Hi Roland.
Thanks! I rejected option 1, as I still want to combine these with other files later, so having a "database" of chunks is too awkward.
Nevertheless, option 2 --- hdf5_slicer with the syntax you suggested --- seems to have fixed my problem
Bernard
On 26 July 2016 at 11:53, Roland Haas rhaas@aei.mpg.de wrote:
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:
- 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.
- 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). _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
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