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

Chronological Thread 
  • From: Jozsef Bakosi <jbakosi AT>
  • To: "Adelmann Andreas (PSI)" <andreas.adelmann AT>
  • Cc: "h5part AT" <h5part AT>, "Gsell Achim (PSI)" <achim.gsell AT>
  • Subject: Re: [H5part] Extending H5Part to particles + changing-topology tetrahedron meshes
  • Date: Tue, 25 Oct 2016 13:50:05 -0600

Hi Andy,

Yes, I have seen h5hut but since at the time I was only interested in
I just used H5Part. However, now I would be interested in it more and looked
it again and saw that there is capability in there to save unstructured meshes
too. This would be great, if it worked in parallel. According to the web site
does not yet work in parallel. I also have not found documentation on the API
for H5hut. I would be interested in exploring how much work is missing to make
it fulfill the requirements I am aiming for.

I am available for live conversation, possibly via skype, google hangout, or
phone. Please let me know if someone is interested in pursuing this and want
have a live discussion on it.

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

On 10.25.2016 19:15, Adelmann Andreas (PSI) wrote:
> Dear Jozef Achim Gsell the main developer of H5Part (we call it now
> H5hut) and can definitively
> explain you more in detail. We have in H5hut the capability to store
> block structured fields (scalar and vector)
> that is working for your points 1 … 3, not sure about 4. We are also
> working on and off on unstructured grids. The latter does not have
> priority on our side but (==off)
> but definitely you are very welcome to join forces.
> Sure Achim can give more details. Maybe we should have a Skype (or
> hangouts) meeting to discuss details.
> Cheers Andreas
> ------
> Dr. sc. math. Andreas (Andy) Adelmann
> Staff Scientist
> Paul Scherrer Institut WBBA/219 CH-5232 Villigen PSI
> Phone Office: xx41 56 310 42 33 Fax: xx41 56 310 31 91
> Phone Home: xx41 62 891 91 44
> -------------------------------------------------------
> Friday: ETH CAB F37 +41 44 632 75 22
> ============================================
> The more exotic, the more abstract the knowledge,
> the more profound will be its consequences.
> Leon Lederman
> ============================================
> On 24 Oct 2016, at 18:22, Jozsef Bakosi <[1]jbakosi AT> wrote:
> 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 data
> 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 steps.
> I have been using ExodusII ([2]
> for this
> purpose, which works okay, satisfying (1) and (2), but not (3), and (4)
> can only
> be fulfilled with separate files per time step. Considering that
> ExodusII saves
> a single file per parallel rank already, having to save a new file per
> time step
> 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 of
> 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
> particles).
> My questions are:
> 1. Does anyone know of an existing library that satisfies all the above
> requirements?
> 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 be
> 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.
> Thanks,
> Jozsef
> --
> Jozsef Bakosi
> Computational Physics and Algorithms (CCS-2)
> MS D413, Los Alamos National Laboratory
> Los Alamos, NM 87545, USA
> email: [3]jbakosi AT
> phone: 505-665-0950
> fax: 505-665-4972
> References
> 1. mailto:jbakosi AT
> 2.
> 3. mailto:jbakosi AT

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