[gmx-users] Error with MPICH

[Szilárd Páll]

That kind of cmake invocation with MPI on without setting the
compilers to the MPI wrappers can often fail depending on how well the
MPI installation is detected by cmake. Try setting CMAKE_C_COMPILER
and CMAKE_CXX_COMPILER variables to the MPI compiler wrappers, i.e.
mpicc/mpic++ or similar.
--
Szilárd


On Fri, Aug 18, 2017 at 2:34 PM, Souparno Adhikary
<souparnoa91 at gmail.com> wrote:
> My CMAKE was like this:
>
> /root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4
>
> I have compiled mpich2 with --enable-shared option.
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
>
> On Fri, Aug 18, 2017 at 6:01 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> If libmpich.so is available after building with --enabled-shared, then the
>> MPI wrapper compilers should take care of this. If you want more help, we
>> need to at least see how you called cmake, using mpicc and mpic++, and more
>> information about what was wrong than "it still doesn't work." :-)
>>
>> Mark
>>
>> On Fri, Aug 18, 2017 at 12:02 PM Souparno Adhikary <souparnoa91 at gmail.com>
>> wrote:
>>
>> > Hi,
>> >
>> > I was installing GROMACS-5.1.4 with MPI option in the server. It yielded
>> > the following error,
>> >
>> > [  6%] Linking CXX shared library ../../lib/libgromacs_mpi.so
>> > /usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation
>> R_X86_64_32
>> > against `.rodata.str1.8' can not be used when making a shared object;
>> > recompile with -fPIC
>> > /usr/local/lib/libmpich.a: could not read symbols: Bad value
>> > collect2: ld returned 1 exit status
>> > make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1
>> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>> > make: *** [all] Error 2
>> >
>> > As the available suggestions on the internet suggested, I recompiled the
>> > mpich with --enable-shared option and also setting the CXXFLAGS as -fPIC.
>> > It still doesn't work.
>> >
>> > Can you please help?
>> >
>> > Souparno Adhikary,
>> > CHPC Lab,
>> > Department of Microbiology,
>> > University of Calcutta.
>> > --
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