CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > OpenFOAM Installation on Windows, Mac and other Unsupported Platforms

Mac OS X - extrudeMesh and addr2line4Mac.py

Register Blogs Members List Search Today's Posts Mark Forums Read

Reply
 
LinkBack Thread Tools Display Modes
Old   December 7, 2013, 20:11
Default Mac OS X - extrudeMesh and addr2line4Mac.py
  #1
Senior Member
 
Pierre-Olivier Dallaire
Join Date: Mar 2009
Location: Montreal, Quebec, Canada
Posts: 185
Rep Power: 8
podallaire is on a distinguished road
Hi,

I'm facing some challenges when using extrudeMesh and wondering if it could be related to addr2line4Mac.py. I have cases that crash without any reason (mostly segmentation fault) and the same cases run no problem under Linux machines. Could it has to do something with addr2line4Mac.py and the fact that I'm running OpenFOAM under Mavericks ?

I have a clean install of Mavericks, gcc 4.6 compiled from sources and everything works pretty well with OpenFoam except extrudeMesh.

Let me know if you guys experience the same problems.

Thanks

PO
podallaire is offline   Reply With Quote

Old   December 8, 2013, 14:38
Default
  #2
Super Moderator
 
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 8,488
Blog Entries: 34
Rep Power: 86
wyldckat is just really nicewyldckat is just really nicewyldckat is just really nicewyldckat is just really nice
Greetings Pierre-Olivier,

Example of the output you're seeing would come in handy, in order to try and figure out the problem.

Also, an example case or an indication of a tutorial where this happens, would also be helpful.

In addition, did you do anything to "addr2line4Mac.py" during the installation procedure?

Best regards,
Bruno
wyldckat is offline   Reply With Quote

Old   December 8, 2013, 19:19
Default
  #3
Assistant Moderator
 
Bernhard Gschaider
Join Date: Mar 2009
Posts: 3,915
Rep Power: 40
gschaider will become famous soon enoughgschaider will become famous soon enough
Quote:
Originally Posted by podallaire View Post
Hi,

I'm facing some challenges when using extrudeMesh and wondering if it could be related to addr2line4Mac.py. I have cases that crash without any reason (mostly segmentation fault) and the same cases run no problem under Linux machines. Could it has to do something with addr2line4Mac.py and the fact that I'm running OpenFOAM under Mavericks ?

I have a clean install of Mavericks, gcc 4.6 compiled from sources and everything works pretty well with OpenFoam except extrudeMesh.

Let me know if you guys experience the same problems.

Thanks

PO
No. addr2line is only involved BECAUSE a problem occurred. Usually at a failure OF dumps a stack-trace with (if this debug-information is present) the names of the source files and the lines in that source-file. On Mac OS X there is no API to get that information directly (or at least I didn't find it). addr2line.py is a utility that gets the address where the problem occurred calls gdb, asks for the source file information on that address and returns it. Sometimes this doesn't work.

But it is only called when a problem occurs. So as Bruno said an output of the error would be helpful
__________________
Note: I don't use "Friend"-feature on this forum out of principle. Ah. And by the way: I'm not on Facebook either. So don't be offended if I don't accept your invitation/friend request
gschaider is offline   Reply With Quote

Old   December 9, 2013, 12:25
Default
  #4
Senior Member
 
Pierre-Olivier Dallaire
Join Date: Mar 2009
Location: Montreal, Quebec, Canada
Posts: 185
Rep Power: 8
podallaire is on a distinguished road
Quote:
Originally Posted by gschaider View Post
No. addr2line is only involved BECAUSE a problem occurred. Usually at a failure OF dumps a stack-trace with (if this debug-information is present) the names of the source files and the lines in that source-file. On Mac OS X there is no API to get that information directly (or at least I didn't find it). addr2line.py is a utility that gets the address where the problem occurred calls gdb, asks for the source file information on that address and returns it. Sometimes this doesn't work.

But it is only called when a problem occurs. So as Bruno said an output of the error would be helpful
Hi guys,

the extrudeMesh process in the wingMotion tutorial fails for me

Code:
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Selecting extrudeModel linearNormal
Extruding from patch using model linearNormal
Not collapsing any edges after extrusion

Extruding patches 1(front) on mesh "../wingMotion_snappyHexMesh"

Create mesh for time = 0

Adding overall 0 processor patches.
Moving mesh to layer0 points since differ from original points - this can happen for wedge extrusions.

Testing:"../wingMotion_snappyHexMesh/system/fvSchemes"
Mesh bounding box : (-1.67021e+45 -2.58578e+45 -2.31584e+77) (3.53806e+44 9.23849e+44 0.15)
        with span : (2.02401e+45 3.50962e+45 2.31584e+77)
Merge distance    : 0

Writing mesh to "/Volumes/OpenFOAM/OpenFOAM-2.2.x/tutorials/incompressible/pimpleDyMFoam/wingMotion/wingMotion2D_simpleFoam/constant/region0"

End
Anything similar on your machines ? Pretty sure that it worked well under Mountain Lion, not sure what is going on here.

Thanks

Last edited by wyldckat; December 28, 2013 at 14:00. Reason: Added [CODE][/CODE]
podallaire is offline   Reply With Quote

Old   December 11, 2013, 15:48
Default
  #5
Assistant Moderator
 
Bernhard Gschaider
Join Date: Mar 2009
Posts: 3,915
Rep Power: 40
gschaider will become famous soon enoughgschaider will become famous soon enough
Quote:
Originally Posted by podallaire View Post
Hi guys,

the extrudeMesh process in the wingMotion tutorial fails for me

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Selecting extrudeModel linearNormal
Extruding from patch using model linearNormal
Not collapsing any edges after extrusion

Extruding patches 1(front) on mesh "../wingMotion_snappyHexMesh"

Create mesh for time = 0

Adding overall 0 processor patches.
Moving mesh to layer0 points since differ from original points - this can happen for wedge extrusions.

Testing:"../wingMotion_snappyHexMesh/system/fvSchemes"
Mesh bounding box : (-1.67021e+45 -2.58578e+45 -2.31584e+77) (3.53806e+44 9.23849e+44 0.15)
with span : (2.02401e+45 3.50962e+45 2.31584e+77)
Merge distance : 0

Writing mesh to "/Volumes/OpenFOAM/OpenFOAM-2.2.x/tutorials/incompressible/pimpleDyMFoam/wingMotion/wingMotion2D_simpleFoam/constant/region0"

End

Anything similar on your machines ? Pretty sure that it worked well under Mountain Lion, not sure what is going on here.

Thanks
Works for me (2.2.x pulled 3 weeks ago).

Go to the snappy-case and do "checkMesh -constant". I think that that case is already messed up. If the snapped mesh is already faulty then remove it. Redo blockMesh and check that (sounds silly, I know)
__________________
Note: I don't use "Friend"-feature on this forum out of principle. Ah. And by the way: I'm not on Facebook either. So don't be offended if I don't accept your invitation/friend request
gschaider is offline   Reply With Quote

Old   December 18, 2013, 22:24
Default
  #6
Senior Member
 
Pierre-Olivier Dallaire
Join Date: Mar 2009
Location: Montreal, Quebec, Canada
Posts: 185
Rep Power: 8
podallaire is on a distinguished road
Quote:
Originally Posted by gschaider View Post
Works for me (2.2.x pulled 3 weeks ago).

Go to the snappy-case and do "checkMesh -constant". I think that that case is already messed up. If the snapped mesh is already faulty then remove it. Redo blockMesh and check that (sounds silly, I know)
Sorry for the delay. I tried this without any success, I still get weird numbers in the extruded mesh. Also, I have noted that in this example, the blockMesh side patches are set to "empty" patches before running snappy and it's kept this way for the extruding process as well. Is this a good practice ?

Don,t know what is wrong with my extrudeMesh - I also recompiled with a different gcc version but same results.

Thanks
podallaire is offline   Reply With Quote

Old   December 28, 2013, 14:05
Default
  #7
Super Moderator
 
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 8,488
Blog Entries: 34
Rep Power: 86
wyldckat is just really nicewyldckat is just really nicewyldckat is just really nicewyldckat is just really nice
Greetings to all!

@Pierre-Olivier: Let's try to isolate the problem. If you run this command:
Code:
find $FOAM_TUTORIALS -name Allrun | xargs grep extrude
you'll find several tutorials that use extrudeMesh.
So try to run each tutorial, to double check if this is a problem with extrudeMesh or with the tutorial you've been testing.
If any other tutorial presents the same problem, it will be easier to assess what might be going on.

Because I vaguely remember seeing such a bug, but it was a long time ago and with an older version of OpenFOAM.

Best regards,
Bruno
wyldckat is offline   Reply With Quote

Old   February 9, 2014, 19:23
Default
  #8
Senior Member
 
Pierre-Olivier Dallaire
Join Date: Mar 2009
Location: Montreal, Quebec, Canada
Posts: 185
Rep Power: 8
podallaire is on a distinguished road
Hi,

sorry for the delay on responding to this. I actually cannot run the test: I updated my git installation this week and I'm having challenges recompiling libOpenFAM. Something is wrong with db/dynamicLibrary/codedBase/codedBase.C

Anybody haven the same issue ? I also tried using Clang and the appropriate patches, same problem.

Thanks

PO
podallaire is offline   Reply With Quote

Old   February 13, 2014, 20:02
Default
  #9
Assistant Moderator
 
Bernhard Gschaider
Join Date: Mar 2009
Posts: 3,915
Rep Power: 40
gschaider will become famous soon enoughgschaider will become famous soon enough
Quote:
Originally Posted by podallaire View Post
Hi,

sorry for the delay on responding to this. I actually cannot run the test: I updated my git installation this week and I'm having challenges recompiling libOpenFAM. Something is wrong with db/dynamicLibrary/codedBase/codedBase.C

Anybody haven the same issue ? I also tried using Clang and the appropriate patches, same problem.

Thanks

PO
"something is wrong" is a bit unspecific. If I hadn't already fixed that problem I wouldn't have bothered any further. Attached is a patch that fixes a problem about codedBase (not sure whether it is yours) and which I will fold into the general Mac-patch later this weekend

fixCodeBase.patch
__________________
Note: I don't use "Friend"-feature on this forum out of principle. Ah. And by the way: I'm not on Facebook either. So don't be offended if I don't accept your invitation/friend request
gschaider is offline   Reply With Quote

Old   February 16, 2014, 00:16
Default
  #10
Senior Member
 
Pierre-Olivier Dallaire
Join Date: Mar 2009
Location: Montreal, Quebec, Canada
Posts: 185
Rep Power: 8
podallaire is on a distinguished road
Thanks for the patch !

I recompiled, works great, no issue so far. I don't understand what was wrong with extrudeMesh - I ran some cases including the wing motion tutorial without any problem ?! I'll keep testing but so far so good
podallaire is offline   Reply With Quote

Reply

Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On



All times are GMT -4. The time now is 12:06.