Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
On 9/2/10 11:46 AM, Carsten Kutzner wrote: On Sep 2, 2010, at 11:42 AM, Rossen Apostolov wrote: Hi, Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf). I'll release a 4.5.1 right now. Hi Rossen, in ./src/tools/CMakeLists.txt the program gmx_rmsdist.c is doubly listed. Maybe you want to fix that also. It gives a warning only, though. Thanks Carsten! I fixed that. Strangely, I was getting a warning about it. Rossen Carsten A very short lived 4.5 (RIP) :) Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
On Sep 2, 2010, at 11:42 AM, Rossen Apostolov wrote: > > Hi, > > Yes, cmake is broken:) We forgot to add some of the cmake specific files for > distribution (which is created using autoconf). > > I'll release a 4.5.1 right now. Hi Rossen, in ./src/tools/CMakeLists.txt the program gmx_rmsdist.c is doubly listed. Maybe you want to fix that also. It gives a warning only, though. Carsten > > A very short lived 4.5 (RIP) :) > > Rossen > > On 9/2/10 11:23 AM, Christian Mücksch wrote: >> Dear all, >> >> so I downloaded Gromacs-4.5 and tried to compile the gpu-version with cmake >> version 2.8.0 as stated in the gpu installation instructions as >> >> export OPENMM_ROOT_DIR=/usr/local/openmm >> cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 >> make mdrun >> make install-mdrun >> >> But I get a few errors: >> >> - >> >> -- The C compiler identification is GNU >> -- The CXX compiler identification is GNU >> -- Check for working C compiler: /usr/bin/gcc >> -- Check for working C compiler: /usr/bin/gcc -- works >> -- Detecting C compiler ABI info >> -- Detecting C compiler ABI info - done >> -- Check for working CXX compiler: /usr/bin/c++ >> -- Check for working CXX compiler: /usr/bin/c++ -- works >> -- Detecting CXX compiler ABI info >> -- Detecting CXX compiler ABI info - done >> -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' >> or 'svn'. CTest update will not work. >> CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): >> CPack license resource file: >> "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallLicense.txt" >> could not be found. >> Call Stack (most recent call first): >> /usr/share/cmake-2.8/Modules/CPack.cmake:707 (cpack_check_file_exists) >> CMakeLists.txt:40 (include) >> >> >> CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): >> CPack readme resource file: >> "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallInfo.txt" >> could not be found. >> Call Stack (most recent call first): >> /usr/share/cmake-2.8/Modules/CPack.cmake:708 (cpack_check_file_exists) >> CMakeLists.txt:40 (include) >> >> >> CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): >> CPack welcome resource file: >> "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallWelcome.txt" >> could not be found. >> Call Stack (most recent call first): >> /usr/share/cmake-2.8/Modules/CPack.cmake:709 (cpack_check_file_exists) >> CMakeLists.txt:40 (include) >> >> >> -- Performing Test CFLAGS_WARN >> -- Performing Test CFLAGS_WARN - Success >> -- Performing Test CFLAGS_EXCESS_PREC >> -- Performing Test CFLAGS_EXCESS_PREC - Failed >> -- Performing Test CFLAGS_COPT >> -- Performing Test CFLAGS_COPT - Success >> -- Performing Test CFLAGS_NOINLINE >> -- Performing Test CFLAGS_NOINLINE - Success >> -- Performing Test CXXFLAGS_WARN >> -- Performing Test CXXFLAGS_WARN - Success >> -- Performing Test CXXFLAGS_EXCESS_PREC >> -- Performing Test CXXFLAGS_EXCESS_PREC - Failed >> -- Performing Test CXXFLAGS_COPT >> -- Performing Test CXXFLAGS_COPT - Success >> -- Performing Test CXXFLAGS_NOINLINE >> -- Performing Test CXXFLAGS_NOINLINE - Success >> -- No external FFT libraries needed for the OpenMM build, using fftpack! >> -- Threads not compatible with OpenMM build, disabled! >> CMake Warning at CMakeLists.txt:183 (message): >> CPU-based acceleration turned off, OpenMM does not support/need any! >> >> >> -- Looking for include files HAVE_STRING_H >> -- Looking for include files HAVE_STRING_H - found >> -- Looking for include files HAVE_MATH_H >> -- Looking for include files HAVE_MATH_H - found >> -- Looking for include files HAVE_LIMITS_H >> -- Looking for include files HAVE_LIMITS_H - found >> -- Looking for include files HAVE_MEMORY_H >> -- Looking for include files HAVE_MEMORY_H - found >> -- Looking for include files HAVE_UNISTD_H >> -- Looking for include files HAVE_UNISTD_H - found >> -- Looking for include files HAVE_PWD_H >> -- Looking for include files HAVE_PWD_H - found >> -- Looking for include files HAVE_STDINT_H >> -- Looking for include files HAVE_STDINT_H - found >> -- Looking for include files HAVE_STDLIB_H >> -- Looking for include files HAVE_STDLIB_H - found >> -- Looking for include files HAVE_PTHREAD_H >> -- Looking for include files HAVE_PTHREAD_H - found >> -- Looking for include files HAVE_DIRENT_H >> -- Looking for include files HAVE_DIRENT_H - found >> -- Looking for include files HAVE_INTTYPES_H >> -- Looking for include files HAVE_INTTYPES_H - found >> -- Looking for include files HAVE_REGEX_H >> -- Looking for include files HAVE_REGEX_H - found >> -- Looking for include files HAVE_SYS_TYPES_H >> -- Looking for include files HAVE_SYS_TYPES_H - found >> -- Looking for include files HAVE_SYS_STAT_H >> -- Looking for include files HAVE_SYS_STAT_H - found >> -- Looking for include files HAV
Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
Hi, Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf). I'll release a 4.5.1 right now. A very short lived 4.5 (RIP) :) Rossen On 9/2/10 11:23 AM, Christian Mücksch wrote: Dear all, so I downloaded Gromacs-4.5 and tried to compile the gpu-version with cmake version 2.8.0 as stated in the gpu installation instructions as export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 make mdrun make install-mdrun But I get a few errors: - -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work. CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack license resource file: "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallLicense.txt" could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:707 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack readme resource file: "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallInfo.txt" could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:708 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack welcome resource file: "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallWelcome.txt" could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:709 (cpack_check_file_exists) CMakeLists.txt:40 (include) -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Failed -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Failed -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- No external FFT libraries needed for the OpenMM build, using fftpack! -- Threads not compatible with OpenMM build, disabled! CMake Warning at CMakeLists.txt:183 (message): CPU-based acceleration turned off, OpenMM does not support/need any! -- Looking for include files HAVE_STRING_H -- Looking for include files HAVE_STRING_H - found -- Looking for include files HAVE_MATH_H -- Looking for include files HAVE_MATH_H - found -- Looking for include files HAVE_LIMITS_H -- Looking for include files HAVE_LIMITS_H - found -- Looking for include files HAVE_MEMORY_H -- Looking for include files HAVE_MEMORY_H - found -- Looking for include files HAVE_UNISTD_H -- Looking for include files HAVE_UNISTD_H - found -- Looking for include files HAVE_PWD_H -- Looking for include files HAVE_PWD_H - found -- Looking for include files HAVE_STDINT_H -- Looking for include files HAVE_STDINT_H - found -- Looking for include files HAVE_STDLIB_H -- Looking for include files HAVE_STDLIB_H - found -- Looking for include files HAVE_PTHREAD_H -- Looking for include files HAVE_PTHREAD_H - found -- Looking for include files HAVE_DIRENT_H -- Looking for include files HAVE_DIRENT_H - found -- Looking for include files HAVE_INTTYPES_H -- Looking for include files HAVE_INTTYPES_H - found -- Looking for include files HAVE_REGEX_H -- Looking for include files HAVE_REGEX_H - found -- Looking for include files HAVE_SYS_TYPES_H -- Looking for include files HAVE_SYS_TYPES_H - found -- Looking for include files HAVE_SYS_STAT_H -- Looking for include files HAVE_SYS_STAT_H - found -- Looking for include files HAVE_SYS_TIME_H -- Looking for include files HAVE_SYS_TIME_H - found -- Looking for include files HAVE_RPC_RPC_H -- Looking for include files HAVE_RPC_RPC_H - found -- Looking for include files HAVE_RPC_XDR_H -- Looking for include files HAVE_RPC_XDR_H - found -- Looking for include files HAVE_XMMINTRIN_H -- Looking for include files HAVE_XMMINTRIN_H - found -- Looking for include files HAVE_EMMINTRIN_H -- Looking for include files HAVE_EMMINTRIN_H - found -- Looking for include files HAVE_PMMINTRIN_H -- Looking for include
Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
Today, I have made similar observations and recorded them in the Bugzilla database here http://bugzilla.gromacs.org/show_bug.cgi?id=539 For now, I do not think cmake works properly. autotools have been fine for me, however. Mark - Original Message - From: Christian Mücksch Date: Thursday, September 2, 2010 19:26 Subject: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5 To: gmx-users@gromacs.org > Dear all, > > so I downloaded Gromacs-4.5 and tried to compile the gpu-version > with cmake version 2.8.0 as stated in the gpu installation > instructions as > > export OPENMM_ROOT_DIR=/usr/local/openmm > cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 > make mdrun > make install-mdrun > > But I get a few errors: > > - > > -- The C compiler identification is GNU > -- The CXX compiler identification is GNU > -- Check for working C compiler: /usr/bin/gcc > -- Check for working C compiler: /usr/bin/gcc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- CTest cannot determine repository type. Please set > UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work. > CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): > CPack license resource file: > "/home/c_muecksch/gpu_Install_Linux/gromacs- > 4.5/admin/InstallLicense.txt" could not be found. > Call Stack (most recent call first): > /usr/share/cmake-2.8/Modules/CPack.cmake:707 > (cpack_check_file_exists) CMakeLists.txt:40 (include) > > > CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): > CPack readme resource file: > "/home/c_muecksch/gpu_Install_Linux/gromacs- > 4.5/admin/InstallInfo.txt" could not be found. > Call Stack (most recent call first): > /usr/share/cmake-2.8/Modules/CPack.cmake:708 > (cpack_check_file_exists) CMakeLists.txt:40 (include) > > > CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): > CPack welcome resource file: > "/home/c_muecksch/gpu_Install_Linux/gromacs- > 4.5/admin/InstallWelcome.txt" could not be found. > Call Stack (most recent call first): > /usr/share/cmake-2.8/Modules/CPack.cmake:709 > (cpack_check_file_exists) CMakeLists.txt:40 (include) > > > -- Performing Test CFLAGS_WARN > -- Performing Test CFLAGS_WARN - Success > -- Performing Test CFLAGS_EXCESS_PREC > -- Performing Test CFLAGS_EXCESS_PREC - Failed > -- Performing Test CFLAGS_COPT > -- Performing Test CFLAGS_COPT - Success > -- Performing Test CFLAGS_NOINLINE > -- Performing Test CFLAGS_NOINLINE - Success > -- Performing Test CXXFLAGS_WARN > -- Performing Test CXXFLAGS_WARN - Success > -- Performing Test CXXFLAGS_EXCESS_PREC > -- Performing Test CXXFLAGS_EXCESS_PREC - Failed > -- Performing Test CXXFLAGS_COPT > -- Performing Test CXXFLAGS_COPT - Success > -- Performing Test CXXFLAGS_NOINLINE > -- Performing Test CXXFLAGS_NOINLINE - Success > -- No external FFT libraries needed for the OpenMM build, using > fftpack!-- Threads not compatible with OpenMM build, disabled! > CMake Warning at CMakeLists.txt:183 (message): > CPU-based acceleration turned off, OpenMM does not > support/need any! > > > -- Looking for include files HAVE_STRING_H > -- Looking for include files HAVE_STRING_H - found > -- Looking for include files HAVE_MATH_H > -- Looking for include files HAVE_MATH_H - found > -- Looking for include files HAVE_LIMITS_H > -- Looking for include files HAVE_LIMITS_H - found > -- Looking for include files HAVE_MEMORY_H > -- Looking for include files HAVE_MEMORY_H - found > -- Looking for include files HAVE_UNISTD_H > -- Looking for include files HAVE_UNISTD_H - found > -- Looking for include files HAVE_PWD_H > -- Looking for include files HAVE_PWD_H - found > -- Looking for include files HAVE_STDINT_H > -- Looking for include files HAVE_STDINT_H - found > -- Looking for include files HAVE_STDLIB_H > -- Looking for include files HAVE_STDLIB_H - found > -- Looking for include files HAVE_PTHREAD_H > -- Looking for include files HAVE_PTHREAD_H - found > -- Looking for include files HAVE_DIRENT_H > -- Looking for include files HAVE_DIRENT_H - found > -- Looking for include files HAVE_INTTYPES_H > -- Looking for include files HAVE_INTTYPES_H - found > -- Looking for include files HAVE_REGEX_H > -- Looking for include files HAVE_REGEX_H - found > -- Looking for include fil
[gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
Dear all, so I downloaded Gromacs-4.5 and tried to compile the gpu-version with cmake version 2.8.0 as stated in the gpu installation instructions as export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 make mdrun make install-mdrun But I get a few errors: - -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work. CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack license resource file: "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallLicense.txt" could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:707 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack readme resource file: "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallInfo.txt" could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:708 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack welcome resource file: "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallWelcome.txt" could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:709 (cpack_check_file_exists) CMakeLists.txt:40 (include) -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Failed -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Failed -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- No external FFT libraries needed for the OpenMM build, using fftpack! -- Threads not compatible with OpenMM build, disabled! CMake Warning at CMakeLists.txt:183 (message): CPU-based acceleration turned off, OpenMM does not support/need any! -- Looking for include files HAVE_STRING_H -- Looking for include files HAVE_STRING_H - found -- Looking for include files HAVE_MATH_H -- Looking for include files HAVE_MATH_H - found -- Looking for include files HAVE_LIMITS_H -- Looking for include files HAVE_LIMITS_H - found -- Looking for include files HAVE_MEMORY_H -- Looking for include files HAVE_MEMORY_H - found -- Looking for include files HAVE_UNISTD_H -- Looking for include files HAVE_UNISTD_H - found -- Looking for include files HAVE_PWD_H -- Looking for include files HAVE_PWD_H - found -- Looking for include files HAVE_STDINT_H -- Looking for include files HAVE_STDINT_H - found -- Looking for include files HAVE_STDLIB_H -- Looking for include files HAVE_STDLIB_H - found -- Looking for include files HAVE_PTHREAD_H -- Looking for include files HAVE_PTHREAD_H - found -- Looking for include files HAVE_DIRENT_H -- Looking for include files HAVE_DIRENT_H - found -- Looking for include files HAVE_INTTYPES_H -- Looking for include files HAVE_INTTYPES_H - found -- Looking for include files HAVE_REGEX_H -- Looking for include files HAVE_REGEX_H - found -- Looking for include files HAVE_SYS_TYPES_H -- Looking for include files HAVE_SYS_TYPES_H - found -- Looking for include files HAVE_SYS_STAT_H -- Looking for include files HAVE_SYS_STAT_H - found -- Looking for include files HAVE_SYS_TIME_H -- Looking for include files HAVE_SYS_TIME_H - found -- Looking for include files HAVE_RPC_RPC_H -- Looking for include files HAVE_RPC_RPC_H - found -- Looking for include files HAVE_RPC_XDR_H -- Looking for include files HAVE_RPC_XDR_H - found -- Looking for include files HAVE_XMMINTRIN_H -- Looking for include files HAVE_XMMINTRIN_H - found -- Looking for include files HAVE_EMMINTRIN_H -- Looking for include files HAVE_EMMINTRIN_H - found -- Looking for include files HAVE_PMMINTRIN_H -- Looking for include files HAVE_PMMINTRIN_H - not found. -- Looking for include files HAVE_SMMINTRIN_H -- Looking for include files HAVE_SMMINTRIN_H - not found. -- Looking for include files HAVE_IO_H -- Looking for include files HAVE_IO_H - not found. -- Looking for strcasecmp --
