[MOAB-dev] Polyhedra elements in parallell

[Vijay S. Mahadevan]

James,

There is a PR that Iulian created to fix this issue.

https://bitbucket.org/fathomteam/moab/pull-request/106/ghosting-polyhedra-elements/

Can you fetch from the repo and test against the branch:
iulian07/ghost_polyhedra to see if the bug has been fixed ? If you can
confirm, we will review and merge the PR.

Vijay

On Tue, Apr 28, 2015 at 4:04 PM, Grindeanu, Iulian R.
<iulian at mcs.anl.gov> wrote:
> Hi Jim,
>
> I am able to reproduce the error when I use ghosting
>
> mpiexec -np 2 mbconvert -O PARALLEL=READ_PART -O
> PARTITION=PARALLEL_PARTITION -O PARALLEL_RESOLVE_SHARED_ENTS -o
> PARALLEL=WRITE_PART -O PARALLEL_GHOSTS=3.0.1 twoPolyhedra.p2.h5m jj.h5
>
> It is a bug, thank you for reporting it. It is related to polyhedra
> elements, most likely.
>
> I am looking at it,
> thanks,
> Iulian
>
>
>
>
> ________________________________
> From: WARNER, JAMES E. (LARC-D309) [james.e.warner at nasa.gov]
> Sent: Tuesday, April 28, 2015 3:26 PM
>
> To: Grindeanu, Iulian R.; moab-dev at mcs.anl.gov
> Subject: Re: [MOAB-dev] Polyhedra elements in parallell
>
> Hi Iulian,
>
> Thanks for the quick response…
>
> I am able to run that 'mbconvert' command in parallel as well without error.
>
> Where I am running into an issue is when I try to read the partitioned mesh
> file (twoPolyhedra.p2.h5m) into a finite element code using the
> DMMoabLoadFromFile(…) function on two processors. I get the following error
> after calling DMMoabLoadFromFile() :
>
> "
> ParallelComm.cpp:2928: moab::ErrorCode
> moab::ParallelComm::get_local_handles(moab::EntityHandle*, int, const
> std::vector<long unsigned int>&): Assertion `ID_FROM_HANDLE(from_vec[i]) <
> (int) new_ents.size()' failed.
> "
>
> However, reading the unpartitioned mesh (twoPolyhedra.p1.h5m) on one
> processor works fine.
>
> -Jim
>
>
> From: <Grindeanu>, "Iulian R." <iulian at mcs.anl.gov>
> Date: Tuesday, April 28, 2015 2:58 PM
> To: "WARNER, JAMES E. (LARC-D309)" <james.e.warner at nasa.gov>,
> "moab-dev at mcs.anl.gov" <moab-dev at mcs.anl.gov>
> Subject: RE: [MOAB-dev] Polyhedra elements in parallell
>
> Hi Jim,
> I was able to "mbconvert" in parallel your file, with a command like
> mpiexec -np 2 mbconvert -O PARALLEL=READ_PART -O
> PARTITION=PARALLEL_PARTITION -O PARALLEL_RESOLVE_SHARED_ENTS -o
> PARALLEL=WRITE_PART twoPolyhedra.p2.h5m jj.h5m
>
> mbpart created correctly the partitions, (each with one element).
>
> What options do you use when you load the file in parallel?
>
> You can add also an option like -O DEBUG_IO=2, it will output more debug
> info during reading
>
>  So what options do you pass when loading the file?
>
> Thanks,
> Iulian
>
> ________________________________
> From: WARNER, JAMES E. (LARC-D309) [james.e.warner at nasa.gov]
> Sent: Tuesday, April 28, 2015 12:47 PM
> To: Grindeanu, Iulian R.; moab-dev at mcs.anl.gov
> Subject: Re: [MOAB-dev] Polyhedra elements in parallell
>
> Hi Iulian,
>
> I fixed the bug I mentioned previously but still get the same MOAB error
> when reading the mesh with two partitions. Attached here are the original
> (.p1.) and partitioned (.p2.) meshes. Let me know if you have any
> suggestions when you get a chance to take a look. Thanks a lot!
>
> Best,
> Jim
>
>
> From: <WARNER>, "WARNER, JAMES E. (LARC-D309)" <james.e.warner at nasa.gov>
> Date: Monday, April 27, 2015 5:00 PM
> To: "Grindeanu, Iulian R." <iulian at mcs.anl.gov>, "moab-dev at mcs.anl.gov"
> <moab-dev at mcs.anl.gov>
> Subject: Re: [MOAB-dev] Polyhedra elements in parallell
>
> Hi Iulian,
>
> The face that the two polyhedron elements have in common was given a
> different ID in each element's connectivity… so that is probably the issue.
> I'm going to look into fixing that and I'll let you know if it's resolved
> afterwards. Sorry about that!
>
> -Jim
>
>
> From: <Grindeanu>, "Iulian R." <iulian at mcs.anl.gov>
> Date: Monday, April 27, 2015 4:42 PM
> To: "WARNER, JAMES E. (LARC-D309)" <james.e.warner at nasa.gov>,
> "moab-dev at mcs.anl.gov" <moab-dev at mcs.anl.gov>
> Subject: RE: [MOAB-dev] Polyhedra elements in parallell
>
>
> my guess is that mbpart (with default options) distributed all faces to
> different processors, so maybe meshes are not "complete" in the partition; I
> think that mbpart will need to change for polyhedral meshes.
> As Rajeev said, can you send your mesh files (before and after partitioning)
> ?
> Thanks,
> Iulian
> ________________________________
> From:moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf
> of WARNER, JAMES E. (LARC-D309) [james.e.warner at nasa.gov]
> Sent: Monday, April 27, 2015 3:12 PM
> To: moab-dev at mcs.anl.gov
> Subject: [MOAB-dev] Polyhedra elements in parallell
>
> Hello,
>
> I generated a MOAB finite element mesh with polyhedra elements that works
> fine on one processor. However, when I use mbpart to generate two partitions
> and run my finite element code in parallel, I get the following error when
> calling DMMoabLoadFromFile() :
>
> "
> ParallelComm.cpp:2928: moab::ErrorCode
> moab::ParallelComm::get_local_handles(moab::EntityHandle*, int, const
> std::vector<long unsigned int>&): Assertion `ID_FROM_HANDLE(from_vec[i]) <
> (int) new_ents.size()' failed.
> "
>
> Ultimately, I'd like to use MOAB's polyhedra elements to implement arbitrary
> user-defined finite elements in the code I work on, but as a simple initial
> test I am trying to create a mesh with just two 3D bricks using MBPOLYHEDRON
> rather than MBHEX. I first generate 2D quad elements for the six facets of
> each 3D element and use an array of these facets as the connectivity for
> each polyhedron element, according to the documentation. I don't get any
> warning or error messages when generating the input mesh file or when
> calling mbpart to partition the mesh, only when trying to read it into the
> finite element code in parallel. And again, it appears to be working
> correctly in serial.
>
> It's possible I am overlooking something in my code for generating the mesh,
> so if you can provide any info about the error above and what may be causing
> it I'd appreciate it!
>
> Thanks a lot,
> -Jim
>
>
>
>