error Zero sized dimension for non-unlimited dimension
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
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
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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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
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
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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participants (2)
-
Jean-Claude Passy
-
Matthew Turk