Mailman 3 January 2019 - yt-users

overplot ~100,000 points onto a figure
by Huanqing 16 Jan '19

16 Jan '19

Hi, I want to overlie >100,000 points onto a plot. Using annotate_marker I have no issue with a small number of points, however if I want to plot more than 10,0000 points to overlie, it takes almost an hour to produce that plot. Here is the code I use: for ipar in range(len(xpMpc)): slc.annotate_marker(ds.arr([xpMpc[ipar],ypMpc[ipar],zpMpc[ipar]],'Mpc').in_units('code_length'),coord_system='data',marker='.',plot_args={'color':'cyan','s':1,'alpha':0.3}) I wonder is there any way I can speed this up? Thank you very much, Huanqing

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2D Profile Plots for User Defined Fields
by piyush.suneet＠gmail.com 14 Jan '19

14 Jan '19

Hello, I have an hdf5 data file from FLASH which I analyze through yt. I use the yt_createprofile function to make a 2D profile plot of density and temperature as mentioned on the website: import yt ds = yt.load("some_hdf5_data") dd = ds.all_data() center = ds.arr([64.0, 64.0, 64.0], 'code_length') rvir = ds.quan(1, "pc") sph = ds.sphere(center, rvir) profile = yt.create_profile(sph, ['density', 'temperature'], n_bins=[128, 128], fields=['cell_mass'], weight_field=None) plot = yt.PhasePlot.from_profile(profile) plot.save() However, I would also like to make a plot of the number density. Say, I define numdens = dd['density']/1.67e-24 How can I use 'numdens' to plot the same profile plot?

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RuntimeError when Accessing Exodus II Data
by andfranklin3＠gmail.com 11 Jan '19

11 Jan '19

Hi all, I'm trying to access Exodus II Data from a [MOOSE](https://mooseframework.inl.gov/) application. I'm following the instructions provided [here](http://yt-project.org/doc/examining/loading_data.html#exodus-ii-data). My particular script is follows: ```python import yt file_name = "results.e" ds = yt.load(file_name, step=-1) time = float(ds.current_time) ad = ds.all_data() ad["connect1", "rho"] ``` where ("connect1", "rho") is a valid field. This script fails on the last line with a traceback and the following error message: ``` RuntimeError: Region right edge[0] < left edge: width = 0.0 ``` The particular MOOSE simulation consists of two, 1D meshes. Would anyone know why I'm getting this error and how to overcome it? Thanks in advance, Andrew

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Error making a movie with RAMSES data
by Vadlamani Samhitha 09 Jan '19

09 Jan '19

Hi, I'm trying to make a movie by depositing particles on to the mesh: > import yt > > from yt.visualization.volume_rendering.api import MeshSource > > from yt.units import Myr > > import yt.visualization.eps_writer as eps > > from yt.data_objects.particle_filters import add_particle_filter > > import pylab as plt > > plt.switch_backend('agg') > > > def star_filter(pfilter,data): > > age = data["all", "particle_age"] > > filter = age.in_units('Myr') > 0 > > return filter > > add_particle_filter("new_stars", function=star_filter, filtered_type="all", > requires=["particle_age"]) > > > ini=19 > > fin=21 > > CMAP = 'hot' > > VMIN = 1e3 > > VMAX = 1e10 > > for x in range(ini, fin): filename= "/lunarc/nobackup/users/samvad/FINAL-50-0.5/output/output_%0*d/info_%0*d.txt" % (5,x,5,x) ds=yt.load(filename) time = ds.current_time ds.add_particle_filter("new_stars") ms =MeshSource(ds, ('deposit', 'new_stars_density')) sc.add_camera(ds) camera_position = ds.arr([0, 0, 0], 'code_length') cam.focus = ds.domain_center north_vector = ds.arr([0, 0, 0], 'dimensionless') cam.width = ds.arr([ 400, 400, 400], 'kpc') cam.resolution = (800, 800) > cam.set_position(camera_position, north_vector) # actually make the image here im = ms.render(cam, cmap=CMAP, color_bounds=(VMIN, VMAX)) plt.clf() fig = plt.gcf() ax = plt.gca() ax.imshow(im, interpolation='nearest', origin='lower') p = ax.imshow(ms.data, visible=False, cmap=CMAP, vmin=VMIN, vmax=VMAX) cb = fig.colorbar(p) cb.set_label(field_name[1]) ax.text(25, 750, 'time = %.2e' % time, color='k') > ax.axes.get_xaxis().set_visible(False) plt.savefig('movie_frames/test_%.3d' % x) But ending up with error: Traceback (most recent call last): File "movie_new_stars.py", line 32, in <module> ms =MeshSource(ds, ('deposit', 'new_stars_density')) File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/render_source.py", line 536, in __init__ self.build_volume_embree() File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/render_source.py", line 593, in build_volume_embree mesh_id = int(ftype[-1]) - 1 > ValueError: invalid literal for int() with base 10: 't' Any leads on this are highly appreciated. >

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[ANN] 2019 Scipy Conference: Call for Proposals
by Nathan Goldbaum 08 Jan '19

08 Jan '19

SciPy 2019, the 18th annual Scientific Computing with Python conference, will be held July 8-14, 2019 in Austin, Texas. The annual SciPy Conference brings together over 800 participants from industry, academia, and government to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. The call for abstracts for SciPy 2019 for talks, posters and tutorials is now open. The deadline for submissions is February 10, 2019. Conference Website: https://www.scipy2019.scipy.org/ Submission Website: https://easychair.org/conferences/?conf=scipy2019 Talks and Posters (July 10-12, 2019) In addition to the general track, this year will have specialized tracks focused on: - Data Driven Discoveries (including Machine Learning and Data Science) - Open Source Communities (Sustainability) Mini Symposia - Science Communication through Visualization - Neuroscience and Cognitive Science - Image Processing - Earth, Ocean, Geo and Atmospheric Science There will also be a SciPy Tools Plenary Session each day with 2 to 5 minute updates on tools and libraries. Tutorials (July 8-9, 2019) Tutorials should be focused on covering a well-defined topic in a hands-on manner. We are looking for useful techniques or packages, helping new or advanced Python programmers develop better or faster scientific applications. We encourage submissions to be designed to allow at least 50% of the time for hands-on exercises even if this means the subject matter needs to be limited. Tutorials will be 4 hours in duration. In your tutorial application, you can indicate what prerequisite skills and knowledge will be needed for your tutorial, and the approximate expected level of knowledge of your students (i.e., beginner, intermediate, advanced). Instructors of accepted tutorials will receive a stipend.

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Running Rockstar
by Nick Gnedin 08 Jan '19

08 Jan '19

I have a question about running Rockstar. It appears that yt runs each writer, each reader, and the main server each on a separate MPI rank. 002 yt : [ERROR ] 2019-01-08 11:39:05,929 6 reader + 6 writers + 1 server != 7 mpi However, Rockstar documentation (https://bitbucket.org/gfcstanford/rockstar#markdown-header-more-complete-se…) recommends setting both numbers of readers and writers to the number of available ranks. Is there any reason why we cannot run reader and writer tasks on the same rank? n

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Re: Installation error
by Nick Gnedin 07 Jan '19

07 Jan '19

I listed the commands I executed - just git clone and python3 setup.py build. I cannot use pip, on BW it first tries to uninstall the system-wide distribution of yt, so their Python expert suggested I try setup.py. On 1/7/19 12:24 PM, Nathan Goldbaum wrote: > Hi Nick, > > This "setup.py build" thing is new to me. It's not a setup.py command > we've ever supported or documented for use with yt. I wonder why the > blue waters staff told you to use it. > > That said, I'm not able to reproduce the failure you're seeing (python3 > setup.py build runs without error after making a fresh clone of the yt > repo). > > What branch and changeset are you building yt from? > > What were the rest of the steps in the installation instructions you > were trying to follow? > > I bet if you do "pip install ." inside of your checkout of the > repository, things will "just work". However since I'm not able to > reproduce the failure you're seeing you may run into the same issue with > "pip install". If that happens answering the questions above will allow > me to do additional debugging steps on my local machine. > > -Nathan > > On Mon, Jan 7, 2019 at 12:03 PM Nick Gnedin <ngnedin(a)gmail.com > <mailto:ngnedin@gmail.com>> wrote: > > > Folks, > > I am getting an error trying to install the latest version of yt using > setup.py (I have to use this method per BlueWaters staff instructions): > > ----------------------------- > >git clone https://ngnedin@github.com/yt-project/yt.git > <https://urldefense.proofpoint.com/v2/url?u=https-3A__ngnedin-40github.com_y…> > ... > Checking out files: 100% (1258/1258), done. > > >cd yt > yt >python3 setup.py build > ... > [48/48] Cythonizing yt/utilities/lib/write_array.pyx > reading manifest template 'MANIFEST.in' > no previously-included directories found matching > 'doc/source/reference/api/generated' > no previously-included directories found matching 'doc/build' > writing manifest file 'yt.egg-info/SOURCES.txt' > error: can't copy 'yt/analysis_modules': doesn't exist or not a > regular file > > yt > > -------------------- > > Thank you, > > Nick > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > <mailto:yt-users@python.org> > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> >

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Installation error
by Nick Gnedin 07 Jan '19

07 Jan '19

Folks, I am getting an error trying to install the latest version of yt using setup.py (I have to use this method per BlueWaters staff instructions): ----------------------------- >git clone https://ngnedin@github.com/yt-project/yt.git ... Checking out files: 100% (1258/1258), done. >cd yt yt >python3 setup.py build ... [48/48] Cythonizing yt/utilities/lib/write_array.pyx reading manifest template 'MANIFEST.in' no previously-included directories found matching 'doc/source/reference/api/generated' no previously-included directories found matching 'doc/build' writing manifest file 'yt.egg-info/SOURCES.txt' error: can't copy 'yt/analysis_modules': doesn't exist or not a regular file yt > -------------------- Thank you, Nick

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Derived field depending on sections of simulation
by Paco Holguin 03 Jan '19

03 Jan '19

Hi, I've been trying to get this derived field to work, but it's more complicated to define than anything I've done before. I am working in a plane parallel geometry. I want to make a field that contains gas surface density below (i.e. from z=0 to z=current cell) the given cell. I naively thought I could filter the whole data set 'ad' inside of the function def (field, data) definition using ad['z'] < data['z'], but data['z'] is not a single value from cell. What I can think of right now is to find a gas density profile (accumulated) and then interpolate that function when I want to use it in a derived field. Maybe I'm missing something here. ad = ds.all_data() def _sigma_n_z(field,data): current_z = np.absolute(data['z']) all_z = np.absolute(ad['z']) z_cut = (all_z < current_z) m_tot = np.sum( ad[('gas','cell_mass')]*z_cut) return (m_tot / (area)**2).in_units('Msun/pc**2') Thanks for the help! -Paco

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