[MOAB-dev] h5m with data

Tue Nov 10 06:55:28 CST 2015

MOAB already provides an array of formats that can be inter-converted
from/to h5m. We should see if there are other formats provided by
meshio that may be useful to integrate directly into MOAB so that we
can increase the extent of I/O formats.

The Paraview plugin is there specifically to visualize a h5m file
directly. You can always convert h5m->vtk and read that without the
extension but you end up losing something during conversion due to the
nature/description of file formats.

Vijay

On Tue, Nov 10, 2015 at 6:06 AM, Nico Schlömer <nico.schloemer at gmail.com> wrote:
> Sounds good!
> For the meantime, I've created MeshIO [1,2] to convert between various mesh
> file formats, including H5M. This makes installing a ParaView extension
> unnecessary, at least if you can afford to copy your mesh into another
> format. I'll put it to the test with one of my applications this week and
> see if I finally get to read actual data with MAOB. :)
>
> Cheers,
> Nico
>
> [1] https://pypi.python.org/pypi/meshio
> [2] https://github.com/nschloe/meshio
>
> On Mon, Nov 9, 2015 at 1:32 PM Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>
>> > Something that would have helped me avoid this extra work is MOAB
>> > offering
>> > first-class support for an established standard format (Exodus, VTK,
>> > XDMF
>> > come to mind).
>>
>> Nico, we will be happy to work with you to add support for more
>> standard formats. In the realm of parallel I/O, there are very few
>> solutions that scale well to beyond 10K processors and this is an
>> active area of improvement in MOAB. There is already support for
>> legacy VTK and we are planning to add readers/writers for VTK-m in the
>> next year. Perhaps if we converge on your needs better, we can choose
>> either Nemesis or XDMF based formats as an alternate format too.
>>
>> Vijay
>>
>> On Mon, Nov 9, 2015 at 4:29 AM, Nico Schlömer <nico.schloemer at gmail.com>
>> wrote:
>> > Thanks everyone; I'll plow my way through the format, trying to
>> > integrate it
>> > better with the conversion tools I have at hand. Once I'm through that I
>> > think I'll be able to integrate it with my application too.
>> >
>> > Something that would have helped me avoid this extra work is MOAB
>> > offering
>> > first-class support for an established standard format (Exodus, VTK,
>> > XDMF
>> > come to mind).
>> >
>> > Anyhow, I'll probably ask one or two more questions about the format
>> > here,
>> > so your help is still appreciated! :)
>> >
>> > --Nico
>> >
>> > On Mon, Nov 9, 2015 at 5:55 AM Vijay S. Mahadevan <vijay.m at gmail.com>
>> > wrote:
>> >>
>> >> Nico, as Patrick mentioned, Tags are the abstract ways to represent,
>> >> serialize and manipulate data associated with entities in a MOAB mesh.
>> >> Tags can be associated directly with entities such as vertex or
>> >> element, or you could choose to create sets of entities and associate
>> >> data to these sets. So based on this degree of representation, we have
>> >> the terminology that a tag can be dense or sparse. This is just an
>> >> internal way to store these tags to optimize memory layout and does
>> >> slightly affect how data is serialized/read-back to/from h5m files.
>> >>
>> >> Now in terms of usage, just get the tag handle, and you can either
>> >> read or write to the tag by using tag_get_data and tag_set_data
>> >> respectively.
>> >>
>> >> The SetsNTags [1], VisTags [2] examples show how to read the data
>> >> stored in h5m. You can use set_tag_data to write this a priori. If
>> >> needed, we can also create a simplistic example to create/manipulate
>> >> tag data on a mesh, but I think this may be overkill. Let me know if
>> >> this would help though.
>> >>
>> >> Vijay
>> >>
>> >> [1]
>> >> ftp://ftp.mcs.anl.gov/pub/fathom/moab-docs/SetsNTags_8cpp-example.html
>> >> [2]
>> >> ftp://ftp.mcs.anl.gov/pub/fathom/moab-docs/VisTags_8cpp-example.html
>> >>
>> >> On Sun, Nov 8, 2015 at 8:32 PM, Patrick Shriwise <shriwise at wisc.edu>
>> >> wrote:
>> >> > Hey Nico,
>> >> >
>> >> > Ok. There doesn't appear to be a great example for applying data.
>> >> > Applying
>> >> > data works in a very similar way to the way you retrieve tagged data,
>> >> > using
>> >> > tag_set_data with a Tag which can be created for a certain type of
>> >> > data
>> >> > with
>> >> > a given name by calling tag_get_handle with the MBCREAT option at the
>> >> > end.
>> >> > I'd like to be clear that you can apply/retrieve data from MOAB
>> >> > Entities
>> >> > or
>> >> > MOAB EntitySets. So you can either apply data directly to entities
>> >> > like
>> >> > vertices or you can group them together in a set and apply data to
>> >> > that
>> >> > set
>> >> > instead. For the purpose you're indicating, it sounds like it'd be
>> >> > best
>> >> > to
>> >> > apply the data directly to the vertices.
>> >> >
>> >> > Sample code for creating a MOAB Tag:
>> >> >   Tag name_tag;
>> >> >   rval = mdbImpl->tag_get_handle(NAME_TAG_NAME, NAME_TAG_SIZE,
>> >> > MB_TYPE_OPAQUE,
>> >> >                                  name_tag, MB_TAG_SPARSE |
>> >> > MB_TAG_CREAT);
>> >> > Cheers,
>> >> >
>> >> > Patrick C. Shriwise
>> >> > Research Fellow
>> >> > University of Wisconsin - Madison
>> >> > Engineering Research Building - Rm. 428
>> >> > 1500 Engineering Drive
>> >> > Madison, WI 53706
>> >> > (608) 446-8173
>> >> >
>> >> > On 11/08/15 21:01, Nico Schlömer wrote:
>> >> >
>> >> > In both ways, actually. I need to build h5m files from data and I
>> >> > need
>> >> > to
>> >> > extract data from h5m meshes.
>> >> > With [1], I'm digging my way through understanding the sets group
>> >> > now.
>> >> >
>> >> > --Nico
>> >> >
>> >> > [1] https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB/h5m
>> >> >
>> >> > On Mon, Nov 9, 2015 at 2:53 AM Patrick Shriwise <shriwise at wisc.edu>
>> >> > wrote:
>> >> >>
>> >> >> Hi Nico,
>> >> >>
>> >> >> I see. I may have misunderstood your problem. It seems you're trying
>> >> >> to
>> >> >> apply data to the mesh. Is that right?
>> >> >>
>> >> >>
>> >> >> Cheers,
>> >> >>
>> >> >> Patrick C. Shriwise
>> >> >> Research Fellow
>> >> >> University of Wisconsin - Madison
>> >> >> Engineering Research Building - Rm. 428
>> >> >> 1500 Engineering Drive
>> >> >> Madison, WI 53706
>> >> >> (608) 446-8173
>> >> >>
>> >> >> On 11/08/15 20:03, Nico Schlömer wrote:
>> >> >>
>> >> >> Thanks Patrick for your reply.
>> >> >>
>> >> >> I'm still having problems where data should be stores. In a h5m
>> >> >> file, I
>> >> >> see tags, I see sets with tags in them, and it seems they are
>> >> >> somehow
>> >> >> related, but I don't know where and how to put the actual data. I
>> >> >> would
>> >> >> help
>> >> >> to see a file with some mesh and a custom data element in it, e.g.,
>> >> >> an
>> >> >> array
>> >> >> of values associated with the vertices.
>> >> >>
>> >> >> Cheers,
>> >> >> Nico
>> >> >>
>> >> >> On Sun, Nov 8, 2015 at 9:20 PM Patrick Shriwise <shriwise at wisc.edu>
>> >> >> wrote:
>> >> >>>
>> >> >>> Hi Nico,
>> >> >>>
>> >> >>> The vertex data should be stored in MOAB tags. You can access these
>> >> >>> tags
>> >> >>> via their name. There is a set of conventions for the tag names in
>> >> >>> an
>> >> >>> Exodus
>> >> >>> file (here I think). However, if the tag has a custom name and
>> >> >>> isn't
>> >> >>> recognized by the Exodus reader, then the data might not be read in
>> >> >>> from the
>> >> >>> Exodus file and as a result won't be saved into the .h5m. Do you
>> >> >>> have
>> >> >>> an
>> >> >>> idea of what the tag name might be for your data?
>> >> >>>
>> >> >>> There's also a good example here of how to access the tag data on
>> >> >>> an
>> >> >>> entity. The example I linked you to accesses EntitySets rather than
>> >> >>> Entities, but they work the same way.
>> >> >>>
>> >> >>> If you think the data might be in the .h5m, you can use
>> >> >>> tag_get_tags_on_entity to get all of the tags on a vertex and then
>> >> >>> check for
>> >> >>> the tag data you're looking for. An easier way of doing this in the
>> >> >>> cmd line
>> >> >>> is by using mbsize -t <your_file>.h5m to print out the count by
>> >> >>> tag.
>> >> >>>
>> >> >>> Hope this helps!
>> >> >>>
>> >> >>> Cheers,
>> >> >>>
>> >> >>> Patrick C. Shriwise
>> >> >>> Research Fellow
>> >> >>> University of Wisconsin - Madison
>> >> >>> Engineering Research Building - Rm. 428
>> >> >>> 1500 Engineering Drive
>> >> >>> Madison, WI 53706
>> >> >>> (608) 446-8173
>> >> >>>
>> >> >>> On 11/08/15 13:43, Nico Schlömer wrote:
>> >> >>>
>> >> >>> Hi everyone,
>> >> >>>
>> >> >>> I have an Exodus file with vertex data in it (i.e., "a function"
>> >> >>> defined
>> >> >>> on the vertices). When converting this file to h5m, where does the
>> >> >>> vertex
>> >> >>> data go? And how to I retrieve the data after having it read with
>> >> >>> `load_file()`?
>> >> >>>
>> >> >>> Cheers,
>> >> >>> Nico
>> >> >>>
>> >> >>>
>> >> >>
>> >> >