[gmx-users] Message-ID:
Hey Mark, I tried to set the CMAKE_LIBRARY_PATH to an actual file, because it cannot be found by cmake if I left it out, but it is there. Greetings Kim > > Ursprüngliche Nachricht: > > Von: Kim Jessica Novacek <kim.j.nova...@campus.lmu.de> > > An: gromacs.org_gmx-users@maillist.sys.kth.se > > Kopie: > > Datum: Mon Oct 12 15:31:58 CEST 2015 > > > > Although I did let out the Xeon Phi Command there is still the same make > > error. > > Greetings > > Kim > > > > > > /usr/bin/ld: cannot find -lcudart > > /usr/bin/ld: cannot find -lmpi > > collect2: error: ld returned 1 exit status > > make[2]: *** [bin/gmx_mpi] Fehler 1 > > make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2 > > make[1]: *** Auf noch nicht beendete Prozesse wird gewartet … > > /usr/bin/ld: cannot find -lcudart > > /usr/bin/ld: cannot find -lmpi > > collect2: error: ld returned 1 exit status > > make[2]: *** [bin/template] Fehler 1 > > make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2 > > make: *** [all] Fehler 2 > > > > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc > > -DGMX_MPI=ON > > -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit > > -DCMAKE_INSTALL_PREFIX=/usr > /l > > ocal/GROMACS -DGMX_FFT_LIBRARY=fftw3 > > -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a > -DCMAKE_BUILD_T > > YPE=DEBUG -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON > > -DCMAKE_C_FLAGS="-sta > ti > > c" -DCMAKE_CXX_FLAGS="-static" -DCMAKE_SKIP_RPATH=YES > > -DCMAKE_PREFIX_PATH=/usr/lib/cuda > > -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so > > -DCMAKE_PREFIX_PATH=/usr/include/ > li > > bxml2/libxml > -- 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] Message-ID:
Although I did let out the Xeon Phi Command there is still the same make error. Greetings Kim /usr/bin/ld: cannot find -lcudart /usr/bin/ld: cannot find -lmpi collect2: error: ld returned 1 exit status make[2]: *** [bin/gmx_mpi] Fehler 1 make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2 make[1]: *** Auf noch nicht beendete Prozesse wird gewartet … /usr/bin/ld: cannot find -lcudart /usr/bin/ld: cannot find -lmpi collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Fehler 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2 make: *** [all] Fehler 2 cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DCMAKE_INSTALL_PREFIX=/usr/local/GROMACS -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a -DCMAKE_BUILD_TYPE=DEBUG -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS="-static" -DCMAKE_CXX_FLAGS="-static" -DCMAKE_SKIP_RPATH=YES -DCMAKE_PREFIX_PATH=/usr/lib/cuda -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so -DCMAKE_PREFIX_PATH=/usr/include/libxml2/libxml -- 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] installation of gromacs
When I try to the install gromacs with the given commands in cmake I get the following error message in make. Can u please help me out? Thanks a lot Greetings Kim J. Novacek /usr/bin/ld: cannot find -lcudart /usr/bin/ld: cannot find -lmpi collect2: error: ld returned 1 exit status make[2]: *** [bin/gmx_mpi] Fehler 1 make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2 make[1]: *** Auf noch nicht beendete Prozesse wird gewartet … /usr/bin/ld: cannot find -lcudart /usr/bin/ld: cannot find -lmpi cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DCMAKE_INSTALL_PREFIX=/usr/local/GROMACS -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a -DCMAKE_BUILD_TYPE=DEBUG -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS="-static" -DCMAKE_CXX_FLAGS="-static" -DCMAKE_SKIP_RPATH=YES -DCMAKE_PREFIX_PATH=/usr/lib/cuda -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so -DCMAKE_PREFIX_PATH=/usr/include/libxml2/libxml -DCMAKE_TOOLCHAIN_FILE=Platform/XeonPhi -DCMAKE_PREFIX_PATH=/usr/bin/mpich -- 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] problem after installation
hello, I was at this step of the installation: GROMACS installs the script GMXRC in the bin subdirectory of the installation directory (e.g. /usr/local/gromacs/bin/GMXRC), which you should source from your shell: source /your/installation/prefix/here/bin/GMXRC It will detect what kind of shell you are running and set up your environment for using GROMACS. You may wish to arrange for your login scripts to do this automatically; please search the web for instructions on how to do this for your shell. Many of the GROMACS programs rely on data installed in the share/gromacs subdirectory of the installation directory. By default, the programs will use the environment variables set in the GMXRC script, and if this is not available they will try to guess the path based on their own location. This usually works well unless you change the names of directories inside the install tree. If you still need to do that, you might want to recompile with the new install location properly set, or edit the GMXRC script. is the GMXRC script the gmx[...].bash file? when I try source with this file nothing happens. What do I have to do, when the installation is done to run gromacs? Is there a user interface? Thanks in advance Kim J. Novacek -- 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.
