Broken volume rendering
by Matthew Turk
Hi all,
I broke volume rendering (via yt.extensions.volume_rendering) some
time ago, and I only just realized it today when some people were
getting corrupted images. It took a while to come up because I
avoided re-generating the Cython/C code that actually conducts the
volume rendering; however, recently I updated this code and pushed it
to the repository, and that's when the errors started showing up.
The exact error was in mercurial changeset 3007999e2518 (May 30),
which I merged into trunk in revision 1754 (June 24). These dates are
not necessarily the dates at which the error showed up, however, as
the re-cythonization probably did not occur at those times. The error
was in the optimization of division by the inverse of the vector
direction; the rays to cast were passed to partitioned bricks and to
avoid too much division of 64-bit floats, I changed it to be a
multiplication against the inverse.
To calculate the inverse, I did something similar to this:
for i in range(3):
iv_dir[i] = 1.0/v_dir[0]
The error, of course, being that I was dividing by v_dir[0] for all
three values.
I identified this by using the hg bisect command, where I found a good
revision and a bad revision and it executed the necessary tests to
figure out where the code took a turn for the worse. I've committed
fixes in hg changeset f0960f4f6bed, svn trunk r1804 and svn yt-1.7
r1805.
I'm really sorry for the troubles, and I hope that it hasn't cost
anyone too much time. There may still be some lingering bugs, so
please let me know if you run into any more bad images or difficulties
with the volume rendering. You can get an updated yt by doing "yt
instinfo -u".
-Matt
8 years, 5 months
yt-2.0: a brief poll
by j s oishi
Hi all,
yt-2.0 is coming soon, and the development team is starting to think
about what needs to be done before we can release it. We would really
love some user input as to what we should focus our energies on. To
this end, I've made a very short survey that we would really
appreciate your participation in. Please go to
http://spreadsheets.google.com/viewform?formkey=dFpwNHR2MHV2dlFTNEZrN2lEM...
and fill in your opinions. If you have any other comments, feel free
to email me directly or reply on list.
Thanks so much,
Jeff
on be behalf of the yt-development team
8 years, 5 months
halo density profiling
by Irina Dvorkin
Hello All,
I'm trying to use the halo profiler, without much success.
If I want to plot the density, do I need to use the weight_field?
It says weight_field=None in the manual, but
weight_field='CellMassMsun' in the cookbook.
Is it the same for Dark_Matter_Density?
Also, where can I see a list of things the halo profiler can in
principle do? I coudn't find it on the site.
Thanks a lot for your help,
Irina
8 years, 5 months
yt file problems
by Stephen Skory
Hi all,
I am running a script that does a for loop over a set of time ordered data
dumps. I am fairly consistently getting this error, but at different points in
the for loop cycle. This suggests that this is a file system error (this is on
Triton), but I'm not sure. Does anyone have any ideas of why things would fail
here in an inconsistent fashion? Thanks!
File "./camera.py", line 167, in <module>
pf = load(dirs[count])
File
"/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/convenience.py",
line 77, in load
return output_type_registry[candidates[0]](*args, **kwargs)
File
"/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/OutputTypes.py",
line 59, in __new__
_pf_store.check_pf(obj)
File
"/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py",
line 152, in check_pf
self.insert_pf(pf)
File
"/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py",
line 166, in insert_pf
self.flush_db()
File
"/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py",
line 182, in flush_db
self._write_out()
File
"/home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py",
line 197, in _write_out
os.rename("%s.tmp" % fn, fn)
OSError: [Errno 2] No such file or directory
_______________________________________________________
sskory(a)physics.ucsd.edu o__ Stephen Skory
http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
________________________________(_)_\(_)_______________
8 years, 5 months
Flashfields error on install
by Cameron Hummels
Hey everyone:
I just pulled the newest version of yt and installed it on kraken.
It installed OK (installing locally HDF5, zlib, libpng and python). I
remembered to swap the PGI modules to the GNU modules. Unfortunately,
when I go to run it I get the following error involving "FLASHFields":
$ yt
Traceback (most recent call last):
File "/nics/b/home/chummels/source/yt-x86_64/bin//yt", line 9, in
<module>
load_entry_point('yt==2.0dev', 'console_scripts', 'yt')()
File
"/nics/b/home/chummels/source/yt-x86_64/lib/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",
line 299, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File
"/nics/b/home/chummels/source/yt-x86_64/lib/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",
line 2229, in load_entry_point
return ep.load()
File
"/nics/b/home/chummels/source/yt-x86_64/lib/python2.6/site-packages/distribute-0.6.10-py2.6.egg/pkg_resources.py",
line 1948, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/nics/b/home/chummels/source/yt/yt/command_line.py", line 26,
in <module>
from yt.mods import *
File "/nics/b/home/chummels/source/yt/yt/mods.py", line 32, in <module>
import yt.lagos as lagos
File "/nics/b/home/chummels/source/yt/yt/lagos/__init__.py", line 79,
in <module>
from FLASHFields import *
ImportError: No module named FLASHFields
I've never seen this error, and I investigated a bit but couldn't find
much about it. Any ideas from people? What is this mysterious
FLASHFields module?
Cameron
8 years, 5 months
Quick Tkinter poll
by Matthew Turk
Hi all,
If you have a second, I'd really appreciate your help with figuring
out where Tkinter is available: inside the TeraGrid, on your personal
machines, on other supercomputing centers, etc etc. This form:
http://spreadsheets.google.com/viewform?formkey=dEhzZXdTbl9ydDJXb3JYSktEd...
will collect your responses, and it describes what to do. You simply
have to run the command: "python2.6 -c 'import Tkinter' " and report
if it throws an ImportError or if it passes without failure.
Thanks very much, and I really appreciate you taking the couple
moments to do this.
-Matt
8 years, 6 months
h5py Issues
by Brian Crosby
In attempting to make a series of projections with halos plotted using the public install of yt on Kraken, I've encountered an odd problem. The job terminates without giving an apparent error statement in the output files, but rather ends with this cryptic (at least to me) mess:
h5py._stub.IOError File "h5g.pyx", line 104, in h5py.h5g.GroupIter.__init__ (h5py/h5g.c:1248)
File "h5g.pyx", line 104, in h5py.h5g.GroupIter.__init__ (h5py/h5g.c:1248)
: Addr overflow (Invalid arguments to routine: Address overflowed)
h5py._stub.IOError: Addr overflow (Invalid arguments to routine: Address overflowed)
return func(*args, **kwds)
File "h5g.pyx", line 317, in h5py.h5g.GroupID.get_num_objs (h5py/h5g.c:2482)
return func(*args, **kwds)
File "h5g.pyx", line 317, in h5py.h5g.GroupID.get_num_objs (h5py/h5g.c:2482)
return func(*args, **kwds)
File "h5g.pyx", line 317, in h5py.h5g.GroupID.get_num_objs (h5py/h5g.c:2482)
return func(*args, **kwds)
File "h5g.pyx", line 317, in h5py.h5g.GroupID.get_num_objs (h5py/h5g.c:2482)
File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/h5py-1.2.1-py2.6-linux-x86_64.egg/h5py/_sync.py", line 88, in wrap
Does anyone have an idea what could be causing this problem?
Thanks,
Brian
8 years, 6 months
zlim, phase plots
by david collins
Hi, all--
I'm trying to save a phase plot, then re-load and re-plot, and do this
into an axes object I've pre- defined. (I want to put several phase
plots into a multi-tile frame)
I'm presently doing:
the_plot = raven.PlotTypes.PhasePlot(phase
,[xfield,yfield,zfield],14,'algae',axes=axes)
(where phase is the unpickled phase object)
then
fig.save_fig(output_name)
(where axes is contained in fig) This works just fine. The problem
I'm running into is setting the zlim on the phase plot. If I do:
the_plot = raven.PlotTypes.PhasePlot(phase
,[xfield,yfield,zfield],14,'algae',axes=axes)
the_plot.set_zlim(a,b)
the zlim doesn't seem to change the actual zlim I find in output_name.
Is that the appropriate place to be setting the zlim for this
operation? Or is there a better place?
Thanks,
d.
--
Sent from my Stone Tablet and carried by my Pterodactyl.
8 years, 6 months
Weighed projections
by Brian Crosby
I'm trying to make a density weighted temperature projection on Kraken, and the weighting seems to be causing problems. I get this error:
Traceback (most recent call last):
File "./s_p_halos.py", line 23, in <module>
p = ph.add_projection("Temperature", 0, weight='Density')
I'm puzzled because this exact same script works on my laptop, albeit with a much smaller data set. Any ideas or suggestions would be greatly appreciated.
Thanks,
Brian
8 years, 6 months
parallelHOP
by Brian Crosby
Hi everyone,
I'm trying to make a merger tree on Kraken using parallelHOP and the public yt installation, but am getting this error:
Traceback (most recent call last):
File "./merger.py", line 9, in <module>
MergerTree(files, database='/lustre/scratch/oshea/PopIII_smallbox/halos.db', halo_finder_function=parallelHF)
NameError: name 'parallelHF' is not defined
All of the requisite Forthon and KD Tree bits seem to be there, and the only thing that I found in the yt install that might be problematic is that I can't access the Forthon directory at /lustre/scratch/proj/yt_common/trunk/src/Forthon-0.8.3/ . I don't know if that could possibly cause problems, but it made me curious. Does anyone have any tips on what's going wrong? Running the exact same script with HaloFinder instead of parallelHF works without problem (just very slowly at lower redshifts).
Thanks,
Brian
8 years, 6 months
