[MOAB-dev] MOAB insights?

Sun Nov 1 13:08:29 CST 2015

I'm writing a little conversion tool from VT*/Exodus to h5m, and I'm having
some trouble with the edges/faces. For example, I can read node and element
info from a VTK file; I can also write it out to a h5m file, see [1].

This file gets read alright by the HelloMOAB example, and reports
```
Number of vertices is 21218
Number of edges is 0
Number of faces is 0
Number of elements is 91215
```
All good.

Now, I would like have edges and faces. Can I create those entities at all?
Or is there a MOAB tool to enrich a given h5m file [1] with edges and faces?

Cheers,
Nico

[1] http://chunk.io/f/836dc0de673947b8ac72ad0181f57862

On Sat, Oct 31, 2015 at 5:34 PM Nico Schlömer <nico.schloemer at gmail.com>
wrote:

> Sounds interesting!
>
>
> > As I said, we use Visit or Paraview (with plugins for moab h5m file)
>
> This is the only thing I'm worried about. I mean, I myself could easily do
> that, but I can't possibly demand this from my users. I already see them
> failing to set up their viewers.
>
> A tool that can convert between h5m, vtk, vtu, exodus etc. would certainly
> help. I already have a tool in place for all of the rest [1]. Perhaps it's
> an easy addition with [2].
> Ideal, as Timothy suggests, would be if MOAB supported (parallel) I/O with
> Exodus or VTU.
>
> Cheers,
> Nico
>
> [1] https://github.com/nschloe/pygmsh/blob/master/tools/pygmsh-convert
> [2] http://www.h5py.org/
>
>
> On Sat, Oct 31, 2015 at 4:56 PM Grindeanu, Iulian R. <iulian at mcs.anl.gov>
> wrote:
>
>> Hi Nico,
>>
>> As I said, we use Visit or Paraview (with plugins for moab h5m file)
>> we partition with mbpart (backend is zoltan or metis, directly)
>> an msh file for gmsh can be partitioned with
>>  mbpart 10 -z RCB screw.msh  screw.h5m
>>
>>
>> partition means we add sets to our h5m file, that can be interpreted by
>> visit plugin
>>
>>
>>
>> the file can be read in parallel/processed by moab application
>>
>> output is another h5m file (with new tags for new solution variables,
>> which can be usually read by visit plugin directly from the file)
>>
>>
>> If the file is too big, we can "extract" with some tools a portion only
>>
>> One issue is mbpart does not work in parallel now, but we will add that
>> in the next release
>>
>>
>> As long as you can read the file (  it was generated by one task), mbpart
>> can partition it
>>
>> Iulian
>>
>> ------------------------------
>> *From:* Nico Schlömer [nico.schloemer at gmail.com]
>> *Sent:* Saturday, October 31, 2015 10:25 AM
>>
>> *To:* Grindeanu, Iulian R.; moab-dev at mcs.anl.gov
>> *Subject:* Re: [MOAB-dev] MOAB insights?
>> > what "standard" do you need ? Do you have an example ?
>>
>> Something that can be consumed by VTK/ParaView or for which there is a
>> sufficiently broad user base (e.g., XDMF).
>>
>> The typical workflow right now:
>>
>> * Use Gmsh [1]/PyGmsh [2] to generate a mesh
>> * use PyGmsh [2]/VTK [3] to translate the file into Exodus (.e)
>> * use decomp from SEACAS [4] to split it into a set (e.g., .e.10.*)
>> * Feed those files in parallel into the code, using STK/SEACAS.
>> * run the code, get the output in split Exodus files
>> * use ejoin from SEACAS to put them back together to one single Exodus
>> file
>> * visualize with Paraview.
>>
>> A crucial part here is the decomp which hooks up to Zoltan to generate a
>> partition. I'm not tied to this, and if there is a tool that, for example,
>> splits VTU files into PVTU, I'd be happy to use that.
>>
>> (Side note: Parallel Exodus is sometimes known as Nemesis, I believe.)
>>
>> What's the typical MOAB workflow? How do you visualize the data?
>>
>> Cheers,
>> Nico
>>
>> [1] http://geuz.org/gmsh/
>> [2] https://pypi.python.org/pypi/pygmsh
>> [3] http://www.vtk.org/
>> [4] https://launchpad.net/~nschloe/+archive/ubuntu/seacas-nightly
>>
>> On Sat, Oct 31, 2015 at 3:57 PM Grindeanu, Iulian R. <iulian at mcs.anl.gov>
>> wrote:
>>
>>> Hi Nico,
>>> maybe you can describe your tool set a little
>>> exodus is supported by moab; what is parallel exodus?
>>>
>>> If your model is described in a series of files, we also have parallel
>>> merge tool, that can be used to stitch models in parallel
>>> (in short, each task loads a file in serial, which is a part in a
>>> partition, then parallel merge can be used to have a global view / access,
>>> identify shared entities and enable ghosting; this assumes that the parts
>>> are "conforming" and not overlapping, as a geometric tolerance is used to
>>> identify common vertices)
>>>
>>> what  "standard" do you need ? Do you have an example ?
>>>
>>> Best Regards,
>>> Iulian
>>>
>>> ------------------------------
>>> *From:* Nico Schlömer [nico.schloemer at gmail.com]
>>> *Sent:* Saturday, October 31, 2015 9:08 AM
>>>
>>> *To:* Grindeanu, Iulian R.; moab-dev at mcs.anl.gov
>>> *Subject:* Re: [MOAB-dev] MOAB insights?
>>> Thanks everyone!
>>>
>>> I believe that right now, I cannot efficiently use MOAB yet. We really
>>> need to be able to read from standardized file formats like XDMF, VTU,
>>> Exodus. This is what the tool set is composed around, and it'd probably
>>> much work to get it right for MOAB's custom HDF5-thing.
>>>
>>> That said, I'd be happy to help out with extending MOAB in these
>>> directions. Perhaps after the release, we can arrange a plan.
>>>
>>> Cheers,
>>> Nico
>>>
>>> On Fri, Oct 30, 2015 at 12:40 AM Grindeanu, Iulian R. <
>>> iulian at mcs.anl.gov> wrote:
>>>
>>>> Hi Nico,
>>>> Sorry I missed your message
>>>> I modified one of the examples to construct all edges and faces, and
>>>> output them in some files
>>>>
>>>> after compiling it, you can launch it with
>>>>
>>>> ./HelloMOAB
>>>>
>>>> or
>>>> ./HelloMOAB <other_file>
>>>>
>>>> other_file can be any file that can be loaded in MOAB, in serial (for
>>>> example, a gmsh file)
>>>>
>>>> for parallel IO, you can look at HelloParMOAB example, or tests in
>>>> test/parallel
>>>>
>>>>
>>>> There is a list of examples on doxygen page, with more links on how is
>>>> data accessed.
>>>> http://ftp.mcs.anl.gov/pub/fathom/moab-docs/examples.html
>>>>
>>>>
>>>>
>>>> Iulian
>>>>
>>>> ------------------------------
>>>> *From:* Nico Schlömer [nico.schloemer at gmail.com]
>>>> *Sent:* Thursday, October 29, 2015 3:37 PM
>>>>
>>>> *To:* Grindeanu, Iulian R.; moab-dev at mcs.anl.gov
>>>> *Subject:* Re: [MOAB-dev] MOAB insights?
>>>> Absolutely!
>>>>
>>>> I'm interested to see
>>>>  * how I/O works,
>>>>  * how edges/faces arecreated,
>>>>  * how relationships are queried (Which cells does this face border on?
>>>> Which nodes does this cell have? etc)
>>>>
>>>> If there's an example in the sources, I'd be more than happy to look at
>>>> that, too, of course.
>>>>
>>>> Cheers,
>>>> Nico
>>>>
>>>>
>>>> On Thu, Oct 29, 2015 at 9:19 PM Grindeanu, Iulian R. <
>>>> iulian at mcs.anl.gov> wrote:
>>>>
>>>>>
>>>>> ------------------------------
>>>>> *From:* Nico Schlömer [nico.schloemer at gmail.com]
>>>>> *Sent:* Thursday, October 29, 2015 12:45 PM
>>>>> *To:* Grindeanu, Iulian R.; moab-dev at mcs.anl.gov
>>>>> *Subject:* Re: [MOAB-dev] MOAB insights?
>>>>>
>>>>> > what means long for you, and what is the size of the mesh on one
>>>>> > rank? what is a cell for you? a polyhedra or a
>>>>> > tet/hex/prism/quad/triangle?
>>>>>
>>>>> For me, long means (much) longer than the actual (linear) solver in
>>>>> the end. On a test cube [1] of 140k tets and 27k nodes, creating edges
>>>>> takes about one minutes, faces about two (on one core that is). The linear
>>>>> solver in the end takes about seven seconds.
>>>>>
>>>>> hmmm, that is too long, indeed.
>>>>>
>>>>> For moab, creating the edges and/or faces for that size of a mesh is
>>>>> on the order  of seconds, on a laptop
>>>>>
>>>>> I will write a small example if you are interested
>>>>>
>>>>>
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