[Paraview-developers] H5Part and H5Hut

[Amit Goel]

Dear John

Few months ago I had asked you the following two questions… returning to those two questions again:

First the questions:

1. Creating H5Part Files: Which version of H5Part should I use for creating “parallel-hdf5 based H5Part” files - H5Hut 1.99.13 or H5Part 1.6.6 ? Is this code on git somewhere ?

2. Reading H5Part Files in PV: As I understand from your email, I shall try pv-4.4 branch after I have created them.

Now the update:

I was able to work with h5part from http://vis.lbl.gov/Research/H5Part/, however I had to extend and fix it with bugs and **needed** enhancements such as support for unsigned integers. I am using H5Part for storing particle data and H5Block for storing cell-wise statistics, i.e. stats of each cell of my grid, for every step.

Now the questions:

1. I am still at dilemma where is the latest H5Part/H5Hut and who is hosting it ? I wish to contribute my work back, it may or may not be accepted… thats another story, so it would be great if someone on this list can shed a light on who is hosting latest and greatest H5Part/H5Hut repository. The emails to H5Hut people from this site have gone nowhere: https://amas.psi.ch/H5hut/. As a lot of people on this list use H5Part/H5Hut heavily so someone must be aware of the originators.

Second is informational only:

2. H5Part files that I produced worked in Paraview out of box, on Mac and On CentOS : Paraview from repository, no need to compile. However of course next step would be to compile with Parallel HDF/H5Part. Paraview is just awesome product.

Since H5Part is part of official compiled binary distribution of paraview so I hope at least someone would know the ground truth repository for H5Part :-).

Regards

Amit


On Sep 9, 2015, at 7:30 AM, Biddiscombe, John A. <biddisco at cscs.ch<mailto:biddisco at cscs.ch>> wrote:

Amit

The only requirement for H5Part files is that the x,y,z arrays and field arrays are in the correctly named groups for each timestep inside the hdf5 file. the h5part library is just a very thin wrapper around hdf5 so you can write h5part files with any ode that can write hdf5, including python etc. just the group/dataset names that matter. all h5part does is set this up for you and provide a simple api for the parallel regions.

I have not used h5hut, but h5part version anything should write out data you can read. I would imagine that h5hut will also work if you tell it to write particle data and not volume fields.

inside pv-meshless there is a vtkH5PartWriter that you can try if your data is in vtk compatible form already.

the pv-4.4 branch of pv-meshless was used recently, so it should work.

JB

From: Amit Goel [mailto:Amit.Goel at ucf.edu]
Sent: 09 September 2015 12:18
To: Biddiscombe, John A.
Cc: Berk Geveci; paraview-developers at paraview.org<mailto:paraview-developers at paraview.org>
Subject: Re: [Paraview-developers] H5Part and H5Hut

Hi John

Thanks a lot for your kind response. There are two parts to my question:

1. Creating H5Part Files: Which version of H5Part should I use for creating “parallel-hdf5 based H5Part” files - H5Hut 1.99.13 or H5Part 1.6.6 ? Is this code on git somewhere ?

2. Reading H5Part Files in PV: As I understand from your email, I shall try pv-4.4 branch after I have created them.

Looking forward for your kind advice on point 1 mentioned above.

Regards

amit



On Sep 9, 2015, at 2:07 AM, Biddiscombe, John A. <biddisco at cscs.ch<mailto:biddisco at cscs.ch>> wrote:

Amit

the version of the reader that I maintain is kept here
https://github.com/biddisco/pv-meshless

It has a number of extensions and options that you will want to ignore.

You will see that the pv-4.4 branch was was tested against the paraview master branch a few months ago. if it doesn’t compile against or work with the latest master, please let me know as I only work on viz/paraview stuff part of my time, so I don’t get to maintain/update this as much as I’d like.

Note:
For parallel partitioning of particle data, you will want the pv-zoltan plugin
https://github.com/biddisco/pv-zoltan

JB

From: Amit Goel [mailto:Amit.Goel at ucf.edu]
Sent: 08 September 2015 23:37
To: Berk Geveci
Cc: Biddiscombe, John A.; paraview-developers at paraview.org<mailto:paraview-developers at paraview.org>
Subject: Re: [Paraview-developers] H5Part and H5Hut

Dear Berk

Thanks a lot for your response.

I was able to open H5part files, albeit with warnings in H5Part. Further, there seems to be multiple versions of H5Part floating around:

H5Hut 1.99.13
H5Part 1.6.6

Although the user manuals on H5Part and H5hut website describe the same structure for H5Part files, but seems like codes did go through a major restructuring. I also looked at code of Paraview H5PartReader plugin but was not able to find which version of H5Part code was embedded in reader. Further the H5Part code files itself have been made part of reader, thus plugin doesnt rely on separately present H5Part libraries.

I dont mind digging in and updating the H5Part Plugin and submit patches, but only if I knew where to find the latest stable version of H5Part itself. :-)

Having said that, I am now trying Gadget HDF5 format as my ultimate goal is to save my particle simulations in some HDF5 format and then render through Paraview.

Are there any other particle formats based on HDF5 that Paraview supports ?

Regards

Amit


On Sep 8, 2015, at 3:36 PM, Berk Geveci <berk.geveci at kitware.com<mailto:berk.geveci at kitware.com>> wrote:

Hi Amit,

I CC'ed John who is the original author of that plugin. Hopefully, he can answer your question.
Maybe there is an updated version of the reader that handles a newer format. We would be
happy to update the plugin if there is a new version of the reader.

It does not look like H5hut is available so I can't speak to it. We are not currently doing any
work on the H5Part reader. As far as I know, we haven't received any user requests asking us
to update or fix it so far.

Best,
-berk

On Fri, Sep 4, 2015 at 4:09 PM, Amit Goel <Amit.Goel at ucf.edu<mailto:Amit.Goel at ucf.edu>> wrote:
Hi

I am new to this list. Please let me know if anyone knows the status of H5Part plugin ? My specific questions are:

1. How to use it exactly. I tried opening a Cavity sample file from pvmeshless site. But it returns errors and warnings.

2. What is status of H5hut and H5Part plugins in forthcoming versions of Paraview ?

Regards

— amit

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