[gmx-users] Gromacs installation problem

[Douglas Houston]

Thanks a lot Mark, that worked (after I did "setenv LD_LIBRARY_PATH  
${LD_LIBRARY_PATH}:/usr/people/douglas/programs/gromacs-4.6.3/install/lib").


Quoting Mark Abraham <mark.j.abraham at gmail.com> on Fri, 12 Jul 2013  
13:22:01 +0100:

> 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
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
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>




_____________________________________________________
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.