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

Mark Abraham mark.j.abraham at gmail.com
Wed Jun 10 12:49:25 CEST 2015 

Hi,

That sounds like a job for the PLUMED documentation! ;-)

Mark

On Wed, Jun 10, 2015 at 11:24 AM <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> 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
> >>>>> >> >>
> >>>>> >> >
> >>>>> >> >
> >>>>> >> >
> >>>>> >>
> >>>>> >>
> >>>>> >> --
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> >>>>> >>
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> >>>>> >>
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