I've recently been trying to use yt's inline analysis functionality with
Enzo and am having some difficultly getting it to work in parallel. I am
using the development tip of yt. In serial, everything works fine, but in
parallel, I get the following error:
It seems that the issue is that yt is not correctly identifying which grids
are available on a given processory for the EnzoDatasetInMemory object.
Does anyone have an idea of how to fix this? Has anyone else seen this?
For reference, my user_script is just this:
from yt.frontends.enzo.api import EnzoDatasetInMemory
ds = EnzoDatasetInMemory()
ad = ds.all_data()
Thanks for any help,
I'm looking to convert particle based quantities into a uniform grid based
quantity (arepo data is input). So say I have a collection of gas elements
with some density rho and x,y,z positions. I want to construct an 256^3
mesh representing the cells in a mesh.
x,y,z,rho --> cic mesh where the values at i,j,k is the smoothed density
are created by the cic algorithm
Now, generalising this more, can I have rho to be any quantity? So now say
I have star particles which similarly have x,y,z but I want to distribute
their luminosity. Again, I want to do it for say the gas velocity field as
well. Is there any general functionality for converting particle quantities
to mesh quantites in yt with the deposit all_cic functionality? I have a
basic code for just x,y,z particle data and distributing that based on
density to a cic (see below)
ad = pf.all_data()
level = int(math.log(ndim,2))
cg = pf.covering_grid(level=level, left_edge=[0,0,0],dims=[ndim,ndim,ndim])
arr = cg['deposit', 'all_cic'],
but I'm not sure what to do for the other variables. Any help is
appreciated in advance.
Does anyone know how to specify the tickmark locations on the colorbar
axis? I am able to do this on the plot axes without issue, but have not
been able to successfully do the same with the colorbar.
Attached is a pic of one of my plots using default colorbar axis ticks. I
have tried to use the following code (and many variants of it I have found
in the python/matplotlib documentation) to specify the location of the
tickmarks, but they don't place the ticks accurately. My data is
temperature plotted over the range of 300K to 5500K and I want to have
tickmarks at 300K, 800K, 3500K, and 4500K. Also attached is pic of my plot
showing an attempted custom colorbar axis.
I'm not sure if it makes a difference, but I made the colormap in
colorbar_axes = p.plots[string].cax
colorbar_axes.yaxis.set_ticks([0, 0.1, 0.8])
Thanks for the help!
Hi Michael, John, Nathan,
My strealines script can be see here:
Modifying the periodicity manually via
ds.periodicity = (True, True, True)
causes the script to appear to execute for a very long time. I have never
seen it run to completion, even for a single streamline. Perhaps I am just
If I do not directly modify the periodicity, the output I have pasted here:
Any help is appreciated.
I have a few plotting questions:
In the above plot, Colorbar range is approximately Mass=10^5-10^9. When
making a plot using ParticlePlot or ParticleProjectionPlot, can I manually
force the range on the colorbar?
2. The label on the colorbar says "Particle Mass". Instead, shouldn't it be
saying something like mass_per_pixel, since the plot is showing the total
number of particles projected along the z-axis? How can we rename the
3. Can contours of mass be added to the above plot, using annotate?
I'm trying to plot 3D streamlines from a FLASH (v.4) dataset. I've based my
streamlines script off the version presented on the yt-project.org website.
I consistently get an error about going up the ghost cells in my volume.
The error message is:
RuntimeError: Error: yt attempted to read outside the boundaries of a
> non-periodic domain along dimension 0.
> Region left edge = -3e+18 code_length, Region right edge = 4.5e+18
> Dataset left edge = 0.0 code_length, Dataset right edge = 1.2e+19
> This commonly happens when trying to compute ghost cells up to the domain
> boundary. Two possible solutions are to load a smaller region that does not
> border the edge or override the periodicity for this dataset.
My FLASH datasets have x/y/zmin = 0.0 and x/y/zmax 1.2e19 cm.
I seems like yt is trying to read outside my domain, or is bumping up
against the guardcells and I have no idea how to prevent it from doing
this. I have tried inspecting the code for an obvious solution. A very
similar error shows up when I try to make 1D profiles of the entire dataset
(dd = ds.all_data()).
is it possible that yt doesn't support volumes where the (0,0,0) coordinate
is a corner of the volume? Any easy solution to the above issue?
I have just learned about yt and I'd like to try it out. I tried to install it using the shell script but i got the following error:I am using Ubuntu 14.04 64 bit.
Installing pip******************************************** FAILURE REPORT:********************************************
bootstrap(tmpdir=tmpdir) File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmp4MGuKb/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module>ImportError: cannot import name HTTPSHandler
I have also attached the last lines from the log file.
Does anyone knows how can this error be fixed?
I’ve run into an error whenever I try to execute any yt command (see yt_run_error.txt, attached because I can’t use “yt pastebin”). I’ve tried following the steps on the help page, including re-installing yt, and I still get this same error. I just installed the latest stable yt version (I can’t execute the command to give you specific numbers) on Mac OS X 10.10.4.
Does anyone know where I should start to fix this?
Astrophysics | Lyman Briggs College
Women’s & Gender Studies | College of Arts & Letters
LGBTQ and Sexuality Studies Specialization
Women in Science, President
Undergraduate Teaching Assistant
Undergraduate Research Assistant
Department of Physics and Astronomy
Michigan State University
I am getting this error when I try to wget the install_script.sh. I even
tried the `--no-check-certificate' option, without success. I have tried on
my macbook and my office machine/supercomputer. No luck.
Let me know if anyone has a clue.
Resolving hg.yt-project.org... 126.96.36.199, 188.8.131.52
Connecting to hg.yt-project.org|184.108.40.206|:80... connected.
HTTP request sent, awaiting response... 302 FOUND
Location: https://bitbucket.org [following]
--2015-07-17 20:36:52-- https://bitbucket.org/
Resolving bitbucket.org... 220.127.116.11, 18.104.22.168
Connecting to bitbucket.org|22.214.171.124|:443... connected.
ERROR: cannot verify bitbucket.org's certificate, issued by
`/C=US/O=DigiCert Inc/OU=www.digicert.com/CN=DigiCert SHA2 Extended
Validation Server CA':
Unable to locally verify the issuer's authority.
To connect to bitbucket.org insecurely, use `--no-check-certificate'.
Unable to establish SSL connection.