[MOAB-dev] MOAB insights?

Sat Oct 31 11:34:05 CDT 2015

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
>>>>
>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/moab-dev/attachments/20151031/345e7fe3/attachment.html>