[MOAB-dev] DMMOAB (PETSc 3.5.1)

[Vijay S. Mahadevan]

Yes, the entities in your sets with PARALLEL_PARTITION tag look badly
segmented. You could try running the original mesh through the mbpart
tool with the reorder option (-R) to get a new mesh with contiguous
entity numbering. Let me know if the behavior reverts when using this
new mesh.

Vijay

On Tue, Aug 19, 2014 at 10:41 AM, Gerd Heber <gheber at hdfgroup.org> wrote:
> Maybe that's what's going on. Attached is the output from "mbsize -ll"
> and the range returned by DMMoabGetAllVertices on process 1.
> There are quite a few gaps. Does that make sense?
>
> G.
>
> -----Original Message-----
> From: Vijay S. Mahadevan [mailto:vijay.m at gmail.com]
> Sent: Tuesday, August 19, 2014 10:27 AM
> To: Gerd Heber
> Cc: MOAB dev
> Subject: Re: [MOAB-dev] DMMOAB (PETSc 3.5.1)
>
> You could use the mbsize tool installed at $MOAB_INSTALL/bin/mbsize with options "-ll" to see all entities
>
> mbsize -ll <filename>
>
> You can track down the PARALLEL_PARTITION tag on entity sets and find out whether the corresponding vertices in the element are number contiguously (in terms of GLOBAL_ID). If this is segmented, internally, things get reverted back to a native PETSc Vec in DMMoab.
> Sorry about this confusion and I should've documented this better.
> This inconsistent behavior needs to change and I'm working on a patch that will possibly perform renumbering on the fly so that contiguous memory access is available for MOAB based Vecs.
>
> Vijay
>
> On Tue, Aug 19, 2014 at 10:13 AM, Gerd Heber <gheber at hdfgroup.org> wrote:
>> What's the best way to verify that? G.
>>
>> -----Original Message-----
>> From: Vijay S. Mahadevan [mailto:vijay.m at gmail.com]
>> Sent: Tuesday, August 19, 2014 9:58 AM
>> To: Gerd Heber
>> Cc: MOAB dev
>> Subject: Re: [MOAB-dev] DMMOAB (PETSc 3.5.1)
>>
>>> DMMoabCreateVector(dm, existing_tag, PETSC_NULL, PETSC_TRUE,
>>> PETSC_FALSE, &X)
>>
>> Yes, this should preserve the values in X vector. There is currently an implementation quirk that underneath the MOAB specific Vec, we check whether the local entities (vertices) are numbered contiguously so that tag_iterate can be used. If that's not the case, it actually creates a native PETSc Vec underneath and manages the memory through that. I am working on a patch to remove this limitation but I'm not sure whether you have hit this issue now.
>>
>> Can you just verify whether your local vertices in the mesh per
>> processor are contiguously arranged ? i.e.,
>>
>> P1: (1-10) P2: (11-20) instead of P1: (1-5,11-15), P2: (6-10, 16-20)
>>
>> I will let you know once this patch is ready (along with a PR to track in PETSc) so that you can try it out.
>>
>> Vijay
>>
>> On Tue, Aug 19, 2014 at 9:49 AM, Gerd Heber <gheber at hdfgroup.org> wrote:
>>> Vijay, here's something that I find confusing, or maybe I'm just doing something wrong.
>>>
>>> I call
>>>
>>> DMMoabCreateVector(dm, existing_tag, PETSC_NULL, PETSC_TRUE,
>>> PETSC_FALSE, &X)
>>>
>>> and would expect X to have the values of existing_tag (non-zero). But X's values are all zero.
>>> Is that the expected behavior?
>>>
>>> Thanks, G.
>>>
>>>
>>>
>>>