yt-users November 2013

yt-users@python.org

41 participants
49 discussions

by david collins

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

5 months, 1 week

Notebook server question

by Andrew Myers

Hello yt users, I have a (perhaps naive) ssh question related to the yt notebook. I would like to run a yt notebook server on machine A. However, machine A cannot be directly accessed via ssh from the wider internet. Instead, I must first ssh into machine B, and then ssh from B to A. Machine B cannot run the notebook server itself. Does anyone know how I can configure things - perhaps by using a more complicated ssh tunnel command - so I that access a notebook server running on machine A through machine B? Thanks, Andrew

6 years, 5 months

Light Cone Projection

by Pengfei Chen

Hi all, I downloaded the example script of light cone projectoin( http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-pr…) to my laptop and changed the Enzo simulation parameter file and redshifts. But when I ran it the following error occurred: File "light_cone_projection.py", line 19, in <module> find_outputs=False) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 158, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 44, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line 131, in simulation find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 81, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py", line 343, in __init__ self._parse_parameter_file() File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 273, in _parse_parameter_file param, vals = (i.strip() for i in line.split("=")) ValueError: need more than 1 value to unpack Does the parameters "near_redshift" and "far_redshift" in LightCone need to be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in enzo parameter file? Does anyone know how to solve this? Thank you all! Pengfei

6 years, 6 months

Running Rockstar Halo Finder to create a merger tree

by Hilary Egan

Hi all, I'm quite confused on a number of points related to running the rockstar halo finder, so I hope its alright that I put all these questions into this one email! 1. I can't seem to run the rockstar halo finder at all without getting this error followed by a segmentation fault and crash. [Warning] Network IO Failure (PID XXXXXX): Connection reset by peer [Network] Packet receive retry count at: 1 It sort of seems like this issue ( http://lists.spacepope.org/htdig.cgi/yt-dev-spacepope.org/2012-November/002…) but I couldn't really figure out what the resolution was from the thread. Im attempting to run this on kraken and it doesn't matter if I use a single compute node or multiple, I get the same error. (I hope this isn't the infiniband issue the docs warned about, I couldn't figure out if that is how kraken is connected and I got an error that the suggested flag doesn't exist so I didn't press the issue.) 2. Whenever I finally do get the halo finder to work, I need the results to be in a form that the merger tree can use. It seems as though the MergerTree needs the results in the same form as the other halo finders give, so would getting the halo list and then dumping it as usual be the appropriate strategy? Ie: rh.run() halo_list = rh.halo_list() halo_list.dump('MergerHalos') 2.5. The docs sort of give mixed messages on whether or not I could just be calling MergerTree with the argument halo_finder_function = RockstarHaloFinder. At this point I've pretty thoroughly convinced myself that I can't, but it would be nice if that was clarified. (Just a thoroughly overwhelmed new user's perspective!) 3. I'm a little confused as to whether or not I have to use a TimeSeriesData object rather than the usual single time output when instantiating the halo finder. Under "Rockstar Halo Finding" it uses TimeSeriesData, unlike the rest of the examples, but under the subheading "Output Analysis" it just uses pf. The "Output Analysis" example also doesn't call the run() method, which leads me to believe something else entirely is going on, but its not quite clear. Thanks! -Hilary

6 years, 9 months

sliceplot and frb problems

by Kathy Eastwood

Dear (very helpful) yt folk: I have been struggling with trying to make a slice plot of some FLASH data that is an odd size; the volume is 1 kpc square in x and y, and 40 kpc tall in z. The grid sizes vary widely, as expected. I have two questions: one, I would like to understand the odd behavior that I get with regular SlicePLots, and I would like some help using the FixedResolutionBuffer, which I *suspect* is the way I want to go, but I have not been able to make it work. I am using the newest version of yt (upgraded this morning!) on Mac OS 10.7.5. The SlicePlot weirdnesses: from yt.mods import * %matplotlib inline import matplotlib.pyplot as plt import matplotlib.image as mpimg import matplotlib.colorbar as cb import numpy as np pf = load("Strat_Box_hdf5_plt_cnt_0064") #First try a 20 kpc tall box slc = SlicePlot(pf, 'x', 'Density',center='c',width=((1,"kpc"),(20.0,"kpc"))) slc.annotate_title('This is a Density plot') slc.save('test_20kpc.png') slc.show() #Please see plot at http://i.imgur.com/N65CNfU.png #Now try a 5 kpc tall plot slc = SlicePlot(pf, 'x', 'Density',center='c',width=((1,"kpc"),(5.0,"kpc"))) slc.annotate_title('This is a Density plot') slc.save('test_5kpc.png') slc.show() #Please see plot at http://i.imgur.com/L1YORNK.png ; note that it seems to filling #a different part of the plotting "window" #Now try a 2 kpc tall plot slc = SlicePlot(pf, 'x', 'Density',center='c',width=((1,"kpc"),(2.0,"kpc"))) slc.annotate_title('This is a Density plot') slc.save('test_2kpc.png') slc.show() #Please see plot at http://i.imgur.com/Bq1WaIP.png ; note that it seems to filling #even MORE of the plotting "window", but that the density labels were cut off a bit. OK, now the part that doesn't work. After reading, I decided that an frb must be the way to go, so I tried frb = FixedResolutionBuffer(slc, (0.0, 1.0, 0.0, 1.0), (1024,1024)) plt.imshow(frb['Density']) plt.savefig('test_figure.png') and I get the following error. Note: I also tried slc.to_frb and that didn't work either. ---------------------------------------------------------------------------AttributeError Traceback (most recent call last)<ipython-input-17-e68719d58ae4> in <module>()----> 1 frb = FixedResolutionBuffer(slc, (0.0, 1.0, 0.0, 1.0), (1024,1024)) 2 plt.imshow(frb['Density']) 3 plt.savefig('test_figure.png') 4 5 /Users/kde/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.pyc in __init__(self, data_source, bounds, buff_size, antialias, periodic) 89 self.antialias = antialias 90 self.data = {}---> 91 self.axis = data_source.axis 92 self.periodic = periodic 93 AttributeError: 'SlicePlot' object has no attribute 'axis' THanks in advance for any help. cheers kathy -- Kathy DeGioia Eastwood, Ph.D. Professor of Physics and Astronomy Northern Arizona University Flagstaff, AZ 86011-6010 Ph: 928-523-7159 FX: 928-523-1371 Kathy.Eastwood(a)nau.edu deliveries: 602 S. Humphreys St., Bldg 19 Rm 209

6 years, 9 months

empty plot issue

by Kathy Eastwood

Hi, helpful folks. Another issue I have been struggling with, which is similar to this thread http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-May/003652… I am working on some FLASH data with the current version of yt using MacOS 10.7.5. Using this exact same data set, I managed to create some nice phaseplots using spheres centered on the densest spot. However, I now want to make some plots for a much larger volume of scientific interest... Here is the code from yt.mods import * %matplotlib inline import matplotlib.pyplot as plt import numpy as np pf = load("Strat_Box_hdf5_plt_cnt_0064") pc = PlotCollection(pf, [0.5, 0.5, 0.5]) plane = pf.h.region([0.5,0.5,0.5],[0.0,0.0,0.4],[1.0,1.0,0.6]) pc.save("plane_cnt_0064") I then get the following error ValueError: Data has no positive values, and therefore can not be log-scaled Following the advice in the thread listed above, John Wise suggested "For your "empty" plot, do you have any gas with densities between 1e-26 and 1e-27 g/cm^3 in this sphere? If there's no gas in this range, then CellVolume will be zero and will give you that error message when it tries to take the log of CellVolume. If you want to manually inspect the CellVolume field, you can print out the following variable pc.plots[-1].data['CellVolume'] which will give you the CellVolume as a function of the x-variable for the last plot you have added to your PlotCollection." The writer did not respond in the next thread, so I'm not sure if this worked. But when I try it, I get the following: KeyError Traceback (most recent call last)<ipython-input-18-71f93f9e2cb6> in <module>()----> 1 pc.plots[-1].data["CellVolume"] /Users/kde/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc in __getitem__(self, key) 160 # This raises a KeyError if it doesn't exist 161 # This is because we explicitly want to add all fields--> 162 return self.field_data[key] 163 164 def __setitem__(self, key, value): KeyError: 'CellVolume' Even though CellVolume is explicitly listed in my list of derived fields... Also, I did try the same command for Density rather than CellVolume, and the numbers were in the e-24 g cm-3 range...in fact, all the numbers were exactly the same. So I don't know if I've screwed up my data container somehow, or if the density values really are too low? any ideas? thanks SO much kathy -- Kathy DeGioia Eastwood, Ph.D. Professor of Physics and Astronomy Northern Arizona University Flagstaff, AZ 86011-6010 Ph: 928-523-7159 FX: 928-523-1371 Kathy.Eastwood(a)nau.edu deliveries: 602 S. Humphreys St., Bldg 19 Rm 209

6 years, 9 months

getting the average density inside a data container

by k.grisdale＠surrey.ac.uk

Hi yt Users I am trying to create a data container that is a cube from which I can extract the average density of the gas inside the cube. I am using Ramses data. When I create a data container using: p6 = load("output_00006/info_00006.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure"]) cen = [0, 0, 0] box = p6.h.region(cen, 0.2/p6['cm'], 0.3/p6['cm’]) print box["Density”] I get this error: TypeError: 'float' object has no attribute ‘__getitem__' I have tried creating a sphere as a data container and this works for the Density, but then when I try to take the AverageDensity in the sphere: sphere = p6.h.sphere(cen, 0.7/p6['cm’]) print sphere['AveragedDensity’] I get this error: enerationInProgress Traceback (most recent call last) <ipython-input-28-574d78c4fb5c> in <module>() ----> 1 print sphere['AveragedDensity'] /Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 187 return self.field_data[f] 188 else: --> 189 self.get_data(f) 190 # Note that this is less succinct so that we can account for the case 191 # when there are, for example, no elements in the object. /Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields) 514 return 515 elif self._locked == True: --> 516 raise GenerationInProgress(fields) 517 # At this point, we want to figure out *all* our dependencies. 518 fields_to_get = self._identify_dependencies(fields_to_get) Any idea what I am doing wrong or if there is another way to go about this? Thanks Kearn

6 years, 9 months

yt-3.0 now a part of yt repository

by Britton Smith

Hi all, After some discussion on the dev mailing list, we've decided to unify the repositories for yt-3.0 and yt. It will still be located in a branch called yt-3.0 in that repository. At some point in the near future the separate yt-3.0 repository will become read-only. This simply means that if you are using yt normally, from the repository here: http://bitbucket.org/yt_analysis/yt you will be able to switch to the yt-3.0 branch more easily. And, if you currently have a fork of the repository yt-3.0, you'll need to switch to using a fork of the main yt repository. This is easy, just fork the main yt repo (unless you already have!) and push your yt-3.0 changes there. Just as it has always been, installing the "stable" and "development" versions from the install script will still only put you on the latest stable and development versions of yt-2.x. Additionally, doing "yt update" will not accidentally switch you from one version to the other. Happy Thanksgiving! Britton and the yt development team

6 years, 9 months

Yt-3.0 Ray Casting Progress bar

by Alex Bogert

Hi Guys, The ray casting progress bar is growing the white space in the ipython notebook when I have it inside of a for loop. I think this is because the progress bar is always being drawn on a new line after each iteration. Alex

6 years, 9 months

Segmentation Fault Analyzing Gasoline (TIPSY) data with yt-3.0

by Samantha Benincasa

Hello, I have been trying to analyze a TIPSY dataset using the new features in yt-3.0. I am unable to do any analysis without getting a segmentation fault. Following the python notebook example for Gasoline, I read in the data using the command: ds = TipsyStaticOutput('test.00001',parameter_file='test.param') When I try to construct a plot collection, I am given the following error: YTDomainOverflow: Particle bounds [ 1.25443703e-02 -5.12246704e+02 -5.46726685e+02] and [ 1.25443703e-02 5.65781677e+02 4.61335541e+02] exceed domain bounds [-0.5 -0.5 -0.5] and [ 0.5 0.5 0.5] If I instead try to manually set the domain bounds in the TipsyStaticOutput command, ds = TipsyStaticOutput('test.00001',parameter_file='test.param',domain_left_edge=[-57,-57,-57],domain_right_edge=[57,57,57]) This gets rid of the domain boundary errors but I still receive a segmentation fault when I try to create the PlotCollection. I am just trying to read the data in so I can make slices/projections in temperature and density. Thank you in advance for the help, Samantha

6 years, 9 months

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yt-users November 2013