Re: [gmx-users] Cannot find gmx_mpi when installing gromacs 5.0
I'd guess your permissions on some part of /users/yli/gromacs-5.0/exec/bin/gmx_mpi are such that you can't access. Mark On Thu, Aug 28, 2014 at 4:06 AM, 朱文鹏 jasonzhu...@gmail.com wrote: Dear all, I am trying to install gromacs 5.0 by cmake on my cluster. But an error occurs when I make install. The module list for environment is given as below: mvapich2/2.0rc1-intel cmake/2.8.12.2 intel/2013.1.106 fftw/3.3.2 And the sequence of commands to execute is: --- cmake ../ \ -DCMAKE_C_COMPILER=mpicc \ -DCMAKE_CXX_COMPILER=mpicxx \ -DGMX_X11=OFF \ -DGMX_MPI=ON \ -DCMAKE_INSTALL_PREFIX=/users/yli/gromacs-5.0/exec \ -DCMAKE_INCLUDE_PATH=/gpfs/runtime/opt/fftw/3.3.2/include \ -DCMAKE_LIBRARY_PATH=/gpfs/runtime/opt/fftw/3.3.2/lib/libfftw3f.a make make install --- Configuration and make finished successfully. There are no errors or warnings on the first two steps. However, an error shows up at the final step of make install as below: --- .. -- Up-to-date: /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/analysismodule.h -- Up-to-date: /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/analysissettings.h -- Up-to-date: /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /users/yli/gromacs-5.0/exec/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:49 (INCLUDE) make: *** [install] Error 1 --- And the executable file gmx_mpi cannot be found anywhere. It is the first time I install the version 5.0. The same installation and environments work for the version 4.6.5. I am wondering if anyone has the same problems when installing gromacs 5.0. I would appreciate it if you have any suggestion to my installation. Thank you very much. Best, Jason -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cannot find gmx_mpi when installing gromacs 5.0
Dear Mark, Thank you for your response. But I can install gromacs 4.6.5 successfully with the same permission. I will still contact the administrator of the cluster. Do you have idea what permissions I should ask them for if I need to install 5.0? Any files or directories, or any permissions to execute files? I don't think it is good for gromacs installation to access some parts needing higher permissions. After all, most of users who need to install gromacs onto cluster are not administrators. Best, Jason Date: Thu, 28 Aug 2014 08:45:40 +0200 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] Cannot find gmx_mpi when installing gromacs 5.0 Message-ID: camnumaqmqgkjdl7rgzfm4ua4ovxspo5r98evumm5zucp1oj...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 I'd guess your permissions on some part of /users/yli/gromacs-5.0/exec/bin/gmx_mpi are such that you can't access. Mark On Thu, Aug 28, 2014 at 4:06 AM, ??? jasonzhu...@gmail.com wrote: Dear all, I am trying to install gromacs 5.0 by cmake on my cluster. But an error occurs when I make install. The module list for environment is given as below: mvapich2/2.0rc1-intel cmake/2.8.12.2 intel/2013.1.106 fftw/3.3.2 And the sequence of commands to execute is: --- cmake ../ \ -DCMAKE_C_COMPILER=mpicc \ -DCMAKE_CXX_COMPILER=mpicxx \ -DGMX_X11=OFF \ -DGMX_MPI=ON \ -DCMAKE_INSTALL_PREFIX=/users/yli/gromacs-5.0/exec \ -DCMAKE_INCLUDE_PATH=/gpfs/runtime/opt/fftw/3.3.2/include \ -DCMAKE_LIBRARY_PATH=/gpfs/runtime/opt/fftw/3.3.2/lib/libfftw3f.a make make install --- Configuration and make finished successfully. There are no errors or warnings on the first two steps. However, an error shows up at the final step of make install as below: --- .. -- Up-to-date: /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/ analysismodule.h -- Up-to-date: /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/ analysissettings.h -- Up-to-date: /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/ cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /users/yli/gromacs-5.0/exec/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:49 (INCLUDE) make: *** [install] Error 1 --- And the executable file gmx_mpi cannot be found anywhere. It is the first time I install the version 5.0. The same installation and environments work for the version 4.6.5. I am wondering if anyone has the same problems when installing gromacs 5.0. I would appreciate it if you have any suggestion to my installation. Thank you very much. Best, Jason -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cannot find gmx_mpi when installing gromacs 5.0
Dear all, I am trying to install gromacs 5.0 by cmake on my cluster. But an error occurs when I make install. The module list for environment is given as below: mvapich2/2.0rc1-intel cmake/2.8.12.2 intel/2013.1.106 fftw/3.3.2 And the sequence of commands to execute is: --- cmake ../ \ -DCMAKE_C_COMPILER=mpicc \ -DCMAKE_CXX_COMPILER=mpicxx \ -DGMX_X11=OFF \ -DGMX_MPI=ON \ -DCMAKE_INSTALL_PREFIX=/users/yli/gromacs-5.0/exec \ -DCMAKE_INCLUDE_PATH=/gpfs/runtime/opt/fftw/3.3.2/include \ -DCMAKE_LIBRARY_PATH=/gpfs/runtime/opt/fftw/3.3.2/lib/libfftw3f.a make make install --- Configuration and make finished successfully. There are no errors or warnings on the first two steps. However, an error shows up at the final step of make install as below: --- .. -- Up-to-date: /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/analysismodule.h -- Up-to-date: /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/analysissettings.h -- Up-to-date: /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /users/yli/gromacs-5.0/exec/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:49 (INCLUDE) make: *** [install] Error 1 --- And the executable file gmx_mpi cannot be found anywhere. It is the first time I install the version 5.0. The same installation and environments work for the version 4.6.5. I am wondering if anyone has the same problems when installing gromacs 5.0. I would appreciate it if you have any suggestion to my installation. Thank you very much. Best, Jason -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
