Mailman 3 September 2014 - yt-dev

Fwd: Blue Waters Advanced User Workshop and yt development workshop
by Matthew Turk 12 Sep '14

12 Sep '14

Hi everyone, As noted below, there's going to be a development workshop for yt at NCSA at University of Illinois Urbana-Champaign, on October 16 and 17. This is going to be a dev workshop, but *everyone* is invited (whether you use Blue Waters or not!). There isn't yet a set schedule, but I hope we can spend time on solidifying support for newer frontends, attaching to running simulations, and hopefully even converting the n-body codes to forest-of-octree from the current implementation. I'm also thinking it might be a good idea to block off an afternoon *just* for converting any analysis modules or analysis code that works on yt 2 but not yt 3. In the next few days I will have information about funding for attendance; please write to me to let me know if you'd like travel support. I can't guarantee anything yet, but I am hoping to have some positive information soon. Hope to see lots of people there! -Matt ---------- Forwarded message ---------- From: <help+bw(a)ncsa.illinois.edu> Date: Mon, Sep 1, 2014 at 3:16 PM Subject: Blue Waters Advanced User Workshop and yt development workshop To: Blue Waters Announcements <noreply(a)ncsa.illinois.edu> We are pleased to announce a three-day, hands-on oriented advanced user workshop about using Blue Waters to its fullest potential. Representatives from Cray, Allinea, PGI and NVIDIA will be on-site to present material and interact with attendees so bring your own code. This work shop is targeting existing or recently allocated, advanced users of Blue Waters. In conjunction with the Blue Waters Advanced User workshop, we are pleased to invite people who are interested in participating in development of the yt project (yt-project.org) to a two-day hands-on development workshop, focusing on parallel and in situ analysis, stabilizing existing data format front-ends, and expanding the capabilities of yt to take advantage of supercomputing resources. Blue Waters Advanced User workshop https://bluewaters.ncsa.illinois.edu/blue-waters-advanced-user-workshop-oct… yt development workshop https://bluewaters.ncsa.illinois.edu/yt-development-workshop-oct-16-17-2014 We hope to see you here.

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How to issue multiple PR's on BitBucket?
by Chris Malone 11 Sep '14

11 Sep '14

Hey devs, I apologize in advance for my naivety... I asked this in IRC, and Kacper was kind enough to provide some insight, but alas I was still having problems getting this to work. I know it involves bookmarks and heads, but I'm still not as familiar with mercurial as I am with git, so this all confuses my gitsense. Also, I know there are others who have this issue - perhaps this should be on the docs page somewhere... Let's say I have my fork of yt wherein I already have a pending PR on BB. I can't simply make changes to my fork and push them in the default branch/bookmark because BB likes to automagically update PRs. What is the recommended procedure for committing and pushing new changes to my fork so that I can issue an additional PR? Do I create a bookmark, then commit my changes, then push that bookmark to BB? If so, how then can I issue a PR from that bookmark - I can't seem to find this on the BB interface. Chris

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Issue #896: Inconsistent total mass in Gadget snapshots spread over multiple files (yt_analysis/yt)
by afitts 10 Sep '14

10 Sep '14

New issue 896: Inconsistent total mass in Gadget snapshots spread over multiple files https://bitbucket.org/yt_analysis/yt/issue/896/inconsistent-total-mass-in-g… afitts: There is a difference in what the total_mass() reports when using a snapshot from a single file and a snapshot from multiple files. What's even stranger is that if you query total_quantity("PartType*_mass") both the single and multiple file snapshots match up. The corresponding snapshots and script can be found here: https://www.dropbox.com/s/2t5pzgwgc7fug9n/massbug.tar.gz?dl=0

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Issue #895: Can't load mass of stars from Gadget snapshots written to multiple files (yt_analysis/yt)
by afitts 10 Sep '14

10 Sep '14

New issue 895: Can't load mass of stars from Gadget snapshots written to multiple files https://bitbucket.org/yt_analysis/yt/issue/895/cant-load-mass-of-stars-from… afitts: I have this recurring problem when using snapshots written to multiple files with Gadget. I'm interested in following the total stellar mass at each time step. However when using multiple files i get the error: http://paste.yt-project.org/show/5107/ when trying to reference particular files. I redid my simulation writing to one file per snapshot and never had a problem referencing the mass of all the stellar particles. Attached you will find the snapshot written to one file (snapshot_025.hdf5) and one written to multiple files (in the snapdir_025).These are from the exact same simulation, the only difference being how many files the snapshots were distributed over. Both cases have been run a second time and the problem has still remained.

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members needed for representative positions
by Britton Smith 09 Sep '14

09 Sep '14

Hi everyone, Members, if you are interested in taking on some leadership within yt, please consider signing yourself to be a representative for one for the five subcomponents: infrastructure, plotting, testing, documentation, and analysis modules. If you have experience with one of these areas or are interested in becoming more involved in planning and/or development, consider yourself right for the position. An area should ideally be represented by at least a two or three people. All that is required is that someone from each subcomponent be present at a monthly hangout to discuss the latest comings and goings. Additionally, if you are the first person to sign up for one area, consider reaching out to a couple others who you think would also be right for the position. If you'd like to sign up, clone the YTEP repo ( https://bitbucket.org/yt_analysis/ytep) and add your name to YTEP-1776 and either issue a PR or just push directly. When changes are pushed to the repo, the document will get automatically rebuilt and will be viewable here: http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-1776.html Britton

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Issue #894: Test suite does not detect load function breakage (yt_analysis/yt)
by Andrew Myers 08 Sep '14

08 Sep '14

New issue 894: Test suite does not detect load function breakage https://bitbucket.org/yt_analysis/yt/issue/894/test-suite-does-not-detect-l… Andrew Myers: This issue came up regarding PR 1190. Currently, if one breaks the code in such a way that the load function fails for certain datasets, the test suite will skip those datasets instead of reporting a failure. IME, breaking the _is_valid methods is really easy to do when doing frontend work, and it be nice if the answer tests reported a failure when this happens. As Nathan suggested in IRC, the requires_ds decorator probably just needs to be made smarter. Responsible: atmyers

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Issue #893: Feature request: specify xyz or zyx order in load_octree (yt_analysis/yt)
by astrofrog 07 Sep '14

07 Sep '14

New issue 893: Feature request: specify xyz or zyx order in load_octree https://bitbucket.org/yt_analysis/yt/issue/893/feature-request-specify-xyz-… astrofrog: The load_octree currently makes assumptions about how to map the 1-d array of quantities into three dimensions. I think it varies fastest along z, then along y, then along x. It would be nice to be able to specify this order using an argument that could be set to either e.g. ``xyz`` or ``zyx``.

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Issue #892: OffAxisProjection yields different results than OnAxisProjection (yt_analysis/yt)
by Cameron Hummels 04 Sep '14

04 Sep '14

New issue 892: OffAxisProjection yields different results than OnAxisProjection https://bitbucket.org/yt_analysis/yt/issue/892/offaxisprojection-yields-dif… Cameron Hummels: ProjectionPlot (on-axis) images and the OffAxisProjectionPlot images (specifying vectors to be on-axis) appear to yield different results: This simple script demonstrates what I'm talking about: http://paste.yt-project.org/show/5049/ Running this script yields 4 images: off_axis_proj.png - http://i.imgur.com/CKbq5iO.png on_axis_proj.png - http://i.imgur.com/2iBucuv.png off_axis_weighted_proj.png - http://i.imgur.com/RQV2REP.png on_axis_weighted_proj.png - http://i.imgur.com/CNWHyQS.png The weighted images are basically the same for both on and off-axis, but the unweighted images are significantly different. Suggestion from @ngoldbaum that perhaps the projection conversion was not being applied correction in the non-weighted off-axis projection. Wanted to make an issue of this problem before I forget about it.

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normination: Chris Malone
by Michael Zingale 03 Sep '14

03 Sep '14

I'd like to nominate Chris Malone for member status. Chris is the one who got me introduced to yt (full disclosure, I was his thesis advisor). Chris has actively hacked on the boxlib stuff (including a PR awaiting two more approvals right now), as well as a number of fixes throughout that you can see in the hg logs, and has taken an active role in answering questions on the yt-user's list. Mike -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

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Nomination: Kenza Arraki
by Matthew Turk 03 Sep '14

03 Sep '14

Hi all, I'd like to nominate Kenza Arraki for membership. Kenza has acted as the representative for the NMSU-ART code, and has spent a considerably amount of time and effort working on making sure it's correctly set up, and usable for the folks using it. I think she would be an excellent liaison for NMSU-ART, and a great addition to the membership ranks. -Matt

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