Mailman 3 September 2012 - yt-users

how to control the pixel size for projection/slice plot in order to use ffmpeg
by Ji Suoqing 13 Sep '12

13 Sep '12

Hi all, Sometimes I use YT to generate time series projection/slice plots, and use ffmpeg to convert these png file to mp4 movie. However, the problem is ffmpeg only recognizes the png file with the pixel number of length being an even number. If the inputted png file size is not even times even, there's the error: [libx264 @ 0x7fcc3c047000] width not divisible by 2 (983x886) Output #0, mp4, to 'movie.mp4': Stream #0:0: Video: h264, yuv420p, 983x886, q=-1--1, 90k tbn, 20 tbc Stream mapping: Stream #0:0 -> #0:0 (png -> libx264) Error while opening encoder for output stream #0:0 - maybe incorrect parameters such as bit_rate, rate, width or height So, is there anyway to control the pixel size of the projection/slice plots to be even? Or, is there a much simpler way to generate a projection/slice movie? Best wishes, Suoqing

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Changing na => np internally
by Matthew Turk 10 Sep '12

10 Sep '12

Hi all, There's been quite a bit of discussion on yt-dev about changing the internal convention in yt of using "na" for numpy (which originally stood for "numarray") to "np", which is the commonly used shorthand. We'll keep around "na" in the yt.mods namespace, which means your scripts should *not* need any adjustment. But, if you have made a number of substantial changes to the internals of yt in your version, any updates after this change is made may pose problems and may need to be hand-modified. If you'd like to contribute to the discussion (we're waiting until next week to make the switch) please do so on yt-dev or here. This change, which touches many many files, was not decided on lightly and we're trying to ensure that the transition is smooth without any external effects. Here's the thread: http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2012-August/00235… (Note that tomorrow starts a new archive month, so you might need to switch the URL for any new messages after today.) Again, this should not pose any issues for you unless you have modified yt internals. If you have done so and would like help updating, please reply to this message or contact yt-dev. Best, Matt

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2D FLASH data
by John Forbes 09 Sep '12

09 Sep '12

Hi all, I'm running into some issues with 2D FLASH data, which seem to be related to the z positions of the data. Nathan has helped me track down the likely culprits, but I haven't come up with a reasonable workaround as of yet. >From what I can tell by inspecting the hdf5 file directly (here's a link to it: http://www.ucolick.org/~jforbes/cloud_hdf5_plt_cnt_0000 ), the z-coordinates are explicitly specified to be 0.0 for each of the root grids (there are 4 in this particular setup), and -1.0 for all other grids. I think the 'dz' field in yt is also somehow being read directly from the hdf5 file, and it is 1 cm for all cells. The problem is that pf.domain_left_edge[2] and pf.domain_right_edge[2] are -8 kpc and 8 kpc respectively, so as-is, yt will give all the data a z-coordinate of -8 kpc, whereas I think it should probably be close to 0 in this particular setup. Even worse, the difference between the z-coordinates explicitly written in the hdf5 file between root and refined blocks means that most of the data will be at z = -8 kpc, but some will be at z=0 (i.e. when the root grid has the maximum-resolution data available at a particular location). Any suggestions would be appreciated. Thank you, John Bonus information: In the IRC channel I mentioned that replacing na.rint(self.grid_left_edge[i]/dx)*dx with na.rint(self.grid_left_edge[i]/(.99999999999*dx))*dx (and the corresponding change for the right edge) in frontends/flash/data_structures.py seemed to sidestep the problem, but in fact it created other problems. The effect was that all the z-data now appeared at -8 kpc, so I thought that would solve any issues stemming from the data having different z-values, but as it turns out that put all the z coordinates just outside grid_left_edge, so for instance calling pc.add_phase_object ran into trouble because it could find no valid data inside the domain. I suspect that part of the problem lies with the for loop at line 146 in frontends/flash/data_structures.py as I claimed on yt-dev, but it seems the problems are a bit deeper.

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Fortran kD tree on Mac OS X 10.8
by Stephen Skory 07 Sep '12

07 Sep '12

Hi all, I have received a report that the Fortran kD tree does not build correctly on Mac OS X 10.8. For Brian Crosby, when he runs: from yt.utilities.kdtree import fKD he gets: ImportError: dlopen(/Users/crosby/yt-x86_64/lib/python2.7/site-packages/yt-2.5dev-py2.7-macosx-10.4-x86_64.egg/yt/utilities/kdtree/fKDpy.so, 2): Symbol not found: _fkdgetpointerchunk_tags_ Referenced from: /Users/crosby/yt-x86_64/lib/python2.7/site-packages/yt-2.5dev-py2.7-macosx-10.4-x86_64.egg/yt/utilities/kdtree/fKDpy.so Expected in: flat namespace I'm wondering if any other users of 10.8 can run the import command above, and tell me what you get? I'd like to narrow this down to Brian's 10.8, or 10.8 in general. If you get an error like "ImportError: No module named fKD", I'd like you to please try the following: - Make sure you have Forthon installed. Try "Forthon" from the command line, if it prints some stuff, you're set. If not, you can get it here http://hifweb.lbl.gov/Forthon/ - Go to your yt install directory, and navigate to the src/yt-hg/yt/utilities/kdtree directory. In there, please type "make". - Navigate up three levels (cd ../../..) and type "python setup.py install" with this done, please try the first import command above again, and if you get an interesting error message, please send it back. Thanks! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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matplotlib issue on kraken
by Eric Hallman 06 Sep '12

06 Sep '12

Hey everyone, so this issue seems like one I've had before, but I searched the lists and don't find this exact issue. On batch jobs on kraken, attempting to do halo finding, I get an almost immediate crash (with an eternal hang until the time limit is reached) due to matplotlib. I've been unable to reproduce it in the interactive queue on kraken, which is frustrating. I'm hoping someone has seen it and can comment. this is with yt/dev on kraken, and I set env variables to MPLCONFIGDIR like so: export MPLCONFIGDIR=${PBS_O_WORKDIR}/.matplotlib/ [ ! -d ${MPLCONFIGDIR} ] && mkdir ${MPLCONFIGDIR} because if you don't, it fails immediately with perm issues. Anyway, it's a simple script and call aprun -n 12 python halo_finding.py --parallel but the details of the script are not too important, since the job fails when yt is imported, as so: Traceback (most recent call last): File "halo_finding.py", line 1, in <module> from yt.mods import * File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/mods.py", line 115, in <module> from yt.visualization.api import \ File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visualization/api.py", line 34, in <module> from plot_collection import \ File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visualization/plot_collection.py", line 26, in <module> from matplotlib import figure File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/figure.py", line 18, in <module> from axes import Axes, SubplotBase, subplot_class_factory File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/axes.py", line 18, in <module> import matplotlib.contour as mcontour File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/contour.py", line 21, in <module> import matplotlib.texmanager as texmanager File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/texmanager.py", line 72, in <module> class TexManager: File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/texmanager.py", line 92, in TexManager os.mkdir(texcache) OSError: [Errno 17] File exists: '/lustre/scratch/hallman/gigaCubes/run1024/.matplotlib/tex.cache' In each case, I have deleted tex.cache before I restart, thinking an old version persisted there, but the same error happens. The most irritating thing is that the job does not kick out of the batch system, so the time continues to run on however many processors you have until the limit is reached (eternal hang!). I hope this is something obvious and I'm just dumb. Let me know. Eric -- Eric Hallman Tech-X Corporation hallman(a)txcorp.com 5621 Arapahoe Ave, Suite A Phone: (720) 254-5833 Boulder, CO 80303 Fax: (303) 448-7756 --

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