (indexed >> by >> > G). >> > >> > Otherwise, release notes (not final): >> > http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x >> > >> > Install guide is at the expected location: >> > http://www.gromacs.org/Documentation/Installation_Instructions >> > >> > Cheers, >> > -- >> > Szilárd >> > >> > >> >> for that gromacs release ?) installed? By the way at present time I >> >> force with the problem of compilation 4.1.1 openMM (i need to compile >> >> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11 >> >> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know. >> >> >> >> >> >> James >> >> >> >> 2013/1/7 James Starlight <jmsstarli...@gmail.com>: >> >> > Hi Szilárd! >> >> > >> >> > As I understood you correctly gromacs-4.6 have specific algorithm >> >> > (independent on openMM?) for gpu-based calculations havent ? If it >> >> > true how I should compilate such new gpu-based gromacs? In the >> >> > gromacs-4.6-beta-3 folder I've found instructuon for the standart >> >> > installation via cmake >> >> > >> >> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF >> >> > >> >> > >> >> > James >> >> > >> >> > 2013/1/7 Szilárd Páll <szilard.p...@cbr.su.se>: >> >> >> Szilárd >> >> -- >> >> 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 >> -- >> 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 >> >> >> >> >> > > > -- > 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