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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