[gmx-users] Installation woe: fatal error: mpi.h: No such file or directory

[Mark Abraham]

Hi,

That seems a lot more complicated than you should need. First, don't run
the whole script as sudo unless you like re-installing OSes. As the install
guide says, you only need the install stage as sudo. You haven't set the
C++ compiler, either, so that might why it hasn't found mpi.h when
compiling a C++ file. You've managed a whole pile of things that don't need
to be managed if you have a normal installation of OpenMPI - the whole
point of using the wrapper compilers is that they already know where to
find the matching headers and libraries.

GROMACSDIR=/SNSlocal/sw/gromacs/gromacs-5.1.3
module load mpi/openmpi-x86_64
mkdir -p $GROMACSDIR/install
mkdir -p $GROMACSDIR/build
cd $GROMACSDIR/build
cmake $GROMACSDIR -DGMX_MPI=ON -DGMX_BUILD_MDRUN_ONLY=ON
-DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_INSTALL_PREFIX=/SNSlocal/sw/gromacs/gromacs-5.1.3/install

If that works, then consider -DBUILD_SHARED_LIBS=off

Mark

On Wed, Aug 3, 2016 at 12:06 AM Jose Borreguero <borreguero at gmail.com>
wrote:

> Dear GROMACS users,
>
> I don't know what's going on, installation "fails to find mpi.h" again and
> again. The error message:
> In file included from
>
> /SNSlocal/sw/gromacs/gromacs-5.1.3/src/gromacs/legacyheaders/types/commrec.h:45:0,
>                  from
>
> /SNSlocal/sw/gromacs/gromacs-5.1.3/src/gromacs/commandline/cmdlineinit.cpp:56:
> /SNSlocal/sw/gromacs/gromacs-5.1.3/src/gromacs/utility/gmxmpi.h:61:17:
> fatal error: mpi.h: No such file or directory
> compilation terminated.
>
> My installation script:
>
> #!/bin/bash
> # To run, issue:
> # $> sudo su - -c /SNSlocal/sw/gromacs/gromacs-5.1.3/myInstall.sh
>
> GROMACSDIR=/SNSlocal/sw/gromacs/gromacs-5.1.3
> module load mpi/openmpi-x86_64
> mkdir -p $GROMACSDIR/install
> mkdir -p $GROMACSDIR/build
> cd $GROMACSDIR/build
>
> cmake $GROMACSDIR -DCMAKE_INCLUDE_PATH=/usr/include/openmpi-x86_64
> -DCMAKE_LIBRARY_PATH=/usr/lib64/openmpi/li\
> b -DCMAKE_PREFIX_PATH=/usr/lib64/openmpi/bin
> -DCMAKE_C_COMPILER=/usr/lib64/openmpi/bin/mpicc -DGMX_MPI=ON -DG\
> MX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_OWN_FFTW=ON
> -DCMAKE_INSTALL_PREFIX=/SNSlocal/sw/gr\
> omacs/gromacs-5.1.3/install
>
> make -j 24
> make install
>
> As you see, I have populated variable CMAKE_INCLUDE_PATH
> Furthermore:
> $> locate mpi.h
> $> /usr/include/openmpi-x86_64/mpi.h
>
> This is what I get by grepping the CMakeCache.txt:
> $> grep "openmpi-x86_64" CMakeCache.txt
> CMakeCache.txt:CMAKE_INCLUDE_PATH:UNINITIALIZED=/usr/include/openmpi-x86_64
>
> and under CMakeFiles/ directory:
> $> grep -R "openmpi-x86_64" *
> CMakeOutput.log:COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_a8886' '-rdynamic' '-I'
> '/usr/include/openmpi-x86_64' '-pthread' '-L/usr/lib64/openmpi/lib'
> '-mtune=generic' '-march=x86-64'
> CMakeOutput.log:  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_a8886'
> '-rdynamic' '-I' '/usr/include/openmpi-x86_64' '-pthread'
> '-L/usr/lib64/openmpi/lib' '-mtune=generic' '-march=x86-64']
>
> The last info, the ignore line seems suspicious but I don't know what it
> means.
> I'm stuck here, please any help will be much appreciated.
>
> Best,
> .Jose
> --
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