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

Tue Jun 9 18:04:50 CEST 2015

Thanks Mark. That seems to have worked. I will now try to do the same with
Plumed.

> Hi Mark,
>
> I will try that and let you know what happens.
>
> Thanks
> James
>
>> Hi,
>>
>> If you're trying to install into your source or build directory, don't
>> do
>> that. You also seem to be running mpich from its build directory, which
>> might be asking for trouble also. Unpack source in one place. Build in
>> one
>> place, however that software prefers it. Install in yet another place.
>> Then
>> use the installed version :-)
>>
>> Mark
>>
>> On Tue, Jun 9, 2015 at 5:15 PM <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>>
>>> 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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>>> >>
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