On Fri, Jul 12, 2013 at 11:18 AM, Douglas Houston <douglasr.hous...@ed.ac.uk> wrote: > Hi, > > I am having trouble installing Gromacs 4.6.3. > > In bash I am using the following sequence of commands: > > cd gromacs-4.6.3 > mkdir build > cd build > CC=/usr/people/douglas/programs/gcc-4.7.3/installation/bin/gcc > ~/programs/cmake-2.8.7/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON > make > sudo make install > > Everything seems to go OK until the 'sudo make install' stage when I get: > > "make: Warning: File `Makefile' has modification time 1.2e+04 s in the > future > CMake Error at cmake/gmxDetectClang30.cmake:36 (try_compile): > Failed to open > > > /usr/people/douglas/programs/gromacs-4.6.3/build/CMakeFiles/CMakeTmp/CMakeLists.txt > > Permission denied > Call Stack (most recent call first): > CMakeLists.txt:301 (gmx_detect_clang_3_0) > > > CMake Error at CMakeLists.txt:946 (add_subdirectory): > add_subdirectory given source "src/contrib/fftw" which is not an existing > directory. > > > CMake Error at CMakeLists.txt:956 (MESSAGE): > Cannot find FFTW 3 (with correct precision - libfftw3f for > single-precision > GROMACS or libfftw3 for double-precision GROMACS). Either choose the > right > precision, choose another FFT(W) library, enable the advanced option to > let > GROMACS build FFTW 3 for you, or use the really slow GROMACS built-in > fftpack library. > > > -- Configuring incomplete, errors occurred! > CMake Error: Unable to open check cache file for write. > /usr/people/douglas/programs/gromacs-4.6.3/build/CMakeFiles/cmake.check_cache > make: *** [cmake_check_build_system] Error 1" > > > I don't understand the 'permission denied' error on opening CMakeLists.txt - > when I 'ls' for this file it's not there at all. The "let gromacs build FFTW > 3 for you" I also don't understand as I'm already using the > -DGMX_BUILD_OWN_FFTW=ON option. > > Any help would be most appreciated.
Your system (or file server) seems a bit broken, if the time seen by root is very different from that of a file just made by a user. Also, you seem to have your build tree's file permissions set so that root can't read the files. I would suggest you plan to install to user file space, as you have done for gcc and cmake, via cmake .. -DCMAKE_INSTALL_PREFIX=/your/full/path/here. Now you side-step the access permissions issue. The subsequent problems are all caused by that. Mark > cheers, > > Doug > > > _____________________________________________________ > Dr. Douglas R. Houston > Lecturer > Room 3.23 > Institute of Structural and Molecular Biology > Michael Swann Building > King's Buildings > University of Edinburgh > Edinburgh, EH9 3JR, UK > Tel. 0131 650 7358 > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > -- > gmx-users mailing list 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list 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. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
