Mailman 3 February 2014 - yt-dev

Trello
by Matthew Turk 26 Feb '14

26 Feb '14

Hi all, I renamed the yt Trello board to be "yt_analysis" so any bookmarks you have might be broken. Sorry about that! https://trello.com/yt_analysis Also, I *really* like Trello. I think we should start using it more, particularly since BB is moving away from issue tracking and toward JIRA integration, which I've been disappointed in. Looks like we could potentially connect services: https://zapier.com/zapbook/bitbucket/trello/ but I don't have the roundtuits to look into this right now. -Matt

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Issue #788: RAMSES AMRKDTree (yt_analysis/yt)
by Sam Skillman 25 Feb '14

25 Feb '14

New issue 788: RAMSES AMRKDTree https://bitbucket.org/yt_analysis/yt/issue/788/ramses-amrkdtree Sam Skillman: Seems broken. the tree seems to have no bricks associated with it after building, and spits out a number of "Failed to Split Grid" errors. Once fixed, respond to the email thread with Joshua Albert Responsible: samskillman

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Speed comparison relative to 2.X
by Nathan Goldbaum 23 Feb '14

23 Feb '14

Hi all, Matt asked me to look at the performance of unitrefactor relative to 2.X and the current 3.0 codebase. I've done that using the following test script: http://paste.yt-project.org/show/4312 The script cycles through a time series, printing out particle masses for each dataset. In a perfect world, this should be an i/o-bound operation. Currently the timings for running this test are as follows: yt 2.x (dd1ca98) 18.37s user 1.43s system 99% cpu 19.997 total yt 3.0 (1b17b7e) 48.76s user 1.81s system 99% cpu 50.743 total yt-3.0 unitrefactor (8131901df14c) 78.72s user 2.00s system 99% cpu 1:20.85 total So about a thirty second difference between each of the versions. Clearly this isn't the best news given that we're moving to 3.0 going forward. That said, I don't think there has been a lot of focus on 3.0 performance, so it's possible (likely even) there's some low-hanging fruit for performance optimizations. There was also a big refactor of how i/o works for Enzo datasets (moving away from hdf5_light_reader toward h5py) - maybe that explains some of the difference between 2.x and 3.0. Hope this is helpful, -Nathan

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Issue #787: particle_specific_angular_momentum fields not working (yt_analysis/yt)
by Britton Smith 23 Feb '14

23 Feb '14

New issue 787: particle_specific_angular_momentum fields not working https://bitbucket.org/yt_analysis/yt/issue/787/particle_specific_angular_mo… Britton Smith: In the unitrefactor, running this script: http://paste.yt-project.org/show/4327/ gives the following: Traceback (most recent call last): File "dqtest.py", line 9, in <module> print sp['particle_specific_angular_momentum_x'] File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 205, in __getitem__ self.get_data(f) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 609, in get_data self._generate_fields(fields_to_generate) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 626, in _generate_fields fd = self._generate_field(field) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 240, in _generate_field tr = self._generate_particle_field(field) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 320, in _generate_particle_field rv = self.pf._get_field_info(*field)(gen_obj) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/fields/derived_field.py", line 181, in __call__ dd = self._function(self, data) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/fields/particle_fields.py", line 168, in _particle_position return data[_ptype, coord_name][:,axi] File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 198, in __getitem__ f = self._determine_fields([key])[0] File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 441, in _determine_fields finfo = self.pf._get_field_info(ftype, fname) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 379, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'Coordinates')' in DD0064. I am able to grab the particle_positions on their own for a data object, but not within this field.

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yt Presentation at SIAM PP14
by Sam Skillman 21 Feb '14

21 Feb '14

Hi all, I just want to let you all know that I'll be giving a short talk on parallelism in yt at a SIAM Parallel Processing meeting ( http://www.siam.org/meetings/pp14/), focused on how we have designed yt to allow for multiple entry points into parallel computations. In any case, I'd like to invite anyone to send me (perhaps off-list) any case studies or examples of when the parallel nature of a yt computation has allowed you to get your science done. Please send over anything, and images/plots are all welcome. I think it would be super cool to just show example after example of yt getting out of the way and letting people *do science*. Anything I use I'll make sure to attribute. My talk is on Friday so send over anything before ... Friday. Talk abstract: http://meetings.siam.org/sess/dsp_talk.cfm?p=61040 Cheers, Sam

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ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
by Matthew Turk 20 Feb '14

20 Feb '14

Hello All! I am pleased to announce that SciPy 2014, the thirteenth annual Scientific Computing with Python conference, will be held this July 6th-12th in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference allows participants from all types of organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. For more information please visit our website: https://conference.scipy.org/scipy2014/ This year the conference has been extended to include an additional day of presentations. During the presentation days SciPy is proud to host the following event and talk types: Keynotes Expert Panels Short Talks Poster Presentations Birds of a Feather Sessions The full program will consist of two days of tutorials by followed by three days of presentations, and concludes with two days of developer sprints on projects of interest to attendees. This year, we are excited to present a job fair for the first time! Specialized Tracks This year we are happy to announce two specialized tracks that run in parallel to the general conference: Scientific Computing in Education Thanks to efforts such as Software Carpentry, the Hacker Within and grassroots Python Bootcamps, teaching scientific computing as a discipline is becoming more widely accepted and recognized as a crucial task in developing scientific literacy. This special track will focus on efforts to promote and develop scientific computing education, as well as related topics such as reproducibility and best practices for scientific computing. Geospatial Data in Science Python has become a core component of organiziing, understanding, and visualizing geospatial data. This track will focus on libraries, tools and techniques for processing Geospatial data of all types and for all purposes -- from low-volume to high-volume, local and global. Domain-specific Mini-symposia Introduced in 2012, mini-symposia are held to discuss scientific computing applied to a specific scientific domain/industry during a half afternoon after the general conference. Their goal is to promote industry specific libraries and tools, and gather people with similar interests for discussions. Mini-symposia on the following topics will take place this year: Astronomy and astrophysics Bioinformatics Geophysics Vision, Visualization, and Imaging Computational Social Science and Digital Humanities Engineering Tutorials Multiple interactive half-day tutorials will be taught by community experts. The tutorials provide conceptual and practical coverage of tools that have broad interest at both an introductory or advanced level. This year, a third track will be added, which target specifically programmers with no prior knowledge of scientific python. Developer Sprints A hackathon environment is setup for attendees to work on the core SciPy packages or their own personal projects. Theconference is an opportunity for developers that are usually physically separated to come together and engage in highly productive sessions. It is also an occasion for new community members to introduce themselves and receive tips from community experts. This year, some of the sprints will be scheduled and announced ahead of the conference. Birds-of-a-Feather (BOF) Sessions Birds-of-a-Feather sessions are self-organized discussions that run parallel to the main conference. The BOFs sessions cover primary, tangential, or unrelated topics in an interactive, discussion setting. This year, some of the BOF sessions will be scheduled and announced ahead of the conference. Important Dates March 14th: Presentation abstracts, poster, tutorial submission deadline. Application for sponsorship deadline. April 17th: Speakers selected April 22nd: Sponsorship acceptance deadline May 1st: Speaker schedule announced May 6th, or 150 registrants: Early-bird registration ends July 6-12th: 2 days of tutorials, 3 days of conference, 2 days of sprints We look forward to a very exciting conference and hope to see you all in Austin this summer! The SciPy2014 Organizers

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Issue #786: missing doc string in ProjectionPlot for width (yt_analysis/yt)
by gsiisg 18 Feb '14

18 Feb '14

New issue 786: missing doc string in ProjectionPlot for width https://bitbucket.org/yt_analysis/yt/issue/786/missing-doc-string-in-projec… gsiisg: In the online documentation for 2.6 and 2.X dev for the function ProjectionPlot, the doc string that is suppose to describe how the argument 'width' works is missing. There also ought to be a note that says the units would be in proper units instead of co-moving somewhere.

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Issue #785: SimulationTimeSeries broken (yt_analysis/yt)
by Britton Smith 18 Feb '14

18 Feb '14

New issue 785: SimulationTimeSeries broken https://bitbucket.org/yt_analysis/yt/issue/785/simulationtimeseries-broken Britton Smith: In the tip of unitrefactor, the following script: http://paste.yt-project.org/show/4315/ gives this error: ``` #!python Traceback (most recent call last): File "test.py", line 4, in <module> for pf in es: File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/time_series.py", line 156, in __iter__ pf = load(o, **self.kwargs) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line 92, in load raise YTOutputNotIdentified(args, kwargs) yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('enzo_tiny_cosmology/32Mpc_32.enzo',) {}, but could not load! ``` This is because of the changes to TimeSeriesData.__new__, which now checks the first argument and (I think) is not the same when being called by a subclass as it is when instantiated directly.

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Issue #784: FLASH 2.5 HDF5 format not supported (yt_analysis/yt)
by Miguel de Val-Borro 17 Feb '14

17 Feb '14

New issue 784: FLASH 2.5 HDF5 format not supported https://bitbucket.org/yt_analysis/yt/issue/784/flash-25-hdf5-format-not-sup… Miguel de Val-Borro: I have some 2-D HDF5 files created with FLASH2.5 that cannot be loaded by yt. The code has been compiled recently and uses a relatively new version of the HDF5 library. Here is the output error message: ``` File "/usr/lib/python2.7/site-packages/yt-2.7dev-py2.7-linux-x86_64.egg/yt/convenience.py", line 78, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/usr/lib/python2.7/site-packages/yt-2.7dev-py2.7-linux-x86_64.egg/yt/frontends/flash/data_structures.py", line 225, in __init__ StaticOutput.__init__(self, filename, data_style) File "/usr/lib/python2.7/site-packages/yt-2.7dev-py2.7-linux-x86_64.egg/yt/data_objects/static_output.py", line 94, in __init__ self._parse_parameter_file() File "/usr/lib/python2.7/site-packages/yt-2.7dev-py2.7-linux-x86_64.egg/yt/frontends/flash/data_structures.py", line 425, in _parse_parameter_file for d in (dimensionality)+range(3-dimensionality): TypeError: unsupported operand type(s) for +: 'int' and 'list' ``` I am attaching the HDF5 plot file to this issue. Is there any possible way to fix this problem?

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Issue #783: HOP and FOF Halo Finders don't allow exclusive non-DM particles (yt_analysis/yt)
by Desika Narayanan 16 Feb '14

16 Feb '14

New issue 783: HOP and FOF Halo Finders don't allow exclusive non-DM particles https://bitbucket.org/yt_analysis/yt/issue/783/hop-and-fof-halo-finders-don… Desika Narayanan: I would find it useful to have the HOP and FOF Halo finders that ship with yt (3.0) be able to identify groups of particles that aren't dark matter particles (in particular, to link together only gas particles). Responsible: MatthewTurk

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