Hi all,<div><br></div><div>The problem is now fixed. I had mistakenly had Jordan move his hdf5 install to another location without remaking yt with an hdf5.cfg that reflected this move. After doing an rm -rf build dist in the yt directory, changing the hdf5.cfg file, and recompiling, the problem is solved.</div>
<div><br></div><div>Britton</div><div><br><div class="gmail_quote">On Mon, Feb 15, 2010 at 9:57 AM, Jordan Thomas Mirocha <span dir="ltr"><<a href="mailto:Jordan.Mirocha@colorado.edu">Jordan.Mirocha@colorado.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Matt,<br>
Here's the output. Density is in there.<br>
<br>
jmirocha@ EnzoTest $ h5ls -r /Users/jmirocha/Research/sims/runs/EnzoTest/RD0038/RD0038.cpu0001<br>
/Grid00000002 Group<br>
/Grid00000002/Dark_Matter_Density Dataset {32, 64, 64}<br>
/Grid00000002/Density Dataset {32, 64, 64}<br>
/Grid00000002/GasEnergy Dataset {32, 64, 64}<br>
/Grid00000002/Temperature Dataset {32, 64, 64}<br>
/Grid00000002/TotalEnergy Dataset {32, 64, 64}<br>
/Grid00000002/particle_index Dataset {40479}<br>
/Grid00000002/particle_mass Dataset {40479}<br>
/Grid00000002/particle_position_x Dataset {40479}<br>
/Grid00000002/particle_position_y Dataset {40479}<br>
/Grid00000002/particle_position_z Dataset {40479}<br>
/Grid00000002/particle_velocity_x Dataset {40479}<br>
/Grid00000002/particle_velocity_y Dataset {40479}<br>
/Grid00000002/particle_velocity_z Dataset {40479}<br>
/Grid00000002/x-velocity Dataset {32, 64, 64}<br>
/Grid00000002/y-velocity Dataset {32, 64, 64}<br>
/Grid00000002/z-velocity Dataset {32, 64, 64}<div class="im"><br>
<br>
Thanks for the help,<br>
Jordan<br>
<br></div><div><div></div><div class="h5">
On Feb 15, 2010, at 9:51 AM, Matthew Turk wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Jordan,<br>
<br>
So can you try running this?<br>
<br>
h5ls -r /Users/jmirocha/Research/sims/runs/EnzoTest/RD0038/RD0038.cpu0001<br>
<br>
and seeing if /Grid00000002/Density is listed? If so, could you copy<br>
here the entire entry for /Grid00000002 ?<br>
<br>
Best,<br>
<br>
Matt<br>
<br>
On Mon, Feb 15, 2010 at 8:49 AM, Jordan Thomas Mirocha<br>
<<a href="mailto:Jordan.Mirocha@colorado.edu" target="_blank">Jordan.Mirocha@colorado.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Matt,<br>
I was also just trying to make a density plot. I ran your script, and<br>
here's what I get:<br>
<br>
Testing existence of datasets.<br>
yt INFO 2010-02-15 09:44:54,574 Storing the binary hierarchy<br>
yt INFO 2010-02-15 09:44:54,578 Gathering a field list (this<br>
may take a moment.)<br>
Warning: divide by zero encountered in divide<br>
Warning: invalid value encountered in sqrt<br>
Warning: invalid value encountered in divide<br>
Warning: invalid value encountered in divide<br>
Warning: invalid value encountered in sqrt<br>
Testing slices through the center of the domain.<br>
Slicing through EnzoGrid_0002, getting 2:0 from a [64 64 32]-shaped grid<br>
Traceback (most recent call last):<br>
File "<stdin>", line 1, in <module><br>
File "mturk.py", line 34, in <module><br>
dv = pf.hierarchy.io._read_data_slice(g, field, axis, ind)<br>
File<br>
"/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",<br>
line 239, in _read_data_slice<br>
(<a href="http://grid.id" target="_blank">grid.id</a>, field), axis, coord).transpose()<br>
HDF5LightReader.ReadingError: ReadHDF5DataSetSlice: Unable to open<br>
/Users/jmirocha/Research/sims/runs/EnzoTest/RD0038/RD0038.cpu0001<br>
<br>
-Jordan<br>
<br>
On Feb 15, 2010, at 9:16 AM, Matthew Turk wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Jordan,<br>
<br>
I have a couple followup questions; which field are you taking a slice<br>
of? Is it a field that is defined everywhere in the simulation, or<br>
only in a few grids?<br>
<br>
I've created a diagnostic script for you; if you could, could you run<br>
this and tell me what it outputs? You'll need to modify the location<br>
of the data, on line 3. If it runs successfully, without any<br>
exceptions, then on line 20 you'll notice that I define the field to<br>
slice as "Density." Could you change that to the field you are<br>
slicing through, and let me know if it runs to completion then?<br>
<br>
You can get the script by either downloading it from<br>
<a href="http://paste.enzotools.org/show/321" target="_blank">http://paste.enzotools.org/show/321</a> or executing this command:<br>
<br>
yt_lodgeit.py --download=321<br>
<br>
Thanks!<br>
<br>
-Matt<br>
<br>
On Sun, Feb 14, 2010 at 6:25 PM, Jordan Thomas Mirocha<br>
<<a href="mailto:Jordan.Mirocha@colorado.edu" target="_blank">Jordan.Mirocha@colorado.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi again,<br>
I tried Matt's snippet of code and hit an error here:<br>
<br>
g = pf.h.grids[0]<br>
yt INFO 2010-02-14 19:20:47,399 Getting the binary<br>
hierarchy<br>
yt INFO 2010-02-14 19:20:47,403 Finished with binary<br>
hierarchy<br>
reading<br>
Warning: divide by zero encountered in divide<br>
Warning: invalid value encountered in sqrt<br>
Warning: invalid value encountered in divide<br>
Warning: invalid value encountered in divide<br>
Warning: invalid value encountered in sqrt<br>
<br>
The remaining steps still worked, ending with<br>
<br>
print rho.shape, rho.min(), rho.max()<br>
(32, 64, 64) 0.001 196.019<br>
<br>
Thanks for the help,<br>
Jordan<br>
<br>
On Feb 14, 2010, at 6:33 PM, Matthew Turk wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
So one thing that is interesting is that, like Britton said, h5py is<br>
throwing the error even though HDF5LightReader (the yt module) is<br>
having the problems. What h5py does, to my understanding, is<br>
intercept all the HDF5 error calls, thus making it a bit more<br>
difficult for us to get a proper error stack back from<br>
HDF5LightReader. What I'd recommend trying, in order to tie down the<br>
error a bit more, is to use h5py to access the data and see what<br>
errors it reports. You can do this with:<br>
<br>
from yt.mods import *<br>
import h5py<br>
pf = load(path_to_your_data)<br>
g = pf.h.grids[0]<br>
h5_file = h5py.File(g.filename)<br>
rho = h5_file["/Grid%08i/Density" % <a href="http://g.id" target="_blank">g.id</a>][:]<br>
print rho.shape, rho.min(), rho.max()<br>
<br>
and then if it has problems, that could lead us to the problem.<br>
<br>
Thanks,<br>
<br>
Matt<br>
<br>
On Sun, Feb 14, 2010 at 3:44 PM, Britton Smith <<a href="mailto:brittonsmith@gmail.com" target="_blank">brittonsmith@gmail.com</a>><br>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
What's strange to me is that it's an h5py error coming from a call to<br>
the<br>
hdf5 light reader, which I didn't think used h5py. Matt, do you have<br>
any<br>
ideas?<br>
Britton<br>
<br>
On Sun, Feb 14, 2010 at 4:38 PM, Jordan Thomas Mirocha<br>
<<a href="mailto:Jordan.Mirocha@colorado.edu" target="_blank">Jordan.Mirocha@colorado.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hello,<br>
The other day I updated to h5py 1.2, and am now getting the following<br>
error message when I try to make projections or slices.<br>
<br>
yt INFO 2010-02-14 16:25:07,976 Created plot collection<br>
with<br>
default plot-center = [0.5, 0.5, 0.5]<br>
yt INFO 2010-02-14 16:25:07,976 Adding plot for axis 2<br>
yt INFO 2010-02-14 16:25:07,981 Storing the binary<br>
hierarchy<br>
yt INFO 2010-02-14 16:25:07,985 Gathering a field list<br>
(this<br>
may take a moment.)<br>
Warning: divide by zero encountered in divide<br>
Warning: invalid value encountered in sqrt<br>
Warning: invalid value encountered in divide<br>
Warning: invalid value encountered in divide<br>
Warning: invalid value encountered in sqrt<br>
Traceback (most recent call last):<br>
File "/Library/Frameworks/Python.framework/Versions/Current/bin/yt",<br>
line<br>
8, in <module><br>
load_entry_point('yt==1.6dev', 'console_scripts', 'yt')()<br>
File<br>
<br>
<br>
"/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",<br>
line 523, in run_main<br>
sys.exit(YT.main())<br>
File<br>
<br>
<br>
"/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",<br>
line 257, in main<br>
return self.cmd(args)<br>
File<br>
<br>
<br>
"/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",<br>
line 280, in cmd<br>
retval = self.onecmd(argv)<br>
File<br>
<br>
<br>
"/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",<br>
line 412, in onecmd<br>
return self._dispatch_cmd(handler, argv)<br>
File<br>
<br>
<br>
"/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",<br>
line 1100, in _dispatch_cmd<br>
return handler(argv[0], opts, *args)<br>
File<br>
<br>
<br>
"/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",<br>
line 205, in arg_iterate<br>
func(self, subcmd, opts, arg)<br>
File<br>
<br>
<br>
"/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",<br>
line 334, in do_plot<br>
else: pc.add_slice(opts.field, ax, center=center)<br>
File<br>
<br>
<br>
"/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",<br>
line 182, in add_slice<br>
return self.__add_slice(PlotTypes.SlicePlot, *args, **kwargs)<br>
File<br>
<br>
<br>
"/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",<br>
line 206, in __add_slice<br>
data_source = self.pf.hierarchy.slice(axis, coord, field,<br>
center=center,<br>
**kwargs)<br>
File<br>
<br>
<br>
"/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",<br>
line 700, in __init__<br>
self._refresh_data()<br>
File<br>
<br>
<br>
"/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",<br>
line 237, in _refresh_data<br>
self.get_data()<br>
File<br>
<br>
<br>
"/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",<br>
line 589, in get_data<br>
for grid in self._get_grids()]<br>
File<br>
<br>
<br>
"/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",<br>
line 43, in save_state<br>
tr = func(self, grid, field)<br>
File<br>
<br>
<br>
"/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",<br>
line 805, in _get_data_from_grid<br>
dv = self.hierarchy.io._read_data_slice(grid, field, self.axis,<br>
wantedIndex) * conv_factor<br>
File<br>
<br>
<br>
"/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",<br>
line 239, in _read_data_slice<br>
(<a href="http://grid.id" target="_blank">grid.id</a>, field), axis, coord).transpose()<br>
h5py._stub.ValueError: Invalid group number (Function arguments: Out<br>
of<br>
range)<br>
<br>
Any ideas?<br>
Thanks,<br>
Jordan<br>
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