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
4 years, 7 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-...)
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
4 years, 9 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/0...)
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
4 years, 11 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
5 years
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/0036...
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
5 years
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
5 years
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
5 years
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
5 years
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
5 years
Problem with covering_grid
by Wolfram Schmidt
Hi,
I want to read in the root-grid data from AMR output produce by Nyx. The
following piece of code used to work a while ago and something similar
can be found in the recipes:
n_levels = 0
pf =load(path)
left=na.amin(pf.h.grid_left_edge,axis=0)
right=na.amax(pf.h.grid_right_edge,axis=0)
resolution = 2**n_levels*pf.domain_dimensions
print n_levels, left, right, resolution
cg = pf.h.covering_grid(n_levels, left_edge=left, right_edge=right,
dims=resolution)
With the current stable yt version, however, I get the following error:
0 [ 0. 0. 0.] [ 2.46880000e+25 1.23440000e+25 1.23440000e+25]
[256, 128, 128]
Traceback (most recent call last):
File "/usr/users/wschmid2/scripts/radial_profile.py", line 71, in
<module>
cg = pf.h.covering_grid(n_levels, left_edge=left, right_edge=right,
dims=resolution)
File
"/home/uni05/wschmid2/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 3706, in __init__
rdx[np.where(dims - 2 * num_ghost_zones <= 1)] = 1 # issue 602
TypeError: list indices must be integers, not tuple
Since the output in the first line produced by the print statement shows
that all parameters are perfectly ok, I don't understant what's the
problem. Can anyone help?
Cheers,
Wolfram
5 years
