[Paraview] [EXTERNAL] Re: exodusII reader & writer in parallel

Fri Jan 20 12:06:23 EST 2017

Hi Greg,

Thanks for the info. I've briefly gone through the ExodusII Sandia report
at http://prod.sandia.gov/techlib/access-control.cgi/1992/922137.pdf but
didn't notice any information on parallel sets. Is that available some
place that I can look at?

Thanks,
Andy

On Thu, Jan 19, 2017 at 12:17 PM, Sjaardema, Gregory D <gdsjaar at sandia.gov>
wrote:

> It is legal to create an exodus file with no nodes and no elements.  If
> that file is part of a parallel set (using file-per-processor mode), then
> that “empty” file should have consistent metadata (block counts, sideset
> counts, …), but it is allowed to have zero nodes and elements.
>
> ..Greg
>
> --
> "A supercomputer is a device for turning compute-bound problems into
> I/O-bound problems”
>
> On 1/13/17, 2:13 PM, "ParaView on behalf of David Thompson" <
> paraview-bounces at paraview.org on behalf of david.thompson at kitware.com>
> wrote:
>
>     Hi all,
>
>     > It's looking like there could be a decent amount of hacking in the
> ExodusII code to get the writer to work properly for this (as well as the
> reader to read it back in without issues). The main issue appears to be
> that NetCDF doesn't allow creating a dimension of 0 length/size. Thus the
> stuff in VTK/ThirdParty/exodusII/vtkexodusII would need to be changed.
>     >
>     > Both the reader and writer make the assumption that if the num_nodes
> dimension exists that there are points to be read in.
>
>     Yes, that is a basic assumption of the Exodus file format: each rank
> is assigned a subset of the cells and nodes in the simulation domain, since
> otherwise there is no state to store. If rank 0 of a simulation has no
> nodes (and thus cannot have cells either), then it should probably not
> participate in writing the Exodus dataset. You could create an MPI
> subcontroller without the rank 0 process and have the writer use that.
>
>     > At this point I'm thinking it's better to modify the reader than the
> writer...
>
>     I would be very wary of this.
>
>         David
>
>     >
>     > On Fri, Jan 13, 2017 at 2:59 PM, Andy Bauer <andy.bauer at kitware.com>
> wrote:
>     > Hi Ken,
>     >
>     > Thanks for the input.
>     >
>     > There is an explicit check in the writer to see if there are any
> points before writing out point data. I took that check out and am hitting
> a NetCDF error that the "num_nodes" dimension isn't specified. It will
> probably take a bit of investigating to fix this but at least you've helped
> me go down the correct path.
>     >
>     > Thanks,
>     > Andy
>     >
>     > On Fri, Jan 13, 2017 at 2:44 PM, Moreland, Kenneth <
> kmorel at sandia.gov> wrote:
>     > Andy,
>     >
>     >
>     >
>     > That sounds like a bug in our Exodus writer to me. I’m not positive,
> but I’m pretty sure that you can specify in Exodus point and cell arrays if
> no grid points or cells exist. The writer is probably making a shortcut and
> skipping that if there is no actual data.
>     >
>     >
>     >
>     > -Ken
>     >
>     >
>     >
>     > From: ParaView [mailto:paraview-bounces at paraview.org] On Behalf Of
> Andy Bauer
>     > Sent: Friday, January 13, 2017 12:00 PM
>     > To: paraview at paraview.org
>     > Subject: [EXTERNAL] [Paraview] exodusII reader & writer in parallel
>     >
>     >
>     >
>     > Hi,
>     >
>     > I'm trying out the ExodusII writer in parallel and had some
> questions about how it should work in general when there isn't any data on
> process 0. Currently what happens in ParaView is that a file for each
> process is written out but the file corresponding to process 0 doesn't have
> any grid information or field data (an example is attached). When I read
> this back into ParaView using the built-in server (i.e. in serial) the
> ExodusII reader gets the proper points and cells but no field data is read
> in.
>     >
>     > So my question is this, does the ExodusII file format allow
> specifying point and cell arrays in a file if no grid points or cells exist?
>     >
>     > I'm tempted to fix this issue by modifying the reader to properly
> pass the field data information to process 0 from another one that has data
> but wanted to get the community's thoughts on this before I go through the
> implementation. The alternative would be to modify the writer to include
> point and cell data information and that's probably a better solution,
> assuming that the ExodusII format allows for that.
>     >
>     > Thanks,
>     >
>     > Andy
>     >
>     > ps. Attached is a sample set of ExodusII files that doesn't have any
> data on parallel.ex2.4.0 in case someone wants to play around with it.
>     >
>     >
>     >
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