Closed tekkamanmaverick closed 5 years ago
Hi @tekkamanmaverick, the current stable version of yt (3.5) does not support arepo data. You will have to clone my arepo
branch of yt from http://github.com/jzuhone/yt
to study arepo data.
Just a warning: the halos in Illustris-1 have far less hot gas than are seen in observations, and they will be pretty faint in X-rays, so I'm not sure how useful this will be. IllustrisTNG will be released next week and the hot gas fraction is much more consistent in that set of simulations.
Thank you.
By the way, have you read this paper(https://arxiv.org/pdf/1811.07414v1.pdf)? Maybe you can add its function to yt.
I can not install your version into my computer.
yt/utilities/lib/mesh_construction.cpp:653:28: fatal error: embree2/rtcore.h: No such file or directory
^
compilation terminated. error: command 'gcc' failed with exit status 1
It looks like you have pyembree installed in your python stack. Do you use it? If not, just delete it and try recompiling.
Btw, yt issues should be discussed at the yt repository issue page, so i’m closing this one and please open one there.
I still can not install the arepo version.
Cython.Compiler.Errors.CompileError: yt/utilities/lib/particle_kdtree_tools.pyx
I find no issue page in https://github.com/jzuhone/yt.
Hi @tekkamanmaverick,
You will need to be more specific in reporting errors--please report the entire traceback instead of just one line.
from cykdtree.kdtree cimport KDTree, uint64_t
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pxd:4:0: 'cykdtree/kdtree/uint64_t.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
int step
cdef int set_axes_range(axes_range *axes, int skipaxis)
cdef int find_neighbors(np.float64_t * pos, np.float64_t[:, ::1] tree_positions,
BoundedPriorityQueue queue, KDTree * c_tree,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pxd:15:52: 'KDTree' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef int set_axes_range(axes_range *axes, int skipaxis)
cdef int find_neighbors(np.float64_t * pos, np.float64_t[:, ::1] tree_positions,
BoundedPriorityQueue queue, KDTree * c_tree,
uint64_t skipidx, axes_range * axes) nogil except -1
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pxd:16:24: 'uint64_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
cimport cython
from cpython.exc cimport PyErr_CheckSignals
from cykdtree.kdtree cimport PyKDTree, KDTree, Node, uint64_t, uint32_t
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:22:0: 'cykdtree/kdtree/PyKDTree.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
cimport cython
from cpython.exc cimport PyErr_CheckSignals
from cykdtree.kdtree cimport PyKDTree, KDTree, Node, uint64_t, uint32_t
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:22:0: 'cykdtree/kdtree/Node.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
cimport cython
from cpython.exc cimport PyErr_CheckSignals
from cykdtree.kdtree cimport PyKDTree, KDTree, Node, uint64_t, uint32_t
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:22:0: 'cykdtree/kdtree/uint32_t.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
def generate_smoothing_length(np.float64_t[:, ::1] tree_positions,
PyKDTree kdtree, int n_neighbors):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:61:30: 'PyKDTree' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return np.asarray(smoothing_length)
@cython.boundscheck(False)
@cython.wraparound(False)
cdef int find_neighbors(np.float64_t * pos, np.float64_t[:, ::1] tree_positions,
BoundedPriorityQueue queue, KDTree * c_tree,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:117:52: 'KDTree' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
@cython.wraparound(False)
cdef int find_neighbors(np.float64_t * pos, np.float64_t[:, ::1] tree_positions,
BoundedPriorityQueue queue, KDTree * c_tree,
uint64_t skipidx, axes_range * axes) nogil except -1:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:118:24: 'uint64_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
@cython.boundscheck(False)
@cython.wraparound(False)
cdef int find_knn(Node* node,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:133:18: 'Node' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.wraparound(False)
cdef int find_knn(Node* node,
BoundedPriorityQueue queue,
np.float64_t[:, ::1] tree_positions,
np.float64_t* pos,
uint32_t skipleaf,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:137:18: 'uint32_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef int find_knn(Node* node,
BoundedPriorityQueue queue,
np.float64_t[:, ::1] tree_positions,
np.float64_t* pos,
uint32_t skipleaf,
uint64_t skipidx,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:138:18: 'uint64_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
axes)
return 0
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline int cull_node(Node* node,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:158:26: 'Node' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline int cull_node(Node* node,
np.float64_t* pos,
BoundedPriorityQueue queue,
uint32_t skipleaf,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:161:26: 'uint32_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return (ndist > queue.heap[0] and queue.size == queue.max_elements)
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline int process_node_points(Node* node,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:188:36: 'Node' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
smoothing_lengths: arrays of floats with shape (n_particles, )
The calculated smoothing lengths
"""
cdef int i
cdef KDTree * c_tree = kdtree._tree
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:82:9: 'KDTree' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
@cython.wraparound(False)
cdef int find_neighbors(np.float64_t * pos, np.float64_t[:, ::1] tree_positions,
BoundedPriorityQueue queue, KDTree * c_tree,
uint64_t skipidx, axes_range * axes) nogil except -1:
cdef Node* leafnode
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:119:9: 'Node' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
axes_range * axes,
) nogil except -1:
cdef int k
cdef np.float64_t v
cdef np.float64_t tpos, ndist = 0
cdef uint32_t leafid
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:167:9: 'uint32_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
np.float64_t[:, ::1] positions,
np.float64_t* pos,
int skipidx,
axes_range * axes,
) nogil except -1:
cdef uint64_t i, k
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:195:9: 'uint64_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
BoundedPriorityQueue queue, KDTree * c_tree,
uint64_t skipidx, axes_range * axes) nogil except -1:
cdef Node* leafnode
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:122:29: Cannot convert 'float64_t *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
sq_dist = 0.0
k = axes.start
while k < axes.stop:
tpos = positions[i, k] - pos[k]
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:205:29: Invalid index for memoryview specified, type <error>
Error compiling Cython file:
------------------------------------------------------------
...
sq_dist = 0.0
k = axes.start
while k < axes.stop:
tpos = positions[i, k] - pos[k]
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:205:40: Invalid index type '<error>'
Error compiling Cython file:
------------------------------------------------------------
...
BoundedPriorityQueue queue, KDTree * c_tree,
uint64_t skipidx, axes_range * axes) nogil except -1:
cdef Node* leafnode
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:122:28: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
BoundedPriorityQueue queue, KDTree * c_tree,
uint64_t skipidx, axes_range * axes) nogil except -1:
cdef Node* leafnode
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:122:28: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
BoundedPriorityQueue queue, KDTree * c_tree,
uint64_t skipidx, axes_range * axes) nogil except -1:
cdef Node* leafnode
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:122:21: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
BoundedPriorityQueue queue, KDTree * c_tree,
uint64_t skipidx, axes_range * axes) nogil except -1:
cdef Node* leafnode
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:122:28: Constructing Python tuple not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
BoundedPriorityQueue queue, KDTree * c_tree,
uint64_t skipidx, axes_range * axes) nogil except -1:
cdef Node* leafnode
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:122:29: Converting to Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
process_node_points(leafnode, queue, tree_positions, pos, skipidx, axes)
# Traverse the rest of the kdtree to finish the neighbor list
find_knn(c_tree.root, queue, tree_positions, pos, leafnode.leafid, skipidx,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:126:19: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
process_node_points(leafnode, queue, tree_positions, pos, skipidx, axes)
# Traverse the rest of the kdtree to finish the neighbor list
find_knn(c_tree.root, queue, tree_positions, pos, leafnode.leafid, skipidx,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:126:19: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
process_node_points(leafnode, queue, tree_positions, pos, skipidx, axes)
# Traverse the rest of the kdtree to finish the neighbor list
find_knn(c_tree.root, queue, tree_positions, pos, leafnode.leafid, skipidx,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:126:62: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
# Make an initial guess based on the closest node
leafnode = c_tree.search(&pos[0])
process_node_points(leafnode, queue, tree_positions, pos, skipidx, axes)
# Traverse the rest of the kdtree to finish the neighbor list
find_knn(c_tree.root, queue, tree_positions, pos, leafnode.leafid, skipidx,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:126:62: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
uint64_t skipidx,
axes_range * axes,
) nogil except -1:
# if we aren't a leaf then we keep traversing until we find a leaf, else we
# we actually begin to check the leaf
if not node.is_leaf:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:143:15: Truth-testing Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
uint64_t skipidx,
axes_range * axes,
) nogil except -1:
# if we aren't a leaf then we keep traversing until we find a leaf, else we
# we actually begin to check the leaf
if not node.is_leaf:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:143:15: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
axes_range * axes,
) nogil except -1:
# if we aren't a leaf then we keep traversing until we find a leaf, else we
# we actually begin to check the leaf
if not node.is_leaf:
if not cull_node(node.less, pos, queue, skipleaf, axes):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:144:29: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
axes_range * axes,
) nogil except -1:
# if we aren't a leaf then we keep traversing until we find a leaf, else we
# we actually begin to check the leaf
if not node.is_leaf:
if not cull_node(node.less, pos, queue, skipleaf, axes):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:144:29: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
) nogil except -1:
# if we aren't a leaf then we keep traversing until we find a leaf, else we
# we actually begin to check the leaf
if not node.is_leaf:
if not cull_node(node.less, pos, queue, skipleaf, axes):
find_knn(node.less, queue, tree_positions, pos, skipleaf, skipidx,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:145:25: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
) nogil except -1:
# if we aren't a leaf then we keep traversing until we find a leaf, else we
# we actually begin to check the leaf
if not node.is_leaf:
if not cull_node(node.less, pos, queue, skipleaf, axes):
find_knn(node.less, queue, tree_positions, pos, skipleaf, skipidx,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:145:25: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
# we actually begin to check the leaf
if not node.is_leaf:
if not cull_node(node.less, pos, queue, skipleaf, axes):
find_knn(node.less, queue, tree_positions, pos, skipleaf, skipidx,
axes)
if not cull_node(node.greater, pos, queue, skipleaf, axes):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:147:29: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
# we actually begin to check the leaf
if not node.is_leaf:
if not cull_node(node.less, pos, queue, skipleaf, axes):
find_knn(node.less, queue, tree_positions, pos, skipleaf, skipidx,
axes)
if not cull_node(node.greater, pos, queue, skipleaf, axes):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:147:29: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
if not node.is_leaf:
if not cull_node(node.less, pos, queue, skipleaf, axes):
find_knn(node.less, queue, tree_positions, pos, skipleaf, skipidx,
axes)
if not cull_node(node.greater, pos, queue, skipleaf, axes):
find_knn(node.greater, queue, tree_positions, pos, skipleaf,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:148:25: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
if not node.is_leaf:
if not cull_node(node.less, pos, queue, skipleaf, axes):
find_knn(node.less, queue, tree_positions, pos, skipleaf, skipidx,
axes)
if not cull_node(node.greater, pos, queue, skipleaf, axes):
find_knn(node.greater, queue, tree_positions, pos, skipleaf,
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:148:25: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int k
cdef np.float64_t v
cdef np.float64_t tpos, ndist = 0
cdef uint32_t leafid
if node.leafid == skipleaf:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:169:19: Truth-testing Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int k
cdef np.float64_t v
cdef np.float64_t tpos, ndist = 0
cdef uint32_t leafid
if node.leafid == skipleaf:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:169:19: Operation not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int k
cdef np.float64_t v
cdef np.float64_t tpos, ndist = 0
cdef uint32_t leafid
if node.leafid == skipleaf:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:169:11: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int k
cdef np.float64_t v
cdef np.float64_t tpos, ndist = 0
cdef uint32_t leafid
if node.leafid == skipleaf:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:169:22: Converting to Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
return True
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:175:13: Truth-testing Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
return True
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:175:13: Operation not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
return True
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:175:11: Converting to Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
return True
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:175:29: Indexing Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
return True
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:175:19: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:176:37: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:176:37: Operation not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:176:33: Indexing Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:176:23: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:176:39: Converting to Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:177:15: Truth-testing Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:177:15: Operation not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:177:13: Converting to Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:177:32: Indexing Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
k = axes.start
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:177:21: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
tpos = v - node.right_edge[k]
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:178:21: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
tpos = v - node.right_edge[k]
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:178:21: Operation not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
tpos = v - node.right_edge[k]
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:178:19: Converting to Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
tpos = v - node.right_edge[k]
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:178:38: Indexing Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
while k < axes.stop:
v = pos[k]
if v < node.left_edge[k]:
tpos = node.left_edge[k] - v
elif v > node.right_edge[k]:
tpos = v - node.right_edge[k]
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:178:27: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
int skipidx,
axes_range * axes,
) nogil except -1:
cdef uint64_t i, k
cdef np.float64_t tpos, sq_dist
for i in range(node.left_idx, node.left_idx + node.children):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:197:13: Coercion from Python not allowed without the GIL
Error compiling Cython file:
------------------------------------------------------------
...
int skipidx,
axes_range * axes,
) nogil except -1:
cdef uint64_t i, k
cdef np.float64_t tpos, sq_dist
for i in range(node.left_idx, node.left_idx + node.children):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:197:13: Iterating over Python object not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
int skipidx,
axes_range * axes,
) nogil except -1:
cdef uint64_t i, k
cdef np.float64_t tpos, sq_dist
for i in range(node.left_idx, node.left_idx + node.children):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:197:18: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
int skipidx,
axes_range * axes,
) nogil except -1:
cdef uint64_t i, k
cdef np.float64_t tpos, sq_dist
for i in range(node.left_idx, node.left_idx + node.children):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:197:18: Constructing Python tuple not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
int skipidx,
axes_range * axes,
) nogil except -1:
cdef uint64_t i, k
cdef np.float64_t tpos, sq_dist
for i in range(node.left_idx, node.left_idx + node.children):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:197:23: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
int skipidx,
axes_range * axes,
) nogil except -1:
cdef uint64_t i, k
cdef np.float64_t tpos, sq_dist
for i in range(node.left_idx, node.left_idx + node.children):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:197:48: Operation not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
int skipidx,
axes_range * axes,
) nogil except -1:
cdef uint64_t i, k
cdef np.float64_t tpos, sq_dist
for i in range(node.left_idx, node.left_idx + node.children):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:197:38: Accessing Python attribute not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
int skipidx,
axes_range * axes,
) nogil except -1:
cdef uint64_t i, k
cdef np.float64_t tpos, sq_dist
for i in range(node.left_idx, node.left_idx + node.children):
^
------------------------------------------------------------
yt/utilities/lib/particle_kdtree_tools.pyx:197:54: Accessing Python attribute not allowed without gil
Traceback (most recent call last):
File "setup.py", line 429, in <module>
python_requires='>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*'
File "/work/share/software/miniconda2/lib/python2.7/site-packages/setuptools/__init__.py", line 143, in setup
return distutils.core.setup(**attrs)
File "/work/share/software/miniconda2/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/work/share/software/miniconda2/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/work/share/software/miniconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/work/share/software/miniconda2/lib/python2.7/site-packages/setuptools/command/develop.py", line 38, in run
self.install_for_development()
File "/work/share/software/miniconda2/lib/python2.7/site-packages/setuptools/command/develop.py", line 134, in install_for_development
self.run_command('egg_info')
File "/work/share/software/miniconda2/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/work/share/software/miniconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/work/share/software/miniconda2/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 296, in run
self.find_sources()
File "/work/share/software/miniconda2/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 303, in find_sources
mm.run()
File "/work/share/software/miniconda2/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 534, in run
self.add_defaults()
File "/work/share/software/miniconda2/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 570, in add_defaults
sdist.add_defaults(self)
File "/work/share/software/miniconda2/lib/python2.7/site-packages/setuptools/command/py36compat.py", line 36, in add_defaults
self._add_defaults_ext()
File "/work/share/software/miniconda2/lib/python2.7/site-packages/setuptools/command/py36compat.py", line 119, in _add_defaults_ext
build_ext = self.get_finalized_command('build_ext')
File "/work/share/software/miniconda2/lib/python2.7/distutils/cmd.py", line 312, in get_finalized_command
cmd_obj.ensure_finalized()
File "/work/share/software/miniconda2/lib/python2.7/distutils/cmd.py", line 109, in ensure_finalized
self.finalize_options()
File "setup.py", line 346, in finalize_options
self.distribution.ext_modules)
File "/work/share/software/miniconda2/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 1086, in cythonize
cythonize_one(*args)
File "/work/share/software/miniconda2/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 1209, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: yt/utilities/lib/particle_kdtree_tools.pyx
@tekkamanmaverick install this package first, sorry I forgot about it: https://github.com/ngoldbaum/cykdtree
Thank you!
I have trouble with installing cykdtree.
building 'cykdtree.parallel_utils' extension gcc -pthread -B /work/share/software/miniconda2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Icykdtree -I/work/share/software/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/work/share/software/miniconda2/lib/python2.7/site-packages/mpi4py -I/work/share/software/miniconda2/include/python2.7 -c cykdtree/parallel_utils.cpp -o build/temp.linux-x86_64-2.7/cykdtree/parallel_utils.o -std=c++03 g++ -I/work/share/software/miniconda2/include -DBOOST_MATH_DISABLE_FLOAT128 -m64 -Wl,-rpath,/work/share/software/miniconda2/lib -L/work/share/software/miniconda2/lib -I/work/share/software/miniconda2/include -L/work/share/software/miniconda2/lib -lmpicxx -Wl,-rpath -Wl,/work/share/software/miniconda2/lib -Wl,--enable-new-dtags -lmpi gcc: error: g++: No such file or directory error: command 'gcc' failed with exit status 1
It looks like you have no g++ compiler.
$ which g++ /usr/bin/g++
I sure I have.
gcc: error: g++: No such file or directory
This is the error for some reason regardless. I would make an issue on the cykdtree github page.
Something else, now that I am noticing it in your error message--yt-4.0 will not support Python 2.7 when it is released. I am not sure what the current status is while it is in development, but I would not expect everything in yt-4.0 to work properly unless you use Python 3.
Hi John, I want to use the data of Illustris-1 to study x-ray observation. However, when I try to use yt directly load the data, the program will crash (dump core). Then I think maybe I can use yt to load the individual fields of the data. As the moving-mesh data, I feel it is not suitable to be loaded as generic particle data or generic array data. So how can I load the Illustris-1 data? Thank you.