CFD Online Discussion Forums

CFD Online Discussion Forums (http://www.cfd-online.com/Forums/)
-   OpenFOAM Installation on Windows, Mac and other Unsupported Platforms (http://www.cfd-online.com/Forums/openfoam-installation-windows-mac/)
-   -   Compile OF 2.3 on Mac OS X .... the patch (http://www.cfd-online.com/Forums/openfoam-installation-windows-mac/130113-compile-2-3-mac-os-x-patch.html)

gschaider February 19, 2014 19:39

Compile OF 2.3 on Mac OS X .... the patch
 
Hi!

With a 2 day delay after OF 2.3 was released here comes the patch for Mac OS X.

This time I decided to distribute it differently: it is found in the OF-extend SVN-repository at

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

This should make sure that always the latest patch is found in the same location.

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.

As a guidline for installation have a look at http://openfoamwiki.net/index.php/In...OpenFOAM_2.2.2 but check the README first for differences.

It is possible that I forgot necessary packages to install via MacPorts. So whoever wants to write an updated recipe for installation ...

Compared to previous patches the patch has the enhancements described in http://www.cfd-online.com/Forums/ope...tml#post475721

Also the code that produces the stack-traces has been partially rewritten and some ugly hacks have been removed (should work with OS X 10.5 or later)

gschaider February 20, 2014 13:24

Quote:

Originally Posted by gschaider (Post 475782)
Hi!

With a 2 day delay after OF 2.3 was released here comes the patch for Mac OS X.

This time I decided to distribute it differently: it is found in the OF-extend SVN-repository at

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

Pushed an updated version of the patch. This fixes some weird problems with Gcc47-compilations. Currently the state (for me: your milage may vary) is this:

- Gcc48 compiles. But foamyQuadMesh and foamyHexMesh crash (this seems to be a problem with CGAL and happens for me on Linux machines and gcc48 too)
- Clang34: compiles and works. In Debug-mode the stack-trace is incomplete
- Gcc47: compiles and seems to work completely

For the time being I'll stick with Gcc47

podallaire February 20, 2014 17:20

Thanks for the patch, greatly appreciated ! I successfully compiled with gcc-4.6 and I did not use Macport.

Regards,

PO

mkatgert February 28, 2014 13:03

Thanks, i managed to compile it nicely under 10.7.5. Some remarks though (keep in mind i have very limited experience with terminal-driven Unix-editing...)

- i was a little over-eager and unpacked the OpenFoam tar-files with the OS X GUI unzip utility. This appeared to work but it messed up the directory structure. Took me a while to figure out where all the error messages in the patch came from...

- since MacPorts changed the openmpi stuff (it told me to use 'port install openmpi-default') parallel snappyHexMesh isn't working, because there's no 'mpirun' executable or alias in the /bin directory. There however are multiple mpi-files in the /opt/local/bin folder:

Code:

mpic++-mpich-mp                mpicxx                        mpiexec-openmpi-mp        mpif90
mpicc                        mpicxx-mpich-mp                mpiexec.hydra-mpich-mp        mpif90-mpich-mp
mpicc-mpich-mp                mpicxx-openmpi-mp        mpif77                        mpif90-openmpi-mp
mpicc-openmpi-mp        mpiexec                        mpif77-mpich-mp                mpirun-mpich-mp
mpichversion-mpich-mp        mpiexec-mpich-mp        mpif77-openmpi-mp        mpivars-mpich-mp

Which one is the right one to alias? Or hasn't OpenMPI installed correctly?

- if i type 'ulimit -n 1024' straight into terminal, it works without an error message. The same line in bashrc gives the error:

Code:

-bash: ulimit: open files: cannot modify limit: Operation not permitted
Any thoughts on that?

Excuse if these two questions have been answered before; I have not been able to find the answers...

gschaider February 28, 2014 13:27

Quote:

Originally Posted by mkatgert (Post 477324)
Thanks, i managed to compile it nicely under 10.7.5. Some remarks though (keep in mind i have very limited experience with terminal-driven Unix-editing...)

- i was a little over-eager and unpacked the OpenFoam tar-files with the OS X GUI unzip utility. This appeared to work but it messed up the directory structure. Took me a while to figure out where all the error messages in the patch came from...

If you think that this point was not stressed enough on the Wiki page you used for instructions (I assume you did) feel free to edit the page in such a way that you say "then I would have seen this".
[QUOTE=mkatgert;477324]
- since MacPorts changed the openmpi stuff (it told me to use 'port install openmpi-default') parallel snappyHexMesh isn't working, because there's no 'mpirun' executable or alias in the /bin directory. There however are multiple mpi-files in the /opt/local/bin folder:

Code:

mpic++-mpich-mp                mpicxx                        mpiexec-openmpi-mp        mpif90
mpicc                        mpicxx-mpich-mp                mpiexec.hydra-mpich-mp        mpif90-mpich-mp
mpicc-mpich-mp                mpicxx-openmpi-mp        mpif77                        mpif90-openmpi-mp
mpicc-openmpi-mp        mpiexec                        mpif77-mpich-mp                mpirun-mpich-mp
mpichversion-mpich-mp        mpiexec-mpich-mp        mpif77-openmpi-mp        mpivars-mpich-mp

Which one is the right one to alias? Or hasn't OpenMPI installed correctly?
[/CODE]

mpicc is the "one that links to the currently selected MPI-impolementation" (which is either a OpenMPI or a MPICH-implementation). Which one is used can be seen (and changed) with "port select mpi" ("port help select" is your friend). The current version of the patch finds out which version this is and selects everything accordingly. So you should be fine

Quote:

Originally Posted by mkatgert (Post 477324)
- if i type 'ulimit -n 1024' straight into terminal, it works without an error message. The same line in bashrc gives the error:

Code:

-bash: ulimit: open files: cannot modify limit: Operation not permitted

No idea what is causing this. I take the easy route and blame 10.7

mkatgert March 1, 2014 10:38

Thanks a lot for the reply. I tried all i could with regard to mpirun, but it suddenly started working after i uninstalled and reinstalled openmpi-default.

Regarding the ulimit error: if i type in terminal ulimit -n 1024 and immediately type ulimit -n 2048 after that i trigger the same error. Probably a weird thing with ulimit under os x. I saw that the ulimit value is changed twice in bashrc (first by the manually added ulimit -n 1024 command and after that in (around) line 255: ulimit -n 8192)

The second command triggers the error. Since the second command apparently is triggered, i figured i might as well delete the first command...

gschaider March 1, 2014 10:50

Quote:

Originally Posted by mkatgert (Post 477429)
Thanks a lot for the reply. I tried all i could with regard to mpirun, but it suddenly started working after i uninstalled and reinstalled openmpi-default.

Regarding the ulimit error: if i type in terminal ulimit -n 1024 and immediately type ulimit -n 2048 after that i trigger the same error. Probably a weird thing with ulimit under os x. I saw that the ulimit value is changed twice in bashrc (first by the manually added ulimit -n 1024 command and after that in (around) line 255: ulimit -n 8192)

The second command triggers the error. Since the second command apparently is triggered, i figured i might as well delete the first command...

The mpi-problem: That was probably the postinstall-script of the package making things "right"

Concerning ulimit: I think this is "normal". Not sure about Linux but I definitely remember this "you can only change limits once"-behaviour from Tru64 on our Alphas (years ago).

egp March 1, 2014 11:00

With the latest self update in MacPorts, you need to be a bit more specific. In the original port install, use openmpi-gcc46

sudo port install gcc46 openmpi-gcc46 boost cgal ccache flex bison

When this is complete, use the select port

sudo port select --set mpi openmpi-gcc46-fortran

This sets all the proper symlinks in /opt/local/bin and eliminates the need to do this by hand (see 4.3, item 6 in wiki). I also use the select port to set symlinks for python27 and ipython27.

Eric

[QUOTE=gschaider;477328]If you think that this point was not stressed enough on the Wiki page you used for instructions (I assume you did) feel free to edit the page in such a way that you say "then I would have seen this".
Quote:

Originally Posted by mkatgert (Post 477324)
- since MacPorts changed the openmpi stuff (it told me to use 'port install openmpi-default') parallel snappyHexMesh isn't working, because there's no 'mpirun' executable or alias in the /bin directory. There however are multiple mpi-files in the /opt/local/bin folder:

Code:

mpic++-mpich-mp        mpicxx            mpiexec-openmpi-mp    mpif90
mpicc            mpicxx-mpich-mp        mpiexec.hydra-mpich-mp    mpif90-mpich-mp
mpicc-mpich-mp        mpicxx-openmpi-mp    mpif77            mpif90-openmpi-mp
mpicc-openmpi-mp    mpiexec            mpif77-mpich-mp        mpirun-mpich-mp
mpichversion-mpich-mp    mpiexec-mpich-mp    mpif77-openmpi-mp    mpivars-mpich-mp

Which one is the right one to alias? Or hasn't OpenMPI installed correctly?
[/CODE]

mpicc is the "one that links to the currently selected MPI-impolementation" (which is either a OpenMPI or a MPICH-implementation). Which one is used can be seen (and changed) with "port select mpi" ("port help select" is your friend). The current version of the patch finds out which version this is and selects everything accordingly. So you should be fine



No idea what is causing this. I take the easy route and blame 10.7


redAbbot March 2, 2014 21:06

I'm not having luck with the patch:

bash-3.2$ patch -p1<OpenFOAM-2.3.x-Mac.patch
patch unexpectedly ends in middle of line
patch: **** Only garbage was found in the patch input.


It's unclear to me if I have to install the SurfaceGCALFix patch, but I tried anyway and got a different error:

bash-3.2$ patch -p1<SurfaceCGALFix.patch
patching file applications/utilities/surface/surfaceFeatureExtract/surfaceFeatureExtract.C
Hunk #1 FAILED at 48.
1 out of 1 hunk FAILED -- saving rejects to file applications/utilities/surface/surfaceFeatureExtract/surfaceFeatureExtract.C.rej

gschaider March 3, 2014 12:16

Quote:

Originally Posted by redAbbot (Post 477632)
I'm not having luck with the patch:

bash-3.2$ patch -p1<OpenFOAM-2.3.x-Mac.patch
patch unexpectedly ends in middle of line
patch: **** Only garbage was found in the patch input.


Seems that your download of the patch is incomplete. The last lines of the patch should be:
Code:

--- /dev/null
+++ b/wmake/rules/darwinIntel64Gcc/mplibOPENMPI
@@ -0,0 +1,3 @@
+PFLAGS    = -DOMPI_SKIP_MPICXX
+PINC      = -I$(MPI_ARCH_PATH)/include
+PLIBS      = -L$(MPI_ARCH_PATH)/lib -lmpi


esujby March 4, 2014 00:46

help please
 
hello guys please need your help, i did try to apply the patch using git but i ended up getting something like this: please tell me what to do thanks

nasirs-imac:OpenFOAM-2.3.0 nasiryakubu$ git apply OpenFOAM-2.3.0.patch
OpenFOAM-2.3.0.patch:753: trailing whitespace.
handle =
OpenFOAM-2.3.0.patch:1311: trailing whitespace.

OpenFOAM-2.3.0.patch:1340: trailing whitespace.

OpenFOAM-2.3.0.patch:1579: trailing whitespace.
c++DBUG =
OpenFOAM-2.3.0.patch:1605: trailing whitespace.
cDBUG =
fatal: corrupt patch at line 1944
nasirs-imac:OpenFOAM-2.3.0 nasiryakubu$

gschaider March 4, 2014 18:03

Quote:

Originally Posted by esujby (Post 477845)
hello guys please need your help, i did try to apply the patch using git but i ended up getting something like this: please tell me what to do thanks

nasirs-imac:OpenFOAM-2.3.0 nasiryakubu$ git apply OpenFOAM-2.3.0.patch
OpenFOAM-2.3.0.patch:753: trailing whitespace.
handle =
OpenFOAM-2.3.0.patch:1311: trailing whitespace.

OpenFOAM-2.3.0.patch:1340: trailing whitespace.

OpenFOAM-2.3.0.patch:1579: trailing whitespace.
c++DBUG =
OpenFOAM-2.3.0.patch:1605: trailing whitespace.
cDBUG =
fatal: corrupt patch at line 1944
nasirs-imac:OpenFOAM-2.3.0 nasiryakubu$

Seems like git is very picky about what it expects in a patch (1944 is the correct length of the original patch so it can't be an incomplete downlod). Try applying the patch with the patch utility and then commiting the changes into git

esujby March 28, 2014 19:01

help please: hello gschaider.
 
i tried applying the patch using terminal and i still get the same thing i dont know why, any recommendations please?
i am quite new to using terminal and have to use openfoam for my phd project.

thanks

nas

gschaider March 31, 2014 19:41

Quote:

Originally Posted by esujby (Post 482727)
i tried applying the patch using terminal and i still get the same thing i dont know why, any recommendations please?
i am quite new to using terminal and have to use openfoam for my phd project.

thanks

nas

I have no idea why your patch-utility is so picky with a patch that seems to work for others. Could you report the output of 'which patch' and also 'patch -v' to make sure that you're using the standard.

Also: the command-line you're using

alexeym April 1, 2014 03:36

Hi,

well, I guess esujby is still trying to use 'git patch' to apply the patch instead of just using 'patch -p1'. There are two solutions:

1. Use 'patch -p1' as suggested by gschaider

2. Run

Code:

sed -i 's/[ \t]*$//' OpenFOAM-2.3.x-Mac.patch
to remove trailing white space, before applying patch with 'git patch' command.

esujby April 1, 2014 07:05

please help!!!
 
Quote:

Originally Posted by gschaider (Post 483096)
I have no idea why your patch-utility is so picky with a patch that seems to work for others. Could you report the output of 'which patch' and also 'patch -v' to make sure that you're using the standard.

Also: the command-line you're using

Hello Gschaider,

i have done as you requested, please find the following output reports bellow:

Last login: Mon Mar 31 04:35:24 on ttys000
nasirs-imac:~ nasiryakubu$ which patch
/usr/bin/patch
nasirs-imac:~ nasiryakubu$ patch -v
patch 2.5.8
Copyright (C) 1988 Larry Wall
Copyright (C) 2002 Free Software Foundation, Inc.

This program comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of this program
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING.

written by Larry Wall and Paul Eggert
nasirs-imac:~ nasiryakubu$

esujby April 1, 2014 07:21

Quote:

Originally Posted by alexeym (Post 483144)
Hi,

well, I guess esujby is still trying to use 'git patch' to apply the patch instead of just using 'patch -p1'. There are two solutions:

1. Use 'patch -p1' as suggested by gschaider

2. Run

Code:

sed -i 's/[ \t]*$//' OpenFOAM-2.3.x-Mac.patch
to remove trailing white space, before applying patch with 'git patch' command.

Hello Alexey,

thanks for your reply. i have tried to follow the exact same step you posted on this link:
http://matveichev.blogspot.co.uk/201...0-on-os-x.html

all seems fine, i have gone through the notes section and its associated installations but the problem is at stage 7.

i have tried installing using "git apply" and this is what i get:

Last login: Tue Apr 1 12:09:00 on ttys000
nasirs-imac:~ nasiryakubu$ git apply /Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch
/Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch:753: trailing whitespace.
handle =
/Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch:1311: trailing whitespace.

/Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch:1340: trailing whitespace.

/Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch:1579: trailing whitespace.
c++DBUG =
/Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch:1605: trailing whitespace.
cDBUG =
error: applications/solvers/combustion/fireFoam/Make/options: No such file or directory
error: applications/solvers/compressible/rhoSimpleFoam/rhoSimplecFoam/Make/options: No such file or directory
error: applications/solvers/heatTransfer/chtMultiRegionFoam/chtMultiRegionSimpleFoam/Make/options: No such file or directory
error: applications/solvers/incompressible/adjointShapeOptimizationFoam/Make/options: No such file or directory
error: applications/solvers/incompressible/simpleFoam/SRFSimpleFoam/Make/options: No such file or directory
error: applications/solvers/lagrangian/icoUncoupledKinematicParcelFoam/Make/options: No such file or directory
error: applications/solvers/lagrangian/icoUncoupledKinematicParcelFoam/icoUncoupledKinematicParcelDyMFoam/Make/options: No such file or directory
error: applications/solvers/lagrangian/reactingParcelFilmFoam/Make/options: No such file or directory
error: applications/solvers/multiphase/multiphaseEulerFoam/Make/options: No such file or directory
error: applications/utilities/mesh/generation/blockMesh/Make/options: No such file or directory
error: applications/utilities/mesh/generation/foamyQuadMesh/Make/options: No such file or directory
error: applications/utilities/mesh/generation/snappyHexMesh/Make/options: No such file or directory
error: applications/utilities/mesh/manipulation/renumberMesh/Make/options: No such file or directory
error: applications/utilities/miscellaneous/expandDictionary/Make/options: No such file or directory
error: applications/utilities/miscellaneous/foamDebugSwitches/Make/options: No such file or directory
error: applications/utilities/parallelProcessing/reconstructParMesh/Make/options: No such file or directory
error: applications/utilities/postProcessing/dataConversion/foamToEnsight/Make/options: No such file or directory
error: applications/utilities/postProcessing/miscellaneous/execFlowFunctionObjects/Make/options: No such file or directory
error: applications/utilities/postProcessing/turbulence/R/Make/options: No such file or directory
error: applications/utilities/postProcessing/turbulence/createTurbulenceFields/Make/options: No such file or directory
error: applications/utilities/postProcessing/velocityField/Pe/Make/options: No such file or directory
error: applications/utilities/postProcessing/wall/wallShearStress/Make/options: No such file or directory
error: applications/utilities/postProcessing/wall/yPlusLES/Make/options: No such file or directory
error: applications/utilities/postProcessing/wall/yPlusRAS/Make/options: No such file or directory
error: applications/utilities/preProcessing/applyBoundaryLayer/Make/options: No such file or directory
error: bin/addr2line4Mac.py: already exists in working directory
error: etc/bashrc: No such file or directory
error: etc/config/CGAL.sh: No such file or directory
error: etc/config/metis.sh: No such file or directory
error: etc/config/paraview.sh: No such file or directory
error: etc/config/scotch.sh: No such file or directory
error: etc/config/settings.sh: No such file or directory
error: etc/controlDict: No such file or directory
error: src/OSspecific/POSIX/POSIX.C: No such file or directory
error: src/OSspecific/POSIX/clockTime/clockTime.H: No such file or directory
error: src/OSspecific/POSIX/fileStat.C: No such file or directory
error: src/OSspecific/POSIX/printStack.C: No such file or directory
error: src/OSspecific/POSIX/signals/sigFpe.C: No such file or directory
error: src/OSspecific/POSIX/signals/sigFpe.H: No such file or directory
error: src/OpenFOAM/db/dictionary/functionEntries/codeStream/codeStream.C: No such file or directory
error: src/OpenFOAM/db/dynamicLibrary/codedBase/codedBase.C: No such file or directory
error: src/OpenFOAM/db/dynamicLibrary/dynamicCode/dynamicCode.C: No such file or directory
error: src/OpenFOAM/db/dynamicLibrary/dynamicCode/dynamicCode.H: No such file or directory
error: src/OpenFOAM/primitives/Scalar/doubleFloat.H: No such file or directory
error: src/conversion/ensight/part/ensightPart.C: No such file or directory
error: src/conversion/ensight/part/ensightPartIO.C: No such file or directory
error: src/dynamicMesh/fvMeshDistribute/fvMeshDistributeTemplates.C: No such file or directory
error: src/dynamicMesh/meshCut/refineCell/refineCell.H: No such file or directory
error: src/fvOptions/Make/options: No such file or directory
error: src/meshTools/meshTools/meshTools.H: No such file or directory
error: src/parallel/decompose/ptscotchDecomp/Make/options: No such file or directory
error: src/parallel/decompose/scotchDecomp/Make/options: No such file or directory
error: src/renumber/Allwmake: No such file or directory
error: src/renumber/SloanRenumber/Make/options: No such file or directory
error: src/sampling/sampledSurface/writers/ensight/ensightPTraits.H: No such file or directory
error: wmake/Makefile: No such file or directory
error: wmake/rules/darwinIntel64Clang/c: already exists in working directory
error: wmake/rules/darwinIntel64Clang/c++: already exists in working directory
error: wmake/rules/darwinIntel64Clang/c++Debug: already exists in working directory
error: wmake/rules/darwinIntel64Clang/c++Opt: already exists in working directory
error: wmake/rules/darwinIntel64Clang/c++Prof: already exists in working directory
error: wmake/rules/darwinIntel64Clang/cDebug: already exists in working directory
error: wmake/rules/darwinIntel64Clang/cOpt: already exists in working directory
error: wmake/rules/darwinIntel64Clang/cProf: already exists in working directory
error: wmake/rules/darwinIntel64Clang/general: already exists in working directory
nasirs-imac:~ nasiryakubu$



and when i use " patch -p1" i get:

nasirs-imac:~ nasiryakubu$ patch -p1</Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch
can't find file to patch at input line 7
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|# HG changeset patch
|# Parent c484792c3c037623473c0a8f11a5e52e66c0e929
|
|diff --git a/applications/solvers/combustion/fireFoam/Make/options b/applications/solvers/combustion/fireFoam/Make/options
|--- a/applications/solvers/combustion/fireFoam/Make/options
|+++ b/applications/solvers/combustion/fireFoam/Make/options
--------------------------
File to patch:


I also tried to remove the white trailing spaces you told me to do use the code "sed -i 's/[ \t]*$//' " and i got:

Last login: Tue Apr 1 12:20:50 on ttys000
nasirs-imac:~ nasiryakubu$ sed -i 's/[ \t]*$//'/Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch
sed: -i may not be used with stdin
nasirs-imac:~ nasiryakubu$

please i am more than happy to have someone run my imac using logmein or skype to help install it on my computer if anyone is willing to help.

thanks

kind regards

nas

alexeym April 1, 2014 07:47

Well,

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).

2. The patches are different. I.e. if you'd downloaded the patch here, you should follow instructions given here, if you downloaded patch from blog post, you have to follow instructions in the blog post.

3. To apply patch you have to go to the source folder, from your reply I can deduce, that you are trying to apply patch in your home folder. Surely it will fail as there is no original files in your home folder. Your

Code:

nasirs-imac:~ nasiryakubu$ git apply /Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch
should be

Code:

nasirs-imac:~ nasiryakubu$ cd /Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0
nasirs-imac:OpenFOAM-2.3.0 nasiryakubu$ patch -p1 < OpenFOAM-2.3.x-Mac.patch

4. I guess you've forgotten space before OpenFOAM-2.3.x-Mac.patch during invocation of sed.

esujby April 1, 2014 08:23

Quote:

Originally Posted by alexeym (Post 483204)
Well,

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).

2. The patches are different. I.e. if you'd downloaded the patch here, you should follow instructions given here, if you downloaded patch from blog post, you have to follow instructions in the blog post.

3. To apply patch you have to go to the source folder, from your reply I can deduce, that you are trying to apply patch in your home folder. Surely it will fail as there is no original files in your home folder. Your

Code:

nasirs-imac:~ nasiryakubu$ git apply /Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0/OpenFOAM-2.3.x-Mac.patch
should be

Code:

nasirs-imac:~ nasiryakubu$ cd /Volumes/OpenFOAM-v2.3/OpenFOAM-2.3.0
nasirs-imac:OpenFOAM-2.3.0 nasiryakubu$ patch -p1 < OpenFOAM-2.3.x-Mac.patch

4. I guess you've forgotten space before OpenFOAM-2.3.x-Mac.patch during invocation of sed.



Hello Alexy,

did thesame procedure but got:

Last login: Tue Apr 1 12:35:13 on ttys000
nasirs-imac:~ nasiryakubu$ cd /Volumes/OpenFOAM-v2.3
nasirs-imac:OpenFOAM-v2.3 nasiryakubu$ ls -lstr
total 0
0 drwxr-xr-x@ 8 nasiryakubu staff 918 30 Mar 20:39 ThirdParty-2.3.0
0 drwxr-xr-x@ 7 nasiryakubu staff 272 31 Mar 00:24 clang+llvm-3.3-x86_64-apple-darwin12 2
0 drwx------@ 2 nasiryakubu staff 3162 31 Mar 01:09 stl
0 drwxr-xr-x@ 8 nasiryakubu staff 714 31 Mar 01:19 boost_1_55_0
0 drwxr-xr-x@ 9 nasiryakubu staff 646 31 Mar 04:42 OpenFOAM-2.3.0
nasirs-imac:OpenFOAM-v2.3 nasiryakubu$ cd OpenFOAM-2.3.0
nasirs-imac:OpenFOAM-2.3.0 nasiryakubu$ ls -lstr
total 336
0 drwxr-xr-x@ 5 nasiryakubu staff 782 11 Feb 11:59 wmake
0 drwxr-xr-x@ 16 nasiryakubu staff 646 11 Feb 11:59 tutorials
0 drwxr-xr-x@ 36 nasiryakubu staff 1258 11 Feb 11:59 src
0 drwxr-xr-x@ 6 nasiryakubu staff 272 11 Feb 11:59 doc
0 drwxr-xr-x@ 5 nasiryakubu staff 204 11 Feb 11:59 applications
8 -rw-r--r--@ 1 nasiryakubu staff 1587 11 Feb 11:59 README.org
16 -rw-r--r--@ 1 nasiryakubu staff 7611 11 Feb 11:59 README.html
72 -rw-r--r--@ 1 nasiryakubu staff 35647 11 Feb 11:59 COPYING
8 -rwxr-xr-x@ 1 nasiryakubu staff 932 11 Feb 11:59 Allwmake
0 drwxr-xr-x@ 3 nasiryakubu staff 2142 30 Mar 21:03 bin
128 -rw-r--r--@ 1 nasiryakubu staff 64691 30 Mar 22:10 OpenFOAM-2.3.x-Mac.patch
0 drwxr-xr-x@ 6 nasiryakubu staff 374 30 Mar 22:29 etc
104 -rw-r--r-- 1 nasiryakubu staff 51144 31 Mar 04:30 OpenFOAM-2.3.0-2.patch
nasirs-imac:OpenFOAM-2.3.0 nasiryakubu$ patch -p1 < OpenFOAM-2.3.x-Mac.patch
patching file applications/solvers/combustion/fireFoam/Make/options
Hunk #1 FAILED at 36.
Hunk #2 FAILED at 55.
2 out of 2 hunks FAILED -- saving rejects to file applications/solvers/combustion/fireFoam/Make/options.rej
patching file applications/solvers/compressible/rhoSimpleFoam/rhoSimplecFoam/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]

i clicked enter till the end and got:
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/solvers/compressible/rhoSimpleFoam/rhoSimplecFoam/Make/options.rej
patching file applications/solvers/heatTransfer/chtMultiRegionFoam/chtMultiRegionSimpleFoam/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/solvers/heatTransfer/chtMultiRegionFoam/chtMultiRegionSimpleFoam/Make/options.rej
patching file applications/solvers/incompressible/adjointShapeOptimizationFoam/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/solvers/incompressible/adjointShapeOptimizationFoam/Make/options.rej
patching file applications/solvers/incompressible/simpleFoam/SRFSimpleFoam/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/solvers/incompressible/simpleFoam/SRFSimpleFoam/Make/options.rej
patching file applications/solvers/lagrangian/icoUncoupledKinematicParcelFoam/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/solvers/lagrangian/icoUncoupledKinematicParcelFoam/Make/options.rej
patching file applications/solvers/lagrangian/icoUncoupledKinematicParcelFoam/icoUncoupledKinematicParcelDyMFoam/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/solvers/lagrangian/icoUncoupledKinematicParcelFoam/icoUncoupledKinematicParcelDyMFoam/Make/options.rej
patching file applications/solvers/lagrangian/reactingParcelFilmFoam/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file applications/solvers/lagrangian/reactingParcelFilmFoam/Make/options.rej
patching file applications/solvers/multiphase/multiphaseEulerFoam/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/solvers/multiphase/multiphaseEulerFoam/Make/options.rej
patching file applications/utilities/mesh/generation/blockMesh/Make/options
Hunk #1 FAILED at 6.
1 out of 1 hunk FAILED -- saving rejects to file applications/utilities/mesh/generation/blockMesh/Make/options.rej
patching file applications/utilities/mesh/generation/foamyQuadMesh/Make/options
patching file applications/utilities/mesh/generation/snappyHexMesh/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/mesh/generation/snappyHexMesh/Make/options.rej
patching file applications/utilities/mesh/manipulation/renumberMesh/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/mesh/manipulation/renumberMesh/Make/options.rej
patching file applications/utilities/miscellaneous/expandDictionary/Make/options
patching file applications/utilities/miscellaneous/foamDebugSwitches/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/miscellaneous/foamDebugSwitches/Make/options.rej
patching file applications/utilities/parallelProcessing/reconstructParMesh/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/parallelProcessing/reconstructParMesh/Make/options.rej
patching file applications/utilities/postProcessing/dataConversion/foamToEnsight/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file applications/utilities/postProcessing/dataConversion/foamToEnsight/Make/options.rej
patching file applications/utilities/postProcessing/miscellaneous/execFlowFunctionObjects/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/postProcessing/miscellaneous/execFlowFunctionObjects/Make/options.rej
patching file applications/utilities/postProcessing/turbulence/R/Make/options
Hunk #1 FAILED at 8.
1 out of 1 hunk FAILED -- saving rejects to file applications/utilities/postProcessing/turbulence/R/Make/options.rej
patching file applications/utilities/postProcessing/turbulence/createTurbulenceFields/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/postProcessing/turbulence/createTurbulenceFields/Make/options.rej
patching file applications/utilities/postProcessing/velocityField/Pe/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/postProcessing/velocityField/Pe/Make/options.rej
patching file applications/utilities/postProcessing/wall/wallShearStress/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/postProcessing/wall/wallShearStress/Make/options.rej
patching file applications/utilities/postProcessing/wall/yPlusLES/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/postProcessing/wall/yPlusLES/Make/options.rej
patching file applications/utilities/postProcessing/wall/yPlusRAS/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/postProcessing/wall/yPlusRAS/Make/options.rej
patching file applications/utilities/preProcessing/applyBoundaryLayer/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file applications/utilities/preProcessing/applyBoundaryLayer/Make/options.rej
The next patch would create the file bin/addr2line4Mac.py,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file bin/addr2line4Mac.py.rej
patching file etc/bashrc
Hunk #1 succeeded at 204 (offset 5 lines).
Hunk #2 succeeded at 252 (offset 11 lines).
patching file etc/config/CGAL.sh
Hunk #1 succeeded at 46 with fuzz 2 (offset 11 lines).
patching file etc/config/metis.sh
patching file etc/config/paraview.sh
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file etc/config/paraview.sh.rej
patching file etc/config/scotch.sh
patching file etc/config/settings.sh
Hunk #1 FAILED at 46.
Hunk #2 succeeded at 237 with fuzz 1 (offset 78 lines).
Hunk #3 succeeded at 623 (offset 78 lines).
Hunk #4 succeeded at 684 (offset 78 lines).
Hunk #5 succeeded at 822 (offset 78 lines).
1 out of 5 hunks FAILED -- saving rejects to file etc/config/settings.sh.rej
patching file etc/controlDict
patching file src/OSspecific/POSIX/POSIX.C
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file src/OSspecific/POSIX/POSIX.C.rej
patching file src/OSspecific/POSIX/clockTime/clockTime.H
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/OSspecific/POSIX/clockTime/clockTime.H.rej
patching file src/OSspecific/POSIX/fileStat.C
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/OSspecific/POSIX/fileStat.C.rej
patching file src/OSspecific/POSIX/printStack.C
Hunk #1 FAILED at 33.
Hunk #2 FAILED at 58.
Hunk #3 FAILED at 102.
Hunk #4 FAILED at 117.
Hunk #5 FAILED at 129.
Hunk #6 FAILED at 179.
Hunk #7 FAILED at 198.
Hunk #8 succeeded at 385 (offset 123 lines).
Hunk #9 succeeded at 415 (offset 123 lines).
Hunk #10 succeeded at 456 (offset 123 lines).
7 out of 10 hunks FAILED -- saving rejects to file src/OSspecific/POSIX/printStack.C.rej
patching file src/OSspecific/POSIX/signals/sigFpe.C
Hunk #1 succeeded at 54 with fuzz 2 (offset 12 lines).
Hunk #2 FAILED at 100.
Hunk #3 succeeded at 215 with fuzz 1 (offset 29 lines).
Hunk #4 succeeded at 342 with fuzz 2 (offset 50 lines).
Hunk #5 FAILED at 388.
2 out of 5 hunks FAILED -- saving rejects to file src/OSspecific/POSIX/signals/sigFpe.C.rej
patching file src/OSspecific/POSIX/signals/sigFpe.H
Hunk #1 succeeded at 63 with fuzz 2 (offset 8 lines).
Hunk #2 FAILED at 91.
1 out of 2 hunks FAILED -- saving rejects to file src/OSspecific/POSIX/signals/sigFpe.H.rej
patching file src/OpenFOAM/db/dictionary/functionEntries/codeStream/codeStream.C
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/OpenFOAM/db/dictionary/functionEntries/codeStream/codeStream.C.rej
patching file src/OpenFOAM/db/dynamicLibrary/codedBase/codedBase.C
Hunk #1 FAILED at 228.
Hunk #2 FAILED at 246.
Hunk #3 FAILED at 266.
Hunk #4 FAILED at 279.
4 out of 4 hunks FAILED -- saving rejects to file src/OpenFOAM/db/dynamicLibrary/codedBase/codedBase.C.rej
patching file src/OpenFOAM/db/dynamicLibrary/dynamicCode/dynamicCode.C
Hunk #1 succeeded at 98 with fuzz 2 (offset 48 lines).
Hunk #2 FAILED at 387.
1 out of 2 hunks FAILED -- saving rejects to file src/OpenFOAM/db/dynamicLibrary/dynamicCode/dynamicCode.C.rej
patching file src/OpenFOAM/db/dynamicLibrary/dynamicCode/dynamicCode.H
Hunk #1 FAILED at 109.
Hunk #2 FAILED at 222.
2 out of 2 hunks FAILED -- saving rejects to file src/OpenFOAM/db/dynamicLibrary/dynamicCode/dynamicCode.H.rej
patching file src/OpenFOAM/primitives/Scalar/doubleFloat.H
Hunk #1 succeeded at 51 with fuzz 2 (offset 20 lines).
patching file src/conversion/ensight/part/ensightPart.C
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/conversion/ensight/part/ensightPart.C.rej
patching file src/conversion/ensight/part/ensightPartIO.C
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file src/conversion/ensight/part/ensightPartIO.C.rej
patching file src/dynamicMesh/fvMeshDistribute/fvMeshDistributeTemplates.C
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/dynamicMesh/fvMeshDistribute/fvMeshDistributeTemplates.C.rej
patching file src/dynamicMesh/meshCut/refineCell/refineCell.H
patching file src/fvOptions/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/fvOptions/Make/options.rej
patching file src/meshTools/meshTools/meshTools.H
patching file src/parallel/decompose/ptscotchDecomp/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/parallel/decompose/ptscotchDecomp/Make/options.rej
patching file src/parallel/decompose/scotchDecomp/Make/options
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/parallel/decompose/scotchDecomp/Make/options.rej
patching file src/renumber/Allwmake
patching file src/renumber/SloanRenumber/Make/options
Hunk #1 FAILED at 1.
1 out of 1 hunk FAILED -- saving rejects to file src/renumber/SloanRenumber/Make/options.rej
patching file src/sampling/sampledSurface/writers/ensight/ensightPTraits.H
patching file wmake/Makefile
The next patch would create the file wmake/rules/darwinIntel64Clang/c,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/c.rej
The next patch would create the file wmake/rules/darwinIntel64Clang/c++,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/c++.rej
The next patch would create the file wmake/rules/darwinIntel64Clang/c++Debug,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/c++Debug.rej
The next patch would create the file wmake/rules/darwinIntel64Clang/c++Opt,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/c++Opt.rej
The next patch would create the file wmake/rules/darwinIntel64Clang/c++Prof,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/c++Prof.rej
The next patch would create the file wmake/rules/darwinIntel64Clang/cDebug,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/cDebug.rej
The next patch would create the file wmake/rules/darwinIntel64Clang/cOpt,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/cOpt.rej
The next patch would create the file wmake/rules/darwinIntel64Clang/cProf,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/cProf.rej
The next patch would create the file wmake/rules/darwinIntel64Clang/general,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/general.rej
patching file wmake/rules/darwinIntel64Clang/mplib
patching file wmake/rules/darwinIntel64Clang/mplibMACPORTMPICH
patching file wmake/rules/darwinIntel64Clang/mplibMACPORTOPENMPI
The next patch would create the file wmake/rules/darwinIntel64Clang/mplibOPENMPI,
which already exists! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file wmake/rules/darwinIntel64Clang/mplibOPENMPI.rej
patching file wmake/rules/darwinIntel64Dragonegg/c
patching file wmake/rules/darwinIntel64Dragonegg/c++
patching file wmake/rules/darwinIntel64Dragonegg/c++Debug
patching file wmake/rules/darwinIntel64Dragonegg/c++Opt
patching file wmake/rules/darwinIntel64Dragonegg/c++Prof
patching file wmake/rules/darwinIntel64Dragonegg/cDebug
patching file wmake/rules/darwinIntel64Dragonegg/cOpt
patching file wmake/rules/darwinIntel64Dragonegg/cProf
patching file wmake/rules/darwinIntel64Dragonegg/general
patching file wmake/rules/darwinIntel64Dragonegg/mplib
patching file wmake/rules/darwinIntel64Dragonegg/mplibMACPORTMPICH
patching file wmake/rules/darwinIntel64Dragonegg/mplibMACPORTOPENMPI
patching file wmake/rules/darwinIntel64Dragonegg/mplibOPENMPI
patching file wmake/rules/darwinIntel64Gcc/c
patching file wmake/rules/darwinIntel64Gcc/c++
patching file wmake/rules/darwinIntel64Gcc/c++Debug
patching file wmake/rules/darwinIntel64Gcc/c++Opt
patching file wmake/rules/darwinIntel64Gcc/c++Prof
patching file wmake/rules/darwinIntel64Gcc/cDebug
patching file wmake/rules/darwinIntel64Gcc/cOpt
patching file wmake/rules/darwinIntel64Gcc/cProf
patching file wmake/rules/darwinIntel64Gcc/general
patching file wmake/rules/darwinIntel64Gcc/mplib
patching file wmake/rules/darwinIntel64Gcc/mplibMACPORTMPICH
patching file wmake/rules/darwinIntel64Gcc/mplibMACPORTOPENMPI
patching file wmake/rules/darwinIntel64Gcc/mplibOPENMPI

alexeym April 1, 2014 08:31

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.


All times are GMT -4. The time now is 08:28.