[Trilinos-Users] Exodus and MPI
Shota Soga
ssoga at ncsu.edu
Wed Dec 14 09:28:48 MST 2011
HI Andrea,
You should add path to your environmental variable.
If you use bash, run the following code:
PATH=/path/to/chaco/exec/:${PATH}
if you use tcsh, then
setenv PATH /path/to/chaco/:${PATH}
Then, Sundance can find chaco. Check if your path is properly set by
echo ${PATH}
Shota
On Wed, Dec 14, 2011 at 9:09 AM, Andrea Penza <pepe.aero at alice.it> wrote:
> Hi Kevin,
>
> I've installed Chaco doing command make in the dir:
>
> /home/andrea/Projects/trilinos-10.8.3-Source/MyApps/MeshPartitioner/Chaco-2.2/code
>
> After that, I found the executable file "chaco" in the dir:
>
> /home/andrea/Projects/trilinos-10.8.3-Source/MyApps/MeshPartitioner/Chaco-2.2/exec
>
> in this path I've generated the partitionExo.exe file from the source
> file that you've sent to me.
> Trying to execute it my system gave this response:
>
> andrea at andrea-MacBookPro:~/Projects/trilinos-10.8.3-Source/MyApps/MeshPartitioner/Chaco-2.2/exec$
> time ./partitionExo.exe
> Teuchos::GlobalMPISession::GlobalMPISession(): started processor with
> name andrea-MacBookPro and rank 0!
> 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]
> sh: chaco: not found
>
>
> --------------------------------
> and the execution is never ending. Is there something wrong in how I've
> installed Chaco?
> Thanks to everyone for the support.
> Kind regards,
>
> Andrea
>
>
>
>
> On mar, 2011-12-13 at 18:37 -0600, Kevin Long wrote:
> >
> > 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> 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
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Shota Soga
> > > > > > Graduate Assistant at North Carolina State University
> > > > > >
> > > > > >
> > > > > > Email: ssoga at ncsu.edu
> > > > > > URL:http://abdelk.ne.ncsu.edu/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
> > > > http://software.sandia.gov/mailman/listinfo/trilinos-users
> > >
> >
> >
> > --
> > 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
> > http://software.sandia.gov/mailman/listinfo/trilinos-users
>
>
>
>
> _______________________________________________
> Trilinos-Users mailing list
> 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
URL:http://abdelk.ne.ncsu.edu/<http://abdelk.ne.ncsu.edu/wiki/index.php/Shota_Soga>
w/
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