[gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger at mrc-lmb.cam.ac.uk]

You may be right. I get the same errors from trying to compile non-PLUMED
normal GROMACS 5.0.4 as when I try with PLUMED (after removing duplicate
instruction to link PLUMED).

Make abruptly stops at this point with no clear error (using VERBOSE=1).

Linking CXX executable ../../bin/gmx_mpi
cd /lmb/home/jkrieger/bin/gromacs-mpi/src/programs && /usr/bin/cmake -E
cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/lmb/home/jkrieger/bin/mpich-3.1.4-build/bin/mpicxx    -mavx    -Wextra
-Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function
 -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops  -Wno-array-bounds  
    CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o
CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
CMakeFiles/view_objlib.dir/view/view.cpp.o  -o ../../bin/gmx_mpi -rdynamic
../../lib/libgromacs_mpi.so.0.0.0 -fopenmp -ldl -lrt -lm -lz
../contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a -lblas -llapack -lblas
-llapack -Wl,-rpath,/lmb/home/jkrieger/bin/gromacs-mpi/lib:
/usr/bin/cmake -E cmake_progress_report
/lmb/home/jkrieger/bin/gromacs-mpi/CMakeFiles
[100%] Built target gmx
/usr/bin/cmake -E cmake_progress_start
/lmb/home/jkrieger/bin/gromacs-mpi/CMakeFiles 0

Make install then complains that it cannot find gmx_mpi:

CMake Error at src/programs/cmake_install.cmake:42 (FILE):
  file INSTALL cannot find "/lmb/home/jkrieger/bin/gromacs-mpi/bin/gmx_mpi".
Call Stack (most recent call first):
  src/cmake_install.cmake:40 (INCLUDE)
  cmake_install.cmake:49 (INCLUDE)

> Hi,
>
> Anything. I think I understood that you can't install non-PLUMED normal
> GROMACS in MPI mode, in which case the main suspect is your MPI
> infrastructure, e.g. it was compiled with a different / incompatible
> compiler from the one you're using now.
>
> Mark
>
> On Tue, Jun 9, 2015 at 4:23 PM <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>
>> Hi Mark,
>>
>> Sorry I missed your message as I had forgotten I needed to enable
>> receiving messages. What MPI test program did you have in mind?
>>
>> Best wishes
>> James
>>
>> > More details are available on the plumed forum google group at
>> >
>> https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ
>> >
>> >> Hi,
>> >>
>> >> I have successfully installed plumed-2.1.2 (I believe with MPI
>> >> capabilities) and patched it onto gromacs-5.0.4, I am now trying to
>> >> install the gromacs and it's not working. Here are my errors from
>> make:
>> >>
>> >> collect2: error: ld returned 1 exit status
>> >> src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for
>> >> target
>> >> 'lib/libgromacs_mpi.so.0.0.0' failed
>> >> make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1
>> >> CMakeFiles/Makefile2:1948: recipe for target
>> >> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
>> >> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>> >> Makefile:146: recipe for target 'all' failed
>> >> make: *** [all] Error 2
>> >>
>> >> I have successfully installed the latest gcc compilers and tried to
>> tell
>> >> gromacs to use them with the following command (not sure if this is
>> >> right):
>> >> ccmake ../gromacs-5.0.4/ -DGMX_BUILD_OWN_FFTW=ON
>> >> -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/gcc-5.1.0-build/bin/gcc
>> >>
>> >> In any case I get similar errors using the default compilers on my
>> >> system.
>> >>
>> >> I am installing on a front-end node of our cluster at the LMB, which
>> has
>> >> a
>> >> shared filesystem.
>> >>
>> >> Please let me know if there's anything else I need to tell you so
>> that
>> >> you
>> >> can help.
>> >>
>> >> Many thanks
>> >> James
>> >>
>> >
>> >
>> >
>>
>>
>> --
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