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

[Mark Abraham]

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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