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OF 1.9 (aka OF 2.1) on Mac OS X

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Old   September 24, 2012, 12:10
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  #121
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BCD, you should have kept reading
See post #89: OF 1.9 (aka OF 2.1) on Mac OS X - and see #90 as well, just in case...
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Old   September 24, 2012, 13:36
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Originally Posted by BCD View Post
Thanks Bruno,
I really appreciate your wisdom & tenacity here.

wmake failed, here's the log,
PLEASE don't post logs in RTF-format

Anyway: from the log it seems that this part of the patch was not correctly applied:
Code:
diff --git a/applications/utilities/postProcessing/turbulence/R/Make/options b/applications/utilities/postProcessing/turbulence/R/Make/options
--- a/applications/utilities/postProcessing/turbulence/R/Make/options
+++ b/applications/utilities/postProcessing/turbulence/R/Make/options
@@ -7,6 +7,7 @@
 
 EXE_LIBS = \
     $(FOAM_LIBBIN)/postCalc.o \
+    -lincompressibleTurbulenceModel \
     -lincompressibleRASModels \
     -lincompressibleTransportModels \
     -lfiniteVolume \
I think this fix for the R-utility was already in the original patch so recheck if the patch was correctly applied
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Old   September 27, 2012, 09:27
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Great, thanks, no more cookies - we have OF working, of sorts.

I did a complete reinstallation and followed the various steps again. I think perhaps the first time I had applied both the gcc42 and gcc46 patches,
I also needed to edit the various options files, per post #89 here and delete the bottom lines in the ThirdParty patch per #4. Thanks so much guys, it's great to finally have lift-off.

the cavity case runs great and per post #39 running touch (enter casename).foam generates a file that ParaView can open.

sorry about the txt/rtf mixup, won't happen again!
Oh, and I've stepped up my post-reading diligence.

Last edited by BCD; September 27, 2012 at 16:18. Reason: read the manual :)
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Old   October 2, 2012, 09:49
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Dear all,

unfortunately I deleted my installation I used for creating the manual. So I followed it again myself, see http://openfoamwiki.net/index.php/Ho...using_ParaView
using Mac OS X 10.6.8 with GCC 4.6 for OpenFOAM 2.1.1-221db2718bbb.

There were a few errors during the compilation process, so I would be glad if somebody could confirm that they're harmless. EDIT: Ok, one who could read has a clear advantage. I corrected the problem with the 'R', see OF 1.9 (aka OF 2.1) on Mac OS X ran wcleanAll and Allwmake again. No errors anymore.

I tested with the icoFoam and fireFoam solver their tutorial cases and they're working.
Then I copied the disk image to a OS X 10.8.2 installation with Mac port's GCC 4.6 installed. It is working just out of the box without recompiling. I hope this is a good message for all who wait for migration.

Cheers,

Michael
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File Type: gz make.tar.gz (1.0 KB, 9 views)

Last edited by lithos; October 2, 2012 at 11:12.
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Old   October 2, 2012, 15:48
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Hi Michael,

You're getting the same errors the other people have gotten as well. Read the post #122 for the fix!
And if that doesn't do it, check post #121 for more post references

Best regards,
Bruno
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Old   October 7, 2012, 02:30
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Dear all,

I've installed Openfoam on Mac, and it was working properly until I installed gnuplot. And now, everytime I source the bashrc file, the following lines come up:

-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamEtcFile: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamEtcFile: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamEtcFile: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamEtcFile: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted

Has anyone seen this before? Thanks for your time.
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Old   October 7, 2012, 07:12
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Quote:
Originally Posted by gpeng View Post
Dear all,

I've installed Openfoam on Mac, and it was working properly until I installed gnuplot. And now, everytime I source the bashrc file, the following lines come up:

-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamEtcFile: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamEtcFile: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamEtcFile: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamEtcFile: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted
-bash: /Users/Gary/OpenFOAM/OpenFOAM-2.1.1/bin/foamCleanPath: /bin/sh: bad interpreter: Operation not permitted

Has anyone seen this before? Thanks for your time.
Could you be a bit more specific? Which version of Mac OS X? How did you install gnuplot? (I recommend MacPorts)

Hae you tried executing /bin/sh in the terminal?
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Old   October 7, 2012, 08:24
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Quote:
Originally Posted by gschaider View Post
Could you be a bit more specific? Which version of Mac OS X? How did you install gnuplot? (I recommend MacPorts)

Hae you tried executing /bin/sh in the terminal?
Hi, thanks for your reply, I am using mountain lion. And I am not too sure about MacPorts, the way I installed it is just downloading a folder and make install after compiling it.

The following link is the one I referred to:
http://bhou.wordpress.com/2011/09/13...mac-os-x-lion/

Any suggestions?
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Old   October 7, 2012, 11:00
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Quote:
Originally Posted by gpeng View Post
Hi, thanks for your reply, I am using mountain lion. And I am not too sure about MacPorts, the way I installed it is just downloading a folder and make install after compiling it.

The following link is the one I referred to:
http://bhou.wordpress.com/2011/09/13...mac-os-x-lion/

Any suggestions?
First: it seems that this is an OS-problem not an OF-problem.

Try whether /bin/sh is still a valid shell because the output you posted suggests otherwise (try to execute it) like I suggested above.

My guess is that something went wrong during the execution of the installation (which you probably did with sudo): /bin/sh was overwritten by a malfunctioning script for instance.

That is one of the reason why one should use a package manager like MacPorts, Fink or HomeBrew to install additional command-line software like gnuplot on Mac OS X: for gnuplot Mac OS X is just another architecture and not regularly tested whereas with MacPort you can be sure that it was installed on Mac OS X at least once
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Old   October 7, 2012, 22:00
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Quote:
Originally Posted by gschaider View Post
First: it seems that this is an OS-problem not an OF-problem.

Try whether /bin/sh is still a valid shell because the output you posted suggests otherwise (try to execute it) like I suggested above.

My guess is that something went wrong during the execution of the installation (which you probably did with sudo): /bin/sh was overwritten by a malfunctioning script for instance.

That is one of the reason why one should use a package manager like MacPorts, Fink or HomeBrew to install additional command-line software like gnuplot on Mac OS X: for gnuplot Mac OS X is just another architecture and not regularly tested whereas with MacPort you can be sure that it was installed on Mac OS X at least once
Sorry, I actually don't know anything about programming.. do you mean running the file named sh in the folder called bin? I couldn't find it..

Yeah, I think I did type sudo to get the gnuplot installed..Does that mean I will have to re-install open foam?!..
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Old   October 8, 2012, 03:58
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Sorry, I actually don't know anything about programming..
Then you're exactly the kind of person that should use a package manager like MacPorts, Fink or Homebrew (Google them) to install stuff like Gnuplot (those people who "know about programming" usually use them .... because they know)

Quote:
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do you mean running the file named sh in the folder called bin? I couldn't find it..
On the shell just enter /bin/sh (or even better "/bin/sh --version"). If it isn't a bash then you've got a problem

Quote:
Originally Posted by gpeng View Post
Yeah, I think I did type sudo to get the gnuplot installed..Does that mean I will have to re-install open foam?!..
Don't think so. The problem started with the gnuplot installation if I understand you correctly. But trying a reinstall can't hurt
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Old   October 8, 2012, 08:31
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Quote:
Originally Posted by gschaider View Post
On the shell just enter /bin/sh (or even better "/bin/sh --version"). If it isn't a bash then you've got a problem

Don't think so. The problem started with the gnuplot installation if I understand you correctly. But trying a reinstall can't hurt
Thanks, I entered /bin/sh and got the following:
GNU bash, version 3.2.48(1)-release (x86_64-apple-darwin12)
Copyright (C) 2007 Free Software Foundation, Inc.

Does that mean the shell is overwritten?...

Sorry to annoy you, but I really hope not to go through that painful installation process, any way to replace the shell?
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Old   October 8, 2012, 19:04
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Originally Posted by gpeng View Post
Thanks, I entered /bin/sh and got the following:
GNU bash, version 3.2.48(1)-release (x86_64-apple-darwin12)
Copyright (C) 2007 Free Software Foundation, Inc.

Does that mean the shell is overwritten?...

Sorry to annoy you, but I really hope not to go through that painful installation process, any way to replace the shell?
That was false alarm on my part: if the shell was overwritten you'd have all kinds of other problems

I have no idea what the problem could be. Google for "bash bad interpreter permission denied" and you'll find all kinds of solutions (but I haven't got the time to sort out which one fits your case).
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Old   October 9, 2012, 07:07
Default New version of the patch - Setting NaN
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Hi!

One missing feature was the support of the FOAM_SETNAN environment variable (this is mainly for people developing).

I attach two patch files:

- one with the patch implementing this feature (it assumes that the rest has been already applied)
- a complete patch (the old patch plus the the above patch plus minor adaptions)

The patch overrides the way memory is allocated and only has been tested on 10.7 (things are a little bit different on 10.6 and older - it SHOULD take care of it). I only have this machine so I can't test on different OS-versions

If somebody who already has a working version of OF on a Mac and either 10.6 or older or 10.8 (or newer ) could test it I would be grateful:

- apply feature patch
- recompile OF
- run a tutorial case
- export FOAM_SETNAN=1
- run a tutorial case

If the last step fails (process hangs etc) unapply the patch and report.

Of course: if it works (especially on 10.8) please report too

Bernhard

PS: Newcomers who have a non 10.7-system should use the old version of the patch until there is a positive feedback for their OS-version
Attached Files
File Type: patch SetNanMac.patch (5.1 KB, 412 views)
File Type: patch OpenFOAM-2.1.x-Mac_20121009.patch (41.5 KB, 449 views)
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Old   October 12, 2012, 06:01
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hello everybody,
i just wanted to compile and run openfoam but there are so many errors that i stopped the compilation. i don't know how to solve the problem, can you guys please help me? thanks...

first error:

Making all in mca/vprotocol/pessimist
CC mca_vprotocol_pessimist_la-vprotocol_pessimist.lo
In file included from vprotocol_pessimist.c:11:0:
vprotocol_pessimist.h:20:52: fatal error: vprotocol_pessimist_sender_based_types.h: No such file or directory
compilation terminated.
make[3]: *** [mca_vprotocol_pessimist_la-vprotocol_pessimist.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

the rest of the make.log is attached...
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Old   October 12, 2012, 06:46
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hello everybody,
i just wanted to compile and run openfoam but there are so many errors that i stopped the compilation. i don't know how to solve the problem, can you guys please help me? thanks...

first error:

Making all in mca/vprotocol/pessimist
CC mca_vprotocol_pessimist_la-vprotocol_pessimist.lo
In file included from vprotocol_pessimist.c:11:0:
vprotocol_pessimist.h:20:52: fatal error: vprotocol_pessimist_sender_based_types.h: No such file or directory
compilation terminated.
make[3]: *** [mca_vprotocol_pessimist_la-vprotocol_pessimist.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

the rest of the make.log is attached...
From the names of the files I'd say that this happens during the compilation of OpenMPI. Are you using the version supplied in the regular ThirdParty-tarball?

But I can't comment on this because I use the MPI supplied by MacPorts (I prefer to compile as little as possible myself). Maybe you'll have a look in the regular OpenMPI-channels whether there are problems with compilation on a Mac
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Old   October 12, 2012, 06:57
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From the names of the files I'd say that this happens during the compilation of OpenMPI. Are you using the version supplied in the regular ThirdParty-tarball?

But I can't comment on this because I use the MPI supplied by MacPorts (I prefer to compile as little as possible myself). Maybe you'll have a look in the regular OpenMPI-channels whether there are problems with compilation on a Mac
i followed the instructions from the given tutorial. when i type mpirun -V the terminal returns: mpirun (Open MPI) 1.6.2
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Old   October 12, 2012, 08:18
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i followed the instructions from the given tutorial. when i type mpirun -V the terminal returns: mpirun (Open MPI) 1.6.2
This one? http://openfoamwiki.net/index.php/Ho...enFOAM_v21_Mac Then you've got the MacPorts-openMPI and that should be fine. Wondering why it tries to compile the ThirdPArty OpenMPI anyway. But I haven't compiled my Mac-OF from scratch for a long time so I can't say. Is this the only failure you get (haven't looked at the log-file)
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Old   October 12, 2012, 08:23
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Originally Posted by gschaider View Post
This one? http://openfoamwiki.net/index.php/Ho...enFOAM_v21_Mac Then you've got the MacPorts-openMPI and that should be fine. Wondering why it tries to compile the ThirdPArty OpenMPI anyway. But I haven't compiled my Mac-OF from scratch for a long time so I can't say. Is this the only failure you get (haven't looked at the log-file)
the posted error is the first i get in the log-file, but there are plenty of other errors. i need to run openfoam for an university-project, would be great if somebody finds a solution for my problem... otherwise i will try to install ubuntu with bootcamp, but i don't want to run two seperate os on my mac.
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Old   October 12, 2012, 15:58
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Greetings to all!

@matzbanni: From your log, while building "libtriSurface.dylib", this happened:
Quote:
Code:
make: *** wait: Interrupted system call.  Stop.
make: *** Waiting for unfinished jobs....
make: *** [Make/darwinIntel64Gcc46DPOpt/readSTLASCII.o] Interrupt: 2
make: *** wait: Interrupted system call.  Stop.
This is veeeeeeeeery strange! This should not happen, unless someone or something made a kill or sent a signal to kill it off. And the worse is that it happened more than once!!

How many cores did you specify in "WM_NCOMPPROCS"? And how many does your machine have? And how much RAM?

As for Open-MPI: apparently the instructions do not specify how to tell OpenFOAM and wmake which MPI version to be looking for
Since I don't have a Mac to confirm this... Please try this and let us know if it works:
  1. Edit OpenFOAM's "etc/bashrc" file.
  2. Find the line that defines "WM_MPLIB":
    Code:
    export WM_MPLIB=OPENMPI
  3. Set it to this:
    Code:
    export WM_MPLIB=SYSTEMOPENMPI
  4. Just in case, start a new terminal.
  5. Try running Allwmake once again, as instructed.
Best regards,
Bruno
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