[gmx-users] GROMACS 4.6v - Myrinet2000
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 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=$LD_LIBRARY_PATH:/backup/sicnas/gromacs/lib:/opt/mpi/lib /opt/mpi/bin/mpirun -machinefile /backup/sicnas/npt101/machine -np 16 /backup/sicnas/gromacs/bin/mdrun_mpi -s /backup/sicnas/npt101/topol.tpr -v -- Hrachya Astsatryan Head of HPC Laboratory, Institute for Informatics and Automation Problems, National Academy of Sciences of the Republic of Armenia 1, P. Sevak str., Yerevan 0014, Armenia t: 374 10 284780 f: 374 10 285812 e: hr...@sci.am skype: tighra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.6v - Myrinet2000
On Mon, Apr 8, 2013 at 2:28 AM, Hrachya Astsatryan hr...@sci.am wrote: Dear all, We have installed the latest version of Gromacs (version 4.6) on our cluster by the following step: * cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/**backup/sicnas/gromacs -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON With this command, you're building Gromacs' internal FFT rather than using FFTW. Your performance will be much better if you use FFTW. See the installation instructions for more information. -Justin The interconnection of the cluster is Myrinet2000 and the driver is MX (and mpich 1.3.1). The job scripts (see below) and different simulations show that there is no adequate performance (usually it should be 2-3 time more). Could you, pls. help us to overcome the problem in order to get better performance? With regards, Hrach #PBS -l nodes=8:ppn=2 ##PBS -l walltime=360:00 #PBS -q armcluster #PBS -e 33mM_16_new.err #PBS -o 33mM_16_new.log ## Specify the shell to be bash #PBS -S /bin/bash export LD_LIBRARY_PATH=$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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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 listgmx-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
Re: [gmx-users] GROMACS 4.6v - Myrinet2000
On Mon, Apr 8, 2013 at 1:37 PM, Justin Lemkul jalem...@vt.edu wrote: 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. No, the GMX_BUILD_OWN_FFTW option will simply tell the build system to download FFTW 3.3(.3?), build it, and link it statically against mdrun. I'm just realizing that the naming of the option allows it to be confused with GROMACS' built-in (=own) fftpack (which is typically at 2-3x+ slower). Unfortunately, the install guide refers to the option as -DGMX_BUILD_OWN_FFTW=ON which means that even Google can't find it. http://www.gromacs.org/Documentation/Installation_Instructions#3.4.1._FFTW Cheers, -- Szilard -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 listgmx-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/Searchbefore 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 listgmx-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 listgmx-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
