[gmx-users] Installing gromacs 4.6.6 with gsl 1.16

[Justin Lemkul]

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

>
> 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

==================================================