[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 14:22:04 CEST 2015 

Hi,

That's why you use a wrapper compiler - if you run cmake and tell it to use
the 1.8.5 wrapper compiler, you're good. But probably there will be no
significant difference unless more recent MPI supports your network
hardware better (in which case you should probably be using the MPI the
sysadmins have set up).

Mark

On Wed, Jun 10, 2015 at 2:14 PM <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> Yes that fixed it. I now have an mpi-aware version that works.
>
> I realise this is perhaps a separate issue now but it would be good to use
> the latest compiler version. My default is openmpi-1.5.4 and I could get
> openmpi-1.8.5 now. How would I go about setting up wrappers for that?
>
> Many thanks again
> James
>
> > Firstly the problem of finding PLUMED is now fixed.
> >
> > I appear to also have a problem that my mdrun_mpi isn't mpi-aware but
> > rather starts an individual mdrun process on each node requested. I think
> > this might be related to this bug http://redmine.gromacs.org/issues/572
> > and am trying whether using the mpicc and mpicxx wrappers fixes it.
> >
> >> 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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