pickle
by Elizabeth Tasker
Hi,
A bigger problem....
The lastest version of yt
The current version of the code is:
---
a519b8754ba8 (yt) tip
---
has problems with pickle. If I pickle a data set and then try and
unpickle it, I see:
unpickle core data
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
/home/tasker/yt/src/yt-hg/scripts/iyt in <module>()
338
339 #file = open('cores.pickle','rb')
--> 340 allcloudcores = cPickle.load(file('cores.pickle', 'rb'))
341 file.close()
342
/home/tasker/yt/src/yt-hg/yt/data_objects/data_containers.pyc in
_reconstruct_object(*args, **kwargs)
3676 else: new_args.append(arg)
3677 pfs = ParameterFileStore()
-> 3678 pf = pfs.get_pf_hash(pfid)
3679 cls = getattr(pf.h, dtype)
3680 obj = cls(*new_args)
/home/tasker/yt/src/yt-hg/yt/utilities/parameter_file_storage.pyc in
get_pf_hash(self, hash)
106 def get_pf_hash(self, hash):
107 """ This returns a parameter file based on a hash. """
--> 108 return self._convert_pf(self._records[hash])
109
110 def get_pf_ctid(self, ctid):
KeyError: (('283b7c4d88671dbff7acf083098da6ae',), <function
_reconstruct_object at 0x272c938>,
('283b7c4d88671dbff7acf083098da6ae', 'region', array([ 16., 16.,
16.]), array([ 0., 0., 0.]), array([ 32., 32., 32.]),
{'disk_center': array([16, 16, 16]), 'center': array([ 16., 16.,
16.]), 'bulk_velocity': array([ 0., 0., 0.]), 'disk_vector':
array([0, 0, 1]), 'disk_radius': array([ 0.1 , 0.1358, 0.1716,
0.2074, 0.2432, 0.279 ,
The fact it mentions the field parameters in the last line, might mean
it's an error introduced because of the corrections to them (that I
have been demanding!)?
The script I have works fine (pickles and all) on yt version:
---
16e8d749a806 (yt) tip
---
Elizabeth
7 years, 2 months
field parameters (you know I want to use them everywhere...)
by Elizabeth Tasker
Hi,
Two small problems:
1. Another issue with field parameters. I can't pass them to a slice
if the derived field also needs ValidateSpatial.
i.e.
def _EffectivePotential(field, data):
center = na.array(data.get_field_parameter("disk_center"))
h_vec = na.array(data.get_field_parameter("disk_vector"))
omega = na.array(data.get_field_parameter("thiscore_omega"))
.
.
blah
.
.
add_field("EffectivePotential", function=_EffectivePotential,
validators=[ValidateSpatial(1, ["x-velocity", "y-velocity",
"z-velocity", "x", "y", "z"])])
p = pc.add_slice("EffectivePotential", 2,
field_parameters={"disk_vector":disk_vector,
"disk_center":disk_center, "thiscore_omega":core_omega[c]})
can't find its field parameters but if I change the end line of the function to:
add_field("EffectivePotential", function=_EffectivePotential)
everything is fine.
It actually seems to work OK even without the ValidateSpatial (I have
cross products in the function so pain has the potential to happen
without the full data) so perhaps this isn't a problem, but I think it
is a small bug?
2. For some reason, yt has decided to save all my image files in:
/home/tasker/.yt/my_plugins.py_Slice_z_EffectivePotential.png
This is less than intuitive. Does anyone know why and how I can stop it?
Thanks!
Elizabeth
7 years, 2 months
Registration for yt workshop in January 2012 is open
by matthewturk＠gmail.com
If you have trouble viewing or submitting this form, you can fill it out
online:
https://docs.google.com/spreadsheet/viewform?formkey=dElGU0sxcXRHNmlCZW5G...
yt workshop 2012 registration
Registration is now open for the yt workshop, to be held at the FLASH
center in Chicago, from Jan 24-26, 2012. This workshop will start with
basic yt usage, move on to advanced and parallel usage, and then finally
address how to modify, extend and contribute to yt. For more information,
see the blog post:
http://blog.yt-project.org/announcing-the-2012-yt-workshop and keep an eye
on http://yt-project.org/workshop2012/ for more info. We have secured
housing in downtown Chicago (near the river, just off Michigan Avenue) that
we are able to book double-occupancy rooms for $99/night, pre-tax. We are
eagerly pursuing funding opportunities and are very optimistic about their
prospects, but we are still waiting on funding for participant costs. If we
are able to secure funding, it will likely cover hotel costs for most
attendees as well as a number of small travel grants. We have reserved the
block of rooms for four nights, starting the 23rd and including the final
day of the conference, to encourage attendance at all three days. We also
hope to offer a social gathering and a trip to the Adler planetarium during
the workshop. This is the registration form: PLEASE FILL IT OUT EVEN IF YOU
FILLED OUT THE PREVIOUS SURVEY. We have used the pre-registration form to
gauge interest, secure accommodations, and request funding, and we are now
looking for binding commitments. There are also several questions here that
will help us in constructing a set of talks and tutorials for the first
portion of the workshop. If you indicate you would like to stay in the
hotel block of rooms, we will contact you with more information about
securing your reservation. Organizing Committee: Matthew Turk, Britton
Smith, John ZuHone (For inquiries: workshop2012(a)yt-project.org )
Name *
Email address *
I would like to stay in the block of rooms allocated for the workshop.
These rooms are at below-market prices and will cost $99/night plus tax per
room. Preference will be given to those willing to share a room;
assignments and roommate information can be decided later.
Yes (and I am willing to share a room)
Yes (and I am unwilling to share a room)
No
I require funding for: Hotel funding may be contingent on sharing a room.
While we are still awaiting information about funding, we are optimistic
that both hotel and limited travel grants will be available.
Hotel
Travel
What is your skill level with yt?
What is your skill level with Python / NumPy / matplotlib?
If appropriate, what would you consider your primary simulation code to be?
Enzo
FLASH
RAMSES
Boxlib-based code
Chombo-based code
ART
Gadget
Other:
Position What position do you currently occupy?
Undergraduate student
Graduate student
Postdoctoral Researcher
Faculty
Staff Scientist
Other:
Do you have any dietary concerns that may be relevant?
Any other comments or suggestions?
Powered by Google Docs Report Abuse - Terms of Service - Additional Terms
7 years, 2 months
Installing yt without hg
by david collins
Hi there--
I'm on a system that has a pretty fierce firewall so that things like
pip, wget, and mercurial can't see the outside world through any http
based protocol. I got the zips from a different machine and things
worked basically fine until I got to the bit where it tries to install
easy_install. (error below)
Has anyone had experience with such a problem, and have suggestions
for getting around the need for a network connection?
Thanks,
d.
Installing easy_install script to /usr/projects/magnetic/david_c/local/bin
Installing easy_install-2.7 script to /usr/projects/magnetic/david_c/local/bin
Installed /usr/projects/magnetic/david_c/local/lib/python2.7/site-packages/distribute-0.6.21-py2.7.egg
Processing dependencies for distribute==0.6.21
Finished processing dependencies for distribute==0.6.21
After install bootstrap.
Creating /usr/projects/magnetic/david_c/local/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info
Creating /usr/projects/magnetic/david_c/local/lib/python2.7/site-packages/setuptools.pth
Searching for pip
Reading http://pypi.python.org/simple/pip/
Download error on http://pypi.python.org/simple/pip/: timed out --
Some packages may not be found!
Reading http://pypi.python.org/simple/pip/
Download error on http://pypi.python.org/simple/pip/: timed out --
Some packages may not be found!
Couldn't find index page for 'pip' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading http://pypi.python.org/simple/
Download error on http://pypi.python.org/simple/: timed out -- Some
packages may not be found!
No local packages or download links found for pip
error: Could not find suitable distribution for Requirement.parse('pip')
--
Sent from my computer.
7 years, 2 months
only_on_root
by Christine Simpson
Hi,
I'm trying to run a script with parallel yt that does some non-yt io.
I'm a little confused about how to use only_on_root.
Here is a test script I've tried:
from yt.mods import *
from yt.visualization.api import PlotCollection
import matplotlib.colorbar as cb
path =
"/scratch/01112/tg803911/halo88_therm_feed_3.7e-6_LW_RadiationShield_lmax12/DD0010/"
fn = "output_0010"
pf = load(path+fn)
pc = PlotCollection(pf)
pc.add_projection("Density",0)
pc.set_width(20,'kpc')
pc.save(fn)
filename = 'hello_world'
file = only_on_root(open(filename,'w'))
only_on_root(file.write("hello_world \n"))
only_on_root(file.close())
Pasted below is the error. I'm uncertain about the syntax of
only_on_root. Do I just wrap it around normal commands? Also, it seems
that the write command is trying to execute on all the processors. That
shouldn't be happening, right?
P007 yt : [INFO ] 2011-11-22 09:50:20,558 Saved
output_0010_Projection_x_Density.png
P008 yt : [INFO ] 2011-11-22 09:50:20,558 Saved
output_0010_Projection_x_Density.png
P009 yt : [INFO ] 2011-11-22 09:50:20,560 Saved
output_0010_Projection_x_Density.png
Traceback (most recent call last):
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
File "test_parallel_yt.py", line 19, in <module>
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
only_on_root(file.write("hello_world \n"))
AttributeError : only_on_root(file.write("hello_world \n"))
'NoneType' object has no attribute 'write'
P010 yt : [INFO ] 2011-11-22 09:50:20,561 Saved
output_0010_Projection_x_Density.png
AttributeErrorP011 yt : [INFO ] 2011-11-22 09:50:20,561 Saved
output_0010_Projection_x_Density.png
: 'NoneType' object has no attribute 'write'
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
Traceback (most recent call last):
AttributeError: File "test_parallel_yt.py", line 19, in <module>
'NoneType' object has no attribute 'write'
P005 yt : [INFO ] 2011-11-22 09:50:20,562 Saved
output_0010_Projection_x_Density.png
P004 yt : [INFO ] 2011-11-22 09:50:20,562 Saved
output_0010_Projection_x_Density.png
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
P002 yt : [INFO ] 2011-11-22 09:50:20,583 Saved
output_0010_Projection_x_Density.png
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
P001 yt : [INFO ] 2011-11-22 09:50:20,589 Saved
output_0010_Projection_x_Density.png
P003 yt : [INFO ] 2011-11-22 09:50:20,589 Saved
output_0010_Projection_x_Density.png
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
P013 yt : [INFO ] 2011-11-22 09:50:20,593 Saved
output_0010_Projection_x_Density.png
P014 yt : [INFO ] 2011-11-22 09:50:20,593 Saved
output_0010_Projection_x_Density.png
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
P012 yt : [INFO ] 2011-11-22 09:50:20,596 Saved
output_0010_Projection_x_Density.png
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
P015 yt : [INFO ] 2011-11-22 09:50:20,599 Saved
output_0010_Projection_x_Density.png
Traceback (most recent call last):
File "test_parallel_yt.py", line 19, in <module>
only_on_root(file.write("hello_world \n"))
AttributeError: 'NoneType' object has no attribute 'write'
P000 yt : [INFO ] 2011-11-22 09:50:21,410 Saved
output_0010_Projection_x_Density.png
Traceback (most recent call last):
File "test_parallel_yt.py", line 18, in <module>
file = only_on_root(open(filename,'w'))
File
"/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/funcs.py", line 357, in only_on_root
return func(*args, **kwargs)
TypeError: 'file' object is not callable
mpispawn.c:303 Unexpected exit status
Child exited abnormally!
Killing remote processes...DONE
7 years, 3 months
YT on NASA Pleiades
by James Guillochon
I am getting a failure in the "load" statement when trying to run YT on
NASA Pleiades. It seems that it is having problems with the numpy package.
Here is the traceback:
http://paste.yt-project.org/show/1947/
My script is just:
from yt.mods import *
> load('filename')
Any ideas?
--
James Guillochon
Department of Astronomy & Astrophysics
University of California, Santa Cruz
jfg(a)ucolick.org
7 years, 3 months
rendering with streamlines
by Bo Zhao
Dear all,
I'm new to yt. Got a very basic question here:
If I want to render a volume image(say "density"), along with some magnetic
or velocity streamlines. Is there a way to plot both together?
Thanks a lot beforehand!
Sincerely
Bo Zhao
======================
7 years, 3 months
re-calculate function
by Elizabeth Tasker
Hi,
Simpler question (I think!)
Can I force yt to re-calculate a derived field? I'd like to call dd["Radius"] muliple times, but changing the position of the center field parameter in the same script. Currently, yt knows it's already calculated dd["Radius"] once and doesn't repeat it, even though "center" has changed. Ideally, I'd like to clear just that field, so yt doesn't go and recalculate any other fields.
Elizabeth
7 years, 3 months
ASCII Data in YT
by vishaalk＠umich.edu
Hi! I am an undergraduate student who is tasked with learning YT. I have
gotten it to to work in command line and in the python shell with the given
data set, but I am tasked with visualizing an ASCII data file of a single
halo. Is it possible to import ASCII data sets with the load() function in
the python shell?
Also, to get my python shell working I have to input $ cd /src/yt-hg/tests
instead of the cd $YT_DEST/src/yt-hg/tests suggested in the orientation
session. Do you know why this might be?
Thank you for your time.
Sincerely,
Vishaal Kalwani
7 years, 3 months
in-situ visualization possible with yt?
by Matthieu Dorier
Hello,
I'm trying to make in-situ visualization available for a simulation,
and I'm considering different softwares for that (VisIt, YT,...).
I've never used YT, so my question is: is it possible to add
some code in a simulation (written in C++) to have some kind of
distributed rendering engine using YT, just like VisIt does with
code-instrumentation?
Thanks,
Matthieu
--
Matthieu Dorier
ENS Cachan, antenne de Bretagne
Département informatique et télécommunication
http://perso.eleves.bretagne.ens-cachan.fr/~mdori307/wiki/
7 years, 3 months
