Hi all,
Have any of the rest of you seen this?
The default IPython logger has a specific format, which only logs warnings and up. The yt logger has a different format, and logs info and up. For some reason, in the IPython console, the correct logging behavior for yt occurs, but not in the notebook. See the following images:
http://i.imgur.com/l3klTE3.png <http://i.imgur.com/l3klTE3.png>
http://i.imgur.com/MIZ1oKK.png <http://i.imgur.com/MIZ1oKK.png>
Basically, the yt logging behavior is not picked up in the notebook, so it uses the default notebook logging behavior.
I’ve seen this on a number of platforms and can’t figure out how this happens. It’s not a big deal, but it’s annoying. Anyone care to venture what is going on?
John
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Hi all,
Have any of the rest of you seen this?
The default IPython logger has a specific format, which only logs warnings and up. The yt logger has a different format, and logs info and up. For some reason, in the IPython console, the correct logging behavior for yt occurs, but not in the notebook (see the attached images).
Basically, the yt logging behavior is not picked up in the notebook, so it uses the default notebook logging behavior.
I’ve seen this on a number of platforms and can’t figure out how this happens. It’s not a big deal, but it’s annoying. Anyone care to venture what is going on?
John
Hi All,
I have just learned about yt for large data visualization and analysis.
It looks like such a wonderful package for getting things done in a
quicker and very high quality kind of manner.
Hence, I wish to employ the package to work with data from an
outputting code called Carpet(http://www.carpetcode.org) built on
top of another code called Cactus (for computational astrophysics
simulations, e.g. merging black holes or neutron stars). Carpet
also performs some adaptive mesh refinement in Cactus, as well
as parallelization tasks (along with handling the I/O tasks). All these
(cactus and Carpet) are part of a community-based code known
as the Einstein Toolkit.
Usually, one would be interested in creating some array of
color-map snap-shots of 2D (2 spatial dimensions, plus the
actual physical quantity) quantities from the resulting
simulation data. Sometimes, such snap-shots could be
meant to compare a certain quantity from various simulations.
My general impression so far, however, is that the package
seems be oriented towards systems that involve 'particles',
like galaxies or similar bodies. Would it support the kind of
data I'm working with (the 2D/3D scalars on refined grids,
vectors, etc)? Or, would I need to try and extend yt to
read/load my kind of data? Two output formats are possible
from my simulations: HDF5 (CarpetIOHDF5, an adaptation of
standard HDF5), and ASCII formats. I would prefer advice on
the use of HDF5 though.
Your advice will be highly appreciated.
Kind regards
Dumsani
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Hi, everyone--
I apologize if this was discussed already. I noticed that in yt3.0,
magnetic field values have take_log=True, by default (these are the
('enzo','Bx') types of fields) Is there an easy way to change that
universally (like in the plugins file, or better something more
fundamental, since I imagine that this will be the desired effect for most
users)
Thanks!
d.
--
-- Sent from a computer.
Fellow yt users:
We at the yt development team want to make yt better for you, the user. We
have prepared a short survey to gain your valuable feedback to help us
understand what is working in yt and what is not. Could you please spare 2
minutes to fill out our survey below?
We plan to collect responses and make available a selection of results
by December
10, so please let us know what you think at the following URL:
http://goo.gl/forms/hRNryOWTPO
On behalf of the yt development team,
Cameron
--
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
Hi everyone,
I'm trying to get a development version of yt going on a remote machine. I
originally installed yt on that machine using Anaconda, and that's been
working well. Since the Anaconda installation takes care of all the
dependencies, I hoped I would just be able to install the development
version and not have to worry about any of that.
I created a directory called yt in my home directory, then cloned the yt
repository:
hg clone https://bitbucket.org/yt_analysis/yt .
Then I ran hg update yt in the same directory, and then
python setup.py develop
also in the same directory. That almost immediately returns with the
following error:
File "setup.py", line 17, in <module>
if StrictVersion(setuptools.__version__) < StrictVersion('0.7.0'):
File "/<homedir>/miniconda/lib/python2.7/distutils/version.py", line 40,
in __init__
self.parse(vstring)
File "/<homedir>/miniconda/lib/python2.7/distutils/version.py", line 107,
in parse
raise ValueError, "invalid version number '%s'" % vstring
ValueError: invalid version number '0.6c11'
I'm not sure what this means. Can anyone shed some light on this for me?
Thanks,
Dan
I know it's being rewritten, thanks to Sam and Cameron and others, but
I'm hoping to use some sort of perspective camera for volume
rendering. (What I'll eventually want is the dome camera which I know
also exists, but wanted to start with a simpler plane-projection
perspective camera.)
What I get: plausible images from the default orthographic Camera, but
reliably blank images from PerspectiveCamera.
If I extract the sampler rays from PerspectiveCamera and plot them, they
always seem to point in the hemisphere away from the given center
point. If I change the sign of Z width, the viewpoint is put on the
opposite side of the data region, and the rays still point away from it.
Also they're extremely short, like .001 or so of the distance from the
viewpoint to the center point - much too short to intersect anything if
the viewpoint is outside of the data volume.
If I hack the sampler vectors in PerspectiveCamera to (a) reverse their
direction and (b) make them many times longer, I do see something.
I don't know whether I'm passing nonsense parameters to
PerspectiveCamera, or whether its current code is really not right...?
A sample program, which contains its own replacement for
Camera.snapshot() that allows for tweaking PerspectiveCamera rays, is in:
http://paste.yt-project.org/show/5240/
Is there a way to restrict yt to only use a subset of the available
processes when it's running in parallel? I have a set of ipython engines
running, and I'm trying to launch a yt script on a subset of them, but it
just hangs. It works fine if I launch the same script on all the processes.
Printing out MPI.COMM_WORLD.Get_size() from the script gives the total
number of engines, not the size of the subset I'm trying to use.
I haven't done a lot of parallel programming, but I would guess that the
running processes are waiting on one that's not running a yt script, since
they can see the total number of processes available, but not the size of
the subset of processes that are actually running a yt script.
Does anyone have any thoughts on how to do this?
Thanks,
Dan
Hi all,
I know that parallelizing a single projection doesn’t really give you that much speed benefit.
But what would happen if I tried to do something like this (please excuse the Python pseudocode):
fields = [big list of fields I want to project]
prj = ds.proj(“ones”, 2)
frb = prj.to_frb(…)
storage = {}
for sto, fd in parallel_objects(fields, storage=storage):
buf = frb[fd]
sto.result_id = fd
sto.result = buf
I did something like this but it hung at the end, which makes me think that I’ve got some kind of blocking operation here that I’m not aware of.
Best,
John
Hi All,
I'm getting an installation failure that I haven't seen before - I'm trying
to install on 10.9.5 OSX, and have xcode and command line tools installed.
The failure I get right off the bat is appended below.
I haven't edited the install script to allow for root install (because I'm
not sure that should be necessary?). But, at the same time, nothing seemed
weird about the Xcode or command line tools installation. Has anyone seen
an error like this before?
Thanks,
-d
********************************************
********************************************
jam:~ desika$ cat yt-x86_64/yt_install.log
cloudy_emissivity.h5: OK
apec_emissivity.h5: OK
hdf5-1.8.11.tar.gz: OK
zlib-1.2.8.tar.gz: OK
bzip2-1.0.6.tar.gz: OK
libpng-1.6.3.tar.gz: OK
freetype-2.4.12.tar.gz: OK
sqlite-autoconf-3071700.tar.gz: OK
zeromq-4.0.4.tar.gz: OK
pyzmq-14.3.1.tar.gz: OK
tornado-4.0.1.tar.gz: OK
Python-2.7.8.tgz: OK
numpy-1.8.2.tar.gz: OK
matplotlib-1.4.0.tar.gz: OK
mercurial-3.1.tar.gz: OK
ipython-2.2.0.tar.gz: OK
h5py-2.3.1.tar.gz: OK
Cython-0.20.2.tar.gz: OK
reason-js-20120623.zip: OK
nose-1.3.4.tar.gz: OK
python-hglib-1.0.tar.gz: OK
sympy-0.7.5.tar.gz: OK
Agreeing to the Xcode/iOS license requires admin privileges, please re-run
as root via sudo.
