Mailman 3 October 2016 - yt-dev

Issue #1290: Halo catalog weirdness under python3 (yt_analysis/yt)
by Nathan Goldbaum Oct. 10, 2016

Oct. 10, 2016

New issue 1290: Halo catalog weirdness under python3 https://bitbucket.org/yt_analysis/yt/issues/1290/halo-catalog-weirdness-und… Nathan Goldbaum: Right now the halo catalog infrastructure does something fishy with field names in python 3. Specifically, take a look at input cell 16 in this notebook: http://yt-project.org/docs/dev/cookbook/halo_analysis_example.html#Plotting… Note how it uses stringified versions of field tuples. The field names are somehow getting converted to strings and this is making it into output files. This isn't what happens in python2.

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Issue #1289: Rockstar doesn't compile on MacOS Sierra (yt_analysis/yt)
by Nathan Goldbaum Oct. 10, 2016

Oct. 10, 2016

New issue 1289: Rockstar doesn't compile on MacOS Sierra https://bitbucket.org/yt_analysis/yt/issues/1289/rockstar-doesnt-compile-on… Nathan Goldbaum: On my machine `make lib` dies with: ``` Undefined symbols for architecture x86_64: "_GROUPIES_fast3tree_box_inside_sphere", referenced from: _GROUPIES_fast3tree_find_sphere_offset in groupies-de8a73.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [lib] Error 1 ``` Looking inside groupies.c, I guess this has something to do with fast3tree.c being directly included into groupies.c maybe?

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Issue #1288: ParticlePlot docstrings don't include all arguments accepted by ParticlePhasePlot and ParticleProjectionPlot (yt_analysis/yt)
by Nathan Goldbaum Oct. 10, 2016

Oct. 10, 2016

New issue 1288: ParticlePlot docstrings don't include all arguments accepted by ParticlePhasePlot and ParticleProjectionPlot https://bitbucket.org/yt_analysis/yt/issues/1288/particleplot-docstrings-do… Nathan Goldbaum: This makes it difficult to see what features are supported by ParticlePlot. We should include all keyword arguments accepted by the classes ParticlePlot delegates to and note if a keyword argument is only accepted by one of them.

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Astropy problem
by Cameron Hummels Oct. 6, 2016

Oct. 6, 2016

Devs, Demitri Muna has written a paper about support for open source software in astronomy. I think much of what he writes applies to the yt project. He is looking for people to sign on as co-authors to this work so that the community as a whole will take note. If you are interested, please check it out and consider signing: http://bit.ly/astropy-problem Cameron

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Re: [yt-dev] Cut Region Failure
by Nathan Goldbaum Oct. 6, 2016

Oct. 6, 2016

Hi Jason, I'm CCing yt-dev here so that this project discussion happens in public. I hope that's ok. Yes, it would be great if you could take a stab at this. Unfortunately the main blocker here is choosing a good, fast, periodic KDTree that can be used easily from within cython. Having this available would be great for many other things besides the CutRegionSelection. We in fact already have a copy of scipy's C KDTree implementation vendored inside yt that we'd like to get rid of. I believe there are plans to either add a dependency on or vendor a fast cython kdtree that Meagan Lang has been working on: https://bitbucket.org/langmm/cykdtree Earlier today I took a stab at implementing a naive O(N^2) search in CutRegionSelector.select_cell. Unfortunately it's very, very slow to do this so we're going to need some sort of acceleration in order to realistically accomplish this, either via .a tree approach or by using a hash search like we're currently doing via python's builtin set object. An alternate way around this that maintains the O(1) speed of the current hashmap-based approach would be to compute unique integer indexes for each cell inside the cut_region and save those instead of just saving the floating point position of each cell. When I originally wrote the CutRegionSelector there wasn't anything like that in yt, but since then we've added a way to compute morton indices for each cell, which should do the trick. In fact, I went ahead and took a stab at this after coming up with that idea while writing this e-mail: https://bitbucket.org/yt_analysis/yt/pull-requests/2405 And unfortunately it still doesn't work perfectly - I still see artifacts (although they're less severe) in the image produced by the test script in the issue. I think my attempt in PR 2405 might be going on the right track - you could try to poke around with it, or test it with your data. Sorry to not have a satisfactory answer here. I was very excited about initially being able to implement cut_region data sources for SlicePlots, but the issue with FLASH data has been an annoying thorn in my side for a while, it would be great if we could figure out a way to fix it once and for all. -Nathan On Sat, Oct 1, 2016 at 4:27 PM, Jason Galyardt <jason.galyardt(a)gmail.com> wrote: > Hi Nathan, > > Unfortunately, contours won't be enough for me -- I need the actual data > region to do analysis on the gas contained within (i.e. more than > visualization). I'm not very familiar with the yt codebase, but I'd like to > see whether it's worth my time to work on this issue. I'm not very familiar > with the yt codebase or Cython, but my programming skills are decent; how > much work do you think this would take? Could I use an existing KDTree > library, such as the one in SciPy or this C implementation > <https://github.com/jtsiomb/kdtree>? > > Thanks, > Jason > > > On Sat, Oct 1, 2016 at 3:44 PM, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > >> Hi Jason, >> >> Unfortunately no. I think I might be able to come back to this issue >> soonish, we're going to be introducing a new fast periodic KDTree which >> could be exploited here. >> >> For now I think you're going to need to make this plot in a different >> way, without using a cut_region. Perhaps by overplotting contours? >> >> Nathan >> >> >> On Saturday, October 1, 2016, Jason Galyardt <jason.galyardt(a)gmail.com> >> wrote: >> >>> Hi Nathan, >>> >>> Is there a previous version of yt in which compound cut regions work? >>> >>> Thanks, >>> Jason >>> >>> ----- >>> >>> Hi Jason, >>> >>> This is a known issue: >>> >>> https://bitbucket.org/yt_analysis/yt/issues/941/cutregionsel >>> ector-doesnt-work-with-some >>> >>> Unfortunately fixing it will require a modification to the cut_region >>> implementation to do a better job of searching for cells that belong to the >>> region for chained selectors. >>> >>> -Nathan >>> >>> On Fri, Sep 30, 2016 at 1:25 PM, Jason Galyardt < >>> jason.galyardt(a)gmail.com> wrote: >>> Dear all, >>> >>> I would like to generate a compound cut region for a FLASH simulation, >>> but the output I'm getting is odd. I've pasted my simple script here: >>> >>> http://paste.yt-project.org/show/6839/ >>> >>> It loads a simulation file, creates a compound cut_region (1e4 K < T < >>> 1e6 K), and applies it to a slice plot. The resulting image is banded, as >>> you can see by the attached plots. Am I missing something, or is this a >>> problem related to yt? >>> >>> FYI, I get the same behavior when I use a projection plot or only one of >>> the conditionals (e.g. T < 1e6 K). I've tried both the stock 3.3.1 version, >>> as well as the self-contained development version that I installed earlier >>> this afternoon using install_script.sh. Let me know if any other info is >>> useful. >>> >>> Cheers, >>> Jason >>> >>> >

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import yt fail
by Molly Peeples Oct. 5, 2016

Oct. 5, 2016

Hi folks, I just updated yt and now I’m getting this: http://pastebin.com/FGGDBTKU I believe I’m on the tip of the dev branch. Ideas? —Molly

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Local access to a pull request
by Jason Galyardt Oct. 3, 2016

Oct. 3, 2016

Dear yt Devs, I'd like to import (pull?) an existing pull request, but I'm having trouble figuring out how to do that. I'm new to developing yt and communal code development in general. I've found the yt development documentation, but what I've read so far is focused on making changes to committed changesets. So, I've created a Bitbucket account, forked yt, and cloned the repository locally. Now what? Thanks, Jason ---- Jason Galyardt University of Georgia

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