Mailman 3 March 2014 - yt-users

Warning: pip install mpi4py may not work as expected
by Nathan Goldbaum March 5, 2014

March 5, 2014

Hi all, Due to a recent change in pip and the python package index system doing $ pip install mpi4py will install mpi4py 0.6.0, a version from 2008. This is due to a recent decision to only allow pip to download packages from pypi for security reasons. I've raised this issue with the mpi4py developers so hopefully this will be fixed soon. For now, mpi4py can be installed via: pip install mpi4py --allow-external mpi4py --allow-insecure mpi4py Or by downloading the source package tarball from the mpi4py package release page on bitbucket and building manually: https://bitbucket.org/mpi4py/mpi4py/downloads Hope that avoids some confused debugging in the future, Nathan

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FLASH polar coordinates support
by Miguel de Val-Borro March 3, 2014

March 3, 2014

Hello, I have tried to plot the results of 2D FLASH simulation using the SlicePlot function and got the attached images using the development versions of yt-2.7 and yt-3.0. It looks like the range in the radial coordinate and the labels are not correct. Also I would like to transform to a Cartesian coordinate system, is this possible for FLASH 2D polar data? Thanks, Miguel

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Re: [yt-users] Yt geometry viewer
by Anthony Scopatz March 3, 2014

March 3, 2014

Hi Andy, Forwarding to the yt-users list. Could you send the exact error message you are seeing? Be Well Anthony On Sun, Mar 2, 2014 at 6:29 PM, Andrew Davis <davisa(a)engr.wisc.edu> wrote: > Hi Anthony > > Are there instructions anywhere how to get this working, do I need a new > branch of yt? > > Thanks > > Andy >

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sliceplot of a cylinder surface
by Yi Feng March 3, 2014

March 3, 2014

Hi, I have done a 3D accretion disk simulation in cartesian coordinate. The disk is centered at the origin and the disk plane is x-y plane. I want to know the disk structure at a fixed radius R, i.e. sqrt(x*x+y*y) equals a constant. It is something like the surface of a cylinder. A slice plot of cylinder surface is helpful. But sliceplot only applies to a flat plane. So how to do a slice plot of a cylinder surface? Thanks a lot! -- Sincerely Yi Feng Department of Astronomy&Astrophysics,UC Santa Cruz

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Memory error and yt in parallel
by Jean-Claude Passy March 2, 2014

March 2, 2014

Hi everyone, I am trying to analyze a unigrid simulation, 512^3 zones. Each dump has a size of ~ 7 GB. I use the following script to get the angular momenta: http://paste.yt-project.org/show/4340/ I am running it on a cluster with 1 core and 16GB. It typically runs fine for the first 2 dumps, then crashes on the third one when asking for AngularMomentumZ. I assume that I must not erase variables correctly. Does someone have any suggestion about how to optimize the script? Also, would that make sense to run the script in parallel or would the root grid be duplicated on all processors? Sorry for the naive questions, and thanks a lot for the help! Cheers, JC

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Light Cone Projection
by Pengfei Chen March 2, 2014

March 2, 2014

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

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