[gmx-users] Installation Problems with Gromacs4.6

[Mark Abraham]

On Fri, Mar 1, 2013 at 7:29 PM, Abhishek Acharya <aacharya at iitk.ac.in>wrote:

> Hello Gromacs Users.
> I have been trying to install Gromacs4.6 on our HPC facility. I think I
> have correctly provided all the necessary mpi and fftw library paths.


OK, but you'll make trouble-shooting easier if you tell us what you've done
:-)
CC=mpicc cmake .. -DCMAKE_PREFIX_PATH=$HOME/softwares/fftw-3.3.3 is the
simplest form likely to work.


> But
> when i try to run configure it gives me the following error:
>
>  CMake Error at cmake/FindFFTW.cmake:105 (message):
>    Could not find fftwf_plan_r2r_1d in
>    /home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at the
>    error message in
>    /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log to
>    find out what went wrong.  If you are using a static lib (.a) make sure
> you
>    have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
>    -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
>  Call Stack (most recent call first):
>    CMakeLists.txt:894 (find_package)
>
> As suggested here I looked into the CMakeError.log file of which I can't
> make any sense.
>
> Source file was:
> #include <mpi.h>
> int main(void) {
>   void* buf;
>   MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD);
> }
> Determining if the function fftwf_plan_r2r_1d exists in the
> /home/aacharya/softwares/fftw-3.3.3/lib failed with the following output:
> Change Dir: /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
>
> Run Build Command:/usr/bin/gmake "cmTryCompileExec2668319475/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
> CMakeFiles/cmTryCompileExec2668319475.dir/build
> gmake[1]: Entering directory
> `/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
> /home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_progress_report
> /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
> 1
> Building C object
> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
> /usr/bin/cc   -Wextra -Wno-missing-field-initializers -Wno-sign-compare
> -Wall -Wno-unused -Wunused-value
> -DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d   -o
> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o   -c
> /home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
> Linking C executable cmTryCompileExec2668319475
> /home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
> CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
> /usr/bin/cc   -Wextra -Wno-missing-field-initializers -Wno-sign-compare
> -Wall -Wno-unused -Wunused-value
> -DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
> -L/home/aacharya/softwares/fftw-3.3.3/lib
> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o  -o
> cmTryCompileExec2668319475 -rdynamic -lm
>

That looks weird. CMake is not trying to link to your FFTW library at all,
but all I can guess with current information is that something with your
call to cmake isn't working.

Mark

CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
> function `main':
> CheckFunctionExists.c:(.text+0x15): undefined reference to
> `fftwf_plan_r2r_1d'
> collect2: ld returned 1 exit status
> gmake[1]: *** [cmTryCompileExec2668319475] Error 1
> gmake[1]: Leaving directory
> `/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTryCompileExec2668319475/fast] Error 2
>
>
> Kindly help. I tried installing 4.5.6 and it got installed without any
> such problems. I need 4.6 because my tpr files are produced in Gromacs4.6
> and I am using the Verlet cutoff scheme.
> Thanks in advance
> With Regards
> Abhishek Acharya
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