[yt-users] error Zero sized dimension for non-unlimited dimension

[Matthew Turk]

Hi JC,

Can you try removing all the .yt files and trying again?  It looks
like they may have been corrupted.

-Matt

On Thu, Jun 3, 2010 at 5:50 PM, Jean-Claude Passy <jcpassy at gmail.com> wrote:
> Dear all,
>
> I am encountering some issues when running the script enclosed:
>
> ######################################################################################################
> loading DM_part/DD0001/CommonEnvelope0001 yt         INFO       2010-06-03
> 17:36:57,270 Storing the binary hierarchy yt         INFO       2010-06-03
> 17:36:57,523 Gathering a field list (this may take a moment.) Traceback
> (most recent call last):   File "script2body.py", line 39, in <module>
> region = data.h.region([0.5, 0.5, 0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
> File "/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/OutputTypes.py",
> line 150, in _get_hierarchy     self.__hierarchy =
> self._hierarchy_class(self, data_style=self.data_style)   File
> "/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line
> 374, in __init__     AMRHierarchy.__init__(self, pf, data_style)   File
> "/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line
> 64, in __init__     self._detect_fields()   File
> "/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line
> 615, in _detect_fields
> self.save_data(list(field_list),"/","DataFields",passthrough=True)   File
> "/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line
> 192, in _save_data     arr = myGroup.create_dataset(name,data=array)   File
> "/rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg/h5py/highlevel.py",
> line 353, in create_dataset     return Dataset(self, name, *args, **kwds)
> File
> "/rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg/h5py/highlevel.py",
> line 856, in __init__     space_id = h5s.create_simple(shape, maxshape)
> File
> "/rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg/h5py/_sync.py",
> line 88, in wrap     return func(*args, **kwds)   File "h5s.pyx", line 106,
> in h5py.h5s.create_simple (h5py/h5s.c:973) h5py._stub.ValueError: Zero sized
> dimension for non-unlimited dimension (Function arguments: Bad value)
> ######################################################################################################
>
> The weird thing is that if I run the script again, it works and then breaks
> when trying to read the next file (DM_part/DD0001/CommonEnvelope0001), and
> so on... Data contain only 2 particles without gas and as far as I remember,
> I could execute those commands without problems before.
>
> I would appreciate if someone could help me with that.
> Thanks a lot,
>
> Jean-Claude
>
> #!/rpod2/jcpassy/yt-x86_64/bin python2.6
>
> import sys
> import commands as C
> import numpy as N
> import pylab as P
> import yt.raven as R
> import yt.lagos as L
>
> filebase = sys.argv[-1]
>
> minSnap = 0
> maxSnap = 401
> skip = 1
>
> t = N.zeros(maxSnap/skip)
>
> X = N.zeros((maxSnap/skip,3,2))
> V = N.zeros((maxSnap/skip,3,2))
> r = N.zeros(maxSnap/skip)
>
>
> X2 = N.zeros((maxSnap/skip,3,2))
> V2 = N.zeros((maxSnap/skip,3,2))
> r2 = N.zeros(maxSnap/skip)
>
> j = 0
>
> for i in range(minSnap,maxSnap,skip):
>
>    # File 1
>
>    filen = 'DM_part/'+ 'DD' + '%04i' % i + '/' + filebase + '%04i' % i
>    print "loading %s" % filen
>    data = L.EnzoStaticOutput(filen,data_style="enzo_packed_3d") # if no gas
>
>    t[j] = data["InitialTime"] * data["years"]
>
>    region = data.h.region([0.5, 0.5, 0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
>
>    i1,i2 = region['particle_index']
>
>    X[j,0,i1],X[j,0,i2] = region['particle_position_x']
>    X[j,1,i1],X[j,1,i2] = region['particle_position_y']
>    X[j,2,i1],X[j,2,i2] = region['particle_position_z']
>
>    V[j,0,i1],V[j,0,i2] = region['particle_velocity_x']
>    V[j,1,i1],V[j,1,i2] = region['particle_velocity_y']
>    V[j,2,i1],V[j,2,i2] = region['particle_velocity_z']
>
>    r[j] = pow((X[j,0,i1] - X[j,0,i2]),2) + pow((X[j,1,i1] - X[j,1,i2]),2) +
> pow((X[j,2,i1] - X[j,2,i2]),2)
>    r[j] = pow(r[j],0.5)
>
>    j = j + 1
>
>
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