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Old   November 11, 2015, 12:05
Default Installing OpenFOAM 3.0.x on Mac OS X with Homebrew
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Oleg Kotsur
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Hi Alexey!

I am trying to compile OpenFOAM-3.0.0 following your guidelines and your newly posted patch for OF3.0.0 on your repository https://github.com/mrklein/openfoam-os-x. I tried both with macports and homebrew, and I managed to compile it both without any bad issues. However when I run the cavity case I always have this issue:

Code:
Starting time loop

Time = 0.005

Courant Number mean: 0 max: 0
smoothSolver:  Solving for Ux, Initial residual = 1, Final residual = 8.90511e-06, No Iterations 19
smoothSolver:  Solving for Uy, Initial residual = 0, Final residual = 0, No Iterations 0
DICPCG:  Solving for p, Initial residual = 1, Final residual = 7.55423e-07, No Iterations 35
time step continuity errors : sum local = 5.03808e-09, global = -7.94093e-21, cumulative = -7.94093e-21
DICPCG:  Solving for p, Initial residual = 0.523588, Final residual = 9.72371e-07, No Iterations 34
time step continuity errors : sum local = 1.07766e-08, global = 2.00426e-19, cumulative = 1.92485e-19
dyld: lazy symbol binding failed: Symbol not found: __ZN4FoamlsERNS_7OstreamEl
  Referenced from: /Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/bin/icoFoam
  Expected in: flat namespace

dyld: Symbol not found: __ZN4FoamlsERNS_7OstreamEl
  Referenced from: /Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/bin/icoFoam
  Expected in: flat namespace

Trace/BPT trap: 5
Basically, I didn't create a new sparse image for particularly this OF version, because I used 2.1 before. So i compiled on the disk image I had created before.

Any response is highly appreciated!
Oleg
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Old   November 11, 2015, 15:00
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Hi,

Unfortunately I can not reproduce the error, so could you please post:

1. Output of "sw_vers"
2. Output of "clang++ --version"
3. Output of "export | grep -E '(FOAM_|WM_|LD_)'" (after you source OpenFOAM's bashrc)

And I also do not create disk image every time new version is released.

@wyldckat

Dear Bruno,

Could you please move the post to separate thread as currently is has nothing to do with version 2.3.

[Moderator note: Done. Moved posts for OpenFOAM 3.0.x from the other thread http://www.cfd-online.com/Forums/ope...-patch-12.html]

Last edited by wyldckat; February 7, 2016 at 15:02. Reason: see "Moderator note:"
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Old   November 11, 2015, 15:07
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Hi, Alexey,

Thank you for a quick reply!

Code:
MacBook-Air-Oleg:cavity oleg$ sw_vers
ProductName:	Mac OS X
ProductVersion:	10.11.1
BuildVersion:	15B42
MacBook-Air-Oleg:cavity oleg$ clang++ --version
Apple LLVM version 7.0.0 (clang-700.1.76)
Target: x86_64-apple-darwin15.0.0
Thread model: posix
MacBook-Air-Oleg:cavity oleg$ source ~/OpenFOAM/OpenFOAM-3.0.x/etc/bashrc 
MacBook-Air-Oleg:cavity oleg$ export | grep -E '(FOAM_|WM_|LD_)'
declare -x DYLD_LIBRARY_PATH="/usr/local/opt/boost/lib:/usr/local/opt/cgal/lib:/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib/openmpi-system:/openmpi-system:/usr/local/lib:/Users/oleg/OpenFOAM/oleg-3.0.x/platforms/darwin64ClangDPInt32Opt/lib:/Users/oleg/OpenFOAM/site/3.0.x/platforms/darwin64ClangDPInt32Opt/lib:/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib:/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib/dummy:/openmpi-system"
declare -x FOAM_APP="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/applications"
declare -x FOAM_APPBIN="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/bin"
declare -x FOAM_ETC="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/etc"
declare -x FOAM_INST_DIR="/Users/oleg/OpenFOAM"
declare -x FOAM_JOB_DIR="/Users/oleg/OpenFOAM/jobControl"
declare -x FOAM_LIBBIN="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib"
declare -x FOAM_MPI="openmpi-system"
declare -x FOAM_RUN="/Users/oleg/OpenFOAM/oleg-3.0.x/run"
declare -x FOAM_SETTINGS=""
declare -x FOAM_SIGFPE=""
declare -x FOAM_SITE_APPBIN="/Users/oleg/OpenFOAM/site/3.0.x/platforms/darwin64ClangDPInt32Opt/bin"
declare -x FOAM_SITE_LIBBIN="/Users/oleg/OpenFOAM/site/3.0.x/platforms/darwin64ClangDPInt32Opt/lib"
declare -x FOAM_SOLVERS="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/applications/solvers"
declare -x FOAM_SRC="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/src"
declare -x FOAM_TUTORIALS="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/tutorials"
declare -x FOAM_USER_APPBIN="/Users/oleg/OpenFOAM/oleg-3.0.x/platforms/darwin64ClangDPInt32Opt/bin"
declare -x FOAM_USER_LIBBIN="/Users/oleg/OpenFOAM/oleg-3.0.x/platforms/darwin64ClangDPInt32Opt/lib"
declare -x FOAM_UTILITIES="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/applications/utilities"
declare -x LD_LIBRARY_PATH="/usr/local/opt/boost/lib:/usr/local/opt/cgal/lib:/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib/openmpi-system:/openmpi-system:/usr/local/lib:/Users/oleg/OpenFOAM/oleg-3.0.x/platforms/darwin64ClangDPInt32Opt/lib:/Users/oleg/OpenFOAM/site/3.0.x/platforms/darwin64ClangDPInt32Opt/lib:/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib:/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib/dummy:/openmpi-system"
declare -x WM_ARCH="darwin64"
declare -x WM_ARCH_OPTION="64"
declare -x WM_CC="clang"
declare -x WM_COMPILER="Clang"
declare -x WM_COMPILER_LIB_ARCH="64"
declare -x WM_COMPILE_OPTION="Opt"
declare -x WM_CXX="clang++"
declare -x WM_DIR="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/wmake"
declare -x WM_LABEL_OPTION="Int32"
declare -x WM_LABEL_SIZE="32"
declare -x WM_LINK_LANGUAGE="c++"
declare -x WM_MPLIB="SYSTEMOPENMPI"
declare -x WM_OPTIONS="darwin64ClangDPInt32Opt"
declare -x WM_OSTYPE="POSIX"
declare -x WM_PRECISION_OPTION="DP"
declare -x WM_PROJECT="OpenFOAM"
declare -x WM_PROJECT_DIR="/Users/oleg/OpenFOAM/OpenFOAM-3.0.x"
declare -x WM_PROJECT_INST_DIR="/Users/oleg/OpenFOAM"
declare -x WM_PROJECT_USER_DIR="/Users/oleg/OpenFOAM/oleg-3.0.x"
declare -x WM_PROJECT_VERSION="3.0.x"
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Old   November 11, 2015, 17:04
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Hi,

Unfortunately I still can not reproduce your problem even after building 3.0.x (previously I tested on 3.0.0). Could you please also post output of

Code:
$ echo $PATH
$ icoFoam -version
Right now I can only suppose, that you are somehow using old version of executables with new libraries.
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Old   November 12, 2015, 03:25
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Hi,

Yes, that looks strange, since I never saw anyone had had the same error.
Basically, I've checked before that there were no interaction between my previous installed version.

Code:
$ echo $PATH
/Users/oleg/OpenFOAM/oleg-3.0.x/platforms/darwin64ClangDPInt32Opt/bin:/Users/oleg/OpenFOAM/site/3.0.x/platforms/darwin64ClangDPInt32Opt/bin:/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/bin:/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/bin:/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/wmake:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/texbin:/Users/oleg/Qt/5.4/clang_64/bin:/Users/oleg/Qt_Tests/bin
Code:
icoFoam -version
sais that there is no option called "version":
Code:
...
Using: OpenFOAM-3.0.x (see www.OpenFOAM.org)
Build: 3.0.x-fddd87acfd83

--> FOAM FATAL ERROR: 
Invalid option: -version


FOAM exiting
also,
Code:
MacBook-Air-Oleg:cavity oleg$ which icoFoam
/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/bin/icoFoam
Thank you very much for help
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Old   November 12, 2015, 03:37
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I think, I got, what was wrong.

It looks like that OpenFOAM wants to link libraries, that end with .so and not with .dylib, because executing pimpleDyMFoam in movingCone tutorial, I had following issue:

Code:
Create time

Create mesh for time = 0

Selecting dynamicFvMesh dynamicMotionSolverFvMesh
Selecting motion solver: velocityComponentLaplacian
--> FOAM Warning : 
    From function dlOpen(const fileName&, const bool)
    in file POSIX.C at line 1183
    dlopen error : dlopen(libfvMotionSolvers.so, 9): image not found
--> FOAM Warning : 
    From function dlLibraryTable::open(const fileName&, const bool)
    in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
    could not load "libfvMotionSolvers.so"
--> FOAM Warning : 
    From function dlLibraryTable::open(const dictionary&, const word&, const TablePtr&)
    in file /Users/oleg/OpenFOAM/OpenFOAM-3.0.x/src/OpenFOAM/lnInclude/dlLibraryTableTemplates.C at line 67
    Could not open library "libfvMotionSolvers.so"



--> FOAM FATAL ERROR: 
solver table is empty

    From function motionSolver::New(const polyMesh& mesh)
    in file motionSolver/motionSolver/motionSolver.C at line 116.

FOAM exiting
If I understood well, the patch should correct this feature.
So, it looks like the patch was not applied properly. But I don't know why..
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Old   November 12, 2015, 03:59
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Well, not quite so. Patch does nothing to tutorials, so all dynamic library names, like one in dynamicMeshDict of movingCone tutorial

Code:
motionSolverLibs ( "libfvMotionSolvers.so" );
end with so, yet on OS X they are built with dylib extension. To use movingCone example, you have to change dynamicMeshDict:

Code:
motionSolverLibs ( "libfvMotionSolvers.dylib" );
and cuttingPlane file in system folder:

Code:
functionObjectLibs ("libsampling.dylib");
After these modifications solver runs without any problems (at least on my laptop, which have exactly the same software installed as yours).

I am still trying to understand what can go wrong, since even emptying LD_LIBRARY_PATH variables and renaming of OpenFOAM folder (two things that come to mind first) did not break anything.

Does the error happen just with icoFoam (it seems blockMesh does its job)?
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Old   November 12, 2015, 04:08
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A little bit more diagnostics, could you also post output of:

Code:
$ otool -L $(which icoFoam)
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Old   November 12, 2015, 10:51
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Quote:
Well, not quite so
Yes, that's true. I forgot that for tutorials, that require dynamic linkage, I should manually change .so on .dylib

Code:
Does the error happen just with icoFoam (it seems blockMesh does its job)?
Apparently it happens for any solver.
pimpleDyMFoam for movingCone tutorial:
Code:
Courant Number mean: 0 max: 0
Time = 5e-06

DICPCG:  Solving for cellMotionUx, Initial residual = 1, Final residual = 7.49026e-09, No Iterations 41
GAMG:  Solving for pcorr, Initial residual = 1, Final residual = 0.0120425, No Iterations 9
time step continuity errors : sum local = 1.21024e-05, global = -1.93129e-06, cumulative = -1.93129e-06
PIMPLE: iteration 1
smoothSolver:  Solving for Ux, Initial residual = 1, Final residual = 0.00518207, No Iterations 1
smoothSolver:  Solving for Uy, Initial residual = 1, Final residual = 0.00630599, No Iterations 1
smoothSolver:  Solving for Uz, Initial residual = 0.130994, Final residual = 0.000745908, No Iterations 1
GAMG:  Solving for p, Initial residual = 1, Final residual = 0.0045295, No Iterations 11
time step continuity errors : sum local = 4.56003e-06, global = -7.17971e-07, cumulative = -2.64927e-06
PIMPLE: iteration 2
smoothSolver:  Solving for Ux, Initial residual = 0.0285794, Final residual = 1.34937e-06, No Iterations 2
smoothSolver:  Solving for Uy, Initial residual = 0.0214531, Final residual = 2.63463e-06, No Iterations 2
smoothSolver:  Solving for Uz, Initial residual = 0.0175449, Final residual = 5.14228e-07, No Iterations 2
GAMG:  Solving for p, Initial residual = 0.00717312, Final residual = 4.74127e-07, No Iterations 15
time step continuity errors : sum local = 5.50739e-08, global = 7.35885e-09, cumulative = -2.64191e-06
dyld: lazy symbol binding failed: Symbol not found: __ZN4FoamlsERNS_7OstreamEl
  Referenced from: /Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/bin/pimpleDyMFoam
  Expected in: flat namespace

dyld: Symbol not found: __ZN4FoamlsERNS_7OstreamEl
  Referenced from: /Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/bin/pimpleDyMFoam
  Expected in: flat namespace

Trace/BPT trap: 5
Libraries, that icoFoam wants to link:
Code:
$ otool -L $(which icoFoam)
/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/bin/icoFoam:
	/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib/libfiniteVolume.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib/libmeshTools.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib/libOpenFOAM.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1225.1.1)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.1.0)
I also tried to check with nm command object list for libfiniteVolume.dylib. There were lots on names, among which there were:
Code:
...
U __ZN4FoamlsERNS_7OstreamEb
U __ZN4FoamlsERNS_7OstreamEc
U __ZN4FoamlsERNS_7OstreamEd
U __ZN4FoamlsERNS_7OstreamEi
U __ZN4FoamlsERNS_7OstreamEj
...
but not __ZN4FoamlsERNS_7OstreamEl, which is logical
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Old   November 12, 2015, 11:08
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The symbol is in

Code:
alexey at daphne in lib$ nm libOpenFOAM.dylib | grep 7OstreamEl
00000000000381d0 T __ZN4FoamlsERNS_7OstreamEl
What if you force loading of libOpenFOAM.dylib in controlDict with

Code:
libs ("libOpenFOAM.dylib");
?
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Old   November 12, 2015, 12:10
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I don't have this symbol in libOpenFOAM.dylib ...

Code:
What if you force loading of libOpenFOAM.dylib in controlDict with

Code:
libs ("libOpenFOAM.dylib");
?
Still the same issue.

I think, it is smth bad with my libOpenFOAM.dylib compiled on my machine. Could you send me, please, your libOpenFOAM.dylib? Since you have the same os x version and other soft as mine, it could work with your build, if the problem is with this lib.
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Old   November 12, 2015, 14:52
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You can try to download it here: https://github.com/mrklein/openfoam-...OpenFOAM.dylib (it is built for WM_LABEL_SIZE=32)
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Old   November 12, 2015, 17:19
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Well, that worked!

Apparently, the thing was in libOpenFOAM.dylib.
Now both icoFoam and pimpleDyMFoam work as they should, though your libOpenFOAM was built with your local dependencies.

However, if I execute any Allrun script for tutorials, it sais, that it can't find libraries, on which libOpenFOAM is dependent:
Code:
MacBook-Air-Oleg:oscillatingInletACMI2D oleg$ cat log.blockMesh 
dyld: Library not loaded: /Users/alexey/OpenFOAM/OpenFOAM-3.0.0/platforms/darwin64ClangDPInt32Opt/lib/dummy/libPstream.dylib
  Referenced from: /Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32Opt/lib/libOpenFOAM.dylib
  Reason: image not found
That is predictable, but it works fine if I manually execute blockMesh, topoSet and pimpleDyMFoam.

That is strange for me.
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Old   November 13, 2015, 02:37
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What if you try to relink your libOpenFOAM.dylib? I.e. remove it from platforms/darwin64ClangDPInt32Opt/lib and rerun Allwmake (or just run wmake in src/OpenFOAM)?

I was thinking about possible differences between our OS installations and can only come up with

1. I have developer mode switched on (DevToolsSecurity -enable), though since you have Qt installed, guess on your laptop it is also on.

2. In El Capitan they introduced System Integrity Protection, so, for example, scripts are run in slightly stripped environment (in particular (DY)LD_LIBRARY_PATH variables are cleared and there were certain difficulties with dynamic libraries).

Did you check Allwmake output? Was there any errors/warnings? Maybe you have log-file of build process?
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Old   November 13, 2015, 04:10
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Quote:
What if you try to relink your libOpenFOAM.dylib?
Yes, I tried it yesterday - same story.
Quote:
In El Capitan they introduced System Integrity Protection
I've heard about it, but I first tried to build it on Mavericks on my laptop several days ago and had the same error. And that was one of the reasons of update to El Capitan I supposed, that the error could disappear.

Quote:
Did you check Allwmake output? Was there any errors/warnings? Maybe you have log-file of build process?
Yes, I checked allwmake log for error messages - nothing found. However I had one error during build process with Lexer, but I corrected it as you proposed in one of your previous posts, i.e. obliged to use /usr/bin/flex.

I have one warning in my build log, but don't think, it concerns this problem:
Code:
$ cat log.Allwmake | grep warning
ld: warning: directory not found for option '-L/Users/oleg/OpenFOAM/OpenFOAM-3.0.x/platforms/darwin64ClangDPInt32OptSYSTEMOPENMPI/lib'
Attached Files
File Type: zip log.Allwmake.zip (98.8 KB, 3 views)
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Old   November 13, 2015, 05:49
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Quote:
What if you try to relink your libOpenFOAM.dylib?
I thought about this once again and decided to manually relink your libOpenFOAM.dylib.
I executed install_name_tool command like described in this blog http://thecourtsofchaos.com/2013/09/...naries-on-osx/

And now everything seems to work fine. Though I don't like this way to solve the problem

If you still have some ideas, I am ready to work them out
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Old   November 13, 2015, 09:03
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I have tried to reproduce the problem starting from scratch: created new user, created new disk image, etc., etc. To exclude influence of current environment setup on build process. I was again unsuccessful. Solvers are running, _ZN4FoamlsERNS_7OstreamEl is on libOpenFOAM.dylib.

Then I vaguely recalled (or it was Macport's ElCapitanProblems page that created these memories) that maybe after the upgrade to El Capitan I have repeated sequence:

Code:
$ xcode-setect --install
$ xcodebuild -license
And before doing so I also has unresolved symbol troubles with my own patches (after installation it is necessary to rebuild OpenFOAM).

Though maybe you have already done this. During weekend I could try to utilize another virgin El Capitan laptop to reproduce your problem.
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Old   November 13, 2015, 15:27
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Thank you Alexey, I really appreciate your help.

Indeed, I didn't install command line tools after the upgrade.
After executing these commands
Code:
$ xcode-select --install
$ xcodebuild -license
I rebuilt OF ones more, but the problem persists.

Would be nice to know the build experience on the virgin laptop, if it doesn't bother you too much
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Old   November 14, 2015, 09:58
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Hi,

Unfortunately I was not able to reproduce your error neither on my laptop under new user account, nor on the new laptop (well, it was not exactly new, yet I never installed Xcode and OpenFOAM there). 3.0.x with the latest patch builds and runs smoothly.

And unfortunately I have run out of ideas what could be wrong.
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Old   November 15, 2015, 14:23
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Oleg Kotsur
Join Date: Nov 2012
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That's all right, thank you, alexey!
I am sure, there is a stupid explanation, because substitution libOpenFOAM.dylib by yours really seems to work. So that is enough for me

Еще раз большое спасибо!
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