[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
Tue Jun 9 20:23:38 CEST 2015
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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>>>> or
>>>> >> send a mail to gmx-users-request at gromacs.org.
>>>> >>
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>>
>>
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>
>
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