Mailman 3 March 2009 - yt-users

Re: [yt-users] yt memory usage
by Stella Offner March 27, 2009

March 27, 2009

Hi Matt, That modified code you sent appears to be an enormous improvement! Slices though the interpolated data array and the AMR data look quite similar, so as far as I can see it is grabbing and interpolating the correct data. I'll let you know if any other issues come up. Thanks for your help and the quick response! Stella

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yt memory usage
by Stella Offner March 27, 2009

March 27, 2009

Hi, I've been working on setting up yt code to interpolate from an AMR dataset to a spherical grid of points. Thanks to help from Jeff, I've used a covering grid to extract the data and then TrilinearFieldInterpolator to derive the values on the grid of points. The problem is that the covering grid allocates the entire data array on the maximum level ~4500^3, which doesn't fit into the memory on the Nersc Davinci machine (72 gb max). I really only need the cells adaject to points in the output grid, which is < 150^3. Is there a more efficient way of using covering_grid or extracting the AMR data that doesn't involve first interpolating the entire region to the maximum level? (The code definitely works for smaller grids/ lower max levels, but I really need to get at the high resolution AMR data). Thanks for your help! Stella

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Output Resolution
by david collins March 26, 2009

March 26, 2009

Hi there-- What's the relationship between the resolution of a plot and the fig_size argument in add_projection? Is there a dpi flag somewhere, or something so I can control the number of pixels in the output image? Thanks, d.

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HaloProfiler help
by Stephen Skory March 21, 2009

March 21, 2009

Hi, (this question refers to code in the trunk version of yt, not the 1.0 version.) I am trying to calculate the virial mass for about 70,000 haloes in a fairly large cosmology simulation. Out of those, I'm only getting about 61,000 lines in VirialQuantities.out, and of those, 20,000 are actually nans. So out of 70,000 haloes from HOP, I have only about 40,000 virial masses. I don't imagine many people have run the HaloProfiler on a dataset this large, but is a 40% error rate typical? Can you suggest any strategies to minimize the number of nans and missing haloes? Is it likely I'm doing something wrong (which is a strong possibility)? Thanks! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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smoothed plots
by david collins March 17, 2009

March 17, 2009

Hi-- Is it possible to smooth plots one gets from plot_collection.add_projection? d. ps. Sorry to people on yt-dev, this is a question for the general user list, not just the dev people. d.

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ParticleMassMsun
by Stephen Skory March 12, 2009

March 12, 2009

Hi, if I do sp["ParticleMassMsun"], are the masses in Msun/h or Msun? Thanks! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Updated Cray XT5 installation instructions
by Stephen Skory March 8, 2009

March 8, 2009

Hello, I've updated the Cray XT5 installation instructions page. There was an omission in the first Python step, and I added a section on running yt on the compute nodes. http://yt.enzotools.org/wiki/CrayXT5Installation Let me know if you see something amiss! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Mac OS X matplotlib WX backend
by Thomas Statler March 3, 2009

March 3, 2009

I've just installed yt on an Intel Mac and am trying to follow the examples for time series plots with iyt. When the pylab.plot statement is executed, the python plot window appears and python hangs (spinning beachball cursor). If I wait long enough a plot eventually shows up but python is still hung. This appears to be a known problem with the Enthought python distribution. (See https://svn.enthought.com/epd/ticket/186 .) I have verified that I get the same behavior using ordinary ipython rather than iyt. Happily there is also a known solution for ipython: simply invoke ipython with the -whtread option. I have tried this and it solves the problem--- in ipython. My question now is how to do the same thing for iyt. Is there a build option somewhere, so that iyt will start ipython with the -wthread flag?

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Re: [yt-users] Mac OS X matplotlib WX backend
by Stephen Skory March 3, 2009

March 3, 2009

Thomas, > Can you try changing the first line to /path/to/yt/bin/ipython -wthread and see > if that works? Just to be perfectly clear, I meant #!/path/to/yt/bin/ipython -wthread _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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