[Paraview] Exodus weirdness

Rick Angelini angel at arl.army.mil
Tue May 12 15:37:49 EDT 2009 

Just to come to closure on this, in my testing against our data based on 
this email exchange, CleanToGrid is not necessary. Running through the 
D3 filter seems to be sufficient for cleaning up the boundary layers in 
the Exodus dataset.

Thanks to all who contributed.



Moreland, Kenneth wrote:
> Actually, I don’t think you should have to run CleanToGrid at all. D3 
> should be merging all coincident points, both locally and globally. 
> The one exception is if the global ids in the Exodus file is wrong. If 
> you think that might be an issue, try turning off the global ids in 
> the Exodus reader.
>
> -Ken
>
>
> On 5/4/09 9:23 AM, "Brian Wylie" <bnwylie at sandia.gov> wrote:
>
>     Also, just a quick observation...
>
>
>     CleanToGrid = Intraprocessor clean up of coincident node points
>     D3 = Interprocessor clean up of coincident node points (through
>     the use of ghost cells).
>
>
>     So I think (I might be corrected) the correct order to do these is
>     CleanToGrid first and then D3. D3 will then have less data to
>     hoist around (by it's nature D3 is a more heavyweight process so
>     any data reduction you can do is good).
>
>
>     Brian Wylie - Org 1424
>     Sandia National Laboratories
>     MS 1323 - Building CSRI/242
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>     -----Original Message-----
>     From: paraview-bounces at paraview.org
>     [mailto:paraview-bounces at paraview.org] On Behalf Of Rick Angelini
>     Sent: Friday, May 01, 2009 9:09 AM
>     To: Weirs, V Gregory
>     Cc: alegra-help; paraview at paraview.org
>     Subject: Re: [Paraview] Exodus weirdness
>
>     I will re-investigate the data to determine if D3 and then
>     CleanToGrid does the trick.
>
>     Weirs, V Gregory wrote:
>     >
>     > OK, without D3 you will always see the processor boundaries. Paraview
>     > is see all the individual .exo files as independent, until you apply
>     > D3. CleanToGrid takes points that are essentially on top of each
>     other
>     > and merges them. Nodes on processor boundaries are written to both
>     > exodus files, so before CleanToGrid you have, effectively, double
>     > valued nodes at processor boundaries; even though the nodes are
>     at the
>     > same location, and the values are actually the same (if we wrote them
>     > out correctly) Paraview is probably trying to interpolate between
>     them
>     > somehow.
>     >
>     > CellToPoint can hide the discrepancy by slightly smoothing the data
>     > when interpolating from cells to points.
>     >
>     > These are possible and sensible explanations, but without seeing the
>     > data we can't be sure. Try D3 and CleanToGrid, and if you can still
>     > see processor boundaries we would want to look deeper, if that's
>     possible.
>     >
>     > Greg
>     >
>     > On 5/1/09 8:27 AM, "Rick Angelini" <angel at arl.army.mil> wrote:
>     >
>     > It's the boundaries from the original simulation. However, running
>     > through the D3 filter and then doing a cell2point seems to clean
>     > up the
>     > boundary edges.
>     >
>     > Thanks
>     >
>     >
>     > Moreland, Kenneth wrote:
>     > > I don't recall seeing anything quite like that before. Are these
>     > > boundaries in question those in the original simulation (noted
>     by the
>     > > file number) or the processes in your visualization (which can be
>     > > annotated with the Process Id Scalars filter)? Does running the
>     data
>     > > through D3 help?
>     > >
>     > > -Ken
>     > >
>     > >
>     > > On 4/30/09 1:30 PM, "Rick Angelini" <angel at arl.army.mil> wrote:
>     > >
>     > > I am working with one of my customers viewing an Exodus dataset
>     > > generated by Alegra(?) using 256p. The dataset loads fine, but
>     seems
>     > > to have an issue at the processor boundaries. When viewing the
>     > > dataset using something like a clip plane or isosurface, the data
>     > > seems
>     > > to be "slipped" (or offset) at each processor boundary - that is,
>     > > there
>     > > appears to be a hard edge at each processor boundary.
>     Unfortunately,
>     > > I'm not able to post an image that represents the problem.
>     > >
>     > > I'm not familiar with the Exodus data format, but it looks like it
>     > > could
>     > > be an issue associate with ghost cells. Either there are no ghost
>     > > cells at the processor boundary layer, or they're possibly being
>     > > mismanaged? Curiously enough, this is the first time we've noticed
>     > > this problem after processing quite a few Exodus datasets. We're
>     > > using the latest production version of Paraview (3.4) and we've
>     also
>     > > been able to duplicate the issue with other visualization tools,
>     > so we
>     > > think this is a problem with this particular Exodus dataset, if
>     > > not the
>     > > Exodus format in general.
>     > >
>     > > Any ideas?
>     > >
>     > >
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>     > >
>     > > **** Kenneth Moreland
>     > > *** Sandia National Laboratories
>     > > ***********
>     > > *** *** *** email: kmorel at sandia.gov
>     > > ** *** ** phone: (505) 844-8919
>     > > *** web: http://www.cs.unm.edu/~kmorel
>     <http://www.cs.unm.edu/%7Ekmorel>
>     > <http://www.cs.unm.edu/%7Ekmorel> <http://www.cs.unm.edu/%7Ekmorel>
>     > >
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> **** Kenneth Moreland
> *** Sandia National Laboratories
> ***********
> *** *** *** email: kmorel at sandia.gov
> ** *** ** phone: (505) 844-8919
> *** web: http://www.cs.unm.edu/~kmorel <http://www.cs.unm.edu/%7Ekmorel>
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