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-   -   [OpenFOAM.org] Compile OF 2.3 on Mac OS X .... the patch (https://www.cfd-online.com/Forums/openfoam-installation/130113-compile-2-3-mac-os-x-patch.html)

alexeym April 16, 2014 06:33

Quote:

Originally Posted by maCrobo (Post 486458)
I didn't know of this source thing either... The problem here is that I don't understand the logic behind all these things I'm doing to compile OpenFoam... Anyway, I did it and it compiled that specific solver.

'source etc/bashrc' is a synonym for '. etc/bashrc' and this step is described in section 4.3 (Final steps) point 9 of the guide on OpenFOAM wiki. You have to do this thing every time you'd like to use OpenFOAM.

Quote:

I have another question: should have I downloaded the patch directly in the Case Sensitive Image, or it is ok that I downloaded on my Downloads system folder where I usually download everything?
In case of patch it doesn't matter, you can do it either way. Cause all source code changes are inside patch file. It even doesn't matter how you name the patch file actually (as long as you use correct name in patch -p1 command) ;)

maCrobo April 16, 2014 08:32

2 Attachment(s)
Before I said something not true, the solver wasn't compiled, here it is where it gives errors:

Code:

/Users/myName/OpenFOAM/OpenFOAM-2.3.x/src/transportModels/incompressible/transportModel/transportModel.H:39:32: fatal error: primitiveFieldsFwd.H: No such file or directory

compilation terminated.
compilation terminated.
make: *** [Make/darwinIntel64Gcc46DPOpt/driftFluxFoam.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [Make/darwinIntel64Gcc46DPOpt/incompressibleTwoPhaseInteractingMixture.o] Error 1

I found 'primitiveFieldsFwd.H' in this folder: "/Volumes/OpenFoam-2.3.x/OpenFOAM-2.3.x/src/OpenFOAM/fields/Fields".

EDIT:

I tried to compile OpenFoam again and I managed to get something done with the following errors (found in the attachments).


Note: I edited applications/solvers/multiphase/driftFluxFoam/Make/options file, added '-ltwoPhaseMixture \' line after 'EXE_LIBS = \' line without running ./Allwmake in driftFluxFoam folder.


I would like to know if everything is working properly. The reason is that today I was talking to a classmate who has Ubuntu and told me I could find the tutorials in the run directory; I don't have a "run" directory in my OpenFoam directory, but I found the tutorials directory directly under the OpenFoam main directory, which is in my Sparse Image. Anyway, what should I do to check?

totalart April 19, 2014 12:29

I have successfully installed OF 2.3.0 following the instruction in Alexey Matveichev's blog. Everything's okay except snappyHexMesh. Following error occurs with SHM(I'm not running parallel).

dyld: Symbol not found: __SCOTCHbgraphbipartststratab
Referenced from: /Users/totalart/OpenFOAM/OpenFOAM-2.3.0/platforms/darwinIntel64ClangDPOpt/lib/openmpi-system/libptscotchDecomp.so
Expected in: flat namespace
in /Users/totalart/OpenFOAM/OpenFOAM-2.3.0/platforms/darwinIntel64ClangDPOpt/lib/openmpi-system/libptscotchDecomp.so
Trace/BPT trap: 5


In the Allwmake log, there was no error but warnings only. Anyone can advise what the problem is?

Many Thanks,
Young-kook

alexeym April 19, 2014 12:44

Hi,

I've reproduced the problem. I'll try to fix it and post updated patch during weekend.

alexeym April 21, 2014 14:05

Hi,

well, it appeared that previous patch had more problems than I though. So here is a new patch for 2.3.0 - https://bitbucket.org/mrklein/openfo...20140421.patch.

Unfortunately, due to the problems with dynamicCode in previous patch, you need to rebuild everything. The list of bugs in previous patch that was fixed in the new one:
- mess with DYLD_LIBRARY_PATH, now I think it is finally correct
- error in Allwmake for ptscotch decomposition method (this was the reason for the error)
- error in wmake/Makefile (OpenFOAM code expected dynamic library to have extension .dylib while in Makefile it was .so, and that breaks dynamicCode functionality)
- Clang over-optimization of limited schemes that lead to FPE

totalart April 23, 2014 09:42

Hi Alexey,
SnappyHexMesh works well now. It seems everything okay so far. Thanks a lot!

RMacReamoinn April 23, 2014 12:47

OpenFOAM-2.3.x - DriftFluxFoam Error 1
 
1 Attachment(s)
Hi,

I am trying to install OpenFOAM-2.3.x on Mac OS Mavericks and I am getting an error I have been unable to resolve. I am new to using the Terminal and I am new to OpenFOAM.

I downloaded the latest version of OpenFOAM from the website and have installed it following the instructions that can be found at:

http://openfoamwiki.net/index.php/In...OpenFOAM_2.2.2

albeit somewhat modified as per the README instructions associated with the OpenFOAM-2.3.0 patch:

http://sourceforge.net/p/openfoam-ex...ches/MacPatch/

However, I keep getting the same error and I am not sure how to rectify it.

make[2]: *** [/Users/username/OpenFOAM/OpenFOAM-2.3.x/platforms/darwinIntel64Gcc46DPOpt/bin/driftFluxFoam] Error 1
make[1]: *** [driftFluxFoam] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [multiphase] Error 2
make: Target `application' not remade because of errors.

In this instance, I did not have ParaView installed on my system and I got the following error.

ERROR: ParaView not found in /Users/username/OpenFOAM/ThirdParty-2.3.x/platforms/darwinIntel64Gcc46/ParaView-4.1.0

But even if I do have ParaView installed when installing OpenFOAM, I still get the same errors listed above. Please find the appropriate log file attached. Hoping you can help.

Réamonn

alexeym April 23, 2014 13:20

Hi,

1. If you take a look at the line above ERROR, you'll see

Code:

WARN: PV3 readers not building: ParaView_VERSION=4.1.0
So I guess, it has found your installation of Paraview, so line with error can be ignored.

2. Are you planning to use driftFluxFoam? If no, you can also ignore the error. If yes, you need to modify Make/options of this solver as it seems that -ltwoPahseMixture is missing there.

RMacReamoinn April 23, 2014 15:22

Thanks Alexey,

At this stage I am just trying to expose myself to OpenFOAM and become familliar with it. Therefore, I have no specific plans to use DriftFluxFoam.

Réamonn

alexeym April 24, 2014 06:30

How to fix build of driftFluxFoam
 
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.

RMacReamoinn April 28, 2014 16:32

Alexey,

Thanks for the help. I have OpenFOAM and ParaView installed and working now. I also included driftFluxFoam correction also and it worked well.

Réamonn

LucaMagher May 8, 2014 14:04

Errors in compiling
 
1 Attachment(s)
Hi guys

I followed the guide and read through this thread. I tried implementing all the suggestions, though, I can't compile yet. I'd love to receive your help, thanks a lot.

There are two things to point out

1) the message when I 'source etc/bashrc' which is
majesty:OpenFOAM-2.3.x ashleybrooks$ source etc/bashrc
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamEtcFile: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamCleanPath: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamCleanPath: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamCleanPath: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamCleanPath: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/etc/config/settings.sh: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/etc/config/aliases.sh: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamEtcFile: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamEtcFile: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamEtcFile: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamEtcFile: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamCleanPath: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamCleanPath: No such file or directory
-bash: /Users/ashleybrooks/OpenFOAM/OpenFOAM-2.3.x/bin/foamCleanPath: No such file or directory
-bash: ulimit: open files: cannot modify limit: Operation not permitted

2) the consequent error message

majesty:OpenFOAM-2.3.x ashleybrooks$ ./Allwmake 2>&1 | tee logName.log
./Allwmake: line 4: wmakeCheckPwd: command not found
Error: Current directory is not $WM_PROJECT_DIR
The environment variables are inconsistent with the installation.
Check the OpenFOAM entries in your dot-files and source them.

alexeym May 9, 2014 03:05

Hi,

it's hard to tell where the problem is (but I guess it's somewhere around foamInstall= line in bashrc). Is the disk image mounted to $HOME/OpenFOAM? Did you modify bashrc? Can you show bashrc if you did modifications?

Roskiki May 13, 2014 01:32

Hi,

I am trying to install OpenFOAM-2.3.x on Mac OS Mavericks and I am getting an error I have been unable to resolve. I am new to using the Terminal and I am new to OpenFOAM.


1 error generated.
make[2]: *** [Make/darwinIntel64ClangDPOpt/tractionDisplacementCorrectionFvPatchVectorField.o] Error 1
SOURCE=solidEquilibriumDisplacementFoam.C ; clang++ -m64 -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -Wno-overloaded-virtual -Wno-unused-comparison -O3 -DNoRepository -ftemplate-depth-100 -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -ItractionDisplacementCorrectionStress -I../solidDisplacementFoam -IlnInclude -I. -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude -fPIC -Ddarwin -c $SOURCE -o Make/darwinIntel64ClangDPOpt/solidEquilibriumDisplacementFoam.o
In file included from solidEquilibriumDisplacementFoam.C:38:
In file included from /Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude/fvCFD.H:7:
In file included from /Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude/fvMesh.H:50:
In file included from /Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/polyMesh.H:45:
In file included from /Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/primitiveMesh.H:54:
In file included from /Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/edgeList.H:32:
In file included from /Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/edge.H:41:
In file included from /Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/linePointRef.H:36:
/Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/line.H:39:10: fatal error: 'PointHit.H' file not found
#include "PointHit.H"
^
1 error generated.
make[2]: *** [Make/darwinIntel64ClangDPOpt/solidEquilibriumDisplacementFoam.o] Error 1
make[2]: Target `/Users/Mowa/OpenFOAM/OpenFOAM-2.3.0/platforms/darwinIntel64ClangDPOpt/bin/solidEquilibriumDisplacementFoam' not remade because of errors.
make[1]: *** [solidEquilibriumDisplacementFoam] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [stressAnalysis] Error 2
make: Target `application' not remade because of

alexeym May 13, 2014 03:07

Hi,

as the error is very similar to the one in the post #28, guess you've cloned repository into case insensitive file system and then copied sources to disk image with case sensitive FS. Is it right?

alexeym May 13, 2014 07:07

Well, if you really checked out sources on case insensitive FS first and after copied them into disk image, then you have to delete these sources, check out them from git repository into disk image (with case sensitive FS) directly and proceed with compilation. I.e. algorithm is something like this:
  1. mkdir -p $HOME/OpenFOAM
  2. hdiutil attach -mountpoint $HOME/OpenFOAM <disk image name>
  3. cd $HOME/OpenFOAM
  4. git clone <repo URL>
  5. cd OpenFOAM-2.3.x
  6. apply patches
  7. edit etc/bashrc
  8. source etc/bashrc
  9. ./Allwmake > log.Allwmake 2>&1

I can if I have to, otherwise I prefer to speak English.

f0208secretx May 13, 2014 11:56

Quote:

Originally Posted by alexeym (Post 483219)
Hi,

try rereading what I've written in my reply. I will repeat it here in bold:

1. the patch here is for OpenFOAM-2.3.x (git version), patch in the blog is for OpenFOAM-2.3.0 (release source packs).

so basically you're trying to apply patch for git version of OpenFOAM (acquired with git clone git://github.com/OpenFOAM/OpenFOAM-2.3.x.git) to the release packs (you've downloaded OpenFOAM-2.3.0.tgz and ThirdParty-2.3.0.tgz from openfoam.org). As a result it fails.

Hello everyone,


I am newbie to OpenFOAM. The installation attempt is made on OS X 10.9.2.

I got an Error for [dummysizes] and [scotch], which I think is related to openmpi? The error messages are as follows:

Code:

gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DSCOTCH_VERSION=6 -DSCOTCH_RELEASE=0 -DSCOTCH_PATCHLEVEL=0 dummysizes.c -o dummysizes -Xlinker --no-as-needed -lz -lm -lrt
ld: unknown option: --no-as-needed
collect2: ld returned 1 exit status
make[2]: *** [dummysizes] Error 1
make[1]: *** [scotch] Error 2
make: *** [scotch] Error 2
+ make realclean

and
Code:

gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DSCOTCH_VERSION=6 -DSCOTCH_RELEASE=0 -DSCOTCH_PATCHLEVEL=0 dummysizes.c -o dummysizes -Xlinker --no-as-needed -lz -lm -lrt
ld: unknown option: --no-as-needed
collect2: ld returned 1 exit status
make[2]: *** [dummysizes] Error 1
make[1]: *** [scotch] Error 2
make: *** [ptscotch] Error 2
+ make realclean

Based on the discussions, I assume this is a problem with the incompatible patch versions. I downloaded OpenFOAM source pack from .org (OpenFOAM-2.3.0.tgz) and the patch from this thread (OpenFOAM-2.3.x-Mac.patch). Hence the problem. The solution to this problem should be removing everything I got so far and redo the whole process using the patch I will download from alexeym's blog: (btw the blog is very clear, thanks!)
HTML Code:

http://matveichev.blogspot.co.uk/2014/02/building-openfoam-230-on-os-x.html
I read the blog and followed it through -- it seems fine when I tried to run the cavity tutorial examples (the steps are listed on the website as well). Question is: under what circumstances will I run into troubles if I just neglect the error messages I got from above, the [dummysizes], [scotch], and [ptscotch]?

I can for sure just run the whole process again since I know where is the problem (or I think I know). I am just taking this as an opportunity to educate myself about how things work, thanks a lot. :)


JHW

alexeym May 14, 2014 07:13

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.

alexeym May 14, 2014 08:23

Hi,

Quote:

Originally Posted by Roskiki (Post 491743)
jais pas bien compri, comment faire le clonage de la source...etc. pourriez vous me le code pour taper sur le terminal?

Cause I don't know what you'd done already, I'll describe whole procedure from the beginning (more or less how I do these things):

1. Create disk image with case sensitive file system. There is a guide in wiki with pictures but I prefer CLI interface:

Code:

$ cd
$ hdiutil create -size 4.4g -type SPARSEBUNDLE -fs HFSX -volname OpenFOAM -fsargs -s OpenFOAM.sparsebundle

This command will create disk image with a name OpenFOAM.sparsebundle in you home folder. Wiki suggests creation of sparseimage type disk image but sparse bundle disk images ... here is a quote from a discussion with my colleague:

Quote:

The only interest of sparseimage are for compatility with OSX < 10.5 and sparsebundle is better with backup.
2. Create mount point for disk image and attach disk image (again it was suggested by my colleague, to have single disk image for all OF versions):

Code:

$ mkdir -p $HOME/OpenFOAM
$ hdiutil attach -mountpoint $HOME/OpenFOAM OpenFOAM.sparsebundle

3. Now you clone sources into the disk image (command for OF 2.3.x):

Code:

$ cd $HOME/OpenFOAM
$ git clone git://github.com/OpenFOAM/OpenFOAM-2.3.x.git

At this point you have sources on case sensitive FS, so now it's time to get patch, apply patch to the sources and run compilation:

Code:

$ cd OpenFOAM-2.3.x
$ curl -L http://sourceforge.net/p/openfoam-extend/svn/HEAD/tree/trunk/Breeder_2.3/distroPatches/MacPatch/OpenFOAM-2.3.x-Mac.patch?format=raw > OpenFOAM-2.3.x-Mac.patch
$ patch -p1 < OpenFOAM-2.3.x-Mac.patch

After these manipulations you need to edit etc/bashrc (I don't know what version of gcc you're using, I don't know if you installed all necessary software dependencies using Macports, so at this points it's all up to you).

After you just

Code:

$ source etc/bashrc
$ ./Allwmake > log.Allwmake 2>&1

and wait.

alexeym May 14, 2014 11:33

If you read the first message of the thread:

Quote:

People who have been through the Mac-patch cycle several times will notice the absence of a ThirdParty-patch: the reason is that all the necessary third-party software (CGAL, metis, scotch) is available at MacPorts with a simple "port install"-command. This is also the recommended way to install the necessary compiler and MacPorts.
So there's no ThirdParty-2.3.x.patch. As I don't use Macports (though I can go to Macports web site and find names of the packages with necessary options I'd rather not) I can't add anything to the quote.

alexeym May 14, 2014 14:35

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 15:48

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 11:09

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 11:53

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 14:54

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

merci encor!!!!

f0208secretx May 17, 2014 02:46

1 Attachment(s)
Quote:

Originally Posted by alexeym (Post 491737)
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 03:09

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 03:16

1 Attachment(s)
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 03:24

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 10:52

Quote:

Originally Posted by alexeym (Post 492495)
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 11:42

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 12:20

error compiling interFoam
 
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 00:05

Quote:

Originally Posted by alexeym (Post 492579)
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 04:56

@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 09:47

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 09:57

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

Code:

-linterfaceProperties

Roskiki May 18, 2014 10:18

thank you very much

f0208secretx May 18, 2014 11:59

1 Attachment(s)
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 12:10

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 14:39

1 Attachment(s)
Quote:

Originally Posted by Roskiki (Post 492689)
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


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