Mailman 3 May 2016 - yt-dev

Issue #1219: Shader files are not installed correctly (yt_analysis/yt)
by Kacper Kowalik May 17, 2016

May 17, 2016

New issue 1219: Shader files are not installed correctly https://bitbucket.org/yt_analysis/yt/issues/1219/shader-files-are-not-insta… Kacper Kowalik: As reported by @a_gilbert ``` copying yt/visualization/volume_rendering/shaders/default.vertexshader -> build/bdist.linux-x86_64/egg warning: install_data: setup script did not provide a directory for 'yt/visualization/volume_rendering/shaders/passthrough.vertexshader' -- installing right in 'build/bdist.linux-x86_64/egg' ``` shaders are … [View More]

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Issue #1218: How to Mock X-ray Observations with Gadget gas particle outputs? (yt_analysis/yt)
by Weiguang Cui May 13, 2016

May 13, 2016

New issue 1218: How to Mock X-ray Observations with Gadget gas particle outputs? https://bitbucket.org/yt_analysis/yt/issues/1218/how-to-mock-x-ray-observat… Weiguang Cui: Dear, I have checked the available examples online, all of them used the mesh outputs. Can I directly use the gas particle (instead of smoothing them into cells) in the photon simulator? Since Veronica's PHOX is originally used for gadget output, it would be nice to apply this X-ray simulator to gadget output directly. … [View More]

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New project members: Bili Dong and Brian Crosby
by Nathan Goldbaum May 12, 2016

May 12, 2016

Hi all, I'd like to nominate two new project members: Bili Dong and Brian Crosby. Both of them have made substantial contributions to the yt codebase: https://bitbucket.org/yt_analysis/yt/commits/all?search=author(qobilidop) https://bitbucket.org/yt_analysis/yt/commits/all?search=author(bcrosby) If you don't know or remember, yt project members are given official recognition on the website and are also given commit bits for all yt repositories on bitbucket. For more details, see YTEP-1776: … [View More]

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PR review hangout: Wednesday May 11, 1:00 PM CDT
by Nathan Goldbaum May 11, 2016

May 11, 2016

Hi all, Here's the link for this week's PR review hangout: https://plus.google.com/b/107728486871834552760/events/cc5o4fqfnp3cg96qb8vh… -Nathan

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Issue #1217: Slicing semi structured grid fails (yt_analysis/yt)
by Kacper Kowalik May 11, 2016

May 11, 2016

New issue 1217: Slicing semi structured grid fails https://bitbucket.org/yt_analysis/yt/issues/1217/slicing-semi-structured-gr… Kacper Kowalik: Following script: ``` #!python import yt import numpy as np xgrid = np.array([-1, -0.65, 0, 0.65, 1]) ygrid = np.array([-1, 0, 1]) zgrid = np.array([-1, -0.447, 0.447, 1]) coords, conn = yt.hexahedral_connectivity(xgrid, ygrid, zgrid) arr = np.ones((len(xgrid)-1, len(ygrid)-1, len(zgrid)-1)) bbox = np.array([[np.min(xgrid),np.max(xgrid)], … [View More]

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(no subject)
by mika harisetry Rafieferantsoa May 11, 2016

May 11, 2016

Hi there, I've been recently using yt. The following code spit an error. Can anyone please help? In [*2*]: import yt In [*3*]: ds = yt.load('/data/snap_008.hdf5') ... In [*5*]: ds.camera() *---------------------------------------------------------------------------* *AttributeError* Traceback (most recent call last) *<ipython-input-5-14e99c8871cc>* in <module>*()* *----> 1* ds*.*camera*()* *AttributeError*: 'GadgetHDF5Dataset' object has no attribute 'camera'

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Particle phase plotting
by John ZuHone May 7, 2016

May 7, 2016

Hi all, I had a question about how we do particle phase plots / 2d profiles. I’ve noticed that we way we do this involves some kind of deposition of the particle data into a grid. This necessitates never allowing one to make log-spaced bins for a particle 2d profile, though you can of course plot them in logspace. This has rather nasty consequences, however, for data which has a huge dynamic range over orders of magnitude and for which log-spaced bins would make a lot of sense. See, for … [View More]

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[ANN] Introducing the yt Hub
by Kacper Kowalik May 6, 2016

May 6, 2016

Hi Everyone! The yt community is proud to announce the release of yt Hub 1.0. The yt Hub (https://hub.yt) is an environment where data can be published, analyzed and shared with other people. The yt Hub relies on multiple open source microservices that are loosely coupled together. At its core we utilize: * Girder - as a data management platform (https://girder.hub.yt) * Jupyter Notebook - for interactive data exploration * Curldrop - for a quick and easy data sharing * … [View More]

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A set of benchmarks
by Jonah Miller May 6, 2016

May 6, 2016

Hi yt-dev, I am developing a frontend for Einstein Toolkit for yt and in the process I generated some crude, preliminary benchmarks which I thought I would share in case anybody is interested. I performed three tests: 1. I just load the dataset and calculate (say) the maximum of some quantity on each grid. 2. I load in the dataset and calculate the maximum of the magnitude of a gradient on each grid. This requires the generation of ghost zones at grid boundaries. 3. I load … [View More]in the dataset and perform a volume rendering. I make a "movie" with 4 frames where I rotate around the volume. Salient details: * I performed these tests with the attached scripts. I turned openmp and MPI off (set OMP_NUM_THREADS=1). * The domain sizes were: 64^3, 128^3, 256^3, and 512^3. * All four datasets have only one refinement level. However the 512^3 dataset has multiple grids on that refinement level. * The size of a dataset ranges from about 10MB for the 64^3 set to 10GB for the 512^3 * All data was performed on a single modern workstation. Details: 2.6GHz clock with AVX2 instructions and a 60MB L3 cache. Results: * Reading in the data is (for the datasets I tested) extremely fast. The 512^3 dataset takes only about 20 seconds to read the whole thing in. * Generating the first frame in a volume render is extremely slow. On the order of 4 minutes for the 512^3 data set. After the first frame is produced, new frames are fast, even with openmp off. With 1 openmp thread, it takes on the order of 10s of seconds for a new frame. * Generating ghost zones is very fast for datasets with only one grid. It is incredibly slow for datasets with multiple grids, dominating the run time. * I attach a plot comparing the three tests. Naively, it seems to me that there must be several sources of overhead when I perform volume rendering that are significantly more costly than simply reading in the data (which seems to be fast). Clearly one of these is the generation of the ghost zones, and another is the actual ray tracing (although the ray tracing itself seems to be quite fast.). However I'm not sure that these two operations alone explain the cost of the volume rendering. I'd love to know other people's experience with benchmarking. Do these costs seem normal, up to an order of magnitude or so? Would you have any insight into what contributes to the cost of generating the first frame when volume rendering? Thanks very much! Best, Jonah Miller [View Less]

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Particle phase plotting
by John Zuhone May 6, 2016

May 6, 2016

Hi all, I had a question about how we do particle phase plots / 2d profiles. I’ve noticed that we way we do this involves some kind of deposition of the particle data into a grid. This necessitates never allowing one to make log-spaced bins for a particle 2d profile, though you can of course plot them in logspace. This has rather nasty consequences, however, for data which has a huge dynamic range over orders of magnitude and for which log-spaced bins would make a lot of sense. See, for … [View More]

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