[petsc-dev] Checkpoint-restart with DMPlex objects

Tue Dec 18 05:54:56 CST 2018

On 17 Dec 2018, at 20:36, Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:

On Mon, Dec 17, 2018 at 12:11 PM Lawrence Mitchell <wence at gmx.li<mailto:wence at gmx.li>> wrote:

> On 17 Dec 2018, at 11:56, Hapla Vaclav <vaclav.hapla at erdw.ethz.ch<mailto:vaclav.hapla at erdw.ethz.ch>> wrote:
>
> Matt, great that your reminded this email. I actually completely missed it that time.
>
>> On 14 Dec 2018, at 19:54, Matthew Knepley via petsc-dev <petsc-dev at mcs.anl.gov<mailto:petsc-dev at mcs.anl.gov>> wrote:

[...]

>> I would like:
>>
>> - To be able to dump the DMPlex, and fields, on N processes
>>
>> I think the current HDF5 does what you want.
>>
>> - To be able to load the DMPlex, and fields, on P processes.  In the first instance, to get things going, I am happy if P=1.
>>
>> I think this also works with arbitrary P, although the testing can be described as extremely thin.
>
> I think we need to be much more precise here. First off, there are now two HDF5 formats:
> 1) PETSC_VIEWER_HDF5_PETSC - store Plex graph serialization
> 2) PETSC_VIEWER_HDF5_XDMF - store XDMF-compatible representation of vertices and cells
> 3) PETSC_VIEWER_HDF5_VIZ slightly extends 2) with some stuff for visualization, you perhaps understand it better
>
> PETSC_VIEWER_DEFAULT/PETSC_VIEWER_NATIVE mean store all three above. I think what Lawrence calls Native should be 1).
>
> The format 1) is currently written in parallel but loaded sequentially
> https://bitbucket.org/petsc/petsc/src/fbb1886742ac2bbe3b4d1df09bff9724d3fee060/src/dm/impls/plex/plexhdf5.c#lines-834
>
> I don't understand, how it can work correctly for a distributed mesh while the Point SF (connecting partitions) is not stored FWICS. I think there's even no PetscSFView_HDF5(). I will check it more deeply soon.
>
> The format 2) is for which I implemented parallel DMLoad().
> Unfortunately, I can't declare it bulletproof until we declare parallel DMPlexInterpolate() as 100% working. I did quite some work towards it in
> https://bitbucket.org/petsc/petsc/pull-requests/1227/dmplexintepolate-fix-orientation-of-faces/
> but as stated in the PR summary, there are still some examples failing because of the wrong Point SF which is partly fixed in knepley/fix-plex-interpolate-sf but it seems it's not yet finished. Matt, is there any chance you could look at it at some point in near future?
>
> I think for Lawrence's purposes, 2) can be used to read the initial mesh file but for checkpointing 1) seems to be better ATM because it dumps everything including interpolated edges & faces, labels and perhaps some more additional information.

OK, so I guess there are two different things going on here:

1. Store the data you need to reconstruct a DMPlex

2. Store the data you need to have a DMPlex viewable via XDMF.

3. Store the data you need to reconstruct a DMPlex AND have it viewable via XDMF.

For checkpointing only purposes, I only really need 1; for viz purposes, one only needs 2; ideally, one would not separate viz and checkpointing files if there is sufficient overlap of data (I think there is), which needs 3.

> I will nevertheless keep on working to improve 2) so that it can store edges & faces & labels in the XDMF-compatible way.
>
>>
>> For dumping, I think I can do DMView(dm) in PETSc "native" format, and that will write out the topology in a global numbering.
>>
>> I would use HDF5.
>>
>> For the field coefficients, I can just VecView(vec).  But there does not appear to be any way of saving the Section so that I can actually attach those coefficients to points in the mesh.
>>
>> Hmm, I will check this right now. If it does not exist, I will write it.
>
> No, it certainly doesn't exist. There is only ASCII view implemented.
>
>>
>> I can do PetscSectionCreateGlobalSection(section), so that I have a the global numbering for offsets, but presumably for the point numbering, I need to convert the local chart into global point numbers using DMPlexCreatePointNumbering?
>>
>> No, all Sections use local points. We do not use global point numbers anywhere in Plex.
>
> True. DMPlex is partition-wise sequential. The only thing which connects the submeshes is the Point SF.

OK, so I think I misunderstood what the dump format looks like then. For parallel store/load cycle when I go from N to P processes what must I do?

If I understand correctly the dump on N processes contains:

For each process, in process-local numbering

 - The DMPlex topology on that process

Now, given that the only thing that connects these local pieces of the DM together is the point SF, as Vaclav says, it must be the case that a reloadable dump file contains that information.

No, the dump contains a completely consistent serial DM. Now I remember why parallel load is not implemented :)
We demand that the dump look identical from any number of procs for all PETSc stuff. Thus we get a global renumbering
and dump with that for all things.

Oh I see. I misunderstood this. More clear to me know - DMPlexCreatePointNumbering() is employed in DMPlexView_HDF5_Internal().

Now, when we load in parallel, we need to use the new parallel loading from Michael.

What exactly do you mean?
If I remember well Michael implemented a parallel MED loader and it uses DMPlexCreateFromCellListParallel() just as my XDMF-HDF5 reader does.
Is this function what you mean by "the new parallel loading"?

Thanks

Vaclav

I have not yet written that, but it should
be straightforward :) So the below is not really right. We need to call parallel load for the topology. Then we need code that
loads the labels and uses the migration SF to redistribute them, but I think that code already exists for redistribution, so we
just hijack it.

  Matt

OK, so to dump a field so that we can reload it we must need:

- topology (in local numbering)
- point SF (connecting the local pieces of the topology together)
- Vector (dofs), presumably in local layout to make things easier
- Section describing the vector layout (local numbering)

So to load, I do:

1. load and distribute topology, and construct new point SF (this presumably gives me a "migration SF" that maps from old points to new points

2. Broadcast the Section over migration SF so that we know how many dofs belong to each point in the new topology

3. Broadcast the Vec over the migration SF to get the dofs to the right place.

Whenever I think of this on paper it seems "easy", but then I occasionally try and sit down and do it and immediately get lost, so I am normally missing something.

What am I missing this time?

Lawrence

--
What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knepley/>

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