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

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Wed Jun 10 11:23:58 CEST 2015


Unfortunately it's still not working. mdrun_mpi gives me the following error:

Fatal error:
Plumed is not available. Check your PLUMED_KERNEL variable.

Any ideas what's wrong now?

> Here is the solution. Thanks to both Giovanni Bussi and Mark Abraham for
> your help.
>
> 0. configure/make/install mpi compilers (separate src, build and install
> directories are used as suggested by MA)
>
> tar -xvzfc mpich-3.1.4.tar.gz mpich-3.1.4-src
> mkdir mpich-3.1.4-build
> mkdir mpich-3.1.4-install
> cd mpich-3.1.4-build
> ../mpich-3.1.4-src/configure
> --prefix=/lmb/home/jkrieger/bin/mpich-3.1.4-install | & tee c.txt
> make VERBOSE=1 | & tee m.txt
> make install VERBOSE=1 | & tee mi.txt
>
> 1. configure/make/install plumed with addition of -fPIC to CFLAGS in
> Makefile.conf before making (plumed-2.1.2 appears to need to be built in
> the src directory)
>
> tar -xvzfc plumed-2.1.2.tgz plumed-2.1.2-src
> mkdir plumed-2.1.2-install
> cd plumed-2.1.2-src
> ./configure --prefix=/lmb/home/jkrieger/bin/plumed-2.1.2-install/
> CC=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
> CXX=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
> manually add -fPIC to CFLAGS in Makefile.conf (done using vi)
> make VERBOSE=1 | & tee m.txt
> make install VERBOSE=1 | & tee mi.txt
> update PATH and LD_LIBRARY_PATH (added to ~/.login on my system and
> applied by logging out and back in again)
>
> 2. patch plumed onto gromacs in --runtime mode (as per recommendation of
> GB)
>
> cd ~/bin
> cp -r gromacs-5.0.4-src/ gromacs-5.0.4-src-plumed/
> mkdir gromacs-5.0.4-build-plumed
> mkdir gromacs-5.0.4-install-plumed
> cd gromacs-5.0.4-src-plumed/
> plumed patch -p --runtime
>
> 3. configure/make/install gromacs with separate src/build/install
> directories (as per recommendation of MA) with removal of duplicate
> reference to Plumed.o from
> build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (as per
> recommendation of GB)
>
> cd ../gromacs-5.0.4-build-plumed
> cmake -DGMX_MPI=ON ../gromacs-5.0.4-src-plumed/ -DGMX_BUILD_OWN_FFTW=ON
> -DCMAKE_INSTALL_PREFIX=/lmb/home/jkrieger/bin/gromacs-5.0.4-install-plumed
> -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
> -DCMAKE_CXX_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
> remove duplicate reference to Plumed.o from
> build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (again with vi)
> make VERBOSE=1 | & tee m.txt
> make install VERBOSE=1 | & tee mi.txt
> update PATH and LD_LIBRARY_PATH (vi ~/.login, log out, log in again)
>
>> 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
>>>>> >> >>
>>>>> >> >
>>>>> >> >
>>>>> >> >
>>>>> >>
>>>>> >>
>>>>> >> --
>>>>> >> Gromacs Users mailing list
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