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

[Perschbacher, Brent M]

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$ 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


_______________________________________________
Trilinos-Users mailing list
Trilinos-Users at software.sandia.gov
http://software.sandia.gov/mailman/listinfo/trilinos-users



-------------- next part --------------
An HTML attachment was scrubbed...
URL: https://software.sandia.gov/pipermail/trilinos-users/attachments/20111213/df406c4a/attachment.html