Re: [gmx-users] gmx 4.6 mpi installation through openmpi?
Sorry, Hrachya Astsatryan, I have no idea in such case. Why not just try to install openmpi and fftw ahead by yourself before installing groamcs? On Mon, Apr 8, 2013 at 4:06 PM, Hrachya Astsatryan hr...@sci.am wrote: 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 -- 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?
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: $ tar -xzvf gromacs-4.6.1.tar.gz $ mkdir build $ cd build $ CMAKE_PREFIX_PATH=/home/ucaizk/ComTools/openmpi:/home/ucaizk/ComTools/fftw cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX =/home/ucaizk/ComTools/gromacs ../gromacs-4.6.1 $ make $ make install 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 -- 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
[gmx-users] gmx 4.6 mpi installation through openmpi?
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
Re: [gmx-users] gmx 4.6 mpi installation through openmpi?
Hi, As the error message states, the reason for the failed configuration is that CMake can't auto-detect MPI which is needed when you are not providing the MPI compiler wrapper as compiler. If you want to build with MPI you can either let CMake auto-detect MPI and just compile with the C compiler or pass CC=mpicc to CMake and use the MPI compiler magic instead of detection. Unfortunately, the new installation instructions don't explain this detail which was in fact briefly mentioned in the deprecated CMake instructions: http://www.gromacs.org/Documentation/Installation_Instructions_4.5/Cmake#MPI_build Cheers, -- Szilárd On Fri, Apr 5, 2013 at 5:12 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 -- 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
