[Trilinos-Users] Exodus and MPI
Kevin Long
kevin.long at ttu.edu
Tue Dec 13 17:37:51 MST 2011
Hi Andrea,
I've attached source for an executable that will drive partitioning of
an exodus mesh. You'll need to install the chaco executable in your path
somewhere (I really should get around to using zoltan...).
Kevin
On 12/13/2011 04:51 PM, Andrea Penza wrote:
> Thanks Kevin, Shota and Brent for yours explanations.
> Tomorrow I will work again on this and I certainly will let you know
> if I have success.
> Thanks again, best regards.
>
> Andrea
>
>
> Il giorno 13/dic/2011, alle ore 23.36, Kevin Long ha scritto:
>
>>
>> Hi Andrea,
>>
>> There are several options as mentioned by Brent and Shota
>>
>> (1) Use the scripts provided with Sundance
>> (2) Use the nem_split/nem_spread utilities bundled with SEACAS
>>
>> Kevin
>>
>> On 12/13/2011 04:20 PM, Andrea Penza wrote:
>>> Hi Shota,
>>>
>>> thanks for your answer.
>>> So, do you think that without a Cubit License it could be impossible
>>> to use parallel computing with an ExodusII mesh?
>>> I've tried also with Triangle mesh file, and the problem was the
>>> same: the system was looking for two splitted mesh file .par . If
>>> I've understood right the python script you named should create this
>>> *.par file...right?
>>> Thanks a lot, kind regards.
>>>
>>> Andrea
>>>
>>>
>>> Il giorno 13/dic/2011, alle ore 23.01, Shota Soga ha scritto:
>>>
>>>> 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
>>>> <mailto: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$
>>>> <mailto: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
>>>>
>>>>
>>>> _______________________________________________
>>>> Trilinos-Users mailing list
>>>> Trilinos-Users at software.sandia.gov
>>>> <mailto:Trilinos-Users at software.sandia.gov>
>>>> http://software.sandia.gov/mailman/listinfo/trilinos-users
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Shota Soga
>>>> Graduate Assistant at North Carolina State University
>>>>
>>>> Email: ssoga at ncsu.edu <mailto:ssoga at ncsu.edu>
>>>> URL:http://abdelk.ne.ncsu.edu/
>>>> <http://abdelk.ne.ncsu.edu/wiki/index.php/Shota_Soga>w/
>>>>
>>>>
>>>
>>
>>
>> --
>> Kevin Long
>> Associate Professor
>> Department of Mathematics and Statistics
>> Texas Tech University
>>
>> "The end of fear is the beginning of wisdom"
>> - Bertrand Russell
>> _______________________________________________
>> Trilinos-Users mailing list
>> Trilinos-Users at software.sandia.gov
>> <mailto:Trilinos-Users at software.sandia.gov>
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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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