[yt-users] Error when open hdf5 file in yt

[Chao Shi]

Hi all,

I'm trying to modify the particle_type of some particles in a hdf5 data
file extract0062.cpu0000 in yt, typing the following command:

for g in pf.h.grids:
    lbhs =
np.logical_and(np.logical_and(g['particle_type']==1,g['particle_index']>=256**3),g['ParticleMassMsun']>1)
      # These two lines are to pick out
    bhs  = np.where(lbhs)[0]

          # particles that I wanted to modify
    if(np.any(g['particle_type'])):
        g['particle_type'][bhs]=9
        f=h5py.File(g.filename)
        ff = f['/Grid%08i'%g.id]['particle_type']
        ff.write_direct(g['particle_type'])
        f.close()

It spited out following error information:

ReadingError                              Traceback (most recent call last)
/home/cshi31/yt-x86_64/src/yt-hg/yt/mods.pyc in <module>()
      1 for g in pf.h.grids:
----> 2     lbhs =
np.logical_and(np.logical_and(g['particle_type']==1,g['particle_index']>=256**3),g['ParticleMassMsun']>1)
      3     bhs  = np.where(lbhs)[0]
      4     if(np.any(g['particle_type'])):
      5         g['particle_type'][bhs]=9

/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
__getitem__(self, key)
    155         """
    156         if not self.field_data.has_key(key):
--> 157             self.get_data(key)
    158         return self.field_data[key]
    159

/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
get_data(self, field, convert)
    188                     return self.field_data[field]
    189                 try:
--> 190                     temp = self.hierarchy.io.pop(self, field)
    191                     self[field] = na.multiply(temp, conv_factor,
temp)
    192                 except self.hierarchy.io._read_exception, exc:

/home/cshi31/yt-x86_64/src/yt-hg/yt/utilities/io_handler.pyc in pop(self,
grid, field)
     59         else:
     60             # We only read the one set and do not store it if it
isn't pre-loaded
---> 61             return self._read_data_set(grid, field)
     62
     63     def peek(self, grid, field):

/home/cshi31/yt-x86_64/src/yt-hg/yt/frontends/enzo/io.pyc in
_read_data_set(self, grid, field)
    183     def _read_data_set(self, grid, field):
    184         return self.modify(hdf5_light_reader.ReadData(grid.filename,
--> 185                 "/Grid%08i/%s" % (grid.id, field)))
    186
    187     def _read_data_slice(self, grid, field, axis, coord):

ReadingError: ReadHDF5DataSet: Unable to open
/home/cshi31/research/SG256-RP/extract0062


So I tried to look where the loop stopped, typed g in the command:

In [37]: g
Out[37]: EnzoGrid_0056

so it stopped at the 56th grid in that file. I tried to see what particles
is contained in this grid, typing g['particle_type'],
it turned out this is what caused the problem:


In [31]: g['particle_type']
---------------------------------------------------------------------------
ReadingError                              Traceback (most recent call last)
/home/cshi31/yt-x86_64/src/yt-hg/yt/mods.pyc in <module>()
----> 1 g['particle_type']

/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
__getitem__(self, key)
    155         """
    156         if not self.field_data.has_key(key):
--> 157             self.get_data(key)
    158         return self.field_data[key]
    159

/home/cshi31/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
get_data(self, field, convert)
    188                     return self.field_data[field]
    189                 try:
--> 190                     temp = self.hierarchy.io.pop(self, field)
    191                     self[field] = na.multiply(temp, conv_factor,
temp)
    192                 except self.hierarchy.io._read_exception, exc:

/home/cshi31/yt-x86_64/src/yt-hg/yt/utilities/io_handler.pyc in pop(self,
grid, field)
     59         else:
     60             # We only read the one set and do not store it if it
isn't pre-loaded
---> 61             return self._read_data_set(grid, field)
     62
     63     def peek(self, grid, field):

/home/cshi31/yt-x86_64/src/yt-hg/yt/frontends/enzo/io.pyc in
_read_data_set(self, grid, field)
    183     def _read_data_set(self, grid, field):
    184         return self.modify(hdf5_light_reader.ReadData(grid.filename,
--> 185                 "/Grid%08i/%s" % (grid.id, field)))
    186
    187     def _read_data_slice(self, grid, field, axis, coord):

ReadingError: ReadHDF5DataSet: Unable to open
/home/cshi31/research/SG256-RP/extract0062.cpu0000

Can anyone help me on this? Thanks very much.

Chao
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