Mailman 3 August 2011 - yt-dev

Interest in a yt Workshop?
by Christopher Moody Sept. 8, 2011

Sept. 8, 2011

Hi all, Earlier today I sent an email on yt-users list mistakenly reporting that there was a yt users' & developers' conference. Now at the moment there isn't one, but after having spoken to Matt a bit, we realized that maybe that's not a bad idea. We came up with a few questions: 1. Virtual or real workshop? 2. What should be the goals? 3. How many people would be interested, and how many could come? 4. Funding sources? We were tentatively considering piggy-backing the Enzo conference, but adding *two* days *before* it. Thoughts? chris

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Introducing the yt hub
by Britton Smith Sept. 1, 2011

Sept. 1, 2011

Good morning yt developers, I am very pleased to introduce to you all the yt hub: http://hub.yt-project.org/. This was one of the main motivations for moving to yt-project.org. Many here might remember the enzotools barn, which was a place for people to submit non-yt related enzo scripts. The barn was very limited in scope and had somewhat poor usability since the submission and registration processes were not at all automated or simple. Those days are over. With the yt hub, users can create their own accounts and submissions themselves. We are aiming for the yt hub to become the place to share all things related to computational astrophysics: yt scripts, simulation code specific scripts, relevant news (like workshop announcements), repositories of scripts for making figures from published papers, etc. Users also have the option of subscribing to the hub, where they will receive email alerts of new submissions. Before we announce this to the full community, it would be great have the site decently populated with submissions. If you have anything that you think other people would be interested in, please post it to the hub. Currently, the recommended method is to create a repository somewhere like bitbucket and to submit the link to that. If you'd like to host you submissions somewhere else, that's fine, too. All comments and feedback are welcome. Hopefully, this can be something really great. Britton Matt

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RFC: Preliminary build of 2.2 docs
by Matthew Turk Aug. 31, 2011

Aug. 31, 2011

Hi all, I've uploaded a build of the docs for 2.2 here: http://yt-project.org/docs/2.2/ (2.2 will go out probably on Friday morning.) There are two new top-level sections: http://yt-project.org/docs/2.2/interacting_with_yt.html http://yt-project.org/docs/2.2/getting_involved.html and Elizabeth Tasker has also added a FAQ section which we can all continue updating. Britton and Stephen have been studiously adding docs as they have developed, so there are a few additional sections under Analysis Modules that are new, as well. I'd love to hear any comments, particularly about those two sections but also covering everything else, if you have them. Cameron is currently writing the "Command Line Utility" section of "Interacting with yt" but I wanted to send this out so that we could have a bit of time to solicit comments before anything goes live. Comments on anything? Feel free, also, if you see something wrong to directly fork: https://bitbucket.org/yt_analysis/yt-doc/fork and issue a pull request. Elizabeth has been doing this and it has been very effective. Thanks very much for *any* thoughts, Matt

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Periodic grid boxes
by Matthew Turk Aug. 24, 2011

Aug. 24, 2011

Hi all, I have been looking at FLASH data today, which suffers from a particular oddity which will impact users of every other code; however, block structured AMR will bring it out more often. In the covering_grid code, we have this routine: def _get_list_of_grids(self, buffer = 0.0): import pdb;pdb.set_trace() if self._grids is not None: return if na.any(self.left_edge - buffer < self.pf.domain_left_edge) or \ na.any(self.right_edge + buffer > self.pf.domain_right_edge): grids,ind = self.pf.hierarchy.get_periodic_box_grids( self.left_edge - buffer, self.right_edge + buffer) ind = slice(None) else: grids,ind = self.pf.hierarchy.get_box_grids( self.left_edge - buffer, self.right_edge + buffer) level_ind = (self.pf.hierarchy.grid_levels.ravel()[ind] <= self.level) sort_ind = na.argsort(self.pf.h.grid_levels.ravel()[ind][level_ind]) self._grids = self.pf.hierarchy.grids[ind][level_ind][(sort_ind,)][::-1] This is used to identify grids that overlap with a given region in space. As you can see, if the grid abuts the domain boundary, yt will look for grids assuming a period. But then that information is basically completely discarded, and all grids are selected. This absolutely *kills* performance. I looked into it, and this dates back several years. Can anyone -- Stephen, Britton, Sam, you have all looked at periodic grids -- think of a reason why we should err on the side of not following the results of get_periodic_box_grids? Or is it safe to remove that line, and improve performance by a factor of tons? Thanks, -Matt

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Enzo parameter file reading change
by Matthew Turk Aug. 21, 2011

Aug. 21, 2011

Hi all, As discussed over on yt-users, people have requested that the parameter file reading be changed for Enzo, to scrape the entire parameter file. I've committed a change and pushed to *my* fork of yt on BitBucket. The change is shorter than this email. https://bitbucket.org/MatthewTurk/yt/changeset/e96282130e63 Please pull this revision and see if it works for your parameter files. It works for mine. If it works globally, I will push to the main repo. A test script is here: http://paste.enzotools.org/show/1751/ which will print out the conversion factors between the two. There are other items to check as well. This is potentially a HUGE change that might have errors, so I ask for your testing on it! If I get several testings, I will push, otherwise I will back it out. There are three things I wanted to bring up: 1) Enzo 3.0 will feature a much better configuration system, making most of this irrelevant. 2) I would like to move away from using the CurrentTimeIdentifer as a unique ID to using MetaDataDatasetUUID as that identifier. This will break existing pickles. I think the natural time to do this is at yt-3.0. [+-][01]? 3) With yt-3.0, I would like to remove the dict-like access to the parameter file we currently have, which currently queries *FOUR* dictionaries in order: units time_units parameters conversion_factors I'd like to split this into at least parameters and units. [+-][01]? -Matt

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yt in MacPorts
by Thomas Robitaille Aug. 20, 2011

Aug. 20, 2011

Dear yt developers, I just wanted to let you know that I've added yt to the MacPorts package manager (http://www.macports.org/). I recently created a page with instructions for how to set up a fully functioning Python distribution for Astronomy with MacPorts: http://astrofrog.github.com/macports-python/ and as of today, you can type: sudo port install py27-yt and yt and all required dependencies will be installed. I'd be happy to advertise this on the users mailing list if you like, or feel free to do it if you prefer. Note that MacPorts relies on stable releases, so I had to use the auto-generated 2.1 tar file on bitbucket, which MacPorts needs to apply a one-line patch to in order to get to compile. Just letting you know so you are aware that this installation method is dependent on the tags. In addition to py27-yt, I created py25-yt and py26-yt (it's easy to have multiple Python versions side by side in MacPorts). Note that it's also possible to install the latest dev version of yt - the easiest way it to install py27-yt as above to get all the dependencies working, then to download the latest source and do python setup.py install --user Let me know if you have any questions about this! Best regards, Thomas Robitaille

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yt-project.org
by Britton Smith Aug. 19, 2011

Aug. 19, 2011

Hi all, As yt has become much more than analysis for Enzo, I think it has outgrown yt.enzotools.org as its host. Without making this longer than it has to be, can I get a +-1 from people on moving from yt.enzotools.org to yt-project.org? We would be not simply remove yt.enzotools.org from existence, but would redirect it to the new url so people won't get lost. Britton Matt

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precision in io
by Geoffrey So Aug. 16, 2011

Aug. 16, 2011

I was wondering if there is a consensus about the precision of the data output by YT should be? I've came upon this question when trying to output ellipsoidal parameters along with halo attributes. With the current setting, the halo attributes are outputted with 9 decimal points, but the ellipsoid parameters determined using the particle's position (when the data is 64 bit) has 16 decimals. I was thinking that it is best to keep whatever precision we have, but Stephen brought up a good point, that the halos are only vaguely defined, that the extra digits are a waste of storage. So I just want to see if anyone even cares, and what we want to go with. Either way, I think it is best to be consistent across the board, having both halo or ellipsoid IO in the same amount of decimals. From G.S.

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Numpy warning supression
by Stephen Skory Aug. 15, 2011

Aug. 15, 2011

Hi all, this may not be a big issue because most people won't be using Geoffrey's new ellipsoidal halo information. However, it may spark discussion about this topic overall and set a useful precedent. I have just finished vectorizing some of Geoffrey's code that is attached to the halo finder code. In so doing, I am allowing NaNs to come into the calculation because it keeps thing simple. Happily, the NaNs only exist where I know the answers can't be, and numpy.nanargmin/max() happily ignores the NaNs. But when I make the NaNs through a divide by zero (and some other stuff) I get warning messages telling me I just did what I knew was going to happen. My question is, do we think that I should try to suppress these warnings? They are accurate, but the math that makes them is done intentionally, so they're not informative. Can I get a +1/0/-1? Thanks! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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Testing!
by Matthew Turk Aug. 12, 2011

Aug. 12, 2011

Hi all, I am writing about testing yt. Right now we have 100 tests (on the nose), and it's super easy to blow through the entire list very rapidly. But, they only cover a tiny fraction of the code base. (The important fraction, but a fraction none the less.) And, they only run on a single dataset, the one that comes with yt. To improve this situation, we need two things. 1. Datasets with some complexity. 2. More tests. == Datasets == So, if you have a dataset you think might present some challenges -- lots of fields, interesting structure, or if it's NOT ENZO, please consider submitting it for testing! *We need more non-Enzo datasets to run these tests on!* I'm happy to set up testing, I just need some interesting datasets from the other codes -- Orion, Castro, Maestro, Nyx, FLASH in particular. I can copy them from wherever, or download from wherever. == Tests == Writing tests is really easy. And if you have written a module for Enzo, you should *really* write a test for it. Make it simple, make it easy, and it doesn't matter if it takes a little while. Here's how to write a test. The best examples are in the yt source repository, under tests/hierarchy_consistency.py and tests/object_field_values.py . There are basically three modes of testing in yt: 1. Testing that something is true or false. This is how some of the hierarchy consistency checks are done. 2. Testing that something remains *nearly* the same. This allows for some relative change between changesets. 3. Testing that something remains *exactly* the same. This allows for no change between changesets. All three basically look the same. To write a test, just open up a file in tests/ and make it look a bit like the object_field_values.py file. For instance, put this at the top: import hashlib import numpy as na from yt.utilities.answer_testing.output_tests import \ YTStaticOutputTest, RegressionTestException, create_test Now, make a new object, called MyModuleTest or something, and inherit from YTStaticOutputTest. Give it a name, and implement "run" and "compare". Inside run, set self.result. Inside compare, accept old_result and compare to self.result. Like this: class MyModuleTest(YTStaticOutputTest): name = "my_module_test" def run(self): self.result = my_module(self.pf) def compare(self, old_value): self.compare_array_delta(old_result, self.result, 0.0) There are lots of compare functions. This example ensures exact results for an array. You can also use hashlib.sha256 to compare things for precise, no delta differences. And if you want to check True/False, just store True or False as self.result. I'm happy to help out with this, but testing all the contributed modules from over the years is a daunting task! Please, if you have worked on analysis modules that you would like ... not to break ... contribute a test or two. It'll help ensure reliability and invariance over time. And if we decide an answer changed, and it was a good change, we can update the test results. Feel free to write back with any questions or comments, and let me know if you have a dataset to contribute! Thanks everyone, Matt

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