[yt-users] Trouble with h5py + FLASH

Nathan Goldbaum goldbaum at ucolick.org
Wed Nov 2 10:41:13 PDT 2011


Hi Matt,

Thanks for the suggestion.  Unfortunately, h5py still crashes:  http://paste.yt-project.org/show/1907/

Nathan Goldbaum
Graduate Student
Astronomy & Astrophysics, UCSC
goldbaum at ucolick.org
http://www.ucolick.org/~goldbaum

On Nov 2, 2011, at 5:13 AM, Matthew Turk wrote:

> Hi Nathan, John,
> 
> This bug is annoying.  Any chance you could try with the latest
> install script, which uses h5py 2.0?  If you re-run the install script
> in place it should simply update the out-of-date dependencies.
> 
> Thanks,
> 
> Matt
> 
> On Wed, Nov 2, 2011 at 2:12 AM, John ZuHone
> <jzuhone at milkyway.gsfc.nasa.gov> wrote:
>> Hi Nathan,
>> 
>> I would suspect that your grid data is probably fine, yes. I'm pretty sure the relevant data structures are essentially identical.
>> 
>> Happy FLASH-ing!
>> 
>> Best,
>> 
>> John
>> 
>> On Nov 2, 2011, at 2:10 AM, Nathan Goldbaum wrote:
>> 
>>> Thanks for looking into this, John.  Adding those two lines fixes my problem.
>>> 
>>> No worries about yt not supporting FLASH2 particle data - as you can see it's not a problem to read it in directly.
>>> 
>>> I haven't had any problems reading in my FLASH2 AMR data using yt.  I get results that are consistent with my old IDL scripts so I don't think there are any conversion issues.
>>> 
>>> On Nov 1, 2011, at 11:00 PM, John ZuHone wrote:
>>> 
>>>> Hi Nathan,
>>>> 
>>>> You'd have to double-check with Matt, but as I recall we didn't design the yt interface to support FLASH2 data. Now, I wouldn't be surprised if it does for the most part, since the grid data is written in almost exactly the same format by design to ease people switching over to FLASH3.
>>>> 
>>>> The particles, however, are a different story. In FLASH2, the particles are a composite HDF5 data structure of ints and doubles, whereas in FLASH3 they are a 2D array of doubles. In the latter case, simplicity was chosen over design sophistication. I know for a fact that yt only supports particle data in FLASH3.
>>>> 
>>>> I'm looking at this file of yours now... I was not aware that the way compound data types work in HDF5 that you get Python dictionaries when you read them in. That is a lot simpler than what I have to do to read FLASH3 particles.
>>>> 
>>>> In any case, I reproduce the error you get. If you add the lines
>>>> 
>>>> del ParticleData
>>>> del f
>>>> 
>>>> after your "f.close()" call, I no longer get the error. This is what we had to do with the previous issue you mentioned. For some reason the FLASH files are sometimes a bit picky about having all objects allocated from the previous read deleted before accessing the file again.
>>>> 
>>>> Best,
>>>> 
>>>> John
>>>> 
>>>> 
>>> 
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