[gmx-users] Gromacs installation problem

[Mark Abraham]

On Fri, Jul 12, 2013 at 11:18 AM, Douglas Houston
<DouglasR.Houston at 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
>
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