[gmx-users] Re: gInstallation Problems with Gromacs4.6

[Abhishek Acharya]

>> Date: Fri, 1 Mar 2013 23:59:36 +0530
>> From: "Abhishek Acharya" <aacharya at iitk.ac.in>
>> Subject: [gmx-users] Installation Problems with Gromacs4.6
>> To: "gromacs maillist" <gmx-users at gromacs.org>
>> Message-ID:
>>         <2ca7063e41d6ddfa7ea411dc3cfe3ad3.squirrel at webmail.iitk.ac.in>
>> Content-Type: text/plain;charset=iso-8859-1
>>
>> 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.
>> 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
> Strange, there is supposed to be a "-lfftw3f" before "-lm". Can you
> tell us what your cmake command line was?
>
>> 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.

Thank you Mark and Christoph for your replies. I solved the installation
problem by configuring gromacs with static libraries. I somehow didn't
notice earlier, there was a note saying that Shared Libraries might be
problematic with MPI.

With Regards
Abhishek