Mailman 3 September 2012 - yt-users

how to control the pixel size for projection/slice plot in order to use ffmpeg
by Ji Suoqing Sept. 13, 2012

Sept. 13, 2012

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 … [View More]

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Changing na => np internally
by Matthew Turk Sept. 10, 2012

Sept. 10, 2012

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-… [View More]

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2D FLASH data
by John Forbes Sept. 8, 2012

Sept. 8, 2012

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 -… [View More]

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Fortran kD tree on Mac OS X 10.8
by Stephen Skory Sept. 7, 2012

Sept. 7, 2012

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/… [View More]

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matplotlib issue on kraken
by Eric Hallman Sept. 5, 2012

Sept. 5, 2012

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 … [View More]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 -- [View Less]

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