Mailman 3 June 2015 - yt-dev

Issue #1034: halo callback docstring issue (yt_analysis/yt)
by Nathan Goldbaum 22 Jun '15

22 Jun '15

New issue 1034: halo callback docstring issue https://bitbucket.org/yt_analysis/yt/issue/1034/halo-callback-docstring-iss… Nathan Goldbaum: The docstring for the virial_quantities halo callback is incorrect. The docstring references a `critical_density` keyword argument, but the actual function signature contains a `critical_overdensity` keyword argument. While fixing this, it would probably be worth giving the rest of the docstrings in this file a once-over.

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Feature Request: Create data set format mapper
by Joseph Smidt 16 Jun '15

16 Jun '15

Not sure if it is better to request features here or on bitbucket so I am doing both [1]. I am doing some code comparisons between Enzo and Gadget and it would be nice if I could map an Enzo data set to Gadget and visa versa. And I am sure it would be nice if YT users could translate data sets between all codes YT can read. YT already reads in and transforms these data sets to match YT's internal structures. It would be a nice feature to be able to map one data set to another for code comparison purposes using the already established plumbing. Thanks. [1] https://bitbucket.org/yt_analysis/yt/issue/1033/create-data-set-format-mapp… -- ------------------------------------------------------------------------ Joseph Smidt <josephsmidt(a)gmail.com> Theoretical Division P.O. Box 1663, Mail Stop B283 Los Alamos, NM 87545 Office: 505-665-9752 Fax: 505-667-1931

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Issue #1033: Create data set format mapper (yt_analysis/yt)
by Joseph Smidt 16 Jun '15

16 Jun '15

New issue 1033: Create data set format mapper https://bitbucket.org/yt_analysis/yt/issue/1033/create-data-set-format-mapp… Joseph Smidt: I am doing some code comparisons between Enzo and Gadget and it would be nice if I could map an Enzo data set to Gadget and visa versa. And I am sure it would be nice if I could translate data sets between all codes YT can read. YT already reads in and transforms these data sets. It would be a nice feature to be able to map one data set to another for code comparison purposes.

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Issue #1032: Projection Plot Image Size Inconsistency (yt_analysis/yt)
by ggoodwin52 12 Jun '15

12 Jun '15

New issue 1032: Projection Plot Image Size Inconsistency https://bitbucket.org/yt_analysis/yt/issue/1032/projection-plot-image-size-… ggoodwin52: I use projection plots to generate images of my simulation marching through time, then combine the images into a video using mencoder. Attached is a sample script I use to generate the images and a sample video. You will notice in the video that the frame "oscillates" as it progresses, which is very distracting from the actual simulation. This oscillation is due to some of the images being rendered with 360 pixels in the vertical direction and others rendered with 359 pixels. Nothing changes in the window height or vertical position of the plot center, as you will see in the attached script. I have tried using different figure sizes, but the result it the same. For the vertical position of the plot center, I tried using both "height/2." and hardcoding in the coordinate (0.16 in this case), but it didn't correct the issue. I have uploaded ten consecutive timesteps which can be used to run the attached script. You will notice that steps 308350, 308400 and 308650 are rendered with 360 pixels in the vertical direction, and all others are rendered with 359 pixels. Here is the tar file for the dataset: http://use.yt/upload/679cc306 I ran this script using the most updated version of development yt as well as 3.1 stable with the same result. Perhaps there is a way to control the number of pixels used, but I could not find this in the yt documentation. Any help is appreciated!

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VR refactor status update
by Matthew Turk 10 Jun '15

10 Jun '15

Hi all, Andrew, Kacper, Allyson and I had a hangout to go over the current state of the VR refactor that Sam started. Where we're at: * Docs need to be written and updated. I have committed to taking this on, and I am starting today. * There are two cameras that need to be ported, the setreo spherical camera and the perspective camera. Suoqing, is there any chance you might be able to take a look at doing this, and issuing a PR to Sam's repository? I ask only because you've been so good at camera porting in the past. :) Once that's done, since there is a backwards-compatible camera interface, I assert that we should consider heavily simply pulling in the code and beginning to migrate. -Matt

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Issue #1031: Bug Report: Memory leak when rendering projection plots in parallel (yt_analysis/yt)
by ggoodwin52 10 Jun '15

10 Jun '15

New issue 1031: Bug Report: Memory leak when rendering projection plots in parallel https://bitbucket.org/yt_analysis/yt/issue/1031/bug-report-memory-leak-when… ggoodwin52: I emailed this bug report out to yt-users before finding this repository, sorry for the double post. I believe I have found a memory leak when iterating through a DatasetSeries in parallel to render projection plots of each data file in the series. I work in a CFD research group and our code is built on boxlib, so I have been using yt to generate images of my simulations. The DatasetSeries's I work with are fairly large, on the order of 6000 to 7000 data sets per series. To expedite the image rendering process, I have been using yt's parallelism to iterate through the series with openmpi. The ram usage, per mpi process, increases steadily throughout the duration of the script's runtime. When running my attached script with 16 mpi processes on a 16 core machine (1 process per core) the ram usage starts at about 2.56 GB per process and gradually increases to over 25 GB per process, at which time the script typically crashes due to insufficient ram on the machine to continue running. My simulations do involve data sets of increasing memory requirements versus simulation time, but not to the scale mentioned above in the corresponding ram increases. I determined that the crashing is due to a memory leak by starting the script over after it crashed, using only the data set files that had not yet been processed (to ensure that the memory required to render the projection of each data set is the same as it was before it crashed by starting over at the same time in the simulation as when it crashed). I also ran this script on my university's cluster, using several different openmpi implementations, and always got the same result. Additionally, the crashes always occur at approximately the same script runtime. Attached to this email is a copy of a script I'm using. I run the script on my 16 core mini-cluster using the command: mpirun -np 16 --cpus-per-proc 1 br0.05_temp.py I also attached a sample image of the projection plots I'm generating. Any help with this bug is appreciated!

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Fwd: [New post] Get your Bearings with HDF Compass
by Matthew Turk 10 Jun '15

10 Jun '15

Compass is a pretty awesome project -- John demoed it at the workshop last fall at NCSA. Could be really fun to explore and to develop plugins for! ---------- Forwarded message ---------- From: HDF BLOG <donotreply(a)wordpress.com> Date: Wed, Jun 10, 2015 at 3:28 PM Subject: [New post] Get your Bearings with HDF Compass To: matthewturk(a)gmail.com The HDF Group posted: "John Readey, The HDF Group We’ve recently announced a new viewer application for HDF5 files: HDF Compass. In this blog post we’ll explore the motivations for providing this tool, review its features, and speculate a bit about future direction for Compas" New post on *HDF BLOG* <https://hdfgroup.org/wp/?author=5> Get your Bearings with HDF Compass <https://hdfgroup.org/wp/2015/06/get-your-bearings-with-hdf-compass/> by The HDF Group <https://hdfgroup.org/wp/?author=5> *John Readey, The HDF Group* [image: HDF Compass] *We’ve recently announced a new viewer application for HDF5 <https://www.hdfgroup.org/HDF5/> files: HDF Compass. In this blog post we’ll explore the motivations for providing this tool, review its features, and speculate a bit about future direction for Compass.* *HDF Compass <https://www.hdfgroup.org/projects/compass/index.html> is a desktop viewer application for HDF5 and other file formats. A free and open source software product, it runs on Mac OS X, Windows, and Linux. * Read more of this post <https://hdfgroup.org/wp/2015/06/get-your-bearings-with-hdf-compass/#more-896> *The HDF Group <https://hdfgroup.org/wp/?author=5>* | June 10, 2015 at 3:26 pm | Tags: data analysis <https://hdfgroup.org/wp/?taxonomy=post_tag&term=data-analysis>, data viewer <https://hdfgroup.org/wp/?taxonomy=post_tag&term=data-viewer>, H5Py <https://hdfgroup.org/wp/?taxonomy=post_tag&term=h5py>, HDF Compass <https://hdfgroup.org/wp/?taxonomy=post_tag&term=hdf-compass>, HDF5 <https://hdfgroup.org/wp/?taxonomy=post_tag&term=hdf5>, HDFView <https://hdfgroup.org/wp/?taxonomy=post_tag&term=hdfview>, Python <https://hdfgroup.org/wp/?taxonomy=post_tag&term=python>, viewer application <https://hdfgroup.org/wp/?taxonomy=post_tag&term=viewer-application> | Categories: HDF Products <https://hdfgroup.org/wp/?taxonomy=category&term=hdf-products>, HDF Technical Insights <https://hdfgroup.org/wp/?taxonomy=category&term=hdf-technical-insights> | URL: http://wp.me/p5C3Aa-es Comment <https://hdfgroup.org/wp/2015/06/get-your-bearings-with-hdf-compass/#respond> See all comments <https://hdfgroup.org/wp/2015/06/get-your-bearings-with-hdf-compass/#comments> Unsubscribe <https://subscribe.wordpress.com/?key=a6573fa999fd789d4be5a9d90cce1746&email…> to no longer receive posts from HDF BLOG. Change your email settings at Manage Subscriptions <https://subscribe.wordpress.com/?key=a6573fa999fd789d4be5a9d90cce1746&email…>. *Trouble clicking?* Copy and paste this URL into your browser: https://hdfgroup.org/wp/2015/06/get-your-bearings-with-hdf-compass/

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Issue #1030: Document the enable_plugins function (yt_analysis/yt)
by Nathan Goldbaum 09 Jun '15

09 Jun '15

New issue 1030: Document the enable_plugins function https://bitbucket.org/yt_analysis/yt/issue/1030/document-the-enable_plugins… Nathan Goldbaum: This function parses the plugins file and allows the fields and functions defined there to be used in a script that imports yt using `import yt`. It needs docstrings, to be present in the API docs, and needs to be mentioned in the documentation section on the plugins file.

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GridsSource in vr refactor
by Matthew Turk 07 Jun '15

07 Jun '15

Hi all, Anybody here know why with the scene refactor, no matter how low I set the opacity of the grids, they (villainously) blot out the sun? Here's a script: http://paste.yt-project.org/show/5608/ Here's the output of new_tf_clip.png: http://i.imgur.com/ZRTz4kR.png and now, what the script calls grids_overlay.png: http://i.imgur.com/fPvVDdP.png I mean, I *must* be missing something, right? -Matt

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ramses length units
by Desika Narayanan 05 Jun '15

05 Jun '15

Hey YT-dev, I've discovered something that I think could maybe be a bug (though maybe not) in the Ramses front end but am unsure about the motivation behind the code so thought I'd check in and try to learn a bit. In frontends/ramses/data_structures.py, I think the length_unit is set to be the length_unit that comes from the info_xxx.txt file multiplied by the box length. For the example yt data sets, this doesn't impact anything because the box lengths are unity. In examining some Agora snapshots, however the box lengths are not unity - one that I'm looking at for example has a boxlen of 600. This results in length units that aren't similar to what the info_xxx.txt file says, and more dramatically, mass units that are very different. For example, in one such snapshot, I read from the info file: boxlen = 0.600000000000000E+03 time = 0.500035810875167E+00 aexp = 0.100000000000000E+01 H0 = 0.100000000000000E+01 omega_m = 0.100000000000000E+01 omega_l = 0.000000000000000E+00 omega_k = 0.000000000000000E+00 omega_b = 0.000000000000000E+00 unit_l = 0.308656802500000E+22 unit_d = 0.157339152800000E-25 unit_t = 0.308687241173998E+17 but if I load this snapshot in yt, I get: >In [2]: print ds.mass_unit 9.9935115109e+46 g >In [3]: print ds.mass_unit.in_units("Msun") 5.02586592269e+13 Msun >In [4]: print ds.length_unit 1.851940815e+24 cm which consequently results in derived quantities from the simulation (like stellar mass) that are totally off (by a factor boxlen**3). So, I'm writing (as a total Ramses novice) to try to understand the motivation behind multiplying the length unit by the boxlen in the frontend, and if I should be accounting for this factor of boxlen**3 in my analysis, or if this is a bona fide bug. Thanks, -desika ps I updated this morning: thundersnow:yt desika$ hg id 8d3663ac217d+ (yt) tip

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