Mailman 3 November 2013 - yt-dev

Issue #731: Simple ProfilePlot script triggers a matplotlib warning (yt_analysis/yt)
by Nathan Goldbaum Nov. 24, 2013

Nov. 24, 2013

New issue 731: Simple ProfilePlot script triggers a matplotlib warning https://bitbucket.org/yt_analysis/yt/issue/731/simple-profileplot-script-tr… Nathan Goldbaum: ``` #!python pf = load("IsolatedGalaxy/galaxy0030/galaxy0030") plot = ProfilePlot(pf.h.all_data(), 'Density', 'Temperature') ``` /usr/local/lib/python2.7/site-packages/matplotlib/axes.py:4747: UserWarning: No labeled objects found. Use label='...' kwarg on individual plots. warnings.warn("No labeled objects found. " Responsible: ngoldbaum

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Announcing: yt 2.6
by Kacper Kowalik Nov. 23, 2013

Nov. 23, 2013

Hi all, We are pleased to announce the release of yt 2.6. This is a major release that includes new features and major updates along with all the bugs identified and fixed since the release of 2.5.5 on August 28. We currently plan for this to be the final major release of the yt 2.X release series, although bug fix releases will continue for the foreseeable future. Please forward this email to other interested parties. Most notable changes include: * Relicensing whole project to BSD 3-clause * Automated absorption line fitting module developed by Hilary Egan * Significant improvement in documentation in a joint effort of the dev team led by Cameron Hummels * Documentation now includes inlined IPython notebooks, thanks to Nathan Goldbaum * RAMSES, ART, Tiger, Maestro and Castro frontends removal as their counterparts in 3.0 branch exceeded them both performance and capability wise. All users of the aforementioned codes are strongly advised to migrate to yt-3.0 * Python stack update, which now features: ipython-1.1.0, hg-2.8, python-2.7.6 numpy-1.7.1 * New ProfilePlot and PhasePlot classes thanks to Britton Smith, Nathan Goldbaum and Matt Turk. Previous mechanisms (i.e. profiles using PlotCollection) are deprecated and will be removed in future versions. * Projections of the Sunyaev-Zeldovich effect using SZpack implemented by John ZuHone * Generating Mock X-ray Photons now possible thanks to John ZuHone * Introduction of Transfer Function Helper by Sam Skillman * Initial support for installing yt with the package management system Conda. * The addition of a frontend for the Pluto code by Andrew Myers * The addition of an OBJ exporter to enable transparent and multi-surface exports of surfaces to Blender and Sketchfab by Jiill Naiman * yt can now export to RADMC3D thanks to Andrew Myers * Considerably (10x+) faster kD-tree building for volume rendering thanks to Sam Skillman * Full integration and demonstration of all available colormaps included in documentation thanks to Cameron Hummels There have also been a number of minor bugs fixed in this release. Some highlights: * Center of the plot in off_axis_projection plots is now calculated correctly, thanks to William Gray * Several enhancements to PlotWindow made by Nathan Goldbaum: - Save accepts paths to directories - Better handling of highly rectangular domains - Axes and colorbars are now toggleable - Nicer output in ipython notebook - eps_writer is now compatible with PlotWindow, thanks to John Wise * yt command line enhancements thanks to Devin Silvia and Matt Turk * Several enhancements to Athena frontend by John ZuHone * Improvements for OSX support (up to Mavericks) * Updates to halo finding routines by Britton Smith We’d also like to recognize the new contributors to the yt 2.x source code and documentation during the yt 2.5 development cycle: * Hilary Egan * John Forbes * William Gray * Stuart Mumford * Jill Naiman * Doug Rudd * Noel Scudder * Elizabeth Tasker If you are using the stable branch of yt from an installation script, you can upgrade using "yt update" or "yt update --all" to upgrade your full dependency stack. If you are using the development branch, you may already have these fixes. A tarball of this release has been uploaded to the Python Package Index (PyPI). Documentation for this release is available at: http://yt-project.org/docs/2.6/ Previous announcements from the 2.5 release cycle can be found at: 2.5.5: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-August/003… 2.5.4: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-July/00371… 2.5.3: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-June/00366… 2.5.2: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-May/003595… 2.5.1: http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2013-March/002988… Thank you very much, Kacper, on behalf of the yt development team

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Re: [yt-dev] 2.6 release todo list
by Kacper Kowalik Nov. 23, 2013

Nov. 23, 2013

On 22.11.2013 18:50, Matthew Turk wrote: > Hi all, > > We're wrapping up the dev hangout, and here are the remaining issues: Just to sum things up and give current status: > * A handful of small documentation blockers remain as of right now. > (Cameron and Stuart are taking care of this.) All outstanding PRs have been merged into yt-docs, all remaining blockers were resolved as fixed > * The 2.6 docs need to be built and uploaded to /docs/2.6 (Kacper is on this.) Tip of yt-docs has been built and uploaded to http://yt-project.org/docs/2.6 > * The yt branch needs to be merged into stable and a tag for 2.6 > created. (I will do this.) https://bitbucket.org/yt_analysis/yt/commits/053487f48672 https://bitbucket.org/yt_analysis/yt/commits/6341229f0b1c > * PyPI upload (Me again) https://pypi.python.org/pypi/yt/2.6 > * The release announcement needs to be sent out to a variety of mailing lists. > > Here's the announcement. Please leave "comments" by right-clicking if > you have anything to suggest or modify: > > https://docs.google.com/document/d/1Lzywsv1VyfgL1KDNA9i9FbKmN23wg2qzDHEcgwt… Announcement is ready and available there ^^. > Anything else? Otherwise, we'll probably push out all but the release > announcement today, then Kacper will send the email tomorrow (Poland > time). In a few minutes I'm heading to bed, so that all you guys on the other side of the Pond have some time to take a deep breath and make sure we hadn't forgotten about anything ;-) If there are no replies to this thread, I'll send it first thing tomorrow. Cheers, Kacper

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New docs build
by Nathan Goldbaum Nov. 22, 2013

Nov. 22, 2013

Hi all, There was a lot of churn last night in preparation for the release, which should happen in the next couple of days. There is an updated build on the website now: http://yt-project.org/docs/dev/ The docs really look great. I’m glad that so much work has been put into improving them - I think they will be much more useful for our users going forward. Even better, with the new inline scripts and notebooks there is a solid platform to add great looking and useful content in the future. If anyone has some spare time, it would be great if we got some eyes on the docs build to look for typos or formatting errors. -Nathan

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Issue #730: include all supported codes in description of how to load data (yt_analysis/yt)
by Cameron Hummels Nov. 22, 2013

Nov. 22, 2013

New issue 730: include all supported codes in description of how to load data https://bitbucket.org/yt_analysis/yt/issue/730/include-all-supported-codes-… Cameron Hummels: right now the page on how to load data describes details surrounding individual supported codes, but it only lists the details for 4 supported codes: http://yt-project.org/docs/dev/examining/supported_frontends_data.html it would be best to have all supported codes have an entry here.

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2.6 release?
by Nathan Goldbaum Nov. 22, 2013

Nov. 22, 2013

Hi all, Cameron just pinged me about a docs issue with a Sizemore about the 2.6 release happening on Friday. Can we hold off on that for another week or two? I'd like to be able to work on ProfilePlot and PhasePlot this weekend. Natha

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Issue #727: 1/2d support for BoxLib codes (yt_analysis/yt)
by Chris Malone Nov. 19, 2013

Nov. 19, 2013

New issue 727: 1/2d support for BoxLib codes https://bitbucket.org/yt_analysis/yt/issue/727/1-2d-support-for-boxlib-codes Chris Malone: As mentioned on the mailing list [here](http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-Nove…, BoxLib support (at least Castro/Maestro) is lacking for one and two dimensional datasets. Responsible: ChrisMalone

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Asking questions on StackOverflow
by Nathan Goldbaum Nov. 19, 2013

Nov. 19, 2013

Hi all, I recently subscribed to the [yt] tag on StackExchange. Now, whenever a question is asked using this tag on any StackExchange site, I will get an e-mail about it, just like if a question is asked on the users or dev list. Currently (as far as I can tell) zero questions have been asked using this tag... If there are a few others who are interested in subscribing to the tag, I think it might be worthwhile to add StackOverflow to the website and docs where we describe how to get help and also announce on the user’s list that StackOverflow is an alternate place to ask questions. While this might split the community somewhat - not everyone will be subscribed to StackOverflow and thus might miss useful info - I think moving some helpful suggestions to StackOverflow will massively improve googleability of common yt issues, allowing us to avoid answering the same questions over and over again. It might also be worthwhile to ask and answer some common yt questions. Off the top of my head, I think we could at least answer how to load various types of datasets into yt. -Nathan

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off axis projection in yt-3.0
by nick moeckel Nov. 17, 2013

Nov. 17, 2013

Hi there, are off axis projections expected to work for all frontends in 3.0? Using Ramses I'm getting some curious results. e.g. p = OffAxisProjectionPlot(ds, [.1, .1, 1], 'Density', north_vector=[0,1,0]) results in http://i.imgur.com/TzTbh7u.png where the whole simulation seemt to be squished into one quadrant. best, Nick

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Issue #726: Segmentation fault after a rockstar script fails on a multi particle mass dataset (yt_analysis/yt)
by Nathan Goldbaum Nov. 17, 2013

Nov. 17, 2013

New issue 726: Segmentation fault after a rockstar script fails on a multi particle mass dataset https://bitbucket.org/yt_analysis/yt/issue/726/segmentation-fault-after-a-r… Nathan Goldbaum: I just tried running the rockstar halo finder on a multi-mass particle dataset and triggered a segmentation fault after the script failed: ``` #! goldbaum at ROUS in ~/Documents/test ○ mpirun -np 4 python test.py --parallel yt : [INFO ] 2013-11-16 22:29:44,695 Global parallel computation enabled: 0 / 4 yt : [INFO ] 2013-11-16 22:29:44,695 Global parallel computation enabled: 1 / 4 yt : [INFO ] 2013-11-16 22:29:44,695 Global parallel computation enabled: 2 / 4 yt : [INFO ] 2013-11-16 22:29:44,695 Global parallel computation enabled: 3 / 4 P000 yt : [INFO ] 2013-11-16 22:29:45,322 Parameters: current_time = 645.817072369 P000 yt : [INFO ] 2013-11-16 22:29:45,322 Parameters: domain_dimensions = [64 64 64] P000 yt : [INFO ] 2013-11-16 22:29:45,325 Parameters: domain_left_edge = [ 0. 0. 0.] P000 yt : [INFO ] 2013-11-16 22:29:45,326 Parameters: domain_right_edge = [ 1. 1. 1.] P000 yt : [INFO ] 2013-11-16 22:29:45,326 Parameters: cosmological_simulation = 1 P000 yt : [INFO ] 2013-11-16 22:29:45,327 Parameters: current_redshift = 0.00139308806408 P000 yt : [INFO ] 2013-11-16 22:29:45,327 Parameters: omega_lambda = 0.7 P000 yt : [INFO ] 2013-11-16 22:29:45,327 Parameters: omega_matter = 0.3 P000 yt : [INFO ] 2013-11-16 22:29:45,327 Parameters: hubble_constant = 0.71 P000 yt : [WARNING ] 2013-11-16 22:29:45,327 The citation for the Rockstar halo finder can be found at P000 yt : [WARNING ] 2013-11-16 22:29:45,327 http://adsabs.harvard.edu/abs/2013ApJ...762..109B P000 yt : [INFO ] 2013-11-16 22:29:45,327 Rockstar is using 1 readers and 2 writers P000 yt : [INFO ] 2013-11-16 22:29:45,333 Starting 'Parsing Hierarchy' P001 yt : [WARNING ] 2013-11-16 22:29:45,327 The citation for the Rockstar halo finder can be found at P001 yt : [WARNING ] 2013-11-16 22:29:45,327 http://adsabs.harvard.edu/abs/2013ApJ...762..109B P001 yt : [INFO ] 2013-11-16 22:29:45,328 Rockstar is using 1 readers and 2 writers P001 yt : [INFO ] 2013-11-16 22:29:45,333 Starting 'Parsing Hierarchy' P002 yt : [WARNING ] 2013-11-16 22:29:45,327 The citation for the Rockstar halo finder can be found at P002 yt : [WARNING ] 2013-11-16 22:29:45,327 http://adsabs.harvard.edu/abs/2013ApJ...762..109B P002 yt : [INFO ] 2013-11-16 22:29:45,328 Rockstar is using 1 readers and 2 writers P002 yt : [INFO ] 2013-11-16 22:29:45,333 Starting 'Parsing Hierarchy' P003 yt : [WARNING ] 2013-11-16 22:29:45,356 The citation for the Rockstar halo finder can be found at P003 yt : [WARNING ] 2013-11-16 22:29:45,356 http://adsabs.harvard.edu/abs/2013ApJ...762..109B P003 yt : [INFO ] 2013-11-16 22:29:45,356 Rockstar is using 1 readers and 2 writers P003 yt : [INFO ] 2013-11-16 22:29:45,363 Starting 'Parsing Hierarchy' P001 yt : [INFO ] 2013-11-16 22:29:45,443 Finishing 'Parsing Hierarchy' P000 yt : [INFO ] 2013-11-16 22:29:45,445 Finishing 'Parsing Hierarchy' P002 yt : [INFO ] 2013-11-16 22:29:45,450 Finishing 'Parsing Hierarchy' P003 yt : [INFO ] 2013-11-16 22:29:45,473 Finishing 'Parsing Hierarchy' P000 yt : [INFO ] 2013-11-16 22:29:45,515 Gathering a field list (this may take a moment.) P000 yt : [INFO ] 2013-11-16 22:29:45,628 Adding unknown field ('io', 'particle_position_y') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'particle_index') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'creation_time') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'dynamical_time') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'particle_position_z') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'particle_position_x') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'metallicity_fraction') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_velocity_z') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_mass') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_velocity_y') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_type') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_velocity_x') to list of fields Traceback (most recent call last): File "test.py", line 8, in <module> rh = RockstarHaloFinder(ts) File "/Users/goldbaum/Documents/yt-3.0/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 216, in __init__ p = self._setup_parameters(ts) File "/Users/goldbaum/Documents/yt-3.0/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 237, in _setup_parameters ptype) yt.utilities.exceptions.YTRockstarMultiMassNotSupported: Particle type 'all' has minimum mass 1.000e+09 and maximum mass 7.820e+11. Multi-mass particles are not currently supported. [ROUS:67873] *** Process received signal *** [ROUS:67873] Signal: Segmentation fault: 11 (11) [ROUS:67873] Signal code: Address not mapped (1) [ROUS:67873] Failing at address: 0x10 [ROUS:67873] [ 0] 2 libsystem_platform.dylib 0x00007fff944c15aa _sigtramp + 26 [ROUS:67873] [ 1] 3 ??? 0x00000001101adb30 0x0 + 4565162800 [ROUS:67873] [ 2] 4 Python 0x000000010fbfa4fd PyObject_Call + 101 [ROUS:67873] [ 3] 5 MPI.so 0x00000001108ea33f __pyx_getprop_6mpi4py_3MPI_4Comm_rank + 63 [ROUS:67873] [ 4] 6 Python 0x000000010fc0a475 getset_get + 58 [ROUS:67873] [ 5] 7 Python 0x000000010fc2a197 _PyObject_GenericGetAttrWithDict + 216 [ROUS:67873] [ 6] 8 Python 0x000000010fc724e3 PyEval_EvalFrameEx + 7320 [ROUS:67873] [ 7] 9 Python 0x000000010fc70721 PyEval_EvalCodeEx + 1638 [ROUS:67873] [ 8] 10 Python 0x000000010fc17caa function_call + 336 [ROUS:67873] [ 9] 11 Python 0x000000010fbfa4fd PyObject_Call + 101 [ROUS:67873] [10] 12 Python 0x000000010fbfa68d call_function_tail + 72 [ROUS:67873] [11] 13 Python 0x000000010fbfa622 PyObject_CallFunction + 195 [ROUS:67873] [12] 14 Python 0x000000010fc2a197 _PyObject_GenericGetAttrWithDict + 216 [ROUS:67873] [13] 15 Python 0x000000010fc724e3 PyEval_EvalFrameEx + 7320 [ROUS:67873] [14] 16 Python 0x000000010fc76aaf fast_function + 182 [ROUS:67873] [15] 17 Python 0x000000010fc73919 PyEval_EvalFrameEx + 12494 [ROUS:67873] [16] 18 Python 0x000000010fc76aaf fast_function + 182 [ROUS:67873] [17] 19 Python 0x000000010fc73919 PyEval_EvalFrameEx + 12494 [ROUS:67873] [18] 20 Python 0x000000010fc70721 PyEval_EvalCodeEx + 1638 [ROUS:67873] [19] 21 Python 0x000000010fc17caa function_call + 336 [ROUS:67873] [20] 22 Python 0x000000010fbfa4fd PyObject_Call + 101 [ROUS:67873] [21] 23 Python 0x000000010fc04f2f instancemethod_call + 174 [ROUS:67873] [22] 24 Python 0x000000010fbfa4fd PyObject_Call + 101 [ROUS:67873] [23] 25 Python 0x000000010fc76274 PyEval_CallObjectWithKeywords + 93 [ROUS:67873] [24] 26 Python 0x000000010fc3fe04 slot_tp_del + 80 [ROUS:67873] [25] 27 Python 0x000000010fc43f83 subtype_dealloc + 286 [ROUS:67873] [26] 28 Python 0x000000010fc16385 frame_dealloc + 110 [ROUS:67873] [27] 29 Python 0x000000010fc9578a tb_dealloc + 101 [ROUS:67873] [28] 30 Python 0x000000010fc95771 tb_dealloc + 76 [ROUS:67873] [29] 31 Python 0x000000010fc26cbf insertdict_by_entry + 242 [ROUS:67873] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 67873 on node ROUS exited on signal 11 (Segmentation fault: 11). -------------------------------------------------------------------------- ``` Test script is here: ``` #! from yt.mods import * from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder import glob as glob ds = load("Enzo_64/DD0043/data0043") ts = TimeSeriesData([ds]) rh = RockstarHaloFinder(ts) rh.run() ```

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