<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>In fact, it looks like upgrading to h5py 2.0 actually broke my ability to read FLASH files - yt crashes whenever I try to directly access the data through a FLASHStaticOutput object. I've pasted a <a href="http://paste.yt-project.org/show/1913/">script</a> that exhibits the problem as well as the corresponding <a href="http://paste.yt-project.org/show/1912/">crash traceback</a>.</div><div><br></div><div>If I go back to h5py1.3.1 the same script does not crash.</div><div><br></div><div>-Nathan</div><br><div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Nathan Goldbaum<br>Graduate Student<br>Astronomy & Astrophysics, UCSC<br><a href="mailto:goldbaum@ucolick.org">goldbaum@ucolick.org</a><br>http://www.ucolick.org/~goldbaum</div></div></div>
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<br><div><div>On Nov 2, 2011, at 10:41 AM, Nathan Goldbaum wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Matt,</div><div><br></div><div>Thanks for the suggestion. Unfortunately, h5py still crashes: <a href="http://paste.yt-project.org/show/1907/">http://paste.yt-project.org/show/1907/</a></div><br><div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Nathan Goldbaum<br>Graduate Student<br>Astronomy & Astrophysics, UCSC<br><a href="mailto:goldbaum@ucolick.org">goldbaum@ucolick.org</a><br><a href="http://www.ucolick.org/~goldbaum">http://www.ucolick.org/~goldbaum</a></div></span></div></div>
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<br><div><div>On Nov 2, 2011, at 5:13 AM, Matthew Turk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Nathan, John,<br><br>This bug is annoying. Any chance you could try with the latest<br>install script, which uses h5py 2.0? If you re-run the install script<br>in place it should simply update the out-of-date dependencies.<br><br>Thanks,<br><br>Matt<br><br>On Wed, Nov 2, 2011 at 2:12 AM, John ZuHone<br><<a href="mailto:jzuhone@milkyway.gsfc.nasa.gov">jzuhone@milkyway.gsfc.nasa.gov</a>> wrote:<br><blockquote type="cite">Hi Nathan,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I would suspect that your grid data is probably fine, yes. I'm pretty sure the relevant data structures are essentially identical.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Happy FLASH-ing!<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">John<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Nov 2, 2011, at 2:10 AM, Nathan Goldbaum wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Thanks for looking into this, John. Adding those two lines fixes my problem.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">No worries about yt not supporting FLASH2 particle data - as you can see it's not a problem to read it in directly.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">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.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On Nov 1, 2011, at 11:00 PM, John ZuHone wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi Nathan,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">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.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">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.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">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.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">In any case, I reproduce the error you get. If you add the lines<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">del ParticleData<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">del f<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">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.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Best,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">John<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">yt-users mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">yt-users mailing list<br></blockquote><blockquote type="cite"><a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br></blockquote><blockquote type="cite"><br></blockquote>_______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br><br>!DSPAM:10175,4eb1340175682950323881!<br><br></div></blockquote></div><br></div></blockquote></div><br></body></html>