[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 17:26:36 CEST 2015


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
>> >> >>
>> >> >
>> >> >
>> >> >
>> >>
>> >>
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-request at gromacs.org.
>> >>
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send
>> > a mail to gmx-users-request at gromacs.org.
>> >
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.
>




More information about the gromacs.org_gmx-users mailing list