[Users] VisIt HDF5 directory-dependent read-in failures?

[Roland Haas]

Hello Bernard,

hdf5_merge will not work with Carpet's chunked output. It does
everything correctly with the exception of not updating the nioprocs
attribute of "Parameters and Global Attributes"

Bascially what I think happened was that you opened the "merged" file
but VisIt kept looking for the .file_1.h5 etc files which it found as
long as the merged file was in the same directory as the original files.

You now have three options: 

1. just open XX.file_0.h5 and VisIt will automatically open file_1.h5
etc.
2. use hdf5_slicer --out3d-cube --match '.*' XX.file_*.h5 XX.h5 to
merge the files
3. fix the merged file using the attached python script.

4. use hdf5_merge from
https://github.com/rhaas80/fileutils/tree/master/hdf5tools using its -u (unchunk) option.

Yours,
Roland

> Hi all.
> 
> I have some Carpet-generated 3D HDF5 data I want to look at in VisIt,
> but have encountered a weird issue trying to read it in, and wondered
> whether anyone else has encountered it.
> 
> The data output is from a single time step, but was chunked, so there
> are 32 separate files that have to be recombined to reconstruct the
> whole data snapshot. I'm using the hdf5_merge utility for this
> purpose. Here's the issue:
> 
> * if I start up VisIt and read the merged data file from the directory
> it was created in, it works fine.
> 
> * if I move/copy the merged data file elsewhere (like down a level in
> the directory tree), and try to get VisIt to read from the new
> location, it fails. Sample error (I tried gluing together just the
> first two chunks for this example):
> 
> ------------------------------------------------------------------------------------------------
> VisIt could not read from the file "<full directory path>/By.xyz.file_0-1.h5".
> 
> The generated error message was:
> 
> There was an error opening <full directory path>/By.xyz.file_0-1.h5.
> It may be an invalid file.  VisIt tried using the following file
> format readers to open the file: CarpetHDF5
> 
> The following error(s) may be helpful in identifying the problem:
> Tried to access an invalid index 1 (Maximum = 0).
> ------------------------------------------------------------------------------------------------
> 
> I have no problem with opening any of the original chunked files,
> regardless of location.
> 
> Has anyone else seen anything like this?
> 
> Thanks,
> 
> Bernard
> 
> P.S. After starting to compose this, I found that *some* of the
> maerged files started working everywhere, while others didn't. It's
> quite confusing.
> 
> P.P.S. This is the latest version of VisIt, installed on OS X 10.11.6
> (El Capitan). I don't know which version of ET produced the original
> data, but my hdf5_merge came from ET two generations back (2015_05).
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