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[H5part] Extending H5Part to particles + changing-topology tetrahedron meshes

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  • From: Jozsef Bakosi <jbakosi AT>
  • To: h5part AT
  • Subject: [H5part] Extending H5Part to particles + changing-topology tetrahedron meshes
  • Date: Mon, 24 Oct 2016 10:22:59 -0600

Hi folks,

I realize H5Part is for particles, but I wonder how much effort the following
would take.

I have been looking for a library that is capable of reading and writing large
data sets (1) in a portable fashion, e.g., using NetCDF and/or HDF5, (2) in
parallel, and (3) preferably to and from a single file. Geometrically, the
sets to be stored are defined at nodes of a tetrahedra-only unstructured mesh
the mesh itself (node coordinates and element connectivity). Additionally, (4)
the mesh (number of nodes + connectivity) may change over different time

I have been using ExodusII ( for this
purpose, which works okay, satisfying (1) and (2), but not (3), and (4) can
be fulfilled with separate files per time step. Considering that ExodusII
a single file per parallel rank already, having to save a new file per time
will not scale for large data and many processors.

I'm also using H5Part to save particles and now I'm thinking that what H5Part
does already might be pretty close to what I need: it can already save a set
point (particle) coordinates + associated field data whose numbers can change
over time steps. This satisfies (1), (2), and (3) while (4) could be satisfied
by adding the capability to save the mesh connectivity, a set of integers
connecting the point IDs (while the points would be saved similarly to

My questions are:

1. Does anyone know of an existing library that satisfies all the above

2. How much work do you think it would be to add the mesh topology information
to H5Part? If it isn't too bad, I would like to contribute this so H5Part can
used to save meshes, field data associated to mesh nodes, as well as the
existing particles and field data associated to particles. I would also extend
the ParaView H5Part reader plugin.

Any thoughts and advice are appreciated.

Jozsef Bakosi
Computational Physics and Algorithms (CCS-2)
MS D413, Los Alamos National Laboratory
Los Alamos, NM 87545, USA
email: jbakosi AT
phone: 505-665-0950
fax: 505-665-4972

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