[MOAB-dev] MOAB insights?

Sun Nov 1 13:53:40 CST 2015

Thanks Tim!

I've fixed a small index bug and it appear to work now.

Cheers,
Nico

On Sun, Nov 1, 2015 at 8:52 PM Timothy Tautges <
timothy.tautges at cd-adapco.com> wrote:

> Call get_adjacencies with the book flag true, requesting all faces from
> elements then all edge's from elems. There's an equivalent itaps call to
> request a full mesh but I forget what it is.
> On Nov 1, 2015 1:09 PM, "Nico Schlömer" <nico.schloemer at gmail.com> wrote:
>
>> 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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