[CIG-SHORT] Pylith "timedependent.homogeneous..." errors

[Ravi Kanda]

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
> 
> 
> On Tuesday 22 January 2008, Ravi Kanda wrote:
>> I am building a 2D elastic model that contains three materials, two fault
>> interfaces, and 8 edge BCs.  Pylith exits with the following errors:
>> " ...
>>   -- pyre.inventory(error)
>>   -- timedependent.homogeneous.materials <- 'slab2D_3M'
>>   -- unrecognized property 'timedependent.homogeneous.materials'
>>   ...
>> "
>> So, every other error is of the form "-- unknown component
>> timedependent.homogeneous.x.y.z", which is probably due to the first error
>> shown above.
>>
>> 1) I would have thought the order would be
>> "timedependent.materials.homogeneous...."
>>
>> 2) Does it matter where the materials and time information are defined
>> (i.e., whether they are defined in the PYLITHAPP.cfg file or the
>> <RUN-PREFIX>.cfg file? I am defining both in the latter.
>>
>> 3) I also want to know if "debug" option is available for Materials, BCs,
>> and Faults, or if it is restricted to Mesh importing.
>>
>> Note on my workflow:
>> -----------------------
>> I am using python scripts to generate the mesh in Cubit, and export it in
>> EXODUS format.  The SpatialDB files for each of the above components, as
>> well as the CFG files are automatically generated from the problem data
>> exported from the Cubit python scripts as well as separately specified
>> run-data, to minimize manual errors.  I checked using Paraview that the
>> mesh, nodesets and material blocks are exported correctly from cubit.
>>
>> For these initial runs, I have manually (and also by using test scripts I
>> wrote) checked that the spatialDB files generated are consistent w.r.t the
>> mesh-domain, units, and property values.  I also checked that the required
>> module definitions of the form: '[pylith.timedependent.x.y.z...]' occur in
>> the CFG files, as indicated in the pylith examples, and that the mesh
>> nodeset and block labels are correctly identified in these files.
>>
>> I have been able to run and visualize output from all the pylith examples
>> without problem, and used the HEX8 and TWOQUAD4 examples to guide the
>> generation my ODB, SPATIALDB, and CFG files.
>>
>> ATTACHMENTS & Specifics:
>> -----------------------
>> I am attaching the screen-output for the run, along with the CFG files, and
>> the material ODB file.  All the required files are in the same run
>> directory (*.cfg, *.odb, *.spatialdb).   I generated containers
>> (slab2D_3M.odb, slab2D_2F.odb, slab2D_8BC.odb) for the above three
>> components using the corresponding templates provided in the Pylith binary
>> distribution.  I also tried variations of the ODB file where I changed the
>> object name at the top to the defaults (MyMatBin, MyBC, or MyFaults),
>> instead of customized names... but I get the same errors.
>>
>>
>> Thanks for your help!
>> Ravi.
>>
>> ---------------------------------------------------------------------
>> 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
>>
>> ----------------------------------------------------------------------
> 
> 

-- 
---------------------------------------------------------------------
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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