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oofem3.0.0 compilation errors with intel mpi compiler (boost 1.59.0)

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Old   November 7, 2015, 13:04
Default oofem3.0.0 compilation errors with intel mpi compiler (boost 1.59.0)
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puneet
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I am unable to install OpenFoam 3.0.0 (with intel compilers), i am listing my build procedure as well as errors:

CC=mpiicc CXX=mpiicpc WM_MPLIB=IMPI WM_CXX=mpiicpc WM_CC=mpiicc WM_PROJECT=OpenFOAM WM_ARCH_OPTION=64 WM_COMPILER=Icc MPI_HOME=/opt/intel/impi/5.0.3.048/ MPI_ROOT=/opt/intel/impi/5.0.3.048/ FOAM_INST_DIR=/root/Downloads//OpenFoam/ WM_CFLAGS="-m64 -fPIC -DMPI_NO_CPPBIND" WM_CXXFLAGS="-m64 -fPIC -DMPI_NO_CPPBIND " source etc/bashrc

an i got:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status

i saw this so i tried setting WM_MPLIB to INTELMPI & IMPI bur error was same.

I went ahead with this bashrc error and did :
CC=mpiicc CXX=mpiicpc WM_MPLIB=IMPI WM_CXX=mpiicpc WM_CC=mpiicc WM_PROJECT=OpenFOAM WM_ARCH_OPTION=64 WM_COMPILER=Icc MPI_HOME=/opt/intel/impi/5.0.3.048/ MPI_ROOT=/opt/intel/impi/5.0.3.048/ FOAM_INST_DIR=/root/Downloads//OpenFoam/ WM_CFLAGS="-m64 -fPIC -DMPI_NO_CPPBIND" WM_CXXFLAGS="-m64 -fPIC -DMPI_NO_CPPBIND " ./Allwmake

and i got :
Making dependency list for source file UOPwrite.C
icpc -std=c++0x -fp-trap=common -fp-model precise -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -diag-disable 2304 -xHost -O2 -DNoRepository -IlnInclude -I. -I/root/Downloads//OpenFoam//OpenFOAM-3.0.0/src/OpenFOAM/lnInclude -I/root/Downloads//OpenFoam//OpenFOAM-3.0.0/src/OSspecific/POSIX/lnInclude -fPIC -c UOPwrite.C -o Make/linux64GccDPInt32OptIMPI/UOPwrite.o
In file included from UOPwrite.C(30):
PstreamGlobals.H(41): catastrophic error: cannot open source file "mpi.h"
#include <mpi.h>
^
compilation aborted for UOPwrite.C (code 4)
make: *** [Make/linux64GccDPInt32OptIMPI/UOPwrite.o] Error 4


in ./wmake/rules/linux64Icc/c++ i did:

CC = mpiicpc -std=c++0x -fp-trap=common -fp-model precise

then i got

mpiicpc -std=c++0x -fp-trap=common -fp-model precise -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -diag-disable 2304 -xHost -O2 -DNoRepository -IlnInclude -I. -I/root/Downloads//OpenFoam//OpenFOAM-3.0.0/src/OpenFOAM/lnInclude -I/root/Downloads//OpenFoam//OpenFOAM-3.0.0/src/OSspecific/POSIX/lnInclude -fPIC -shared -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPInt32OptIMPI/UOPwrite.o Make/linux64GccDPInt32OptIMPI/UIPread.o Make/linux64GccDPInt32OptIMPI/UPstream.o Make/linux64GccDPInt32OptIMPI/PstreamGlobals.o -L/root/Downloads//OpenFoam//OpenFOAM-3.0.0/platforms/linux64GccDPInt32OptIMPI/lib \
-o /root/Downloads//OpenFoam//OpenFOAM-3.0.0/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so
'/root/Downloads//OpenFoam//OpenFOAM-3.0.0/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so' is up to date.
touch: cannot touch `/root/Downloads//OpenFoam//OpenFOAM-3.0.0/platforms/linux64GccDPInt32OptIMPI/src/Pstream/mpi/usingpenmpi-system': No such file or directory


so i manually created directory usng:
mkdir -p /root/Downloads//OpenFoam//OpenFOAM-3.0.0/platforms/linux64GccDPInt32OptIMPI/src/Pstream/mpi/using

and after doing
CC=mpiicc CXX=mpiicpc WM_MPLIB=IMPI WM_CXX=mpiicpc WM_CC=mpiicc WM_PROJECT=OpenFOAM WM_ARCH_OPTION=64 WM_COMPILER=Icc MPI_HOME=/opt/intel/impi/5.0.3.048/ MPI_ROOT=/opt/intel/impi/5.0.3.048/ FOAM_INST_DIR=/root/Downloads//OpenFoam/ WM_CFLAGS="-m64 -fPIC -DMPI_NO_CPPBIND" WM_CXXFLAGS="-m64 -fPIC -DMPI_NO_CPPBIND " ./Allwmake -j20

i got finally stuck at :
Making dependency list for source file ptscotchDecomp.C
mpiicpc -std=c++0x -fp-trap=common -fp-model precise -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -diag-disable 2304 -xHost -O2 -DNoRepository -I/include -I/root/Downloads//OpenFoam//ThirdParty-3.0.0/platforms/linux64IccInt32/scotch_6.0.3/include/openmpi-system -I/usr/include/scotch -I../decompositionMethods/lnInclude -IlnInclude -I. -I/root/Downloads//OpenFoam//OpenFOAM-3.0.0/src/OpenFOAM/lnInclude -I/root/Downloads//OpenFoam//OpenFOAM-3.0.0/src/OSspecific/POSIX/lnInclude -fPIC -c ptscotchDecomp.C -o Make/linux64GccDPInt32OptIMPI/ptscotchDecomp.o
In file included from /opt/intel//impi/5.0.3.048/intel64/include/mpi.h(2275),
from ptscotchDecomp.C(125):
/opt/intel//impi/5.0.3.048/intel64/include/mpicxx.h(2806): error: more than one instance of overloaded function "MPI::Init" has "C" linkage
extern void Init(int &, char **& );
^
In file included from /opt/intel//impi/5.0.3.048/intel64/include/mpi.h(2275),
from ptscotchDecomp.C(125):
/opt/intel//impi/5.0.3.048/intel64/include/mpicxx.h(2808): error: more than one instance of overloaded function "MPI::Init_thread" has "C" linkage
extern int Init_thread(int &, char **&, int );
^
compilation aborted for ptscotchDecomp.C (code 2)
make: *** [Make/linux64GccDPInt32OptIMPI/ptscotchDecomp.o] Error 2



Any help/hint will be very useful!
Awaiting your replies!
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Old   November 17, 2015, 00:20
Default oofem3.0.0 compilation errors with intel mpi compiler (boost 1.59.0)
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puneet
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I am getting following error while compiling OpenFOAM on centos-6.5 with intel mpi compiler:

mpiicpc -std=c++0x -fp-trap=common -fp-model precise -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64IccInt32/scotch_6.0.3/include/intel64/ -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64IccInt32/scotch_6.0.3/include/ -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -diag-disable 2304 -xHost -O2 -DNoRepository -DNDEBUG -DCGAL_INEXACT -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include -I/include -I/include -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/boost-system/include -diag-disable 1224,2026,2305 -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/finiteVolume/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/meshTools/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/parallel/decompose/decompositionMethods/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/edgeMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/fileFormats/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/dynamicMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/surfMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/triSurface/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/sampling/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/mesh/autoMesh/lnInclude -IPrintTable -I/usr/include -IlnInclude -I. -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OpenFOAM/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OSspecific/POSIX/lnInclude -fPIC -c cellSizeControlSurfaces/surfaceCellSizeFunction/surfaceCellSizeFunction/surfaceCellSizeFunction.C -o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/cellSizeControlSurfaces/surfaceCellSizeFunction/surfaceCellSizeFunction/surfaceCellSizeFunction.o
/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/Triangulation_3.h(3604): internal error: conv_class_prvalue_operand_to_lvalue: couldn't convert to ptr
BOOST_FOREACH(Cell_handle& ch,
^

compilation aborted for conformalVoronoiMesh/conformalVoronoiMeshConformToSurface.C (code 4)
make[2]: *** [/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/conformalVoronoiMesh/conformalVoronoiMeshConformToSurface.o] Error 4
make[2]: *** Waiting for unfinished jobs....
/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/Triangulation_3.h(3604): internal error: conv_class_prvalue_operand_to_lvalue: couldn't convert to ptr
BOOST_FOREACH(Cell_handle& ch,
^
Do i need to downgrade version of boost?
Awaiting your replies!!
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Old   November 17, 2015, 17:03
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Quick answer: I have this on my to-do list, but I can only access Intel MPI a trial license and I didn't have enough time this past weekend to look into this.

As for the problem with Boost, what steps did you take for building Boost?
Either way, I suggest that you build both Boost and CGAL with GCC and not with Intel's compilers.
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Old   November 23, 2015, 00:28
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Hi , i was able to get past the boost error , but now i am stuck with :
https://software.intel.com/en-us/for...r/topic/600758

breif VERBOSE log of error:

Making dependency list for source file cfdTools/general/SRF/derivedFvPatchFields/SRFVelocityFvPatchVectorField/SRFVelocityFvPatchVectorField.C
Making dependency list for source file cfdTools/general/SRF/SRFModel/rpm/rpm.C
could not open file fvPatchFields.H for source file cfdTools/general/SRF/derivedFvPatchFields/SRFVelocityFvPatchVectorField/SRFVelocityFvPatchVectorField.C due to No such file or directory
could not open file fixedValueFvPatchFields.H for source file cfdTools/general/SRF/derivedFvPatchFields/SRFVelocityFvPatchVectorField/SRFVelocityFvPatchVectorField.C due to No such file or directory
Making dependency list for source file cfdTools/general/SRF/SRFModel/SRFModel/SRFModel.C
could not open file SRFModel.H for source file cfdTools/general/SRF/SRFModel/rpm/rpm.C due to No such file or directory
could not open file inletOutletFvPatchFields.H for source file cfdTools/general/SRF/derivedFvPatchFields/SRFFreestreamVelocityFvPatchVectorField/SRFFreestreamVelocityFvPatchVectorField.C due to No such file or directory

..............

mpiicpc -std=c++0x -fp-trap=common -fp-model precise -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -diag-disable 2304 -xHost -O2 -DNoRepository -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/finiteVolume/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/dynamicFvMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/dynamicMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/meshTools/lnInclude -IlnInclude -I. -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OpenFOAM/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OSspecific/POSIX/lnInclude -fPIC -shared -Xlinker --add-needed -Xlinker --no-as-needed /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/rawTopoChangerFvMesh/rawTopoChangerFvMesh.o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/movingConeTopoFvMesh/movingConeTopoFvMesh.o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/rawTopoChangerFvMesh/rawTopoChangerFvMesh.o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/movingConeTopoFvMesh/movingConeTopoFvMesh.o -L/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/lib -lfiniteVolume -ldynamicFvMesh -ldynamicMesh -lmeshTools -o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/lib/libtopoChangerFvMesh.so

/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o.bss+0x18): multiple definition of `Foam::topoChangerFvMesh::typeName'
/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o.bss+0x18): first defined here
/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o: In function `Foam::topoChangerFvMesh::topoChangerFvMesh(Foam:: IOobject const&)':
topoChangerFvMesh.C.text+0x0): multiple definition of `Foam::topoChangerFvMesh::topoChangerFvMesh(Foam:: IOobject const&)'
/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o:topoChangerFvMesh.C.text+0x0 ): first defined here
/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o: In function `Foam::topoChangerFvMesh::topoChangerFvMesh(Foam:: IOobject const&)':
topoChangerFvMesh.C.text+0x10): multiple definition of `Foam::topoChangerFvMesh::topoChangerFvMesh(Foam:: IOobject const&)'
/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o:topoChangerFvMesh.C.text+0x1 0): first defined here
/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o: In function `non-virtual thunk to Foam::topoChangerFvMesh::~topoChangerFvMesh()':


so removing duplicate files in the manual compilation resolved the issue:

mpiicpc -std=c++0x -fp-trap=common -fp-model precise -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -diag-disable 2304 -xHost -O2 -DNoRepository -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/finiteVolume/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/dynamicFvMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/dynamicMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/meshTools/lnInclude -IlnInclude -I. -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OpenFOAM/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OSspecific/POSIX/lnInclude -fPIC -shared -Xlinker --add-needed -Xlinker --no-as-needed /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/topoChangerFvMesh/topoChangerFvMesh.o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/rawTopoChangerFvMesh/rawTopoChangerFvMesh.o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/src/topoChangerFvMesh/movingConeTopoFvMesh/movingConeTopoFvMesh.o -L/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/lib -lfiniteVolume -ldynamicFvMesh -ldynamicMesh -lmeshTools -o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/lib/libtopoChangerFvMesh.so

(complete error log at intel forum- in the link!)
I want to know how can i prevent these error in future , i.e. which openfoam source config files/compilation flags should i edit to remove these errors ?
how can i get past this error ?any hint /help will be very useful.

Last edited by puneet336; November 23, 2015 at 16:44.
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Old   November 23, 2015, 01:06
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i was able to find temporary fix for this error:

/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/Triangulation_3.h(3604): internal error: conv_class_prvalue_operand_to_lvalue: couldn't convert to ptr
BOOST_FOREACH(Cell_handle& ch,


i have boost library in a custom path
so i had to give :

mpiicpc -std=c++0x -fp-trap=common -fp-model precise -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -diag-disable 2304 -xHost -O2 -DNoRepository -DNDEBUG -DCGAL_INEXACT -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include -I/include -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies/include -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/boost-system/include -diag-disable 1224,2026,2305 -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/finiteVolume/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/meshTools/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/parallel/decompose/decompositionMethods/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/edgeMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/fileFormats/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/dynamicMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/surfMesh/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/triSurface/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/sampling/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/mesh/autoMesh/lnInclude -IPrintTable -I/usr/include -IlnInclude -I. -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OpenFOAM/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OSspecific/POSIX/lnInclude -fPIC -c cellSizeControlSurfaces/cellSizeFunction/linearSpatial/linearSpatial.C -o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/cellSizeControlSurfaces/cellSizeFunction/linearSpatial/linearSpatial.o

In file included from /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/Modular_arithmetic/Residue_type.h(30),
from /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/Residue.h(31),
from /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/Modular_traits.h(24),
from /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/int.h(30),
from /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/number_type_basic.h(65),
from /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/basic.h(44),
from /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/ThirdParty-3.0.0/platforms/linux64Icc/CGAL-4.7/include/CGAL/Delaunay_triangulation_3.h(27),
from lnInclude/CGALTriangulation3DKernel.H(36),
from lnInclude/CGALTriangulation3Ddefs.H(41),
from lnInclude/conformalVoronoiMesh.H(46),
from lnInclude/cellSizeFunction.H(39),
from cellSizeControlSurfaces/cellSizeFunction/linearSpatial/linearSpatial.H(37),
from cellSizeControlSurfaces/cellSizeFunction/linearSpatial/linearSpatial.C(26):
/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies/include/boost/thread/tss.hpp(34): warning #2289: proper signature for "thread_specific_ptr" is "Type(const Type&)"
thread_specific_ptr(thread_specific_ptr&);

& the file compiled !!

boost was built with gcc compilers , but this does not seem to be intel compiler error!
as i already have :

export PATH=/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies/bin/:$PATH
export C_INCLUDE_PATH=/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies/include/:$C_INCLUDE_PATH
export LD_LIBRARY_PATH=/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies/lib/:$LD_LIBRARY_PATH
export LIBRARY_PATH=/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies/lib/:$LIBRARY_PATH
export CMAKE_PREFIX_PATH=/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies:$CMAKE_PREFIX_PATH


so at time of configure/cmake , the Allwmake script should also include these paths from the environment as priority (i.e. first these , then defaults)!!
is there a way ? any help / hint will be very useful !!

Last edited by puneet336; November 23, 2015 at 16:39.
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Old   November 23, 2015, 16:56
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Hi puneet336,

Something very strange is going on with your installation. The issue you described at the Intel forum and in the post #4 should never happen when building OpenFOAM normally, because the objects (the files "*.o") should only be listed once and not twice.

As for the issue with Boost, edit the file "etc/config/CGAL.sh" that is inside the folder "OpenFOAM-3.0.0" and change this line:
Code:
export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$boost_version
To this:
Code:
export BOOST_ARCH_PATH=$HOME/OpenFOAM/OpenFOAMDependencies
I've taken a bit of a better look at the work-flow you're following and I only then remembered to suggest to you that you can investigate the instructions given here:
You can draw some ideas from there for your installation.

Good luck! Best regards,
Bruno
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Old   November 24, 2015, 13:33
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hi ,
i had build ptscotch at a custom path & specified the path in etc/config/scotch.sh as SCOTCH_ARCH_PATH = /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies but due to FOAM_MPI variable , it is unable to generate include path properly:

Making dependency list for source file ptscotchDecomp.C
could not open file ptscotch.h for source file ptscotchDecomp.C due to No such file or directory
mpiicpc -std=c++0x -fp-trap=common -fp-model precise -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -diag-disable 2304 -xHost -O2 -DNoRepository -DMPICH_SKIP_MPICXX -isystem /home/soft/intel2015//impi/5.0.3.048/include64 -I/include -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies//include/5.0.3.048 -I/usr/include/scotch -I../decompositionMethods/lnInclude -IlnInclude -I. -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OpenFOAM/lnInclude -I/home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/src/OSspecific/POSIX/lnInclude -fPIC -c ptscotchDecomp.C -o /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAM-3.0.0/platforms/linux64IccDPInt32OptINTELMPI/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.o
ptscotchDecomp.C(126): catastrophic error: cannot open source file "ptscotch.h"
#include "ptscotch.h"


is there a way / file where i can manually fix this (without affecting FOAM_MPI value?)

though compilation proceeds if i set
export FOAM_MPI=
but i doubt weather this will work if i start my compilation all over again!, are there any repercussions to this approach?
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Old   November 24, 2015, 16:23
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Quick answer: Since you're using Linux, you can think this the other way around. Instead of changing the configuration files and shell environment variables such as "FOAM_MPI", you can instead use symbolic links for creating links between the paths that OpenFOAM expects to find and the real paths.

For example, OpenFOAM's original setting is this:
Code:
export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_LABEL_OPTION/$SCOTCH_VERSION
For example, if you do these commands:
Code:
mkdir -p $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_LABEL_OPTION/$SCOTCH_VERSION

ln -s /home/cc/vfaculty/puneets.vfaculty/OpenFOAM/OpenFOAMDependencies/include $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_LABEL_OPTION/$SCOTCH_VERSION/include
This will first create the base folder where OpenFOAM expects Scotch to be installed and then the second command will act as if you were copying the folder "include" at "OpenFOAMDependencies" to the folder where OpenFOAM expects to find this "include" folder. If you then run this command:
Code:
ls -l $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_LABEL_OPTION/$SCOTCH_VERSION/include
it should tell you that the "include" folder is pointing to the folder you have at "OpenFOAMDependencies".
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