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Old   November 25, 2016, 10:34
Default Problem installation OpenFOAM-dev
  #1
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Jean bon
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Hello,

I have several problems to install openfoam-dev. I have already installed several version of OpenFOAM (3, 4 and dev once). After a bug in openfoam-dev, I deleted it and I am trying to install the last version of openfoam-dev on a cluster (I have no root rights). I think it is worst than previous installations.

I am following: https://openfoamwiki.net/index.php/I...OAM-dev/Ubuntu

There are no problem until 11.
For 12, this is the log.makeGcc:

Code:
---------------
Already built: gmp-5.1.2
---------------
Already built: mpfr-3.1.2
---------------
Already built: mpc-1.0.1

......

/work/salmon/ThirdParty-dev/gcc-4.8.5/gcc/lto-compress.c:28:18: fatal error: zlib.h: No such file or directory
 #include <zlib.h>
                  ^
compilation terminated.
Makefile:1059: recipe for target 'lto-compress.o' failed
make[3]: *** [lto-compress.o] Error 1
make[3]: *** Waiting for unfinished jobs....
rm gcc.pod
make[3]: Leaving directory '/work/salmon/ThirdParty-dev/build/linux64/gcc-4.8.5/gcc'
Makefile:4156: recipe for target 'all-stage1-gcc' failed
make[2]: *** [all-stage1-gcc] Error 2
make[2]: Leaving directory '/work/salmon/ThirdParty-dev/build/linux64/gcc-4.8.5'
Makefile:18767: recipe for target 'stage1-bubble' failed
make[1]: *** [stage1-bubble] Error 2
make[1]: Leaving directory '/work/salmon/ThirdParty-dev/build/linux64/gcc-4.8.5'
Makefile:885: recipe for target 'all' failed
make: *** [all] Error 2
Error building: gcc-4.8.5
It cannot find zlib.h

Thanks.
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Old   November 29, 2016, 17:00
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  #2
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Quick answer: If you don't have root rights, that make things a bit harder to build.
I've checked some old build scripts I've used and please try the following steps:
  1. Edit the file "makeGcc".
  2. Find and completely remove the following line:
    Code:
    --with-system-zlib \
    so that it then looks like this:
    Code:
            --enable-libstdcxx-allocator=new \
        $GCC_BUILD_OPTIONS \
  3. Save and close the file in the text editor.
Then try running makeGcc again with the same command that you used before.
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Old   December 2, 2016, 05:18
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Jean bon
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Hello,

Thank you for your reply. I tried what you said but it did not work:

Code:
checking where to find the target windmc... host tool
checking whether to enable maintainer-specific portions of Makefiles... no
configure: creating ./config.status
config.status: creating Makefile
+ --disable-multilib MAKEINFO=missing
./makeGcc: line 295: --disable-multilib: command not found
Error building: gcc-4.8.5
What is the problem ? There is zlib. When I do "locate zlib", there are a lot of paths so I do not understand what is going on.

Thank you for your help anyway.
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Old   December 2, 2016, 07:07
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Quick answer: One thing is the ZLib library that is ready to be used by all applications; another is having the header and library definitions file, which is what is missing.

In order for that error message to appear... I don't know what happened. I will have to try it out myself to try and reproduce it.
Nonetheless, could you please provide the "makeGcc" file that you currently have? I ask this because something else might have changed in the file.
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Old   December 2, 2016, 08:54
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Thanks for your quick reply.
I cannot attach the file so I paste it here:


Code:
#!/bin/sh
#------------------------------------------------------------------------------
# =========                 |
# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
#  \\    /   O peration     |
#   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
#    \\/     M anipulation  |
#------------------------------------------------------------------------------
# License
#     This file is part of OpenFOAM.
#
#     OpenFOAM is free software: you can redistribute it and/or modify it
#     under the terms of the GNU General Public License as published by
#     the Free Software Foundation, either version 3 of the License, or
#     (at your option) any later version.
#
#     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
#     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
#     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
#     for more details.
#
#     You should have received a copy of the GNU General Public License
#     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
#
# Script
#     makeGcc
#
# Description
#     Build script for gmp, mpfr and gcc-[4-9].?.?
#
#------------------------------------------------------------------------------

# get default GCC, mpfr, gmp and mpc versions
. $WM_PROJECT_DIR/etc/config.sh/functions
_foamSource $($WM_PROJECT_DIR/bin/foamEtcFile config.sh/compiler)

gmpPACKAGE=${gmp_version:-gmp-5.1.2}
mpfrPACKAGE=${mpfr_version:-mpfr-3.1.2}
mpcPACKAGE=${mpc_version:-mpc-1.0.1}
gccPACKAGE=$gcc_version


#------------------------------------------------------------------------------
# Run from third-party directory only
wmakeCheckPwd "$WM_THIRD_PARTY_DIR" || {
    echo "Error: Current directory is not \$WM_THIRD_PARTY_DIR"
    echo "    The environment variables are inconsistent with the installation."
    echo "    Check the OpenFOAM entries in your dot-files and source them."
    exit 1
}
. etc/tools/ThirdPartyFunctions
#------------------------------------------------------------------------------

usage() {
    exec 1>&2
    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
    cat<<USAGE

usage: ${0##*/} [option] [gmp-VERSION] [mpfr-VERSION] [mpc-VERSION] <gcc-VERSION>
options:
  -no-multilib      for 64-bit systems that don't have 32-bit support
  -help

* build combinations of gmp, mpfr, mpc and gcc
      $gmpPACKAGE
      $mpfrPACKAGE
      $mpcPACKAGE
      $gccPACKAGE

USAGE
    exit 1
}

GCC_BUILD_OPTIONS=""

# Parse options
while [ "$#" -gt 0 ]
do
    case "$1" in
    -h | -help)
        usage
        ;;
    -no-multilib)
        GCC_BUILD_OPTIONS="--disable-multilib"
        shift
        ;;
    gmp-[4-9]*)
        gmpPACKAGE="${1%%/}"
        shift
        ;;
    mpfr-[2-9]*)
        mpfrPACKAGE="${1%%/}"
        shift
        ;;
    mpc-[0-9]*)
        mpcPACKAGE="${1%%/}"
        shift
        ;;
    gcc-[4-9]*)
        gccPACKAGE="${1%%/}"
        shift
        ;;
    *)
        usage "unknown option/argument: '$*'"
        ;;
    esac
done

if [ -z "$gccPACKAGE" ]
then
    usage "Please specify gcc-VERSION"
    exit 1
fi


# Set 32 or 64 bit ABI
case "$WM_ARCH_OPTION" in
32 | 64)
    ABI=$WM_ARCH_OPTION
    ;;
*)
    usage "Please set WM_ARCH_OPTION to either 32 or 64'$*'"
    ;;
esac


#------------------------------------------------------------------------------
# Build/install without compiler name
buildBASE=$WM_THIRD_PARTY_DIR/build/$WM_ARCH$WM_COMPILER_ARCH
installBASE=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH

GCC_ARCH_PATH=$installBASE/$gccPACKAGE
GMP_ARCH_PATH=$installBASE/$gmpPACKAGE
MPFR_ARCH_PATH=$installBASE/$mpfrPACKAGE
MPC_ARCH_PATH=$installBASE/$mpcPACKAGE

#
# Build GMP
#
echo "---------------"
if [ -d $GMP_ARCH_PATH ]
then
    echo "Already built: $gmpPACKAGE"
else
    echo "Starting build: $gmpPACKAGE"
    echo
(
    sourceDIR=$WM_THIRD_PARTY_DIR/$gmpPACKAGE
    buildDIR=$buildBASE/$gmpPACKAGE

    cd $sourceDIR || exit 1
    make distclean 2>/dev/null

    rm -rf $buildDIR
    mkdir -p $buildDIR
    cd $buildDIR

    set -x
    $sourceDIR/configure ABI=$ABI \
        --prefix=$GMP_ARCH_PATH \
        --libdir=$GMP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
        --enable-cxx \
    && make -j $WM_NCOMPPROCS \
    && make install \
    && echo "Built: $gmpPACKAGE"
) || {
    echo "Error building: $gmpPACKAGE"
    exit 1
}
fi

export LD_LIBRARY_PATH="$GMP_ARCH_PATH/lib:$LD_LIBRARY_PATH"

#
# Build MPFR
#
echo "---------------"
if [ -d $MPFR_ARCH_PATH ]
then
    echo "Already built: $mpfrPACKAGE"
else
    echo "Starting build: $mpfrPACKAGE"
    echo
(
    sourceDIR=$WM_THIRD_PARTY_DIR/$mpfrPACKAGE
    buildDIR=$buildBASE/$mpfrPACKAGE

    cd $sourceDIR || exit 1
    make distclean 2>/dev/null

    rm -rf $buildDIR
    mkdir -p $buildDIR
    cd $buildDIR

    set -x
    $sourceDIR/configure ABI=$ABI \
       --prefix=$MPFR_ARCH_PATH \
       --libdir=$MPFR_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
       --with-gmp-include=$GMP_ARCH_PATH/include \
       --with-gmp-lib=$GMP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
    && make -j $WM_NCOMPPROCS \
    && make install \
    && echo "Built: $mpfrPACKAGE"
) || {
    echo "Error building: $mpfrPACKAGE"
    exit 1
}
fi

export LD_LIBRARY_PATH="$MPFR_ARCH_PATH/lib:$LD_LIBRARY_PATH"

#
# Build mpc
#
echo "---------------"
if [ -d $MPC_ARCH_PATH ]
then
    echo "Already built: $mpcPACKAGE"
else
    echo "Starting build: $mpcPACKAGE"
    echo
(
    sourceDIR=$WM_THIRD_PARTY_DIR/$mpcPACKAGE
    buildDIR=$buildBASE/$mpcPACKAGE

    cd $sourceDIR || exit 1
    make distclean 2>/dev/null

    rm -rf $buildDIR
    mkdir -p $buildDIR
    cd $buildDIR

    set -x
    $sourceDIR/configure ABI=$ABI \
        --prefix=$MPC_ARCH_PATH \
        --libdir=$MPC_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
        --with-gmp-include=$GMP_ARCH_PATH/include \
        --with-gmp-lib=$GMP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
        --with-mpfr-include=$MPFR_ARCH_PATH/include \
        --with-mpfr-lib=$MPFR_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
    && make -j $WM_NCOMPPROCS \
    && make install \
    && echo "Built: $mpcPACKAGE"
) || {
    echo "Error building: $mpcPACKAGE"
    exit 1
}
fi


if [ -d "$MPC_ARCH_PATH" ]
then
    export LD_LIBRARY_PATH="$MPC_ARCH_PATH/lib:$LD_LIBRARY_PATH"
fi


#
# Build GCC
# might need 32-bit glibc-devel headers to compile
# E.g. on ubuntu install g++-multilib
#
echo "---------------"
if [ -d $GCC_ARCH_PATH ]
then
    echo "Already built: $gccPACKAGE"
else
    echo "Starting build: $gccPACKAGE"
    echo
(
    sourceDIR=$WM_THIRD_PARTY_DIR/$gccPACKAGE
    buildDIR=$buildBASE/$gccPACKAGE

    cd $sourceDIR || exit 1
    make distclean 2>/dev/null

    rm -rf $buildDIR
    mkdir -p $buildDIR
    cd $buildDIR

    set -x
    $sourceDIR/configure \
        --prefix=$GCC_ARCH_PATH \
        --with-gmp-include=$GMP_ARCH_PATH/include \
        --with-gmp-lib=$GMP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
        --with-mpfr-include=$MPFR_ARCH_PATH/include \
        --with-mpfr-lib=$MPFR_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
        --with-mpc-include=$MPC_ARCH_PATH/include \
        --with-mpc-lib=$MPC_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
        --with-pkgversion=OpenFOAM \
        --enable-languages=c,c++ \
        --enable-__cxa_atexit \
        --enable-libstdcxx-allocator=new \
        --with-system-zlib \
        $GCC_BUILD_OPTIONS \
        MAKEINFO=missing \
    && make -j $WM_NCOMPPROCS \
    && make install \
    && echo "Built: $gccPACKAGE"
) || {
    echo "Error building: $gccPACKAGE"
    exit 1
}
fi


#------------------------------------------------------------------------------
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Old   December 3, 2016, 17:29
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  #6
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Bruno Santos
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Greetings Fabien,

OK, you still have the original file. Please run the following commands:
Code:
cd $WM_THIRD_PARTY_DIR

sed -i -e 's=--with-system-zlib==' makeGcc

./makeGcc -no-multilib > log.makeGcc 2>&1
wmRefresh
The sed command as shown above will properly remove the "--with-system-zlib" entry.

I've tested just now in Ubuntu 12.04 x86_64, without having the "zlib.h" header file in the system, and it worked without problems with this hack.

Best regards,
Bruno
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Old   December 5, 2016, 05:11
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  #7
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Jean bon
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Thank you very much, it works, you are great !

However (yes sorry), I have a second error. For this one, perhaps you cannot do anything but I try, I am not sure. I have seen other messages on it but I have not seen any solutions that work for me.

When I run "./makeParaView -python -mpi -python-lib /usr/lib/libpython2.7.so.1.0 > log.makePV 2>&1", I have a problem with Qmake:

*** Error: cannot find qmake either at $QMAKE_PATH or in current $PATH

When I run locate qmake, I have a lot of paths, for example:

/work/soft/qt/qt-everywhere-opensource-src-4.8.5/qmake/generators/win32/winmakefile.h

So I tried to export this path in the .bashrc file:

Code:
PATH=/work/soft/qt/qt-everywhere-opensource-src-4.8.5:$PATH
export PATH
But I have still the same message.

Again thank you for your help.
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Old   December 27, 2016, 12:48
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  #8
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Quick answer: Sorry for the late reply. You can define the path to qmake directly in the command line, e.g.:
Code:
./makeParaView -qmake /work/soft/qt/qt-everywhere-opensource-src-4.8.5/bin/qmake -python -mpi -python-lib /usr/lib/libpython2.7.so.1.0 > log.makePV 2>&1
Although you should first check if the file even exists there, by running:
Code:
ls -l /work/soft/qt/qt-everywhere-opensource-src-4.8.5/bin/qmake
find /work/soft/qt/qt-everywhere-opensource-src-4.8.5 -name qmake -type f
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Old   January 3, 2017, 05:32
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  #9
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Jean bon
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Thank you,

It works for qmake but there is an other error after. This is the end of the log.makePV:

Code:
-- Looking for sqrt - not found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strchr
-- Looking for strchr - found
-- Looking for strrchr
-- Looking for strrchr - found
-- Looking for strstr
-- Looking for strstr - found
-- Looking for strtol
-- Looking for strtol - found
-- Looking for strtoul
-- Looking for strtoul - found
-- Check size of int
-- Check size of int - done
-- Check size of long
-- Check size of long - done
CMake Error at /work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48/cmake-3.2.1/share/cmake-3.2/Modules/FindPackageHandleStandardArgs.cmake:138 (message):
  Could NOT find OpenGL (missing: OPENGL_INCLUDE_DIR)
Call Stack (most recent call first):
  /work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48/cmake-3.2.1/share/cmake-3.2/Modules/FindPackageHandleStandardArgs.cmake:374 (_FPHSA_FAILURE_MESSAGE)
  /work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48/cmake-3.2.1/share/cmake-3.2/Modules/FindOpenGL.cmake:168 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  VTK/CMake/vtkOpenGL.cmake:63 (find_package)
  VTK/ThirdParty/glew/vtkglew/CMakeLists.txt:3 (include)


-- Configuring incomplete, errors occurred!
See also "/work/salmon/OpenFOAM/ThirdParty-dev/build/linux64Gcc48/ParaView-5.0.1/CMakeFiles/CMakeOutput.log".
See also "/work/salmon/OpenFOAM/ThirdParty-dev/build/linux64Gcc48/ParaView-5.0.1/CMakeFiles/CMakeError.log".
Then, I tried the next step, the Allwmake of the OpenFOAM file and I had the problem of zlib again.

This is the log.make file (just the beginning, where the first error occurs):

Code:
Compiling enabled on 4 cores
Allwmake /work/salmon/OpenFOAM/OpenFOAM-dev
make: Nothing to be done for 'all'.

========================================
Start ThirdParty Allwmake
========================================

========================================
Build MPI libraries if required

    have OPENMPI shared library (openmpi-1.10.2)

========================================
Build Scotch decomposition library scotch_6.0.3
    /work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48DPInt32/scotch_6.0.3
+ cd scotch_6.0.3/src
+ prefixDIR=/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48DPInt32/scotch_6.0.3
+ libDIR=/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48DPInt32/lib
+ mkdir -p /work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48DPInt32/scotch_6.0.3
+ mkdir -p /work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48DPInt32/lib
+ configOpt='prefix=/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48DPInt32/scotch_6.0.3 libdir=/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48DPInt32/lib'
+ '[' -f ../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM ']'
+ rm -f Makefile.inc
+ ln -s ../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM Makefile.inc
+ '[' -f Makefile.inc ']'
+ unset configEnv
+ '[' gcc '!=' gcc ']'
+ make realclean
(cd libscotch ;      make realclean)
make[1]: Entering directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/libscotch'
rm -f *~ *.o lib*.so parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output *dummysizes
make[1]: Leaving directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/libscotch'
(cd scotch ;         make realclean)
make[1]: Entering directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/scotch'
rm -f *~ *.o acpl amk_ccc amk_fft2 amk_grf amk_hy amk_m2 amk_p2 atst gbase gcv *ggath *gmap gmk_hy gmk_m2 gmk_m3 gmk_msh gmk_ub2 gmtst *gord gotst gout *gpart *gscat *gtst mcv mmk_m2 mmk_m3 mord mtst
make[1]: Leaving directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/scotch'
(cd libscotchmetis ; make realclean)
make[1]: Entering directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/libscotchmetis'
rm -f *~ *.o lib*.so
make[1]: Leaving directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/libscotchmetis'
(cd check ;          make realclean)
make[1]: Entering directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/check'
rm -f *~ *.o
rm -f 				\
				test_common_thread		\
				test_scotch_graph_color		\
				test_scotch_graph_map		\
				test_scotch_graph_order		\
				test_scotch_graph_part_ovl	\
				test_scotch_dgraph_band		\
				test_scotch_dgraph_check	\
				test_scotch_dgraph_coarsen	\
				test_scotch_dgraph_grow		\
				test_scotch_dgraph_redist	\
				test_strat_par			\
				test_strat_seq
make[1]: Leaving directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/check'
(cd esmumps ;        make realclean)
make[1]: Entering directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/esmumps'
rm -f *~ common.h *.o lib*.so main_esmumps
make[1]: Leaving directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/esmumps'
rm -f ../bin/* ../include/* ../lib/*
+ make -j 8 scotch
(cd libscotch ;      make VERSION=6 RELEASE=0 PATCHLEVEL=3 scotch && make install)
make[1]: Entering directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/libscotch'
make CC="gcc" CCD="gcc"	\
				scotch.h				\
				scotchf.h				\
				libscotch.so				\
				libscotcherr.so			\
				libscotcherrexit.so
make[2]: Entering directory '/work/salmon/OpenFOAM/ThirdParty-dev/scotch_6.0.3/src/libscotch'
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch.c -o arch.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_cmplt.c -o arch_cmplt.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_cmpltw.c -o arch_cmpltw.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_deco.c -o arch_deco.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_dist.c -o arch_dist.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_hcub.c -o arch_hcub.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_mesh.c -o arch_mesh.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_tleaf.c -o arch_tleaf.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_torus.c -o arch_torus.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_vcmplt.c -o arch_vcmplt.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c arch_vhcub.c -o arch_vhcub.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c common.c -DSCOTCH_COMMON_RENAME -o common.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c common_file.c -DSCOTCH_COMMON_RENAME -o common_file.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c common_file_compress.c -DSCOTCH_COMMON_RENAME -o common_file_compress.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c common_file_uncompress.c -DSCOTCH_COMMON_RENAME -o common_file_uncompress.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c common_integer.c -DSCOTCH_COMMON_RENAME -o common_integer.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c common_memory.c -DSCOTCH_COMMON_RENAME -o common_memory.o
gcc -m64 -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -c common_string.c -DSCOTCH_COMMON_RENAME -o common_string.o
common_file_compress.c:65:18: fatal error: zlib.h: No such file or directory
 #include "zlib.h"
                  ^
common_file_uncompress.c:65:18: fatal error: zlib.h: No such file or directory
 #include "zlib.h"
                  ^
compilation terminated.
There is the same thing for the build of PTScotch.

I wanted to try the same thing as you but I do not find any file where we need zlib.
If you have an idea.

Thank you for your help.
Last edited by FlyingCat; January 4, 2017 at 11:26.
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Old   January 11, 2017, 13:06
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Jean bon
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Hello,

a little update. zlib has been installed and so I could follow the instrutions. For paraFoam, I cannot install it so far but I think I know why (an other library is not in the cluster).

As regards OpenFOAM, I have trouble in the Allwmake. You can forgot the other errors in the other messages. This is the new error:

Code:
wclean ptscotchDecomp
wmake  ptscotchDecomp
wmake ptscotchDecomp
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file ptscotchDecomp.C
g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=64 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -O3  -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -isystem /work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48/openmpi-1.10.2/include -I/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48DPInt64/scotch_6.0.3/include/openmpi-1.10.2 -I/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64Gcc48DPInt64/scotch_6.0.3/include -I/usr/include/scotch -I../decompositionMethods/lnInclude -IlnInclude -I. -I/work/salmon/OpenFOAM/OpenFOAM-dev/src/OpenFOAM/lnInclude -I/work/salmon/OpenFOAM/OpenFOAM-dev/src/OSspecific/POSIX/lnInclude   -fPIC -c ptscotchDecomp.C -o /work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt64OptOPENMPI/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.o
In file included from /opt/sgi/mpt/mpt-2.14/include/mpi.h:1816:0,
                 from ptscotchDecomp.C:36:
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:416:6: error: declaration of C function ‘void PMPI::Init()’ conflicts with
 Init();
      ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:413:1: error: previous declaration ‘void PMPI::Init(int&, char**&)’ here
 Init(int& argc, char**& argv);
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:440:12: error: declaration of C function ‘void PMPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:433:1: error: previous declaration ‘void PMPI::Register_datarep(const char*, void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:445:12: error: declaration of C function ‘void PMPI::Register_datarep(const char*, void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:438:1: error: previous declaration ‘void PMPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, MPI_Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:445:12: error: declaration of C function ‘void PMPI::Register_datarep(const char*, void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:433:1: error: previous declaration ‘void PMPI::Register_datarep(const char*, void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:450:12: error: declaration of C function ‘void PMPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:443:1: error: previous declaration ‘void PMPI::Register_datarep(const char*, void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:450:12: error: declaration of C function ‘void PMPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:438:1: error: previous declaration ‘void PMPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, MPI_Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:450:12: error: declaration of C function ‘void PMPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:433:1: error: previous declaration ‘void PMPI::Register_datarep(const char*, void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), void (*)(void*, PMPI::Datatype&, int, void*, PMPI::Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:899:7: warning: ‘class PMPI::Comm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Comm : public Comm_Null {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1184:7: warning: ‘class PMPI::Intracomm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Intracomm : public Comm {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1220:7: warning: ‘class PMPI::Cartcomm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Cartcomm : public Intracomm {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1269:7: warning: ‘class PMPI::Graphcomm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Graphcomm : public Intracomm {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1313:7: warning: ‘class PMPI::Intercomm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Intercomm : public Comm {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1642:29: warning: declaration of ‘void MPI::Init(int&, char**&)’ with C language linkage [enabled by default]
 Init(int& argc, char**& argv);
                             ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:416:1: warning: conflicts with previous declaration ‘void PMPI::Init()’ [enabled by default]
 Init();
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1645:6: error: declaration of C function ‘void MPI::Init()’ conflicts with
 Init();
      ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1642:1: error: previous declaration ‘void MPI::Init(int&, char**&)’ here
 Init(int& argc, char**& argv);
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1651:54: error: declaration of C function ‘int MPI::Init_thread(int&, char**&, int)’ conflicts with
 int Init_thread(int& argc, char**& argv, int required);
                                                      ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1650:5: error: previous declaration ‘int MPI::Init_thread(int)’ here
 int Init_thread(int);
     ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1684:12: warning: declaration of ‘void MPI::Register_datarep(const char*, void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ with C language linkage [enabled by default]
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:448:1: warning: conflicts with previous declaration ‘void PMPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const PMPI::Datatype&, PMPI::Aint&, void*), void*)’ [enabled by default]
 Register_datarep(const char *, MPI_Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1688:12: error: declaration of C function ‘void MPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1682:1: error: previous declaration ‘void MPI::Register_datarep(const char*, void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1692:12: error: declaration of C function ‘void MPI::Register_datarep(const char*, void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1686:1: error: previous declaration ‘void MPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, MPI_Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1692:12: error: declaration of C function ‘void MPI::Register_datarep(const char*, void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1682:1: error: previous declaration ‘void MPI::Register_datarep(const char*, void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1696:12: error: declaration of C function ‘void MPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1690:1: error: previous declaration ‘void MPI::Register_datarep(const char*, void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1696:12: error: declaration of C function ‘void MPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1686:1: error: previous declaration ‘void MPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, MPI_Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1696:12: error: declaration of C function ‘void MPI::Register_datarep(const char*, int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), int (*)(void*, MPI_Datatype, int, void*, MPI_Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ conflicts with
      void *);
            ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1682:1: error: previous declaration ‘void MPI::Register_datarep(const char*, void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(void*, MPI::Datatype&, int, void*, MPI::Offset, void*), void (*)(const MPI::Datatype&, MPI::Aint&, void*), void*)’ here
 Register_datarep(const char *, Datarep_conversion_function *,
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:2734:7: warning: ‘class MPI::Comm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Comm : public Comm_Null {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:3245:7: warning: ‘class MPI::Intracomm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Intracomm : public Comm {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:3448:7: warning: ‘class MPI::Cartcomm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Cartcomm : public Intracomm {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:3529:7: warning: ‘class MPI::Graphcomm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Graphcomm : public Intracomm {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:3607:7: warning: ‘class MPI::Intercomm’ has virtual functions and accessible non-virtual destructor [-Wnon-virtual-dtor]
 class Intercomm : public Comm {
       ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h: In function ‘void PMPI::Init(int&, char**&)’:
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:4102:41: warning: declaration of ‘void PMPI::Init(int&, char**&)’ with C language linkage [enabled by default]
 _REAL_MPI_::Init(int& argc, char**& argv)
                                         ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:1645:1: warning: conflicts with previous declaration ‘void MPI::Init()’ [enabled by default]
 Init();
 ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:4102:41: error: declaration of C function ‘void PMPI::Init(int&, char**&)’ conflicts with
 _REAL_MPI_::Init(int& argc, char**& argv)
                                         ^
/opt/sgi/mpt/mpt-2.14/include/mpi++.h:416:1: error: previous declaration ‘void PMPI::Init()’ here
 Init();
 ^
/work/salmon/OpenFOAM/OpenFOAM-dev/wmake/rules/General/transform:25: recipe for target '/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt64OptOPENMPI/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.o' failed
make: *** [/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt64OptOPENMPI/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.o] Error 1
I did not find exactly the same error in other topics.

Thank you for your help.
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Old   January 13, 2017, 06:51
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Jean bon
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I succeeded to avoid this error thanks to a modification: I move "#include <mphi.h>" from extern "C" to the rest of include in the file src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C

Now, I have an other error, I think there is a link with the first. When I try to compile solvers, I cannot (this is the same message for each solver):

Code:
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `op_intercept(void*, void*, int*, unsigned int*)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `PMPI::Request::ignored_status'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `mpi_sgi_status_ignore'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `MPI::Op::Is_commutative() const'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `PMPI::Comm::mpi_comm_map'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `MPI::Is_initialized()'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `MPI::Op::Reduce_local(void const*, void*, int, MPI::Datatype const&) const'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `MPI::Op::Free()'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/openmpi-1.10.2/libPstream.so: undefined reference to `PMPI::Comm::ignored_status'
I tried to compile openmpi and then compile openFoam but I have still the same error.
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Old   January 13, 2017, 09:46
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Jean bon
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Update:

Code:
    -lfiniteVolume -lfvOptions -lcompressibleTransportModels -lfluidThermophysicalModels -lspecie -lrhoCentralFoam -lturbulenceModels -lcompressibleTurbulenceModels -lmeshTools -lOpenFOAM -ldl  \
     -lm -o /work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/bin/rhoCentralFoam
/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64/gcc-4.8.5/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../../../x86_64-unknown-linux-gnu/bin/ld: warning: libtriSurface.so, needed by /work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libfiniteVolume.so, not found (try using -rpath or -rpath-link)
/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64/gcc-4.8.5/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../../../x86_64-unknown-linux-gnu/bin/ld: warning: libsurfMesh.so, needed by /work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so, not found (try using -rpath or -rpath-link)
/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64/gcc-4.8.5/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../../../x86_64-unknown-linux-gnu/bin/ld: warning: libfileFormats.so, needed by /work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so, not found (try using -rpath or -rpath-link)
/work/salmon/OpenFOAM/ThirdParty-dev/platforms/linux64/gcc-4.8.5/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../../../x86_64-unknown-linux-gnu/bin/ld: warning: libPstream.so, needed by /work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libOpenFOAM.so, not found (try using -rpath or -rpath-link)
And:

Code:
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::OBJstream::write(Foam::line<Foam::Vector<double>, Foam::Vector<double> const&> const&)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::triSurface::triSurface(Foam::fileName const&)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libOpenFOAM.so: undefined reference to `Foam::reduce(Foam::Vector2D<double>&, Foam::sumOp<Foam::Vector2D<double> > const&, int, int)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::OBJstream::~OBJstream()'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libOpenFOAM.so: undefined reference to `Foam::UPstream::freePstreamCommunicator(int)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::triSurface::triSurface()'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libfiniteVolume.so: undefined reference to `Foam::UPstream::finishedRequest(int)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::triSurface::scalePoints(double)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::OBJstream::write(Foam::Vector<double> const&)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::triSurface::triSurface(Foam::fileName const&)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libOpenFOAM.so: undefined reference to `Foam::UPstream::abort()'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::geometricSurfacePatch::operator==(Foam::geometricSurfacePatch const&) const'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::triSurface::subsetMesh(Foam::List<bool> const&, Foam::List<int>&, Foam::List<int>&) const'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libOpenFOAM.so: undefined reference to `Foam::UPstream::resetRequests(int)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libOpenFOAM.so: undefined reference to `Foam::UPstream::allocatePstreamCommunicator(int, int)'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::triSurface::edgeOwner() const'
/work/salmon/OpenFOAM/OpenFOAM-dev/platforms/linux64Gcc48DPInt32Opt/lib/libmeshTools.so: undefined reference to `Foam::OBJstream::OBJstream(Foam::fileName const&, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber,
That is what I have, I do not know where is the previous error message. I am making some modification and I do not know what is responsible for this new error.

EDIT: Ok now I have again the previous error. I will kill myself.
Last edited by FlyingCat; January 13, 2017 at 12:21.
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Old   January 16, 2017, 08:56
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I solved the problem by

export WM_MPLIB=SYSTEMOPENMPI

I do not know what was the problem, but this command solved it. If a more competent person could explain, it would be useful for everybody I think.
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Old   October 2, 2017, 18:25
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Quote:
Originally Posted by FlyingCat View Post
I solved the problem by

export WM_MPLIB=SYSTEMOPENMPI

I do not know what was the problem, but this command solved it. If a more competent person could explain, it would be useful for everybody I think.
what file do i edit this in? Will it fix my problems with install on RHEL?

I found where the errors appear and it is stating that it cannot find libtrisurface.so (needed by linux64GccDPInt64Debug/lib/libfiniteVoluem.so, not found
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Old   October 3, 2017, 04:31
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Hi,

You need to write this in the terminal before compiling.

However, perhaps it is not your problem, you should give more information about it.

Moreover, I do not know if you copied and pasted "linux64GccDPInt64Debug/lib/libfiniteVoluem.so" but it is written "Voluem". If you copied and pasted, you had to change something in files.
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Old   December 31, 2017, 12:53
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Quick answer: You can edit the file "OpenFOAM*/etc/bashrc" and change the value for "WM_MPLIB".
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