On Mon, Apr 8, 2013 at 2:28 AM, Hrachya Astsatryan <hr...@sci.am> wrote:
> Dear all, > > We have installed the latest version of Gromacs (version 4.6) on our > cluster by the following step: > > * cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/**backup/sicnas/gromacs > -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON > > With this command, you're building Gromacs' internal FFT rather than using FFTW. Your performance will be much better if you use FFTW. See the installation instructions for more information. -Justin > The interconnection of the cluster is Myrinet2000 and the driver is MX > (and mpich 1.3.1). > > The job scripts (see below) and different simulations show that there is > no adequate performance (usually it should be 2-3 time more). > > Could you, pls. help us to overcome the problem in order to get better > performance? > > With regards, > Hrach > > #PBS -l nodes=8:ppn=2 > ##PBS -l walltime=360:00 > #PBS -q armcluster > #PBS -e 33mM_16_new.err > #PBS -o 33mM_16_new.log > ## Specify the shell to be bash > #PBS -S /bin/bash > > export LD_LIBRARY_PATH=$LD_LIBRARY_**PATH:/backup/sicnas/gromacs/** > lib:/opt/mpi/lib > > /opt/mpi/bin/mpirun -machinefile /backup/sicnas/npt101/machine -np 16 > /backup/sicnas/gromacs/bin/**mdrun_mpi -s /backup/sicnas/npt101/topol.**tpr > -v > > > > > > -- > Hrachya Astsatryan > Head of HPC Laboratory, > Institute for Informatics and Automation Problems, > National Academy of Sciences of the Republic of Armenia > 1, P. Sevak str., Yerevan 0014, Armenia > t: 374 10 284780 > f: 374 10 285812 > e: hr...@sci.am > skype: tighra > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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