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 _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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

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 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 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

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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 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 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 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

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Hi all, 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. Britton On Mon, Feb 15, 2010 at 9:57 AM, Jordan Thomas Mirocha < Jordan.Mirocha@colorado.edu> wrote:

Matt, Here's the output. Density is in there.

jmirocha@ EnzoTest $ h5ls -r /Users/jmirocha/Research/sims/runs/EnzoTest/RD0038/RD0038.cpu0001 /Grid00000002 Group /Grid00000002/Dark_Matter_Density Dataset {32, 64, 64} /Grid00000002/Density Dataset {32, 64, 64} /Grid00000002/GasEnergy Dataset {32, 64, 64} /Grid00000002/Temperature Dataset {32, 64, 64} /Grid00000002/TotalEnergy Dataset {32, 64, 64} /Grid00000002/particle_index Dataset {40479} /Grid00000002/particle_mass Dataset {40479} /Grid00000002/particle_position_x Dataset {40479} /Grid00000002/particle_position_y Dataset {40479} /Grid00000002/particle_position_z Dataset {40479} /Grid00000002/particle_velocity_x Dataset {40479} /Grid00000002/particle_velocity_y Dataset {40479} /Grid00000002/particle_velocity_z Dataset {40479} /Grid00000002/x-velocity Dataset {32, 64, 64} /Grid00000002/y-velocity Dataset {32, 64, 64} /Grid00000002/z-velocity Dataset {32, 64, 64}

Thanks for the help, Jordan

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 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 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 > 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

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