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

Wed Jun 10 13:28:16 CEST 2015

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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>>>>>> >>
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