[CIG-SHORT] Pylith "zero-pivot" error

[Ravi Kanda]

Brad,

You are right, I guess Pylith ran without any errors, but PETSc generated 
errors.  I'll try your suggestion for removing faults.

So, Pylith uses the same element numbers as in the EXODUS file?  In that case, 
is there a convention for numbering the new cohesive elements that are generated 
when there is a fault in the domain?  I mean, if Pylith does the numbering by 
object ID and/or geometrically (e.g., left-right, then top-bottom).  I have been 
setting the FIATLAGRANGE flag and from what I understand, FIAT is an "automatic" 
element generator, right?  Would I get more info on this from the FIAT (FENICS) 
web page?

Thanks,
Ravi.
----------------------------------------------------------------------------------

Brad Aagaard wrote:
> Ravi-
> 
> I don't see any error in the run log you sent. It looks like PyLith ran 
> all the way through without any errors.
> 
> The zero-pivot usually means that PETSc encountered an unconstrained 
> DOF. If things didn't run correctly, try running the problem with the 
> same BC but without faults.
> 
> Some things to note:
> 
> (1) The zero-pivot is not associated with distorted cells.
> (2) In exporting the mesh to an Exodus file, CUBIT renumbers everything. 
>  I have no idea what the renumbering is based on. You can look at the 
> exodus file in ParaView to see the renumbered mesh.
> 
> Brad
> 
> 
> Ravi Kanda wrote:
>> Brad,
>>
>> Thanks, the debugging suggestion was very helpful.  Pylith now 
>> "understands" my
>> CFG files. But now, the run fails with the "Detected zero pivot in LU 
>> factorization" error (see attached screen output log).  After checking 
>> the PETSc documentation page, I tried running with the following in my 
>> PYLITHAPP.CFG file:
>> ---------------------------------------------
>> pc_factor_shift_nonzero = true
>> #pc_factor_shift_positive_definite = true
>> ---------------------------------------------
>>
>> A. I get the same error with either/BOTH flags.
>>
>> B. I then ran pylith with the mesh debug flag, "debug = 1", and it 
>> seems like the problem is with element 2982 (?).  On further 
>> investigation of the screen output, this turns out to be a cohesive 
>> element.  So, I am trying to figure out whether there is a problem of 
>> mesh-quality or if it has something to do with cohesive element 
>> generation.
>>
>> C. I used Cubit to generate my mesh, and have visually checked the 
>> mesh quality to make sure there are only a small number of elements 
>> with a poor aspect ratio (and no negative Jacobians).  The imported 
>> mesh has 1265 elements (and only 4 of those elements have "bad" aspect 
>> or edge ratios - i.e. > 4.0).  I am not sure if/how Pylith re-numbers 
>> the imported elements, especially after the cohesive elements are 
>> added to the system - so, I don't know where this element is in the 
>> mesh.  Is it possible to extract this from the pylith debug 
>> information?  I couldn't find any coordinate info listed in the screen 
>> output.
>>
>> D. Also, there are two more error "blocks" starting at lines 134122 
>> and 134167 of the attached log file.  Are these associated with the 
>> zero pivot error above (line 134077)?
>>
>> Thanks again!
>> Ravi.
>>
>> ---------------------------------------------------------------------------------- 
>>
>>
>> Brad Aagaard wrote:
>>> Ravi-
>>>
>>> You have an error when specifying the materials bin. Delete line 38 
>>> of SLAB2D_p2_nx101_Th30.cfg.
>>> What you have translates to:
>>> pylith.timedependent.materials.materials = slab2D_3M
>>> what you mean is:
>>> pylith.timedependent.materials = slab2D_3M
>>>
>>> The easiest way to track down these problems is to use the --help, 
>>> --help-properties, and --help-components arguments to pylith. For 
>>> example, if you ran PyLith with
>>> pylith YOUR_CFG_FILES_HERE --timedependent.help-components
>>> you would find out that PyLith is still using the default materials 
>>> bin (homogeneous). Once you fix your error you should see that PyLith 
>>> is picking up your setting on line XX of your cfg file.
>>>
>>> Brad
>>>
>>>
>>
>> ---------------------------------------------------------------------
>> Ravi Kanda
>> Seismological Laboratory, MC 252-21
>> Division of Geological and Planetary Sciences
>> California Institute of Technology
>>
>> 1200 E. California Blvd., Pasadena, CA 91125
>> Phone: 626-395-6971, Fax: 626-564-0715
>> Web Page: http://www.gps.caltech.edu/~rkanda
>>
>> ----------------------------------------------------------------------
>>
>> For a human being, the unexamined life is not worth living - SOCRATES
>>
>> ----------------------------------------------------------------------
> 

-- 
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Ravi Kanda
Seismological Laboratory, MC 252-21
Division of Geological and Planetary Sciences
California Institute of Technology

1200 E. California Blvd., Pasadena, CA 91125
Phone: 626-395-6971, Fax: 626-564-0715
Web Page: http://www.gps.caltech.edu/~rkanda

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For a human being, the unexamined life is not worth living - SOCRATES

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