[gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT

[Mark Abraham]

Hi,

I suspect MPT has a bug such that one of its headers defines UNDEFINED,
which it should not do. If so, you can change src/gromacs/legacyheaders/names.h
lines 110-1 to read

#define GMX_UNDEFINED       "UNDEFINED"
#define ENUM_NAME(e, max, names)  ((((e) < 0) || ((e) >= (max))) ?
GMX_UNDEFINED : (names)[e])

and you should be fine. If so, please let us know, and please file a bug
report with SGI.

Mark

On Wed, Jan 6, 2016 at 5:33 PM hubert santuz <hubert.santuz at gmail.com>
wrote:

> Hi everyone,
>
> I am trying to install the last version of Gromacs (5.1.1) on our SGI
> cluster.
> The mono-processor compilation went fine and now I would like to compile
> the mdrun MPI version with the SGI MPT (the MPI library of SGI) 2.09
> (and also 2.12)
> Here the cmake command I used:
>
> cmake .. -DGMX_GPU=OFF -DCMAKE_C_COMPILER=gcc
>
> -DCMAKE_INSTALL_PREFIX=/opt/apps/software/pkg/gcc-4.9.0/mpt-2.0.9/gromacs/5.1.1/single
>
>
> -DFFTWF_LIBRARY=/opt/apps/software/pkg/gcc-4.9.0/fftw/3.3.3/single/lib/libfftw3f.so
>
> -DFFTWF_INCLUDE_DIR=/opt/apps/software/pkg/gcc-4.9.0/fftw/3.3.3/single/include
>   -DGMX_MPI=ON -DMPI_C_INCLUDE_PATH=/opt/sgi/mpt/mpt-2.12/include
> -DMPI_C_LIBRARIES=/opt/sgi/mpt/mpt-2.12/lib/libmpi.so
> -DGMX_BUILD_MDRUN_ONLY=ON  -DBUILD_SHARED_LIBS=off
>
>
> The configuration went fine but when I ran make, I have the following
> error:
>
>
> service0:gromacs-5.1.1/build # make
> [  0%] Generating baseversion-gen.c
> Scanning dependencies of target libgromacs
> [  0%] Building C object
>
> src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/compression/bwlzh.c.o
> [...]
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o
> In file included from
>
> /opt/apps/software/src/gromacs/gromacs-5.1.1/src/gromacs/domdec/domdec_setup.cpp:53:0:
>
> /opt/apps/software/src/gromacs/gromacs-5.1.1/src/gromacs/legacyheaders/names.h:110:25:
> erreur: expected unqualified-id before string constant
>   #define UNDEFINED       "UNDEFINED"
>                           ^
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o] Erreur 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Erreur 2
> make: *** [all] Erreur 2
>
> This is strange because, as I said, the mono-processor compilation went
> fine.
> I tried to upgrade the MPT library (2.12) without success.
> I tried Openmpi 1.8.1 and it succeed.
> Is there a compatibility issue with MPT ? I would like to keep this
> library since I achieved better performance with it.
>
> Thanks,
> Hubert
> --
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