Merging a partitioned ascent blueprint extract to single partition

[mlohry]

I have a blueprint hdf5 extract made using ascent in MPI which writes partitioned HDF5 of the pattern

mesh.root
mesh/
mesh/domain_000.hdf5
mesh/domain_001.hdf5
...
mesh/domain_XYZ.hdf5

and I would like to merge these into a single domain. Reading the .root file like so:

  auto h5_id = conduit::relay::io::hdf5_open_file_for_read("mesh.root");
  conduit::Node node;
  conduit::relay::io::hdf5_read(h5_id, node);
  conduit::relay::io::hdf5_close_file(h5_id);
  node.print();

shows field names and partition maps as expected. Then I try to merge these into one partition:

  conduit::Node partition_options;
  partition_options["target"] = 1;
  conduit::Node merged_mesh;
 // conduit::blueprint::mesh::partition(node, partition_options, merged_mesh);
 // conduit::Error Cannot access non-existent child "topologies" from Node(blueprint_index),
 // needs to be passed a subnode apparently.  
  conduit::blueprint::mesh::partition(node["blueprint_index/mesh"], partition_options, merged_mesh);

and it fails with

terminate called after throwing an instance of 'conduit::Error'
message:
Cannot access non-existent child "elements" from Node(blueprint_index/mesh/topologies/topo)

It seems to not be parsing the subfolder HDF5 files so it can't see the "elements" of the individual domain HDF5 files. What am I doing wrong here?

If I open one of the individual HDF5 files directly, I see the "real" topology of that domain as expected, so conceptually I could manually load all these partitions independently and merge them.

[cyrush]

Hi @mlohry here is what you need:

You can load a mesh using the info from the root file and all other needed data files using the method:

conduit::relay::io::blueprint::read_mesh

https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#loading-meshes-from-files

conduit::relay::io::blueprint::read_mesh(const std::string &root_file_path,
                                         conduit::Node &mesh);

After this, the node passed as mesh will contain a verified blueprint mesh that you can feed to re-partition.

[cyrush]

For more context, the root file has metadata the reflects the larger structure of the domain-decomposed mesh and that info points to locations in other hdf5 files. The read_mesh method handles all of the bookkeeping to read things back in.

There is also a mpi version that allows you to read the mesh, but have the domains distributed across MPI tasks.

[mlohry]

Thank you @cyrush , got it.

[mlohry]

@cyrush , got that aspect working, but does this partition merging know about ascent_ghosts? I'm getting holes in the mesh along partition lines when merging to one partition. The partitioned extract is the result of giving blueprint+ascent each partition in 0-based local ordering.