[MOAB-dev] MOAB insights?

Sun Nov 1 14:18:45 CST 2015

Write the partition I'd as a cell variable (in mbpart there's an option for
that) and that will go through to VTK or exo.
On Nov 1, 2015 2:08 PM, "Nico Schlömer" <nico.schloemer at gmail.com> wrote:

> I can convert from VT*, Exodus to h5m now, so I'll probably go ahead and
> see if I can integrate MOAB into our test suite. The serial case seems
> pretty doable, for parallel I/O I'll probably need a little longer.
>
> Btw, is there a way to visualize the partition in ParaView without using
> the plugin? I thought of converting the resulting h5m into VTK, but a MOAB
> bug [1] keeps me from doing so.
>
> Cheers,
> Nico
>
>
> [1]
> https://bitbucket.org/fathomteam/moab/issues/23/mbconvert-cell-array-global_id-with-1
>
> On Sun, Nov 1, 2015 at 8:54 PM Timothy Tautges <
> timothy.tautges at cd-adapco.com> wrote:
>
>> And, you know moab has an exo writer, right? Should only need to add the
>> nemesis records to make that parallel.
>> On Nov 1, 2015 1:52 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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