Mailman 3 July 2010 - yt-users

Broken volume rendering
by Matthew Turk 02 Aug '10

02 Aug '10

Hi all, I broke volume rendering (via yt.extensions.volume_rendering) some time ago, and I only just realized it today when some people were getting corrupted images. It took a while to come up because I avoided re-generating the Cython/C code that actually conducts the volume rendering; however, recently I updated this code and pushed it to the repository, and that's when the errors started showing up. The exact error was in mercurial changeset 3007999e2518 (May 30), which I merged into trunk in revision 1754 (June 24). These dates are not necessarily the dates at which the error showed up, however, as the re-cythonization probably did not occur at those times. The error was in the optimization of division by the inverse of the vector direction; the rays to cast were passed to partitioned bricks and to avoid too much division of 64-bit floats, I changed it to be a multiplication against the inverse. To calculate the inverse, I did something similar to this: for i in range(3): iv_dir[i] = 1.0/v_dir[0] The error, of course, being that I was dividing by v_dir[0] for all three values. I identified this by using the hg bisect command, where I found a good revision and a bad revision and it executed the necessary tests to figure out where the code took a turn for the worse. I've committed fixes in hg changeset f0960f4f6bed, svn trunk r1804 and svn yt-1.7 r1805. I'm really sorry for the troubles, and I hope that it hasn't cost anyone too much time. There may still be some lingering bugs, so please let me know if you run into any more bad images or difficulties with the volume rendering. You can get an updated yt by doing "yt instinfo -u". -Matt

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yt-2.0: a brief poll
by j s oishi 29 Jul '10

29 Jul '10

Hi all, yt-2.0 is coming soon, and the development team is starting to think about what needs to be done before we can release it. We would really love some user input as to what we should focus our energies on. To this end, I've made a very short survey that we would really appreciate your participation in. Please go to http://spreadsheets.google.com/viewform?formkey=dFpwNHR2MHV2dlFTNEZrN2lEMjV… and fill in your opinions. If you have any other comments, feel free to email me directly or reply on list. Thanks so much, Jeff on be behalf of the yt-development team

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halo density profiling
by Irina Dvorkin 29 Jul '10

29 Jul '10

Hello All, I'm trying to use the halo profiler, without much success. If I want to plot the density, do I need to use the weight_field? It says weight_field=None in the manual, but weight_field='CellMassMsun' in the cookbook. Is it the same for Dark_Matter_Density? Also, where can I see a list of things the halo profiler can in principle do? I coudn't find it on the site. Thanks a lot for your help, Irina

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yt file problems
by Stephen Skory 29 Jul '10

29 Jul '10

Hi all, I am running a script that does a for loop over a set of time ordered data dumps. I am fairly consistently getting this error, but at different points in the for loop cycle. This suggests that this is a file system error (this is on Triton), but I'm not sure. Does anyone have any ideas of why things would fail here in an inconsistent fashion? Thanks! File "./camera.py", line 167, in <module> pf = load(dirs[count]) File "/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/convenience.py", line 77, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/OutputTypes.py", line 59, in __new__ _pf_store.check_pf(obj) File "/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 152, in check_pf self.insert_pf(pf) File "/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 166, in insert_pf self.flush_db() File "/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 182, in flush_db self._write_out() File "/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 197, in _write_out os.rename("%s.tmp" % fn, fn) OSError: [Errno 2] No such file or directory _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Flashfields error on install
by Cameron Hummels 28 Jul '10

28 Jul '10

Hey everyone: I just pulled the newest version of yt and installed it on kraken. It installed OK (installing locally HDF5, zlib, libpng and python). I remembered to swap the PGI modules to the GNU modules. Unfortunately, when I go to run it I get the following error involving "FLASHFields": $ yt Traceback (most recent call last): File "/nics/b/home/chummels/source/yt-x86_64/bin//yt", line 9, in <module> load_entry_point('yt==2.0dev', 'console_scripts', 'yt')() File "/nics/b/home/chummels/source/yt-x86_64/lib/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py", line 299, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/nics/b/home/chummels/source/yt-x86_64/lib/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py", line 2229, in load_entry_point return ep.load() File "/nics/b/home/chummels/source/yt-x86_64/lib/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py", line 1948, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/nics/b/home/chummels/source/yt/yt/command_line.py", line 26, in <module> from yt.mods import * File "/nics/b/home/chummels/source/yt/yt/mods.py", line 32, in <module> import yt.lagos as lagos File "/nics/b/home/chummels/source/yt/yt/lagos/__init__.py", line 79, in <module> from FLASHFields import * ImportError: No module named FLASHFields I've never seen this error, and I investigated a bit but couldn't find much about it. Any ideas from people? What is this mysterious FLASHFields module? Cameron

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Quick Tkinter poll
by Matthew Turk 26 Jul '10

26 Jul '10

Hi all, If you have a second, I'd really appreciate your help with figuring out where Tkinter is available: inside the TeraGrid, on your personal machines, on other supercomputing centers, etc etc. This form: http://spreadsheets.google.com/viewform?formkey=dEhzZXdTbl9ydDJXb3JYSktEd2J… will collect your responses, and it describes what to do. You simply have to run the command: "python2.6 -c 'import Tkinter' " and report if it throws an ImportError or if it passes without failure. Thanks very much, and I really appreciate you taking the couple moments to do this. -Matt

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h5py Issues
by Brian Crosby 23 Jul '10

23 Jul '10

In attempting to make a series of projections with halos plotted using the public install of yt on Kraken, I've encountered an odd problem. The job terminates without giving an apparent error statement in the output files, but rather ends with this cryptic (at least to me) mess: h5py._stub.IOError File "h5g.pyx", line 104, in h5py.h5g.GroupIter.__init__ (h5py/h5g.c:1248) File "h5g.pyx", line 104, in h5py.h5g.GroupIter.__init__ (h5py/h5g.c:1248) : Addr overflow (Invalid arguments to routine: Address overflowed) h5py._stub.IOError: Addr overflow (Invalid arguments to routine: Address overflowed) return func(*args, **kwds) File "h5g.pyx", line 317, in h5py.h5g.GroupID.get_num_objs (h5py/h5g.c:2482) return func(*args, **kwds) File "h5g.pyx", line 317, in h5py.h5g.GroupID.get_num_objs (h5py/h5g.c:2482) return func(*args, **kwds) File "h5g.pyx", line 317, in h5py.h5g.GroupID.get_num_objs (h5py/h5g.c:2482) return func(*args, **kwds) File "h5g.pyx", line 317, in h5py.h5g.GroupID.get_num_objs (h5py/h5g.c:2482) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/h5py-1.2.1-py2.6-linux-x86_64.egg/h5py/_sync.py", line 88, in wrap Does anyone have an idea what could be causing this problem? Thanks, Brian

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zlim, phase plots
by david collins 22 Jul '10

22 Jul '10

Hi, all-- I'm trying to save a phase plot, then re-load and re-plot, and do this into an axes object I've pre- defined. (I want to put several phase plots into a multi-tile frame) I'm presently doing: the_plot = raven.PlotTypes.PhasePlot(phase ,[xfield,yfield,zfield],14,'algae',axes=axes) (where phase is the unpickled phase object) then fig.save_fig(output_name) (where axes is contained in fig) This works just fine. The problem I'm running into is setting the zlim on the phase plot. If I do: the_plot = raven.PlotTypes.PhasePlot(phase ,[xfield,yfield,zfield],14,'algae',axes=axes) the_plot.set_zlim(a,b) the zlim doesn't seem to change the actual zlim I find in output_name. Is that the appropriate place to be setting the zlim for this operation? Or is there a better place? Thanks, d. -- Sent from my Stone Tablet and carried by my Pterodactyl.

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Weighed projections
by Brian Crosby 22 Jul '10

22 Jul '10

I'm trying to make a density weighted temperature projection on Kraken, and the weighting seems to be causing problems. I get this error: Traceback (most recent call last): File "./s_p_halos.py", line 23, in <module> p = ph.add_projection("Temperature", 0, weight='Density') I'm puzzled because this exact same script works on my laptop, albeit with a much smaller data set. Any ideas or suggestions would be greatly appreciated. Thanks, Brian

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parallelHOP
by Brian Crosby 20 Jul '10

20 Jul '10

Hi everyone, I'm trying to make a merger tree on Kraken using parallelHOP and the public yt installation, but am getting this error: Traceback (most recent call last): File "./merger.py", line 9, in <module> MergerTree(files, database='/lustre/scratch/oshea/PopIII_smallbox/halos.db', halo_finder_function=parallelHF) NameError: name 'parallelHF' is not defined All of the requisite Forthon and KD Tree bits seem to be there, and the only thing that I found in the yt install that might be problematic is that I can't access the Forthon directory at /lustre/scratch/proj/yt_common/trunk/src/Forthon-0.8.3/ . I don't know if that could possibly cause problems, but it made me curious. Does anyone have any tips on what's going wrong? Running the exact same script with HaloFinder instead of parallelHF works without problem (just very slowly at lower redshifts). Thanks, Brian

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yt-users July 2010