[CIG-LONG] Gale

Thu Sep 25 16:12:55 PDT 2008

Hi Ritske,
is the topography file in the current working directory?
I just tried tibet3D and it ran for the full 10 timesteps.

The error I get if Gale cannot find the topo file is below.
Not sure if this helps,

Regards,

john.

10:33 PM ~/GaleSVN. ( 12.576 Mb )
: fred 2 %; ./bin/Gale input/examples/tibet3D.xml
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: ---------------------  Stack Frames
------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR:       INSTEAD the line number of the start of the function
[0]PETSC ERROR:       is given.
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 2.3.2, Patch 10, Wed Mar 28 19:13:22
CDT 2007 HG revision: d7298c71db7f5e767f359ae35d33cab3bed44428
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./bin/Gale on a linux-gnu named fred by gale Thu Sep 25
22:34:13 2008
[0]PETSC ERROR: Libraries linked from
/home/gale/Petsc/Petsc/lib/linux-gnu-c-debug
[0]PETSC ERROR: Configure run at Fri Aug 22 11:46:27 2008
[0]PETSC ERROR: Configure options
--download-mumps=/home/gale/Petsc/Downloads/MUMPS_4.6.3.tar.gz
--download-blacs=/home/gale/Petsc/Downloads/blacs-dev.tar.gz
--download-scalapack=/home/gale/Petsc/Downloads/scalapack.tgz
--with-blacs=yes --with-scalapack=yes --with-mpi=yes
--with-mpi-dir=/opt/MyMpich2/GCC --prefix=/home/gale/Petsc/Petsc
--with-debugging=yes --with-shared=0
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

> Hi,
> I do have the topography file, so that is not the problem.
> There seems to be something going wrong with PETSC.
> cheers,
> Ritske
>
> ------------------------------------------------------------------------
> -
> Dr Ritske S. Huismans
> Professor in Structural Geology / Tectonics
> Department of Earth Science, University of Bergen
> Allegaten 41, N-5007 Bergen, Norway
> Tel: 	+ (47) 55 58 81 17
> Mob:	+ (47) 92 27 09 30
> Fax: 	+ (47) 55 58 36 60
> http://myweb.dal.ca/huismans/
> ------------------------------------------------------------------------
> -
>
> -----Original Message-----
> From: js at cp.dias.ie [mailto:js at cp.dias.ie]
> Sent: 25. september 2008 21:29
> To: Ritske S. Huismans
> Cc: cig-long at geodynamics.org
> Subject: Re: [CIG-LONG] Gale
>
>
> Hi
> I had a similar problem with tibet3D. It needs the file ascii_topo
> see,
> http://www.geodynamics.org/pipermail/cig-long/2007-December/000050.html
>
> Hope this helps.
>
> Regards,
>
> john
>> Hello Walter,
>>
>> I am a bit stuck on the 3D Gale models. Do you have any more thoughts
> on
>> this?
>>
>> best regards,
>> Ritske
>>
>> -----Original Message-----
>> From: Ritske S. Huismans
>> Sent: 21. september 2008 21:45
>> To: 'Walter Landry'
>> Cc: cig-long at geodynamics.org
>> Subject: RE: [CIG-LONG] Gale
>>
>> Hello Walter,
>>
>> thanks for the  reply.
>>
>> The error message starts like this and continues.
>>
>> [0]PETSC ERROR: [29]PETSC ERROR:
>>
> ------------------------------------------------------------------------
>> [21]PETSC ERROR:
>>
> ------------------------------------------------------------------------
>> [13]PETSC ERROR:
>>
> ------------------------------------------------------------------------
>> [13]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [13]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [13]PETSC ERROR: or see
>>
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html
>> #Signal[13]PETSC ERROR: or try http://valgrind.org on linux or man
>> libgmalloc on Apple to find memory corruption errors
>> [7]PETSC ERROR:
>>
> ------------------------------------------------------------------------
>> [31]PETSC ERROR:
>>
> ------------------------------------------------------------------------
>> [29]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [29]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [29]PETSC ERROR: or see
>>
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html
>> #Signal[29]PETSC ERROR: or try http://valgrind.org on linux or man
>> libgmalloc on Apple to find memory corruption errors
>> [29]PETSC ERROR: likely location of problem given in stack below
>>
>> and continues like this.
>> the 1 cpu job has the same error.
>>
>> Thanks,
>> Ritske
>>
>>
>> "Ritske S. Huismans" <Ritske.Huismans at geo.uib.no> wrote:
>>> Hello,
>>>
>>> I am interested to use Gale for comparison with other ALE codes in
>>> 2D/3D.
>>> I have installed Gale on our system, it runs the basic tests fine.
>>>
>>> some questions / comments that I am happy to get some feedback on:
>>> 1. There are some small differences in model results from visual
>>> comparison with the Gale manual.
>>>
>>> 2. Most notably, the 2D Tibet example does not show plastic
>> localisation
>>> when I run it, not sure what may be different.
>>
>> It has been a while since I ran it, and the implementation of Mohr
>> Coulomb has changed a lot since then.  I should run it again.
>>
>>> 3. I have tried to run the tibet3d.xml example but get memory
> failures
>>> of ptsc, even if I reduce the model resolution to
>>> something small, e.g. 16 x 16 x 4
>>> I have tried to run this last example at 256 cpu with 1 Gb/core. this
>>> should be enough.
>>
>> It may be that petsc is catching a place where Gale is writing to
>> invalid memory.  What is the exact error that you get?  For the small
>> model, can you run it on one processor?
>>
>>> I am especially interested in feedback how to get Gale running for 3D
>>> problems including plastic localisation.
>>> Thanks for any comments you can give in this regard,
>>
>> I am out of town right now, so it will take me a few days to run these
>> models again.
>>
>> Cheers,
>> Walter Landry
>> walter at geodynamics.org
>> _______________________________________________
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>> CIG-LONG at geodynamics.org
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>>
>
>
>