[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 14:14:35 CEST 2015
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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>>>>>>> >>
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