[OpenFOAM.org] Compile OF 2.3 on Mac OS X .... the patch

alexeym · May 14, 2014, 15:35

Hi,

well, describe what exactly you've done, step by step. Show your bashrc file. As Pstream library was not compiled I guess there was other errors before the one you've posted in your message. Can you show full compilation log?

alexeym · May 14, 2014, 16:48

You've got this line in your bashrc:

Code:

export WM_MPLIB=OPENMPI

while it should be

Code:

export WM_MPLIB=SYSTEMOPENMPI

as you have OpenMPI installed system-wide with Macports.

And due to this error in configuration, you've got this error in the very beginning of your compilation log:

Code:

Making dependency list for source file UOPwrite.C
could not open file mpi.h for source file UOPwrite.C due to No such file or directory
Making dependency list for source file UIPread.C
could not open file mpi.h for source file UIPread.C due to No such file or directory
Making dependency list for source file UPstream.C
could not open file mpi.h for source file UPstream.C due to No such file or directory
Making dependency list for source file PstreamGlobals.C
could not open file mpi.h for source file PstreamGlobals.C due to No such file or directory
SOURCE=UOPwrite.C ;  g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -
Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -I/Users/Mowa/OpenFOAM/ThirdParty-2.3
.x/platforms/darwinIntel64Gcc46/openmpi-1.6.5/include -IlnInclude -I. -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/OpenFOAM/lnInclude -
I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -c $SOURCE -o Make/darwinIntel64Gcc46DPOptOPENM
PI/UOPwrite.o
UOPwrite.C:29:17: fatal error: mpi.h: No such file or directory
compilation terminated.
make: *** [Make/darwinIntel64Gcc46DPOptOPENMPI/UOPwrite.o] Error 1

It leads to all other troubles.

alexeym · May 15, 2014, 12:09

Can you post output of

Code:

$ which mpicc

?

Did you execute (I don't know exact syntax of the command, you should read port's man page)

Code:

$ sudo port select --set mpi <version>

?

Until you fix your OpenMPI installation there's no point in compiling OpenFOAM again and again (though, guess without Pstream compilation fails rather quickly). Also maybe it'll be easier for both of us to wait till somebody using Macports (and was able to build OF successfully) post an answer.

alexeym · May 15, 2014, 12:53

Well, maybe there are some stale dep files; as installation of MPI looks OK, try going to $WM_PROJECT_DIR and executing:

Code:

$ wclean all src
$ wclean all applications

to remove old compilation results and then execute ./Allwmake script again.

Roskiki · May 16, 2014, 15:54

OpenFOAM to successfully compile with the same error. SEVERAL solver works except interfoam. how to operate Parafoam?

merci encor!!!!

f0208secretx · May 17, 2014, 03:46

Quote:

Originally Posted by alexeym

Hi,

I don't know much about building OF on OS X with Macport's gcc (I've used it successfully 2 years ago for 2.1.1, after I used Linux, and finally recently I've used clang to build OF on OS X).

Concerning your question about scotch, I've used 'grep -r lscotch *' and 'grep -r lptscotch *' in $WM_PROJECT_DIR to get rough estimation of the applications and libraries using Scotch library, and I guess you won't be able to use:

foamyHexMesh
renumberMesh
decomposePar (with scotch decomposition method)
foamyQuadMesh
snappyHexMesh
redistributePar

Also, since you're referencing to the post where I used clang to build OpenFOAM and your error is with gcc, I don't know what's gone wrong during installation process.

Hi alexeym,

Thanks for getting back to me. I downloaded the patch from your blog and apply them to OpenFOAM-2.3.0 from openfoam.org. I followed all the steps and yet am still getting some errors. I have little ideas on how to solve them, so I posted my log file and hopefully someone can help me with it.

Meanwhile I will try the whole process again. Thanks.

JHW

alexeym · May 17, 2014, 04:09

Well, in addition to the compilation log, please, attach your OpenFOAM's bashrc file. Cause your log file looks rather strange to me: it use g++ in one place and clang++ in other. Also what patch did you use?

f0208secretx · May 17, 2014, 04:16

It seems that I cannot attach another file for my previous post, so I will have to do it here. Sorry for the spam...

I suspect it was because I had not removed everything completely from the failed attempt in the past. I removed the entire folder and am re-doing the whole process. This time it seems more... promising. If you can confirm this conjecture will be the best. Thank you.

I am using the patch linked from your blog:
https://dl.dropboxusercontent.com/u/...-2.3.0-2.patch
https://dl.dropboxusercontent.com/u/...-2.3.0-1.patch

JHW

alexeym · May 17, 2014, 04:24

Though now log file looks more consistent, I don't like the errors with flex (finally they lead to complete fail of installation). Can you post output of

Code:

$ which flex

and

Code:

$ flex --version

commands?

Do you have Macports installed?

f0208secretx · May 17, 2014, 11:52

Quote:

Originally Posted by alexeym

Though now log file looks more consistent, I don't like the errors with flex (finally they lead to complete fail of installation). Can you post output of

Code:

$ which flex

and

Code:

$ flex --version

commands?

Do you have Macports installed?

As follows:

Code:

dhcp-128-253-143-174:OpenFOAM-2.3.0 jui-hsienwang$ which flex
/opt/local/bin/flex
dhcp-128-253-143-174:OpenFOAM-2.3.0 jui-hsienwang$ flex --version
flex 2.5.37
dhcp-128-253-143-174:OpenFOAM-2.3.0 jui-hsienwang$ sudo port
MacPorts 2.2.1
Entering interactive mode... ("help" for help, "quit" to quit)
[OpenFOAM-v2.3/OpenFOAM-2.3.0] > q
Goodbye

The second attempt still failed. I attached the log file and bashrc for your reference. Thanks so much.
https://dl.dropboxusercontent.com/u/...-17-2014-2.zip

JHW

alexeym · May 17, 2014, 12:42

Well,

as you've got Macports installed, you should use the patch from the beginning of the thread (and use gcc installed with Macports for compilation).

My patch rely on the software shipped with OS X (clang, flex etc), so ex. there's no problem with include path for flex. As you've got Macports installed, during compilation clang is used from OS X developer tools, and flex is used from Macports installation, due to certain incompatibilities between these two, you've got the error:

Code:

Make/darwinIntel64ClangDPOpt/STLsurfaceFormatASCII.C:5981:18: error: out-of-line definition of 'LexerInput' does not match any decla
ration in 'yyFlexLexer'
int yyFlexLexer::LexerInput( char* buf, int max_size )
                 ^~~~~~~~~~

Roskiki · May 17, 2014, 13:20

g++-mp-4.6 -m64 -fsignaling-nans -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2 -DNoRepository -ftemplate-depth-100 -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/twoPhaseMixture/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/incompressible/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/interfaceProperties/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/turbulenceModels/incompressible/turbulenceModel -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/finiteVolume/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/fvOptions/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/meshTools/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/sampling/lnInclude -IlnInclude -I. -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/OpenFOAM/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/OSspecific/POSIX/lnInclude -fPIC -Ddarwin -lpthread -L/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib/dummy -lPstream Make/darwinIntel64Gcc46DPOpt/interFoam.o -L/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib \
-limmiscibleIncompressibleTwoPhaseMixture -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lfvOptions -lmeshTools -lsampling -lOpenFOAM -ldl -lpthread -lm -o /Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam
Undefined symbols for architecture x86_64:
"Foam::transportModel::~transportModel()", referenced from:
Foam::incompressibleTwoPhaseMixture::~incompressib leTwoPhaseMixture() in interFoam.o
Foam::immiscibleIncompressibleTwoPhaseMixture::~im miscibleIncompressibleTwoPhaseMixture() in interFoam.o
Foam::immiscibleIncompressibleTwoPhaseMixture::~im miscibleIncompressibleTwoPhaseMixture() in interFoam.o
"Foam::interfaceProperties::calculateK()", referenced from:
Foam::immiscibleIncompressibleTwoPhaseMixture::cor rect() in interFoam.o
_main in interFoam.o
"Foam::incompressibleTwoPhaseMixture::read()", referenced from:
vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in interFoam.o
"Foam::incompressibleTwoPhaseMixture::calcNu() ", referenced from:
Foam::immiscibleIncompressibleTwoPhaseMixture::cor rect() in interFoam.o
_main in interFoam.o
"Foam::incompressibleTwoPhaseMixture::typeName ", referenced from:
Foam::incompressibleTwoPhaseMixture::type() const in interFoam.o
"Foam::interfaceProperties::nearInterface() const", referenced from:
_main in interFoam.o
"Foam::interfaceProperties::surfaceTensionForc e() const", referenced from:
_main in interFoam.o
"typeinfo for Foam::incompressibleTwoPhaseMixture", referenced from:
typeinfo for Foam::immiscibleIncompressibleTwoPhaseMixture in interFoam.o
"vtable for Foam::incompressibleTwoPhaseMixture", referenced from:
Foam::incompressibleTwoPhaseMixture::~incompressib leTwoPhaseMixture() in interFoam.o
Foam::immiscibleIncompressibleTwoPhaseMixture::~im miscibleIncompressibleTwoPhaseMixture() in interFoam.o
Foam::immiscibleIncompressibleTwoPhaseMixture::~im miscibleIncompressibleTwoPhaseMixture() in interFoam.o
NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
"non-virtual thunk to Foam::incompressibleTwoPhaseMixture::read()", referenced from:
vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in interFoam.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make: *** [/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam] Error 1

any idea?

f0208secretx · May 18, 2014, 01:05

Quote:

Originally Posted by alexeym

Well,

as you've got Macports installed, you should use the patch from the beginning of the thread (and use gcc installed with Macports for compilation).

My patch rely on the software shipped with OS X (clang, flex etc), so ex. there's no problem with include path for flex. As you've got Macports installed, during compilation clang is used from OS X developer tools, and flex is used from Macports installation, due to certain incompatibilities between these two, you've got the error:

Code:

Make/darwinIntel64ClangDPOpt/STLsurfaceFormatASCII.C:5981:18: error: out-of-line definition of 'LexerInput' does not match any decla
ration in 'yyFlexLexer'
int yyFlexLexer::LexerInput( char* buf, int max_size )
                 ^~~~~~~~~~

Hi alexeym,

Thanks for getting back to me. I followed the instruction and cloned the git version. While I was following the instruction listed in the wiki, http://openfoamwiki.net/index.php/In...OpenFOAM_2.2.2, I found a line that looks different. In the wiki it says for the file src/renumber/SloanRenumber/Make/options,

Code:

Change this line:
-L$(BOOST_ARCH_PATH)/lib -lboost_thread \
into this:
-L$(BOOST_ARCH_PATH)/lib -lboost_thread-mt \

But instead the file I pulled from github looks like

Code:

LIB_LIBS = \
    -L$(BOOST_ARCH_PATH)/lib -lboost_thread$(BOOST_THREAD_EXTENSION) \
    -lmeshTools \
    -ldecompositionMethods \
    -lrenumberMethods

I wasn't so sure if I can just change it to

Code:

LIB_LIBS = \
    -L$(BOOST_ARCH_PATH)/lib -lboost_thread-mt$(BOOST_THREAD_EXTENSION) \

If I do this naively it appears to cause trouble in the compilation. If you can give me an advise or two will be great. Thanks!

JHW

alexeym · May 18, 2014, 05:56

@Roskiki: I think due to certain errors libincompressibleTransportModels was not built. So you've got undefined symbols.

@f0208secretx: You should leave the line as it is, BOOST_THREAD_EXTENSION variable is filled during environment initialization. If you have single threaded boost version it will be empty, if you've got multithreaded boost version, it will contain "-mt" string.

Roskiki · May 18, 2014, 10:47

I added '-lincompressibleTransportModels \' in Make/option:

EXE_INC = \
-I$(LIB_SRC)/transportModels/twoPhaseMixture/lnInclude \
-I$(LIB_SRC)/transportModels \
-I$(LIB_SRC)/transportModels/incompressible/lnInclude \
-I$(LIB_SRC)/transportModels/interfaceProperties/lnInclude \
-I$(LIB_SRC)/turbulenceModels/incompressible/turbulenceModel \
-I$(LIB_SRC)/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/fvOptions/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/sampling/lnInclude

EXE_LIBS = \
-lincompressibleTransportModels \
-limmiscibleIncompressibleTwoPhaseMixture \
-lincompressibleTurbulenceModel \
-lincompressibleRASModels \
-lincompressibleLESModels \
-lfiniteVolume \
-lfvOptions \
-lmeshTools \
-lsampling

2-wmake:

-limmiscibleIncompressibleTwoPhaseMixture -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lfvOptions -lincompressibleTransportModels -lmeshTools -lsampling -lOpenFOAM -ldl -lpthread -lm -o /Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam
Undefined symbols for architecture x86_64:
"Foam::interfaceProperties::calculateK()", referenced from:
Foam::immiscibleIncompressibleTwoPhaseMixture::cor rect() in interFoam.o
_main in interFoam.o
"Foam::interfaceProperties::nearInterface() const", referenced from:
_main in interFoam.o
"Foam::interfaceProperties::surfaceTensionForc e() const", referenced from:
_main in interFoam.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make: *** [/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam] Error 1

any idea?

LtInterFoam, interFoam and interDyMFoam does not work

alexeym · May 18, 2014, 10:57

If addition of the linking flag helped, add another one:

Code:

-linterfaceProperties

Roskiki · May 18, 2014, 11:18

thank you very much

f0208secretx · May 18, 2014, 12:59

I got a very similar error to Roskiki. Something like

Code:

+ wmake
g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -IincompressibleTwoPhaseInteractingMixture -ImixtureViscosityModels/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/finiteVolume/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/meshTools/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/sampling/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/fvOptions/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/twoPhaseMixture/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/incompressible/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/interfaceProperties/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/TurbulenceModels/turbulenceModels/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/TurbulenceModels/compressible/lnInclude -I./relativeVelocityModels/lnInclude -IlnInclude -I. -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OpenFOAM/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -lpthread -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-macport-gcc46 -lPstream Make/darwinIntel64Gcc46DPOpt/incompressibleTwoPhaseInteractingMixture.o Make/darwinIntel64Gcc46DPOpt/compressibleTurbulenceModels.o Make/darwinIntel64Gcc46DPOpt/driftFluxFoam.o -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib \
	     -ldriftFluxTransportModels -ldriftFluxRelativeVelocityModels -lfiniteVolume -lmeshTools -lsampling -lfvOptions -lincompressibleTransportModels -lturbulenceModels -lcompressibleTurbulenceModels -lOpenFOAM -ldl   -lpthread -lm -o /Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/driftFluxFoam
Undefined symbols for architecture x86_64:
  "Foam::twoPhaseMixture::twoPhaseMixture(Foam::fvMesh const&, Foam::dictionary const&)", referenced from:
      Foam::incompressibleTwoPhaseInteractingMixture::incompressibleTwoPhaseInteractingMixture(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&) in incompressibleTwoPhaseInteractingMixture.o
      Foam::incompressibleTwoPhaseInteractingMixture::incompressibleTwoPhaseInteractingMixture(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&) in incompressibleTwoPhaseInteractingMixture.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/driftFluxFoam] Error 1
make[1]: *** [driftFluxFoam] Error 2

I searched online and people suggested this might be a problem of the different implementations of the standard C++ library after OS X 10.9. The discussion can be found at, for example,
http://stackoverflow.com/questions/1...-9-xcode-5-0-1

Could this be the problem? Or like Roskiki I have some models weren't built? (How do I know?) If I want to manually choose the library libstdc++, where and what should I change? Thanks a lot for your continuous help

JHW

Roskiki · May 18, 2014, 13:10

As there were two posts with error in compilation of this solver, I've decided to post a way to correct it. The guide is valid for commit 6f6bc2f78679cffacf479cb58cc74497bbf3963c (IIRC there's no such problem on Linux, so guess this correction will be valid for later commits as error won't be fixed in repository).

1. Go to $FOAM_APP/solvers/multiphase/driftFluxFoam
2. Open Make/options in an editor
3. Make it look like:

Code:
EXE_INC = \
-IincompressibleTwoPhaseInteractingMixture \
-ImixtureViscosityModels/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/sampling/lnInclude \
-I$(LIB_SRC)/fvOptions/lnInclude \
-I$(LIB_SRC)/transportModels \
-I$(LIB_SRC)/transportModels/twoPhaseMixture/lnInclude \
-I$(LIB_SRC)/transportModels/incompressible/lnInclude \
-I$(LIB_SRC)/transportModels/interfaceProperties/lnInclude \
-I./relativeVelocityModels/lnInclude

EXE_LIBS = \
-lfiniteVolume \
-lmeshTools \
-lsampling \
-lfvOptions \
-lincompressibleTransportModels \
-ltwoPhaseMixture \
-ldriftFluxTransportModels \
-ldriftFluxRelativeVelocityModels
in fact it's just addition of a line "-ltwoPhaseMixture \" after "-lincompressibleTransportModels \"

4. run wmake

Solver should compile now without errors.

from alexym

f0208secretx · May 18, 2014, 15:39

Quote:

Originally Posted by Roskiki

As there were two posts with error in compilation of this solver, I've decided to post a way to correct it. The guide is valid for commit 6f6bc2f78679cffacf479cb58cc74497bbf3963c (IIRC there's no such problem on Linux, so guess this correction will be valid for later commits as error won't be fixed in repository).

1. Go to $FOAM_APP/solvers/multiphase/driftFluxFoam
2. Open Make/options in an editor
3. Make it look like:

Code:
EXE_INC = \
-IincompressibleTwoPhaseInteractingMixture \
-ImixtureViscosityModels/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/sampling/lnInclude \
-I$(LIB_SRC)/fvOptions/lnInclude \
-I$(LIB_SRC)/transportModels \
-I$(LIB_SRC)/transportModels/twoPhaseMixture/lnInclude \
-I$(LIB_SRC)/transportModels/incompressible/lnInclude \
-I$(LIB_SRC)/transportModels/interfaceProperties/lnInclude \
-I./relativeVelocityModels/lnInclude

EXE_LIBS = \
-lfiniteVolume \
-lmeshTools \
-lsampling \
-lfvOptions \
-lincompressibleTransportModels \
-ltwoPhaseMixture \
-ldriftFluxTransportModels \
-ldriftFluxRelativeVelocityModels
in fact it's just addition of a line "-ltwoPhaseMixture \" after "-lincompressibleTransportModels \"

4. run wmake

Solver should compile now without errors.

from alexym

Hi,

Thanks for the reply. It does fix one of the errors. But I still have errors from other solvers, in particular,

in interFoam:

Code:

+ wmake
g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/twoPhaseMixture/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/incompressible/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/interfaceProperties/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/turbulenceModels/incompressible/turbulenceModel -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/finiteVolume/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/fvOptions/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/meshTools/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/sampling/lnInclude -IlnInclude -I. -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OpenFOAM/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -lpthread -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-macport-gcc46 -lPstream Make/darwinIntel64Gcc46DPOpt/interFoam.o -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib \
	     -limmiscibleIncompressibleTwoPhaseMixture -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lfvOptions -lmeshTools -lsampling -lOpenFOAM -ldl   -lpthread -lm -o /Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam
Undefined symbols for architecture x86_64:
  "Foam::transportModel::~transportModel()", referenced from:
      Foam::incompressibleTwoPhaseMixture::~incompressibleTwoPhaseMixture() in interFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in interFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in interFoam.o
  "Foam::interfaceProperties::calculateK()", referenced from:
      Foam::immiscibleIncompressibleTwoPhaseMixture::correct()     in interFoam.o
      _main in interFoam.o
  "Foam::incompressibleTwoPhaseMixture::read()", referenced from:
      vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in interFoam.o
  "Foam::incompressibleTwoPhaseMixture::calcNu()", referenced from:
      Foam::immiscibleIncompressibleTwoPhaseMixture::correct()     in interFoam.o
      _main in interFoam.o
  "Foam::incompressibleTwoPhaseMixture::typeName", referenced from:
      Foam::incompressibleTwoPhaseMixture::type() const in interFoam.o
  "Foam::interfaceProperties::nearInterface() const", referenced from:
      _main in interFoam.o
  "Foam::interfaceProperties::surfaceTensionForce() const", referenced from:
      _main in interFoam.o
  "typeinfo for Foam::incompressibleTwoPhaseMixture", referenced from:
      typeinfo for Foam::immiscibleIncompressibleTwoPhaseMixture in interFoam.o
  "vtable for Foam::incompressibleTwoPhaseMixture", referenced from:
      Foam::incompressibleTwoPhaseMixture::~incompressibleTwoPhaseMixture() in interFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in interFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in interFoam.o
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "non-virtual thunk to Foam::incompressibleTwoPhaseMixture::read()", referenced from:
      vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in interFoam.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam] Error 1

in interDyMFoam:

Code:

+ wmake interDyMFoam
g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -I.. -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/twoPhaseMixture/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/incompressible/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/interfaceProperties/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/turbulenceModels/incompressible/turbulenceModel -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/finiteVolume/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/dynamicMesh/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/dynamicFvMesh/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/meshTools/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/fvOptions/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/sampling/lnInclude -IlnInclude -I. -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OpenFOAM/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -lpthread -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-macport-gcc46 -lPstream Make/darwinIntel64Gcc46DPOpt/interDyMFoam.o -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib \
	     -limmiscibleIncompressibleTwoPhaseMixture -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -ldynamicMesh -ldynamicFvMesh -ltopoChangerFvMesh -lmeshTools -lfvOptions -lsampling -lOpenFOAM -ldl   -lpthread -lm -o /Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interDyMFoam
Undefined symbols for architecture x86_64:
  "Foam::transportModel::~transportModel()", referenced from:
      Foam::incompressibleTwoPhaseMixture::~incompressibleTwoPhaseMixture() in interDyMFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in interDyMFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in interDyMFoam.o
  "Foam::interfaceProperties::calculateK()", referenced from:
      Foam::immiscibleIncompressibleTwoPhaseMixture::correct()     in interDyMFoam.o
      _main in interDyMFoam.o
  "Foam::incompressibleTwoPhaseMixture::read()", referenced from:
      vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in interDyMFoam.o
  "Foam::incompressibleTwoPhaseMixture::calcNu()", referenced from:
      Foam::immiscibleIncompressibleTwoPhaseMixture::correct()     in interDyMFoam.o
      _main in interDyMFoam.o
  "Foam::incompressibleTwoPhaseMixture::typeName", referenced from:
      Foam::incompressibleTwoPhaseMixture::type() const in interDyMFoam.o
  "Foam::interfaceProperties::nearInterface() const", referenced from:
      _main in interDyMFoam.o
  "Foam::interfaceProperties::surfaceTensionForce() const", referenced from:
      _main in interDyMFoam.o
  "typeinfo for Foam::incompressibleTwoPhaseMixture", referenced from:
      typeinfo for Foam::immiscibleIncompressibleTwoPhaseMixture in interDyMFoam.o
  "vtable for Foam::incompressibleTwoPhaseMixture", referenced from:
      Foam::incompressibleTwoPhaseMixture::~incompressibleTwoPhaseMixture() in interDyMFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in interDyMFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in interDyMFoam.o
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "non-virtual thunk to Foam::incompressibleTwoPhaseMixture::read()", referenced from:
      vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in interDyMFoam.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interDyMFoam] Error 1

in porousInterFoam:

Code:

+ wmake porousInterFoam
g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -I.. -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/twoPhaseMixture/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/incompressible/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/interfaceProperties/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/turbulenceModels/incompressible/turbulenceModel -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/finiteVolume/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/meshTools/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/fvOptions/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/sampling/lnInclude -IlnInclude -I. -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OpenFOAM/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -lpthread -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-macport-gcc46 -lPstream Make/darwinIntel64Gcc46DPOpt/porousInterFoam.o -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib \
	     -limmiscibleIncompressibleTwoPhaseMixture -lincompressibleTransportModels -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lmeshTools -lfvOptions -lsampling -lOpenFOAM -ldl   -lpthread -lm -o /Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/porousInterFoam
Undefined symbols for architecture x86_64:
  "Foam::interfaceProperties::calculateK()", referenced from:
      Foam::immiscibleIncompressibleTwoPhaseMixture::correct()     in porousInterFoam.o
      _main in porousInterFoam.o
  "Foam::interfaceProperties::nearInterface() const", referenced from:
      _main in porousInterFoam.o
  "Foam::interfaceProperties::surfaceTensionForce() const", referenced from:
      _main in porousInterFoam.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/porousInterFoam] Error 1

in LTSInterFoam:

Code:

+ wmake LTSInterFoam
g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -I.. -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/twoPhaseMixture/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/incompressible/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/interfaceProperties/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/turbulenceModels/incompressible/turbulenceModel -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/finiteVolume/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/meshTools/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/fvOptions/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/sampling/lnInclude -IlnInclude -I. -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OpenFOAM/lnInclude -I/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -lpthread -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-macport-gcc46 -lPstream Make/darwinIntel64Gcc46DPOpt/LTSInterFoam.o -L/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib \
	     -limmiscibleIncompressibleTwoPhaseMixture -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lmeshTools -lfvOptions -lsampling -lOpenFOAM -ldl   -lpthread -lm -o /Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/LTSInterFoam
Undefined symbols for architecture x86_64:
  "Foam::transportModel::~transportModel()", referenced from:
      Foam::incompressibleTwoPhaseMixture::~incompressibleTwoPhaseMixture() in LTSInterFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in LTSInterFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in LTSInterFoam.o
  "Foam::interfaceProperties::calculateK()", referenced from:
      Foam::immiscibleIncompressibleTwoPhaseMixture::correct()     in LTSInterFoam.o
      _main in LTSInterFoam.o
  "Foam::incompressibleTwoPhaseMixture::read()", referenced from:
      vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in LTSInterFoam.o
  "Foam::incompressibleTwoPhaseMixture::calcNu()", referenced from:
      Foam::immiscibleIncompressibleTwoPhaseMixture::correct()     in LTSInterFoam.o
      _main in LTSInterFoam.o
  "Foam::incompressibleTwoPhaseMixture::typeName", referenced from:
      Foam::incompressibleTwoPhaseMixture::type() const in LTSInterFoam.o
  "Foam::interfaceProperties::surfaceTensionForce() const", referenced from:
      _main in LTSInterFoam.o
  "typeinfo for Foam::incompressibleTwoPhaseMixture", referenced from:
      typeinfo for Foam::immiscibleIncompressibleTwoPhaseMixture in LTSInterFoam.o
  "vtable for Foam::incompressibleTwoPhaseMixture", referenced from:
      Foam::incompressibleTwoPhaseMixture::~incompressibleTwoPhaseMixture() in LTSInterFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in LTSInterFoam.o
      Foam::immiscibleIncompressibleTwoPhaseMixture::~immiscibleIncompressibleTwoPhaseMixture() in LTSInterFoam.o
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "non-virtual thunk to Foam::incompressibleTwoPhaseMixture::read()", referenced from:
      vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in LTSInterFoam.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [/Users/jui-hsienwang/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/LTSInterFoam] Error 1

log file attached for your reference. Thanks

JHW

May 15, 2014, 12:09		#63
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	Can you post output of Code: $ which mpicc ? Did you execute (I don't know exact syntax of the command, you should read port's man page) Code: $ sudo port select --set mpi <version> ? Until you fix your OpenMPI installation there's no point in compiling OpenFOAM again and again (though, guess without Pstream compilation fails rather quickly). Also maybe it'll be easier for both of us to wait till somebody using Macports (and was able to build OF successfully) post an answer.

May 15, 2014, 12:53		#64
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	Well, maybe there are some stale dep files; as installation of MPI looks OK, try going to $WM_PROJECT_DIR and executing: Code: $ wclean all src $ wclean all applications to remove old compilation results and then execute ./Allwmake script again.

May 17, 2014, 04:24		#69
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	Though now log file looks more consistent, I don't like the errors with flex (finally they lead to complete fail of installation). Can you post output of Code: $ which flex and Code: $ flex --version commands? Do you have Macports installed?

May 17, 2014, 12:42		#71
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	Well, as you've got Macports installed, you should use the patch from the beginning of the thread (and use gcc installed with Macports for compilation). My patch rely on the software shipped with OS X (clang, flex etc), so ex. there's no problem with include path for flex. As you've got Macports installed, during compilation clang is used from OS X developer tools, and flex is used from Macports installation, due to certain incompatibilities between these two, you've got the error: Code: Make/darwinIntel64ClangDPOpt/STLsurfaceFormatASCII.C:5981:18: error: out-of-line definition of 'LexerInput' does not match any decla ration in 'yyFlexLexer' int yyFlexLexer::LexerInput( char* buf, int max_size ) ^~~~~~~~~~

May 17, 2014, 13:20	error compiling interFoam	#72
Roskiki New Member Juimo Pierre Join Date: Aug 2012 Posts: 13 Rep Power: 14	g++-mp-4.6 -m64 -fsignaling-nans -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2 -DNoRepository -ftemplate-depth-100 -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/twoPhaseMixture/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/incompressible/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/interfaceProperties/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/turbulenceModels/incompressible/turbulenceModel -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/finiteVolume/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/fvOptions/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/meshTools/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/sampling/lnInclude -IlnInclude -I. -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/OpenFOAM/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/src/OSspecific/POSIX/lnInclude -fPIC -Ddarwin -lpthread -L/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib/dummy -lPstream Make/darwinIntel64Gcc46DPOpt/interFoam.o -L/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/lib \ -limmiscibleIncompressibleTwoPhaseMixture -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lfvOptions -lmeshTools -lsampling -lOpenFOAM -ldl -lpthread -lm -o /Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam Undefined symbols for architecture x86_64: "Foam::transportModel::~transportModel()", referenced from: Foam::incompressibleTwoPhaseMixture::~incompressib leTwoPhaseMixture() in interFoam.o Foam::immiscibleIncompressibleTwoPhaseMixture::~im miscibleIncompressibleTwoPhaseMixture() in interFoam.o Foam::immiscibleIncompressibleTwoPhaseMixture::~im miscibleIncompressibleTwoPhaseMixture() in interFoam.o "Foam::interfaceProperties::calculateK()", referenced from: Foam::immiscibleIncompressibleTwoPhaseMixture::cor rect() in interFoam.o _main in interFoam.o "Foam::incompressibleTwoPhaseMixture::read()", referenced from: vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in interFoam.o "Foam::incompressibleTwoPhaseMixture::calcNu() ", referenced from: Foam::immiscibleIncompressibleTwoPhaseMixture::cor rect() in interFoam.o _main in interFoam.o "Foam::incompressibleTwoPhaseMixture::typeName ", referenced from: Foam::incompressibleTwoPhaseMixture::type() const in interFoam.o "Foam::interfaceProperties::nearInterface() const", referenced from: _main in interFoam.o "Foam::interfaceProperties::surfaceTensionForc e() const", referenced from: _main in interFoam.o "typeinfo for Foam::incompressibleTwoPhaseMixture", referenced from: typeinfo for Foam::immiscibleIncompressibleTwoPhaseMixture in interFoam.o "vtable for Foam::incompressibleTwoPhaseMixture", referenced from: Foam::incompressibleTwoPhaseMixture::~incompressib leTwoPhaseMixture() in interFoam.o Foam::immiscibleIncompressibleTwoPhaseMixture::~im miscibleIncompressibleTwoPhaseMixture() in interFoam.o Foam::immiscibleIncompressibleTwoPhaseMixture::~im miscibleIncompressibleTwoPhaseMixture() in interFoam.o NOTE: a missing vtable usually means the first non-inline virtual member function has no definition. "non-virtual thunk to Foam::incompressibleTwoPhaseMixture::read()", referenced from: vtable for Foam::immiscibleIncompressibleTwoPhaseMixture in interFoam.o ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status make: *** [/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam] Error 1 any idea?

May 14, 2014, 15:35		#61
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	Hi, well, describe what exactly you've done, step by step. Show your bashrc file. As Pstream library was not compiled I guess there was other errors before the one you've posted in your message. Can you show full compilation log?

May 16, 2014, 15:54		#65
Roskiki New Member Juimo Pierre Join Date: Aug 2012 Posts: 13 Rep Power: 14	OpenFOAM to successfully compile with the same error. SEVERAL solver works except interfoam. how to operate Parafoam? merci encor!!!!

May 17, 2014, 04:09		#67
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	Well, in addition to the compilation log, please, attach your OpenFOAM's bashrc file. Cause your log file looks rather strange to me: it use g++ in one place and clang++ in other. Also what patch did you use?

May 18, 2014, 05:56		#74
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	@Roskiki: I think due to certain errors libincompressibleTransportModels was not built. So you've got undefined symbols. @f0208secretx: You should leave the line as it is, BOOST_THREAD_EXTENSION variable is filled during environment initialization. If you have single threaded boost version it will be empty, if you've got multithreaded boost version, it will contain "-mt" string. f0208secretx likes this.

May 18, 2014, 10:47		#75
Roskiki New Member Juimo Pierre Join Date: Aug 2012 Posts: 13 Rep Power: 14	I added '-lincompressibleTransportModels \' in Make/option: EXE_INC = \ -I$(LIB_SRC)/transportModels/twoPhaseMixture/lnInclude \ -I$(LIB_SRC)/transportModels \ -I$(LIB_SRC)/transportModels/incompressible/lnInclude \ -I$(LIB_SRC)/transportModels/interfaceProperties/lnInclude \ -I$(LIB_SRC)/turbulenceModels/incompressible/turbulenceModel \ -I$(LIB_SRC)/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude \ -I$(LIB_SRC)/finiteVolume/lnInclude \ -I$(LIB_SRC)/fvOptions/lnInclude \ -I$(LIB_SRC)/meshTools/lnInclude \ -I$(LIB_SRC)/sampling/lnInclude EXE_LIBS = \ -lincompressibleTransportModels \ -limmiscibleIncompressibleTwoPhaseMixture \ -lincompressibleTurbulenceModel \ -lincompressibleRASModels \ -lincompressibleLESModels \ -lfiniteVolume \ -lfvOptions \ -lmeshTools \ -lsampling 2-wmake: -limmiscibleIncompressibleTwoPhaseMixture -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lfvOptions -lincompressibleTransportModels -lmeshTools -lsampling -lOpenFOAM -ldl -lpthread -lm -o /Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam Undefined symbols for architecture x86_64: "Foam::interfaceProperties::calculateK()", referenced from: Foam::immiscibleIncompressibleTwoPhaseMixture::cor rect() in interFoam.o _main in interFoam.o "Foam::interfaceProperties::nearInterface() const", referenced from: _main in interFoam.o "Foam::interfaceProperties::surfaceTensionForc e() const", referenced from: _main in interFoam.o ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status make: *** [/Users/Mowa/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/interFoam] Error 1 any idea? LtInterFoam, interFoam and interDyMFoam does not work

May 18, 2014, 10:57		#76
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	If addition of the linking flag helped, add another one: Code: -linterfaceProperties

May 18, 2014, 11:18		#77
Roskiki New Member Juimo Pierre Join Date: Aug 2012 Posts: 13 Rep Power: 14	thank you very much

May 18, 2014, 13:10		#79
Roskiki New Member Juimo Pierre Join Date: Aug 2012 Posts: 13 Rep Power: 14	As there were two posts with error in compilation of this solver, I've decided to post a way to correct it. The guide is valid for commit 6f6bc2f78679cffacf479cb58cc74497bbf3963c (IIRC there's no such problem on Linux, so guess this correction will be valid for later commits as error won't be fixed in repository). 1. Go to $FOAM_APP/solvers/multiphase/driftFluxFoam 2. Open Make/options in an editor 3. Make it look like: Code: EXE_INC = \ -IincompressibleTwoPhaseInteractingMixture \ -ImixtureViscosityModels/lnInclude \ -I$(LIB_SRC)/finiteVolume/lnInclude \ -I$(LIB_SRC)/meshTools/lnInclude \ -I$(LIB_SRC)/sampling/lnInclude \ -I$(LIB_SRC)/fvOptions/lnInclude \ -I$(LIB_SRC)/transportModels \ -I$(LIB_SRC)/transportModels/twoPhaseMixture/lnInclude \ -I$(LIB_SRC)/transportModels/incompressible/lnInclude \ -I$(LIB_SRC)/transportModels/interfaceProperties/lnInclude \ -I./relativeVelocityModels/lnInclude EXE_LIBS = \ -lfiniteVolume \ -lmeshTools \ -lsampling \ -lfvOptions \ -lincompressibleTransportModels \ -ltwoPhaseMixture \ -ldriftFluxTransportModels \ -ldriftFluxRelativeVelocityModels in fact it's just addition of a line "-ltwoPhaseMixture \" after "-lincompressibleTransportModels \" 4. run wmake Solver should compile now without errors. from alexym

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