Mailman 3 March 2016 - yt-users

yt-3.2.1 installation error
by Muhammad Latif March 8, 2016

March 8, 2016

Hi all, I'm getting the following error while installing yt-3.2.1 latest release. Any idea what is going on here? thanks in advance, cheers Latif Installing nose-1.3.6 Installing python-hglib-1.6 Installing sympy-0.7.6 Doing yt update, wiping local changes and updating to branch stable install_script.sh: line 1025: cd: /home/latif/YT/yt-x86_64/src/yt-hg/: No such file or directory Installing yt ******************************************** FAILURE REPORT: ******************************************** running install_data copying doc/man/isympy.1 -> /home/latif/YT/yt-x86_64/share/man/man1 running install_egg_info Writing /home/latif/YT/yt-x86_64/lib/python2.7/site-packages/sympy-0.7.6-py2.7.egg-info Collecting jinja2 Using cached Jinja2-2.8-py2.py3-none-any.whl Collecting MarkupSafe (from jinja2) Installing collected packages: MarkupSafe, jinja2 Successfully installed MarkupSafe-0.23 jinja2-2.8 /home/latif/YT/yt-x86_64/bin/python2.7: can't open file 'setup.py': [Errno 2] No such file or directory ******************************************** ******************************************** Failure. Check /home/latif/YT/yt-x86_64/yt_install.log. The last 10 lines are above.

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Flash Particle files and DatasetSeries
by Alex Hill March 7, 2016

March 7, 2016

Hi, I’d like to load particle files with a series of Flash files. If loading a single file, I can do d = yt.load(‘file_hdf5_plt_cnt_0100’, particle_filename=‘file_hdf5_part_0100’) I’d like to do something like ts = yt.DatasetSeries(‘file_hdf5_plt_cnt_0*0’, particle_filename=‘file_hdf5_part_0*0’) or load the particle files after the fact while iterating through the time series. Is this possible? Cheers, Alex --------- Alex Hill Senior Postdoctoral Research Associate Office: KINSC Link L106 Department of Astronomy, Haverford College 370 Lancaster Ave, Haverford, PA 19041 USA phone: +1 484 297 2136 email/iMessage: ashill(a)haverford.edu

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14-hour load time for Enzo dataset with VR, vs. 30 minutes with ProjectionPlot?
by Stuart Levy March 7, 2016

March 7, 2016

Hello yt people, We're trying to render imagery of a pretty large Enzo snapshot (~160GB, in 330,000 grids in 512 HDF5 domains) with yt-3.3dev. On a reasonably fast Linux machine, we can do a ProjectionPlot of a few variables in about 30 minutes, running single-threaded while it scans the data (which is what takes most of the time). Data access pattern: we see it reading through each of the HDF5 files in numerical order (cpu0000, cpu0001, ...), taking a few seconds each, and opening each file exactly once. On the same machine and same dataset, using the volume rendering API, the data-scanning process takes about*14 hours* (not counting any rendering time). (On Blue Waters, Kalina using a similar dataset couldn't get it to finish within a 24-hour wall-clock limit.) Data access pattern: it opens an HDF5 file many times in quick succession, then opens another, then opens the previous file a bunch more times. I'm guessing it grabs one AMR grid from each HDF5 open: open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0074", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0075", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0357", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0357", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0357", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0357", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0357", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0357", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0074", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0075", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0235", O_RDONLY) = 3 open("/fe0/deslsst/renaissance/normal/RD0074/RedshiftOutput0074.cpu0357", O_RDONLY) = 3 This is trouble. Is there anything we can do to make load times less extravagant when using VR on Enzo? What if we ran "ds.index" before I tried running cProfile on it, as in python -m cProfile myscript.py ... Happy to point anyone at the dataset on our systems or BW, but at this scale it's not a very portable problem.

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Conda packages for development version of yt
by Kacper Kowalik March 5, 2016

March 5, 2016

Hi! For those of you that are using yt via conda, we're happy to announce that we now provide conda packages for yt development branch. They're being built each time pull request gets merged into yt repository. We are currently building for linux-64 and osx-64 platforms with py27 and py35 flavours. If you'd like to try, you can update yt using following command: $ conda update -c http://use.yt/with_conda/ yt If you encounter any issue please let us know. Cheers, Kacper

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PPV cube
by David Collins March 3, 2016

March 3, 2016

Hi, Everybody! The PPV cube functionality is completely sweet. Thanks so much! I have one question about it. I built my cube as described by the docs, wrote to a fits file, then read the fits file with yt.load. If I then want the original dumb three dimensional cube, what's the simplest way to get back to it? I usually use >>> ds.index.grids when I want the raw data, but that gives me an odd list of 27 FITS_grid objects. Is covering_grid the way to get back to the raw data in this sense? For this application, I'm working with some other packages that make it easier for me to do mask operations on the cube, rather than use yt regions as I normally would. d. -- -- Sent from a computer.

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Phase diagram using yt
by Adolfo Alsina March 3, 2016

March 3, 2016

Dear all, I am trying to create a phase diagram using yt and I am having some trouble. The code that I am using is attached to this email and also the picture that I get. I have modified the number of bins because I want to have just one point inside each bin. Is the problem related to this modification or is it related to how I load the data? Cheers, Adolfo Alsina.

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RuntimeError with surface
by Slavin, Jonathan March 2, 2016

March 2, 2016

Hi all, I have some 3D data that I'd like to visualize using iso-surfaces. The data are for an explosion at the center and in cartesian coordinates with reflecting boundary conditions on the left edges such that it is expanding in one octant of a 3D space. I have tried a few different approaches and I keep running into the RuntimeError: "Error: yt attempted to read outside the boundaries of a non-periodic domain along dimension 0. ... This commonly happens when trying to compute ghost cells up to the domain boundary. Two possible solutions are to load a smaller region that does not border the edge or override the periodicity for this dataset." So this is after I loaded a smaller region. I don't want to exclude the planes along x = 0, y= 0 and z = 0 because then I'll be excluding the explosion center. It's not clear to me how to "exclude the periodicity for the dataset". Any help would be appreciated. Thanks, Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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Error in making light ray for a gadget dataset
by Bili Dong - Gmail March 1, 2016

March 1, 2016

Hi yt users, I'm trying to make a light ray for a gadget dataset using this script: http://paste.yt-project.org/show/6234/ But I get the following error: ``` /Users/qobilidop/repos/yt/yt/geometry/geometry_handler.py in fcoords(self) 320 c = obj.select_fcoords(self.dobj) 321 if c.shape[0] == 0: continue--> 322 ci[ind:ind+c.shape[0], :] = c 323 ind += c.shape[0] 324 return ci ValueError: could not broadcast input array from shape (81,3) into shape (40,3) ``` My yt is on the changeset d47150dfbde6. I'm wondering if I'm doing it the correct way? And how could I solve the problem? Thanks, Bili

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