On Feb 15, 2010, at 9:51 AM, Matthew Turk wrote:
Hi Jordan,
So can you try running this?
h5ls -r /Users/jmirocha/Research/sims/runs/EnzoTest/RD0038/RD0038.cpu0001
and seeing if /Grid00000002/Density is listed? If so, could you copy
here the entire entry for /Grid00000002 ?
Best,
Matt
On Mon, Feb 15, 2010 at 8:49 AM, Jordan Thomas Mirocha
<Jordan.Mirocha@colorado.edu> wrote:
Hi Matt,
I was also just trying to make a density plot. I ran your script, and
here's what I get:
Testing existence of datasets.
yt INFO 2010-02-15 09:44:54,574 Storing the binary hierarchy
yt INFO 2010-02-15 09:44:54,578 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
Testing slices through the center of the domain.
Slicing through EnzoGrid_0002, getting 2:0 from a [64 64 32]-shaped grid
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "mturk.py", line 34, in <module>
dv = pf.hierarchy.io._read_data_slice(g, field, axis, ind)
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()
HDF5LightReader.ReadingError: ReadHDF5DataSetSlice: Unable to open
/Users/jmirocha/Research/sims/runs/EnzoTest/RD0038/RD0038.cpu0001
-Jordan
On Feb 15, 2010, at 9:16 AM, Matthew Turk wrote:
Hi Jordan,
I have a couple followup questions; which field are you taking a slice
of? Is it a field that is defined everywhere in the simulation, or
only in a few grids?
I've created a diagnostic script for you; if you could, could you run
this and tell me what it outputs? You'll need to modify the location
of the data, on line 3. If it runs successfully, without any
exceptions, then on line 20 you'll notice that I define the field to
slice as "Density." Could you change that to the field you are
slicing through, and let me know if it runs to completion then?
You can get the script by either downloading it from
http://paste.enzotools.org/show/321 or executing this command:
yt_lodgeit.py --download=321
Thanks!
-Matt
On Sun, Feb 14, 2010 at 6:25 PM, Jordan Thomas Mirocha
<Jordan.Mirocha@colorado.edu> wrote:
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 <brittonsmith@gmail.com>
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
<Jordan.Mirocha@colorado.edu> 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
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