Re: [yt-users] h5py error in plot call

15 Feb 2010

      Hi again,
I tried Matt's snippet of code and hit an error here:

g = pf.h.grids[0]
yt         INFO       2010-02-14 19:20:47,399 Getting the binary  
hierarchy
yt         INFO       2010-02-14 19:20:47,403 Finished with binary  
hierarchy reading
Warning: divide by zero encountered in divide
Warning: invalid value encountered in sqrt
Warning: invalid value encountered in divide
Warning: invalid value encountered in divide
Warning: invalid value encountered in sqrt

The remaining steps still worked, ending with

print rho.shape, rho.min(), rho.max()
(32, 64, 64) 0.001 196.019

Thanks for the help,
Jordan

On Feb 14, 2010, at 6:33 PM, Matthew Turk wrote:
...
Hi all,
So one thing that is interesting is that, like Britton said, h5py is
throwing the error even though HDF5LightReader (the yt module) is
having the problems.  What h5py does, to my understanding, is
intercept all the HDF5 error calls, thus making it a bit more
difficult for us to get a proper error stack back from
HDF5LightReader.  What I'd recommend trying, in order to tie down the
error a bit more, is to use h5py to access the data and see what
errors it reports.  You can do this with:
from yt.mods import *
import h5py
pf = load(path_to_your_data)
g = pf.h.grids[0]
h5_file = h5py.File(g.filename)
rho = h5_file["/Grid%08i/Density" % g.id][:]
print rho.shape, rho.min(), rho.max()
and then if it has problems, that could lead us to the problem.
Thanks,
Matt
On Sun, Feb 14, 2010 at 3:44 PM, Britton Smith  
 wrote:
...
What's strange to me is that it's an h5py error coming from a call  
to the
hdf5 light reader, which I didn't think used h5py.  Matt, do you  
have any
ideas?
Britton
On Sun, Feb 14, 2010 at 4:38 PM, Jordan Thomas Mirocha
 wrote:
...
Hello,
The other day I updated to h5py 1.2, and am now getting the  
following
error message when I try to make projections or slices.
yt         INFO       2010-02-14 16:25:07,976 Created plot  
collection with
default plot-center = [0.5, 0.5, 0.5]
yt         INFO       2010-02-14 16:25:07,976 Adding plot for axis 2
yt         INFO       2010-02-14 16:25:07,981 Storing the binary  
hierarchy
yt         INFO       2010-02-14 16:25:07,985 Gathering a field  
list (this
may take a moment.)
Warning: divide by zero encountered in divide
Warning: invalid value encountered in sqrt
Warning: invalid value encountered in divide
Warning: invalid value encountered in divide
Warning: invalid value encountered in sqrt
Traceback (most recent call last):
 File "/Library/Frameworks/Python.framework/Versions/Current/bin/ 
yt", line
8, in <module>
  load_entry_point('yt==1.6dev', 'console_scripts', 'yt')()
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/commands.py",
line 523, in run_main
  sys.exit(YT.main())
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/cmdln.py",
line 257, in main
  return self.cmd(args)
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/cmdln.py",
line 280, in cmd
  retval = self.onecmd(argv)
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/cmdln.py",
line 412, in onecmd
  return self._dispatch_cmd(handler, argv)
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/cmdln.py",
line 1100, in _dispatch_cmd
  return handler(argv[0], opts, *args)
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/commands.py",
line 205, in arg_iterate
  func(self, subcmd, opts, arg)
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/commands.py",
line 334, in do_plot
  else: pc.add_slice(opts.field, ax, center=center)
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/raven/ 
PlotCollection.py",
line 182, in add_slice
  return self.__add_slice(PlotTypes.SlicePlot, *args, **kwargs)
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/raven/ 
PlotCollection.py",
line 206, in __add_slice
  data_source = self.pf.hierarchy.slice(axis, coord, field,  
center=center,
**kwargs)
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/ 
BaseDataTypes.py",
line 700, in __init__
  self._refresh_data()
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/ 
BaseDataTypes.py",
line 237, in _refresh_data
  self.get_data()
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/ 
BaseDataTypes.py",
line 589, in get_data
  for grid in self._get_grids()]
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/ 
BaseDataTypes.py",
line 43, in save_state
  tr = func(self, grid, field)
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/ 
BaseDataTypes.py",
line 805, in _get_data_from_grid
  dv = self.hierarchy.io._read_data_slice(grid, field, self.axis,
wantedIndex) * conv_factor
 File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/ 
DataReadingFuncs.py",
line 239, in _read_data_slice
  (grid.id, field), axis, coord).transpose()
h5py._stub.ValueError: Invalid group number (Function arguments:  
Out of
range)
Any ideas?
Thanks,
Jordan
_______________________________________________
yt-users mailing list
yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________
yt-users mailing list
yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________
yt-users mailing list
yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org