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Dear John
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<div class="">Few months ago I had asked you the following two questions… returning to those two questions again:</div>
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<div class="">First the questions:</div>
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<div class="">1. <u class="">Creating H5Part Files:</u> Which version of H5Part should I use for creating “parallel-hdf5 based H5Part” files - <span class="" style="font-family: 'Times New Roman', serif; font-size: 12pt;">H5Hut 1.99.13 or </span><span class="" style="font-family: 'Times New Roman', serif; font-size: 12pt;">H5Part
1.6.6 ? Is this code on git somewhere ?</span></div>
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</font></div>
<div class=""><font face="Times New Roman, serif" size="3" class="">2. <u class="">Reading H5Part Files in PV</u>: As I understand from your email, I shall try pv-4.4 branch after I have created them.</font></div>
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</font></div>
<div class=""><font face="Times New Roman, serif" size="3" class="">Now the update:</font></div>
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</font></div>
<div class=""><font face="Times New Roman, serif" size="3" class="">I was able to work with h5part from </font><a href="http://vis.lbl.gov/Research/H5Part/" class="">http://vis.lbl.gov/Research/H5Part/</a>, 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.</div>
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<div class="">Now the questions:</div>
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<div class="">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, <b class="">so it would be great if someone on this list can shed a light
on who is hosting latest and greatest H5Part/H5Hut repository</b>. The emails to H5Hut people from this site have gone nowhere: <a href="https://amas.psi.ch/H5hut/" class="">https://amas.psi.ch/H5hut/</a>. As a lot of people on this list use H5Part/H5Hut heavily
so someone must be aware of the originators.</div>
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<div class="">Second is informational only:</div>
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</div>
<div class="">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.</div>
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<div class="">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 :-).</div>
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<div class="">Regards</div>
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<div class="">Amit</div>
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<blockquote type="cite" class="">
<div class="">On Sep 9, 2015, at 7:30 AM, Biddiscombe, John A. <<a href="mailto:biddisco@cscs.ch" class="">biddisco@cscs.ch</a>> wrote:</div>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">Amit<o:p class=""></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">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.<o:p class=""></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">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.<o:p class=""></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">inside pv-meshless there is a vtkH5PartWriter that you can try if your data is in vtk compatible form already.<o:p class=""></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">the pv-4.4 branch of pv-meshless was used recently, so it should work.<o:p class=""></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">JB<o:p class=""></o:p></span></p>
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<p class="MsoNormal"><b class=""><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" class="">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" class=""> Amit Goel [<a href="mailto:Amit.Goel@ucf.edu" class="">mailto:Amit.Goel@ucf.edu</a>]
<br class="">
<b class="">Sent:</b> 09 September 2015 12:18<br class="">
<b class="">To:</b> Biddiscombe, John A.<br class="">
<b class="">Cc:</b> Berk Geveci; <a href="mailto:paraview-developers@paraview.org" class="">
paraview-developers@paraview.org</a><br class="">
<b class="">Subject:</b> Re: [Paraview-developers] H5Part and H5Hut<o:p class=""></o:p></span></p>
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<p class="MsoNormal"><o:p class=""> </o:p></p>
<p class="MsoNormal">Hi John <o:p class=""></o:p></p>
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<p class="MsoNormal">Thanks a lot for your kind response. There are two parts to my question:<o:p class=""></o:p></p>
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<p class="MsoNormal"><o:p class=""> </o:p></p>
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<p class="MsoNormal">1. <u class="">Creating H5Part Files:</u> 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 ?<o:p class=""></o:p></p>
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<p class="MsoNormal"><o:p class=""> </o:p></p>
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<p class="MsoNormal">2. <u class="">Reading H5Part Files in PV</u>: As I understand from your email, I shall try pv-4.4 branch after I have created them.<o:p class=""></o:p></p>
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<p class="MsoNormal"><o:p class=""> </o:p></p>
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<p class="MsoNormal">Looking forward for your kind advice on point 1 mentioned above.<o:p class=""></o:p></p>
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<p class="MsoNormal"><o:p class=""> </o:p></p>
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<p class="MsoNormal">Regards<o:p class=""></o:p></p>
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<p class="MsoNormal"><o:p class=""> </o:p></p>
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<p class="MsoNormal">amit<o:p class=""></o:p></p>
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<p class="MsoNormal">On Sep 9, 2015, at 2:07 AM, Biddiscombe, John A. <<a href="mailto:biddisco@cscs.ch" class="">biddisco@cscs.ch</a>> wrote:<o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">Amit</span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">the version of the reader that I maintain is kept here</span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""><a href="https://github.com/biddisco/pv-meshless" class=""><span style="color:purple" class="">https://github.com/biddisco/pv-meshless</span></a></span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""> </span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">It has a number of extensions and options that you will want to ignore.</span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""> </span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">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.</span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""> </span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">Note:</span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">For parallel partitioning of particle data, you will want the pv-zoltan plugin</span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""><a href="https://github.com/biddisco/pv-zoltan" class=""><span style="color:purple" class="">https://github.com/biddisco/pv-zoltan</span></a></span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class="">JB</span><o:p class=""></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" class=""> </span><o:p class=""></o:p></p>
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<p class="MsoNormal"><b class=""><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" class="">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" class=""> </span></span><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" class="">Amit
Goel [<a href="mailto:Amit.Goel@ucf.edu" class="">mailto:Amit.Goel@ucf.edu</a>]<span class="apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>08 September 2015 23:37<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span>Berk Geveci<br class="">
<b class="">Cc:</b><span class="apple-converted-space"> </span>Biddiscombe, John A.;
<a href="mailto:paraview-developers@paraview.org" class="">paraview-developers@paraview.org</a><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [Paraview-developers] H5Part and H5Hut</span><o:p class=""></o:p></p>
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<p class="MsoNormal">Dear Berk<span class="apple-converted-space"> </span><o:p class=""></o:p></p>
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<p class="MsoNormal">Thanks a lot for your response. <o:p class=""></o:p></p>
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<p class="MsoNormal"> <o:p class=""></o:p></p>
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<p class="MsoNormal">I was able to open H5part files, albeit with warnings in H5Part. Further, there seems to be multiple versions of H5Part floating around:<o:p class=""></o:p></p>
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<p class="MsoNormal"> <o:p class=""></o:p></p>
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<p class="MsoNormal">H5Hut 1.99.13<o:p class=""></o:p></p>
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<p class="MsoNormal">H5Part 1.6.6<o:p class=""></o:p></p>
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<p class="MsoNormal">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.<o:p class=""></o:p></p>
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<p class="MsoNormal">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. :-)<o:p class=""></o:p></p>
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<p class="MsoNormal"> <o:p class=""></o:p></p>
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<p class="MsoNormal">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.<o:p class=""></o:p></p>
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<p class="MsoNormal"> <o:p class=""></o:p></p>
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<p class="MsoNormal">Are there any other particle formats based on HDF5 that Paraview supports ?<o:p class=""></o:p></p>
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<p class="MsoNormal"> <o:p class=""></o:p></p>
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<p class="MsoNormal">Regards<o:p class=""></o:p></p>
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<p class="MsoNormal">Amit<o:p class=""></o:p></p>
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<p class="MsoNormal">On Sep 8, 2015, at 3:36 PM, Berk Geveci <<a href="mailto:berk.geveci@kitware.com" class=""><span style="color:purple" class="">berk.geveci@kitware.com</span></a>> wrote:<o:p class=""></o:p></p>
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<p class="MsoNormal">Hi Amit,<span class="apple-converted-space"> </span><o:p class=""></o:p></p>
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<p class="MsoNormal">I CC'ed John who is the original author of that plugin. Hopefully, he can answer your question.<o:p class=""></o:p></p>
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<p class="MsoNormal">Maybe there is an updated version of the reader that handles a newer format. We would be<o:p class=""></o:p></p>
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<p class="MsoNormal">happy to update the plugin if there is a new version of the reader.<o:p class=""></o:p></p>
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<p class="MsoNormal">It does not look like H5hut is available so I can't speak to it. We are not currently doing any<o:p class=""></o:p></p>
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<p class="MsoNormal">work on the H5Part reader. As far as I know, we haven't received any user requests asking us<o:p class=""></o:p></p>
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<p class="MsoNormal">to update or fix it so far. <o:p class=""></o:p></p>
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<p class="MsoNormal">Best,<o:p class=""></o:p></p>
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<p class="MsoNormal">-berk<o:p class=""></o:p></p>
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<p class="MsoNormal">On Fri, Sep 4, 2015 at 4:09 PM, Amit Goel <<a href="mailto:Amit.Goel@ucf.edu" target="_blank" class=""><span style="color:purple" class="">Amit.Goel@ucf.edu</span></a>> wrote:<o:p class=""></o:p></p>
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<p class="MsoNormal">Hi<br class="">
<br class="">
I am new to this list. Please let me know if anyone knows the status of H5Part plugin ? My specific questions are:<br class="">
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1. How to use it exactly. I tried opening a Cavity sample file from pvmeshless site. But it returns errors and warnings.<br class="">
<br class="">
2. What is status of H5hut and H5Part plugins in forthcoming versions of Paraview ?<br class="">
<br class="">
Regards<br class="">
<br class="">
— amit<br class="">
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