Can yt load the moving-mesh data?

[tekkamanmaverick]

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.

[jzuhone]

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.

[tekkamanmaverick]

Thank you.

[tekkamanmaverick]

By the way, have you read this paper(https://arxiv.org/pdf/1811.07414v1.pdf)? Maybe you can add its function to yt.

[tekkamanmaverick]

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

include "embree2/rtcore.h"

                        ^

compilation terminated. error: command 'gcc' failed with exit status 1

[jzuhone]

It looks like you have pyembree installed in your python stack. Do you use it? If not, just delete it and try recompiling.

[jzuhone]

Btw, yt issues should be discussed at the yt repository issue page, so i’m closing this one and please open one there.

[tekkamanmaverick]

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.

[jzuhone]

Hi @tekkamanmaverick,

You will need to be more specific in reporting errors--please report the entire traceback instead of just one line.

[tekkamanmaverick]

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

[jzuhone]

@tekkamanmaverick install this package first, sorry I forgot about it: https://github.com/ngoldbaum/cykdtree

[tekkamanmaverick]

Thank you!

[tekkamanmaverick]

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

[jzuhone]

It looks like you have no g++ compiler.

[tekkamanmaverick]

$ which g++ /usr/bin/g++

I sure I have.

[jzuhone]

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.

[jzuhone]

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.