<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><div><div>I would like to add that this feature would be *really* nice to have. Flash checkpoint files are huge, and I'm doing large (and going to be much larger) runs. The plot and particle files are nice and small, easy to store and move around. I cringe at the thought of analyzing a 5 M(cpu-hrs) run of checkpoint files for time series data. Let me know if I can help by providing test data files or anything! My OOP and python skills are probably not at the level you'd want for actual code development, but I'll pitch in where I can.<br><br></div>Joshua Wall<br></div>Drexel University<br></div><br><div class="gmail_quote">On Mon, May 11, 2015 at 4:40 PM John ZuHone <<a href="mailto:jzuhone@gmail.com">jzuhone@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div>I don't think we should expect this to work, actually. We never specified that it should, to my knowledge. So we need to implement it.<br><br><span style="font-size:13pt;background-color:rgba(255,255,255,0)">John ZuHone</span><br><div><span style="background-color:rgba(255,255,255,0)">Kavli Center for Astrophysics and Space Research<br>Massachusetts Institute of Technology<br><a>77 Massachusetts Ave.</a>, 37-582G<br><a>Cambridge, MA 02139</a><br>(w) <a href="tel:617-253-2354" target="_blank">617-253-2354</a><br>(m) <a href="tel:781-708-5004" target="_blank">781-708-5004</a><br><a href="mailto:jzuhone@space.mit.edu" target="_blank">jzuhone@space.mit.edu</a><br><a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a><br><a href="http://www.jzuhone.com/" target="_blank">http://www.jzuhone.com</a></span><br style="font-family:UICTFontTextStyleBody"></div></div></div><div dir="auto"><div><br>On May 11, 2015, at 4:31 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Mon, May 11, 2015 at 1:24 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Mon, May 11, 2015 at 1:19 PM, Joshua Wall <span dir="ltr"><<a href="mailto:joshua.e.wall@gmail.com" target="_blank">joshua.e.wall@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Dear users,<br><br></div> Since I'm already 0 for 1 today, I thought I'd also ask about this error I've seen. I'm trying to get the time series of momentum density in the x-dir from a simulation in FLASH where I have both the plot and particle files with:<br><br>############################################################<br><br>ts = yt.load("/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_plt_cnt_0??[!0]",<br> particle_filename='/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0]')<br><br>times = []<br>Mom_x = []<br>Mom_y = []<br><br>for ds in ts:<br> <br> <br> try:<br> ds.add_field("total_px", function=_px, units="kg/s/m**2")<br> ds.add_field("total_py", function=_py, units="kg/s/m**2")<br> except:<br> continue<br><br> dd = ds.all_data()<br><br> Mom_x.append(dd["total_px"])<br> Mom_y.append(dd["total_py"])<br> times.append(ds.current_time.in_units("Myr"))<br><br>###########################################################<br><br></div>But this gives the error:<br><br>---------------------------------------------------------------------------<br>IOError Traceback (most recent call last)<br><ipython-input-3-4be7349ef199> in <module>()<br> 9 Mom_y = []<br> 10 <br>---> 11 for ds in ts:<br> 12 <br> 13 <br><br>/usr/local/lib/python2.7/dist-packages/yt/data_objects/time_series.pyc in __iter__(self)<br> 158 for o in self._pre_outputs:<br> 159 if isinstance(o, types.StringTypes):<br>--> 160 ds = load(o, **self.kwargs)<br> 161 self._setup_function(ds)<br> 162 yield ds<br><br>/usr/local/lib/python2.7/dist-packages/yt/convenience.pyc in load(*args, **kwargs)<br> 78 if c._is_valid(*args, **kwargs): candidates.append(n)<br> 79 if len(candidates) == 1:<br>---> 80 return output_type_registry[candidates[0]](*args, **kwargs)<br> 81 if len(candidates) == 0:<br> 82 if ytcfg.get("yt", "enzo_db") != '' \<br><br>/usr/local/lib/python2.7/dist-packages/yt/frontends/flash/data_structures.pyc in __init__(self, filename, dataset_type, storage_filename, particle_filename, units_override)<br> 206 self._particle_handle = HDF5FileHandler(self.particle_filename)<br> 207 except:<br>--> 208 raise IOError(self.particle_filename)<br> 209 # These should be explicitly obtained from the file, but for now that<br> 210 # will wait until a reorganization of the source tree and better<br><br>IOError: /home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0]<br></div></div></div></div></blockquote><div><br></div></div></div><div>Unfortunately the FLASH frontend is gobbling the error h5py is raising here.</div><div><br></div><div>A quick way to get the real error from h5py would be to replace "raise IOError..." on line 208 with just "raise" and then rerun the script.</div></div></div></div></blockquote><div><br></div><div>Ah, but now that I think about it, I don't think the glob pattern should have made it all the way down to the FLASH I/O layer. Maybe there's a bug in the way we set up time series for FLASH datasets that include particle files?</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span><div dir="ltr"><div><div><div><br>#############################################################<br><br></div>Any ideas?<span><font color="#888888"><br><br></font></span></div><span><font color="#888888">Joshua Wall<br></font></span></div><span><font color="#888888">Drexel University<br></font></span></div>
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