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

Matthew Turk matthewturk at gmail.com
Fri Jun 4 19:54:52 PDT 2010


Hi all,

Just to update, we took this off list but it *was* in fact a bug that
occurred when Enzo hierarchy files included the *full* path, have been
moved out of their original location, and the data_style is explicitly
specified.  In r1738 I believe I have fixed this in trunk.

-Matt

On Thu, Jun 3, 2010 at 6:08 PM, Matthew Turk <matthewturk at gmail.com> wrote:
> 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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>



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