[gmx-users] Trouble compiling gromacs 5.1.2 with plumed 2.2.3

[Mark Abraham]

Hi,

The simplest explanation would be that you're somehow actually using
different MPI compilers for the two stages. You should make sure you're
following the PLUMED installation instructions, and perhaps contact their
forums/whatever also. Your setup seems so vanilla that things should just
be working.

Mark

On Tue, Oct 25, 2016 at 4:39 PM Anna Vernon <lappala.anna at gmail.com> wrote:

> So... I compiled and installed  gmx 5.1.2 on its own and it was fine. I
> patched it up with plumed 2.2.3 and it could not compile anymore.
>
> The error message was this:
>
> usr/bin/ld: ../../lib/libgromacs.so.1.2.0: undefined reference to symbol
> 'MPI_Isend'
> //usr/lib/x86_64-linux-gnu/libmpich.so.12: error adding symbols: DSO
> missing from command line
> collect2: error: ld returned 1 exit status
> share/template/CMakeFiles/template.dir/build.make:99: recipe for target
> 'bin/template' failed
> make[2]: *** [bin/template] Error 1
> CMakeFiles/Makefile2:1745: recipe for target
> 'share/template/CMakeFiles/template.dir/all' failed
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2
>
> this is my gromacs cmake:
>
> cmake .. -DGMX_MPI=on -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
> -DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np -DNUMPROC=2, -DNUMPROC=3,
> -DNUMPROC=4, -DNUMPROC=5, -DNUMPROC=6, -DNUMPROC=7,-DNUMPROC=8
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
> after which i do make  and make, upon which the error message appears.
>
> this is how I configure plumed:
>
> ./configure --enable-mpi CXX="$MPICXX" --prefix=/usr/local
>
> What is going on?
>
> Anna
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