[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] gmx 4.6 mpi installation through openmpi?
Dear Zhikun Cai, Thank you for your quick response. On 4/8/13 11:15 AM, Zhikun Cai wrote: Hi, see installation instruction with CMAKE here: http://www.gromacs.org/Documentation/Installation_Instructions I guess that maybe you need to specify your Openmpi and FFTW installation directories using options CMAKE_PREFIX_PATH. For example, my Openmpi and FFTW were firstly installed in /home/ucaizk/ComTools/openmpi and /home/ucaizk/ComTools/fftw Then, I installed gromacs with command lines below: wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.1.tar.gz $ tar -xzvf gromacs-4.6.1.tar.gz $ mkdir build $ cd build Done $ CMAKE_PREFIX_PATH=/home/ucaizk/ComTools/openmpi:/home/ucaizk/ComTools/fftw export CMAKE_PREFIX_PATH=/opt/mpi (I use an option below to download and install the fftw by gromacs) cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX =/home/ucaizk/ComTools/gromacs ../gromacs-4.6.1 cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/backup/sicnas/gromacs -DGMX_BUILD_OWN_FFTW=ON (I want to install on /backup/sicnas/gromacs, which is shared by nodes) $ make $ make install done! And finally get the following error: /backup/sicnas/gromacs/bin/mdrun_mpi: error while loading shared libraries: libblas.so.3: cannot open shared object file: No such file or directory When above was done, cd to your home directory and add one line to .bashrc file export PATH=$PATH:/home/ucaizk/ComTools/gromacs/bin restart bash shell, then all are done! Hope it helps! Zhikun On Fri, Apr 5, 2013 at 11:12 PM, 라지브간디 ra...@kaist.ac.kr wrote: Dear gmx users, I could able to install gmx4.6.1 without MPI option in my cluster, whereas the MPI fails to install and gives the following error ( used command line cmake .. -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON ) CMake Error at cmake/gmxManageMPI.cmake:161 (message): MPI support requested, but no MPI compiler found. Either set the C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or set the variables reported missing for MPI_C above. Call Stack (most recent call first): CMakeLists.txt:494 (include) I have also installed openmpi 1.5 version. which mpirun shows /usr/bin/mpirun. It seems openmpi installed in /usr/bin/openmpi/ I dont know how to do link this cmake. Please need some suggestion. Thanks. -- 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 -- 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] Help: Gromacs Installation
Dear Mark Abraham all, We used another benchmarking systems, such as d.dppc on 4 processors, but we have the same problem (1 proc use about 100%, the others 0%). After for a while we receive the following error: Working directory is /localuser/armen/d.dppc Running on host wn1.ysu-cluster.grid.am Time is Fri Apr 22 13:55:47 AMST 2011 Directory is /localuser/armen/d.dppc START Start: Fri Apr 22 13:55:47 AMST 2011 p2_487: p4_error: Timeout in establishing connection to remote process: 0 rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32 p2_487: (301.160156) net_send: could not write to fd=5, errno = 32 p0_32738: p4_error: net_recv read: probable EOF on socket: 1 p3_490: (301.160156) net_send: could not write to fd=6, errno = 104 p3_490: p4_error: net_send write: -1 p3_490: (305.167969) net_send: could not write to fd=5, errno = 32 p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32 p1_483: p4_error: net_recv read: probable EOF on socket: 1 rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32 p1_483: (311.171875) net_send: could not write to fd=5, errno = 32 Fri Apr 22 14:00:59 AMST 2011 End: Fri Apr 22 14:00:59 AMST 2011 END We tried new version of Gromacs, but receive the same error. Please, help us to overcome the problem. With regards, Hrach On 4/22/11 1:41 PM, Mark Abraham wrote: On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote: Dear all, I would like to inform you that I have installed the gromacs4.0.7 package on the cluster (nodes of the cluster are 8 core Intel, OS: RHEL4 Scientific Linux) with the following steps: yum install fftw3 fftw3-devel ./configure --prefix=/localuser/armen/gromacs --enable-mpi Also I have downloaded gmxbench-3.0 package and try to run d.villin to test it. Unfortunately it wok fine until np is 1,2,3, if I use more than 3 procs I receive low CPU balancing and the process in hanging. Could you, please, help me to overcome the problem? Probably you have only four physical cores (hyperthreading is not normally useful), or your MPI is configured to use only four cores, or these benchmarks are too small to scale usefully. Choosing to do a new installation of a GROMACS version that is several years old is normally less productive than the latest version. Mark -- 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] Help: Gromacs Installation
Dear Roland, We need to run the GROMACS on the base of the nodes of our cluster (in order to use all computational resources of the cluster), that's why we need MPI (instead of using thread or OpenMP within the SMP node). I can run simple MPI examples, so I guess the problem on the implementation of the Gromacs. Regads, Hrach On 4/27/11 11:29 PM, Roland Schulz wrote: This seems to be a problem with your MPI library. Test to see whether other MPI programs don't have the same problem. If it is not GROMACS specific please ask on the mailinglist of your MPI library. If it only happens with GROMACS be more specific about what your setup is (what MPI library, what hardware, ...). Also you could use the latest GROMACS 4.5.x. It has built in thread support and doesn't need MPI as long as you only run on n cores within one SMP node. Roland On Wed, Apr 27, 2011 at 2:13 PM, Hrachya Astsatryan hr...@sci.am mailto:hr...@sci.am wrote: Dear Mark Abraham all, We used another benchmarking systems, such as d.dppc on 4 processors, but we have the same problem (1 proc use about 100%, the others 0%). After for a while we receive the following error: Working directory is /localuser/armen/d.dppc Running on host wn1.ysu-cluster.grid.am http://wn1.ysu-cluster.grid.am Time is Fri Apr 22 13:55:47 AMST 2011 Directory is /localuser/armen/d.dppc START Start: Fri Apr 22 13:55:47 AMST 2011 p2_487: p4_error: Timeout in establishing connection to remote process: 0 rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32 p2_487: (301.160156) net_send: could not write to fd=5, errno = 32 p0_32738: p4_error: net_recv read: probable EOF on socket: 1 p3_490: (301.160156) net_send: could not write to fd=6, errno = 104 p3_490: p4_error: net_send write: -1 p3_490: (305.167969) net_send: could not write to fd=5, errno = 32 p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32 p1_483: p4_error: net_recv read: probable EOF on socket: 1 rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32 p1_483: (311.171875) net_send: could not write to fd=5, errno = 32 Fri Apr 22 14:00:59 AMST 2011 End: Fri Apr 22 14:00:59 AMST 2011 END We tried new version of Gromacs, but receive the same error. Please, help us to overcome the problem. With regards, Hrach On 4/22/11 1:41 PM, Mark Abraham wrote: On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote: Dear all, I would like to inform you that I have installed the gromacs4.0.7 package on the cluster (nodes of the cluster are 8 core Intel, OS: RHEL4 Scientific Linux) with the following steps: yum install fftw3 fftw3-devel ./configure --prefix=/localuser/armen/gromacs --enable-mpi Also I have downloaded gmxbench-3.0 package and try to run d.villin to test it. Unfortunately it wok fine until np is 1,2,3, if I use more than 3 procs I receive low CPU balancing and the process in hanging. Could you, please, help me to overcome the problem? Probably you have only four physical cores (hyperthreading is not normally useful), or your MPI is configured to use only four cores, or these benchmarks are too small to scale usefully. Choosing to do a new installation of a GROMACS version that is several years old is normally less productive than the latest version. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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 http://cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Help: Gromacs Installation
Dear all, I would like to inform you that I have installed the gromacs4.0.7 package on the cluster (nodes of the cluster are 8 core Intel, OS: RHEL4 Scientific Linux) with the following steps: yum install fftw3 fftw3-devel ./configure --prefix=/localuser/armen/gromacs --enable-mpi Also I have downloaded gmxbench-3.0 package and try to run d.villin to test it. Unfortunately it wok fine until np is 1,2,3, if I use more than 3 procs I receive low CPU balancing and the process in hanging. Could you, please, help me to overcome the problem? Regards, Hrach -- 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
