Mailman 3 April 2017 - yt-users

Re: [yt-users] SSLError when trying to update
by Slavin, Jonathan April 19, 2017

April 19, 2017

Yeah, just after I sent that message I tried other conda updates in my other main environment and got the same problem. So it seems to be a we hosting issue as you said. Jon On Tue, Apr 18, 2017 at 3:49 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Date: Tue, 18 Apr 2017 14:49:19 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] SSLError when trying to update > Message-ID: > <CALO3=5Gb_MSy9CEzNihTcN6pp=+61RkHMqsBPHE8zdzcrP0Xzw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Jon, > > I think this happens when there are web hosting issues with conda. I think > if you give it a little bit of time it should return to normal. > > -Matt > > On Tue, Apr 18, 2017 at 2:46 PM, Slavin, Jonathan <jslavin(a)cfa.harvard.edu > > > wrote: > > > Hi, > > > > I have a conda environment set up to use the development branch of yt. > > When I just now went to update it I got: > > > conda update -c http://use.yt/with_conda/ -c conda-forge yt > > Fetching package metadata ............. > > > > CondaHTTPError: HTTP None None > > for url <None> > > > > An HTTP error occurred when trying to retrieve this URL. > > SSLError(SSLError(SSLError(1, u'[SSL: CERTIFICATE_VERIFY_FAILED] > > certificate verify failed (_ssl.c:590)'),),) > > > > ?I don't get the "None None" bit, but it looks like a problem with the > SSL > > certificate. Or maybe it's something else. Any help would be > appreciated. > > > > Thanks, > > Jon? > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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Some query regarding YT rays
by Arpan Das April 15, 2017

April 15, 2017

Hello, I am using YT to cast rays within some galaxies simulated using ENZO. I am using YTray for the purpose. But I am not sure if there is any way to save the array of cell width through which the rays are passing. I know there are some quantities like ('index', 'radius'), ('index', 'spherical_radius'), ('index', 'virial_radius_fraction'). But I am not sure exactly which one of them is the width of the cell. Any help would be appreciated. Thanking you in advance, *Arpan Das*

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Inverting Plot Axes
by Greta Zhong April 12, 2017

April 12, 2017

Hi everyone! I’m trying to invert the horizontal axis on some simple projection plots. I’m trying to get a projection along the x axis, with y as the vertical and z as the horizontal axis where the horizontal/z axis is inverted, with the horizontal/z axis decreasing from left to right. Here’s the relevant code: ds.coordinates.x_axis[0] = 2 ds.coordinates.x_axis['x'] = 2 ds.coordinates.y_axis[0] = 1 ds.coordinates.y_axis['x'] = 1 This is just assigning the z axis (2) to the horizontal axis and the y axis (1) to the vertical axis. plot1 = yt.ProjectionPlot(ds,"x","velocity_x",weight_field='density') #plot1.plots["velocity_x"].axes.invert_xaxis() plot1.save() plot12 = yt.ProjectionPlot(ds,"x","density") #plot12.plots["density"].axes.invert_xaxis() plot12.save() And then I just use ProjectionPlot to make the plots. As you can see, I commented out a sort of matplotlib-y attempt to invert the horizontal axis, to no effect. I’ve attached two files: the first is what I’m getting with the above code (‘Projection_x_density_actual'), and the second illustrates the orientation I’d like (‘Projection_x_density_rotated'). Unfortunately, I got to the desired orientation by swapping my vertical/horizontal axes like this: ds.coordinates.x_axis[0] = 1 ds.coordinates.x_axis['x'] = 1 ds.coordinates.y_axis[0] = 2 ds.coordinates.y_axis['x'] = 2 and then just rotating the png in preview. I can’t find anything in the documentation about this besides the fact that we can use matplotlib objects to customize plots. I’d really appreciate any help on this! Thanks, Greta

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possible bug in cut_region
by Stephanie Tonnesen April 8, 2017

April 8, 2017

Hi all, So I think I found a bug in cut_region. Right now the directions say you can chain cut regions in two ways: either listing several cut_regions or using one call and an "&". http://yt-project.org/doc/analyzing/filtering.html However, for some extremely mysterious reason, when I do a multi-call to cut_region I get wackadoo numbers, like too high by a couple orders of magnitude. Here is the quick check that should work on IsoGal: ds = yt.load("/data001/stonnes/BPr16vs30arcfo/DD"+loop[i]+"/BPr16vs30arcfo"+loop[i]) disk3 = ds.disk([0.5,0.5,0.5],[0,0,-1.0],(40,"kpc"),(10,"kpc")) diskn = disk3.cut_region(["obj['Metal_Density']/obj['density'] > 0.5"]) diska = diskn.cut_region(["obj['density'] > 1e-25"]) diskd = disk3.cut_region(["(obj['Metal_Density']/obj['density'] > 0.5) & (obj['density'] > 1e-25)"]) print diska.quantities.total_quantity([("gas","cell_mass")]) print disk3.quantities.total_quantity([("gas","cell_mass")]) print diskn.quantities.total_quantity([("gas","cell_mass")]) print diskd.quantities.total_quantity([("gas","cell_mass")]) I am also attaching my whole code, which is a loop, just in case. So here the diska mass is two orders of magnitude larger than any of the others, and diskd is what I would expect with the two selection criteria. Best, Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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Problem Using Installer Script with Cygwin
by Sean Larkin April 8, 2017

April 8, 2017

I am attempting to Install yt to Cygwin, but the install_script always attempt to download Miniconda from a webpage that does not exist. I have attempted to change the url it searches for to the correct one listed here ( https://repo.continuum.io/miniconda/) , but nothing I have tried works. The script used was the default script obtained by the wget http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh command listed in the installation tutorial, which was only modified to also install scypy, astropy, and Rockstar halo finder. Below this is the error message: [hit enter] Awesome! Here we go. Using wget Using sha512sum Downloading http://repo.continuum.io/miniconda/Miniconda2-latest--.sh Installing the Miniconda python environment. ******************************************** FAILURE REPORT: ******************************************** EXECUTING: wget -nv http://repo.continuum.io/miniconda/Miniconda2-latest--.sh https://repo.continuum.io/miniconda/Miniconda2-latest--.sh: 2017-04-05 18:27:36 ERROR 404: Not Found. ******************************************** ******************************************** Failure. Check /home/Cygwin/yt-conda/yt_install.log. The last 10 lines are above.

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transparency and color from two arrays
by Zbyněk Dostál April 6, 2017

April 6, 2017

Dear YT users, I have question about 3D visualization. I have two 3D numpy float arrays with the same dimensions. It is possible to visualize so that the first array will be data and second array will be their transparency? Thank you. Best regards Zbynek Dostal. -- Ing. Zbynek Dostal, Ph.D. Experimental Biophotonics CEITEC | Brno University of Technology Brno, Czech Republic zbynek.dostal(a)ceitec.cz <zbynek.dostal(a)ceitec.vutbr.cz> http://www.biophot.cz

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problem with installing development version of yt on remote host
by Wolfram Schmidt April 5, 2017

April 5, 2017

Hi, I need to install the development version of yt, which is fully capable of reading BoxLib-based datasets (yt-users Digest, Vol 110, Issue 1). While I can do that without problems on my PC, I ran into problems on the remote host where the datasets are produced. I am able to successfully install Anaconda and also the stable yt branch (via conda install yt), but the "nightly conda build" conda install -c http://use.yt/with_conda/ yt fails with the error message Fetching package metadata ... CondaHTTPError: HTTP None None for url <http://use.yt/with_conda/linux-64/repodata.json> Elapsed: None An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way. ConnectionError(MaxRetryError("HTTPConnectionPool(host='use.yt', port=80): Max retries exceeded with url: /with_conda/linux-64/repodata.json (Caused by NewConnectionError('<requests.packages.urllib3.connection.HTTPConnection object at 0x2aaab449ad30>: Failed to establish a new connection: [Errno 113] No route to host',))",),) It turns out that retrying doesn't help. I suspect that traffic through certain ports is blocked. Over the alternative route offered by the yt installation script, even the basic installation fails because some packages cannot be accessed. If anyone knows of other options or a way to circumvent the above problem, please let me know. Best regards, Wolfram

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problem with processing BoxLib data in pure hydro case
by Wolfram Schmidt April 3, 2017

April 3, 2017

Hi, I encountered a problem when processing BoxLib (Nyx) data from pure hydro simulations without particles, using an Anaconda installation of yt. After loading a dataset with yt.load(), I get the following error for ds.field_list: --------------------------------------------------------------------------- KeyError Traceback (most recent call last) <ipython-input-5-5aaf470c0415> in<module>() ----> 1ds.field_list/sw/tools/anaconda3/4.1.1/generic/lib/python3.5/site-packages/yt/data_objects/static_output.py in field_list(self) 459 @property460 def field_list(self):--> 461return self.index.field_list462 463 def create_field_info(self):/sw/tools/anaconda3/4.1.1/generic/lib/python3.5/site-packages/yt/data_objects/static_output.py in index(self) 417 raise RuntimeError("You should not instantiate Dataset.")418 self._instantiated_index = self._index_class( --> 419self, dataset_type=self.dataset_type) 420 # Now we do things that we need an instantiated index for421 # ...first off, we create our field_info now./sw/tools/anaconda3/4.1.1/generic/lib/python3.5/site-packages/yt/frontends/boxlib/data_structures.py in __init__(self, ds, dataset_type) 906 def __init__(self, ds, dataset_type='nyx_native'):907 super(NyxHierarchy, self).__init__(ds, dataset_type)--> 908self._read_particle_header()909 910 def _read_particle_header(self):/sw/tools/anaconda3/4.1.1/generic/lib/python3.5/site-packages/yt/frontends/boxlib/data_structures.py in _read_particle_header(self) 909 910 def _read_particle_header(self):--> 911if not self.ds.parameters["particles"]:912 self.pgrid_info = np.zeros((self.num_grids, 3), dtype='int64')913 returnKeyError: 'particles' Same problem with slices. I am not sure what exactly causes the error here, but since I can load datasets from cosmological simulations with Nyx and process them without problems, I suppose the problem outlined above is somehow related to the missing particles. How can this be fixed? Best Wolfram

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