[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 in place it should simply update the out-of-date dependencies.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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