[Trilinos-Users] [EXTERNAL] Re: Exodus and MPI

[Kevin Long]

The various partitioning scripts in Sundance use pxo, but there's 
nothing special about that suffix.

It would probably be better to run nem_slice and nem_spread if you can 
get them built. If you do please let me know the magic cmake incantation 
you used;  after quite a bit of playing with cmake options I still have 
been unable to get them to build.

Kevin


On 12/13/2011 04:24 PM, Perschbacher, Brent M wrote:
> Andrea,
>   Shota is correct that Sundance is expecting your mesh files to 
> already be decomposed for the number of processors you are running on. 
> The name “square-2-0.pxo” is the common naming scheme for spread 
> files, ie <filename>-<num procs>-<rank>.pxo (I’ve not seen pxo before, 
> it has always been exo in my experience, but maybe that has changed).
>
> There are tools inside of SEACAS for spreading meshes, nem_slice and 
> nem_spread. They should have already been built based on the configure 
> script you sent so you should be able to find them in your build or 
> install directories. Unfortunately I can’t give you much advice on how 
> to use them as it has been several years since I used either tool and 
> I don’t recall any of the specifics. A quick google of nem_spread 
> brought me to 
> http://www.osti.gov/bridge/purl.cover.jsp?purl=/974871-3kTe6Y/, which 
> is about Salinas, but does discuss a bit how to spread files for 
> Salinas using nem_spread. More poking around on google would probably 
> lead you to better information than that as I know that document is old.
>
> I hope this helps,
>
> Brent
>
>
> On 12/13/11 3:01 PM, "Shota Soga" <ssoga at ncsu.edu> wrote:
>
>     HI Andrea,
>
>     When you run Sundance with multi-dore, it asks to distributed mesh
>     by default for parallel computing.
>
>     I do not know how to generate distributed mesh with exodus
>     (probably Cubit can do this?), but in the source directory, I
>     thought there is python script to convert Exodus file to
>     partitioned triangle mesh. Then, use Triangle Mesh reader for
>     partitioned triangle mesh.
>
>     Shota
>
>     On Tue, Dec 13, 2011 at 4:43 PM, Andrea Penza <pepe.aero at alice.it>
>     wrote:
>
>         Hi all,
>
>         I have problems executing Sundance with ExodusII mesh. I'm
>         trying to run
>         it with MPI on the two processors of my DualCore. I've tested
>         MPI and
>         Exodus separately and everything was working.
>         Now the problem is that my system look for two splitted files
>         for the
>         mesh, particularly it search *.pxo file format.
>         The system reports this message at runtime:
>
>         andrea at andrea-MacBookPro:~/Projects/trilinos-10.8.3-Source/MyApps/LaplaceScalar$
>         <andrea at andrea-MacBookPro:%7E/Projects/trilinos-10.8.3-Source/MyApps/LaplaceScalar$>
>         time mpirun -np 2 ./LaplaceScalarExo.exe
>         Teuchos::GlobalMPISession::GlobalMPISession(): started
>         processor with
>         name andrea-MacBookPro and rank 0!
>         Teuchos::GlobalMPISession::GlobalMPISession(): started
>         processor with
>         name andrea-MacBookPro and rank 1!
>         Simulation built using Sundance version 2.3.0 (10 May 2008)
>         Sundance is copyright
>          (C) 2005-2008 Sandia National Laboratories
>          (C) 2007-2008 Texas Tech University
>         and is licensed under the GNU Lesser General Public License,
>         version 2.1
>         [1]
>         Sundance detected exception:
>         /home/andrea/Projects/trilinos-10.8.3-Source/packages/Sundance/src-utils/Utilities/SundancePathUtils.cpp:58:
>
>         Throw number = 1
>
>         Throw test that evaluated to true: true
>
>         could not find file ../Mesh/exodusii/square-2-0.pxo in path
>         {.,
>         /home/andrea/Projects/trilinos-10.8.3-Source/BUILD/packages/Sundance/etc,
>         /usr/local/etc, NOTFOUND/Sundance/meshes,
>         /home/andrea/Projects/trilinos-10.8.3-Source/BUILD/packages/Sundance/examples-tutorial/data,
>         /usr/local/examples-tutorial/data}
>         caught
>         in
>         /home/andrea/Projects/trilinos-10.8.3-Source/packages/Sundance/src-std-mesh/Sources/SundanceExodusMeshReader.cpp:474
>
>         caught
>         in
>         /home/andrea/Projects/trilinos-10.8.3-Source/packages/Sundance/src-std-mesh/Sources/SundanceMeshSource.cpp:69
>
>         test FAILED
>         Sundance detected exception:
>         /home/andrea/Projects/trilinos-10.8.3-Source/packages/Sundance/src-utils/Utilities/SundancePathUtils.cpp:58:
>
>         Throw number = 1
>
>         Throw test that evaluated to true: true
>
>         could not find file ../Mesh/exodusii/square-2-1.pxo in path
>         {.,
>         /home/andrea/Projects/trilinos-10.8.3-Source/BUILD/packages/Sundance/etc,
>         /usr/local/etc, NOTFOUND/Sundance/meshes,
>         /home/andrea/Projects/trilinos-10.8.3-Source/BUILD/packages/Sundance/examples-tutorial/data,
>         /usr/local/examples-tutorial/data}
>         caught
>         in
>         /home/andrea/Projects/trilinos-10.8.3-Source/packages/Sundance/src-std-mesh/Sources/SundanceExodusMeshReader.cpp:474
>
>         caught
>         in
>         /home/andrea/Projects/trilinos-10.8.3-Source/packages/Sundance/src-std-mesh/Sources/SundanceMeshSource.cpp:69
>
>         test FAILED
>
>
>         As you can see, my system look for a
>         file ../Mesh/exodusii/square-2-0.pxo for the process with rank
>         0, and
>         the file ../Mesh/exodusii/square-2-1.pxo for the rank 1.
>         The source mesh file name is square.exo in the dir Mesh/exodusii.
>         Thanks a lot to everyone could help me!
>         Kind regards,
>
>         Andrea
>
>
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>
>
>


-- 
Kevin Long
Associate Professor
Department of Mathematics and Statistics
Texas Tech University

"The end of fear is the beginning of wisdom"
- Bertrand Russell

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