[gmx-users] Installing gromacs 4.6.6 with gsl 1.16

[B P]

On Mon, Sep 1, 2014 at 4:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/1/14, 3:26 AM, B P wrote:
>
>> Dear Gromacs users,
>> am trying to install gromacs 4.6.6 with GSL.
>>
>> I have installed fftw3 and GSL in separate directories on Desktop and
>> linked them to Gromacs in the follwing command.
>>
>> /home/user1/Desktop/cmake-2.8.12.2-Linux-i386/bin/ccmake ../ -DGMX_MPI=ON
>> -DGMX_SIMD=SSE2 -DGMX_DOUBLE=ON
>> -DCMAKE_INSTALL_PREFIX=/home/user1/Desktop/newgro/ -DBUILD_SHARED_LIBS=ON
>> -DGMX_FFT_LIBRARY=FFTW3 -DFFTW_LIBRARIES="/home/user1/Desktop/fftw/"
>> -DFFTW_INCLUDE="/home/user1/Desktop/fftw/" -DGMX_GSL=ON
>>
>>
> You're using FFTW_LIBRARIES and FFTW_INCLUDE incorrectly.  The LIBRARIES
> variable needs to point to the actual libraries, and the INCLUDE variable
> needs to point the the /include subdirectory.  Or make your life easy by
> dropping both and setting -DCMAKE_PREFIX_PATH=/home/user1/Desktop/fftw
>
> -Justin


Thanks Justin. Problem solved.


>
>
>
>> I have set  the path to GSL libary and include paths in the options given
>> by ccmake toggle.
>>
>> Gromacs gets configured with many warnings displaying following error
>> message.
>>
>> -- Configuring done
>> WARNING: Target "template" requests linking to directory
>> "/home/user1/Desktop/fftw".  Targets may link only to libraries.  CMake is
>> dropping the item.
>> WARNING: Target "gmx" requests linking to directory
>> "/home/user1/Desktop/fftw".  Targets may link only to libraries.  CMake is
>> dropping the item.
>> WARNING: Target "gmx" requests linking to directory
>> "/home/user1/Desktop/fftw".  Targets may link only to libraries.  CMake is
>> dropping the item.
>> WARNING: Target "md" requests linking to directory
>> "/home/user1/Desktop/fftw".  Targets may link only to libraries.  CMake is
>> dropping the item.
>> WARNING: Target "g_luck" requests linking to directory
>> "/home/user1/Desktop/fftw".  Targets may link only to libraries.  CMake is
>> dropping the item.
>> WARNING: Target "gmxpreprocess" requests linking to directory
>> "/home/user1/Desktop/fftw".  Targets may link only to libraries.  CMake is
>> dropping the item.
>> WARNING: Target "md" requests linking to directory
>> "/home/user1/Desktop/fftw".  Targets may link only to libraries.  CMake is
>> dropping the item.
>> WARNING: Target "gmxpreprocess" requests linking to directory
>> "/home/user1/Desktop/fftw".  Targets may link only to libraries.  CMake is
>> dropping the item.
>> WARNING: Target "g_protonate" requests linking to directory
>> "/home/user1/Desktop/fftw".  Targets may link only to libraries.  CMake is
>> dropping the item.
>> .
>> .
>> .
>> .
>> .
>>
>>
>> I issued make command. It started compiling and stopped displaying
>> following error.
>>
>> Linking C executable template
>> cd /home/user1/Desktop/newgro/gromacs-4.6.6/build/share/template &&
>> /home/user1/Desktop/cmake-2.8.12.2-Linux-i386/bin/cmake -E
>> cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
>> /usr/bin/cc  -msse2    -Wextra -Wno-missing-field-initializers
>> -Wno-sign-compare -Wall -Wno-unused -Wunused-value   -fomit-frame-pointer
>> -funroll-all-loops  -O3 -DNDEBUG    -Wl,--export-dynamic
>> CMakeFiles/template.dir/template.c.o  -o template -rdynamic
>> ../../src/gmxlib/libgmx_mpi_d.so.8 /usr/local/lib/libmpi.so -ldl -lm -lrt
>> -lnsl -lutil -ldl -lm -lrt -lnsl -lutil -ldl -lm -lpthread -fopenmp
>> -Wl,-rpath,/home/user1/Desktop/newgro/gromacs-4.6.6/
>> build/src/gmxlib:/usr/local/lib
>>
>> ../../src/gmxlib/libgmx_mpi_d.so.8: undefined reference to `fftw_version'
>> collect2: ld returned 1 exit status
>> make[2]: *** [share/template/template] Error 1
>> make[2]: Leaving directory `/home/user1/Desktop/newgro/
>> gromacs-4.6.6/build'
>> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> make[1]: Leaving directory `/home/user1/Desktop/newgro/
>> gromacs-4.6.6/build'
>> make: *** [all] Error 2
>>
>>
>> Where could be the possible error?
>>
>> PS. FFTW3 installed without any error. I have chosen to install all the
>> files in the same directory. So, the include and lib files are present in
>> the fftw folder on Desktop.
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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