Hi,
On Mon, Mar 5, 2012 at 11:11 AM, Matthew Brett <matthew.br...@gmail.com> wrote:
> Hi,
>
> On Sun, Mar 4, 2012 at 11:53 PM, Mark Wiebe <mwwi...@gmail.com> wrote:
>> On Sun, Mar 4, 2012 at 10:34 PM, Matthew Brett <matthew.br...@gmail.com>
>> wrote:
>>>
>>> <snip>
>>> > $ export NPY_SEPARATE_COMPILATION=1
>>>
>>> Thanks, that did it:
>>>
>>> 9194b3af704df71aa9b1ff2f53f169848d0f9dc7 is the first bad commit
>>>
>>> Let me know if I can debug further,
>>
>>
>> That commit was a rewrite of np.concatenate, and I've traced the test
>> function you got the crash in. The only call to concatenate is as follows:
>>
>>>>> a = np.array([True], dtype=object)
>>>>> np.concatenate((a,)*3)
>> array([True, True, True], dtype=object)
>>>>>
>>
>> Can you try this and see if it crashes?
>
> No, that doesn't crash.
>
> Further investigation revealed the crash to be:
>
> (bare-env)[matthew@vagus ~]$ nosetests
> ~/dev_trees/numpy/numpy/lib/tests/test_io.py:TestFromTxt.test_with_masked_column_various
> nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
> Test masked column ... Bus error
>
> Accordingly:
>
> In [1]: import numpy as np
>
> In [2]: from StringIO import StringIO
>
> In [3]: data = StringIO('True 2 3\nFalse 5 6\n')
>
> In [4]: test = np.genfromtxt(data, dtype=None, missing_values='2,5',
> usemask=True)
>
> In [6]: from numpy import ma
>
> In [7]: control = ma.array([(1, 2, 3), (0, 5, 6)], mask=[(0, 1, 0),
> (0, 1, 0)], dtype=[('f0', bool), ('f1', bool), ('f2', int)])
>
> In [8]: test == control
> Bus error
>
>> Another thing you can do is compile with debug information enabled, then run
>> the crashing case in gdb. This will look something like this:
>>
>> $ export CFLAGS=-g
>> $ rm -rf build # make sure it's a fresh build from scratch
>> $ python setup.py install --prefix=<dir> # or however you do it
>> [... build printout]
>> $ gdb python <script/options>
>> [... gdb info]
>> (gdb) run
>> [... script runs]
>> Program received signal SIGSEGV, Segmentation fault,
>> [crash address]
>> (gdb) backtrace
>> [full backtrace printout]
>>
>> Such a backtrace would be immensely helpful in tracking down why it's
>> crashing.
>
> I'll get back to you with this.
<atest.py>
from StringIO import StringIO
import numpy as np
from numpy import ma
data = StringIO('True 2 3\nFalse 5 6\n')
test = np.genfromtxt(data, dtype=None, missing_values='2,5',
usemask=True)
control = ma.array([(1, 2, 3), (0, 5, 6)], mask=[(0, 1, 0), (0, 1, 0)],
dtype=[('f0', bool), ('f1', bool), ('f2', int)])
test == control
</atest.py
gdb python
run atest.py
backtrace full attached.
See you,
Matthew
#0 0xf79b75a4 in _aligned_strided_to_strided_size4_srcstride0 (dst=0xffffacc8 "\377\377\255h", dst_stride=0, src=0x8d3dca "", __NPY_UNUSED_TAGGEDsrc_stride=0,
N=1, __NPY_UNUSED_TAGGEDsrc_itemsize=4, __NPY_UNUSED_TAGGEDdata=0x0) at numpy/core/src/multiarray/lowlevel_strided_loops.c.src:196
temp = 7
#1 0xf7956380 in PyArray_CastRawArrays (count=1, src=0x8d3dca "", dst=0xffffacc8 "\377\377\255h", src_stride=0, dst_stride=0, src_dtype=0xf7adacd4,
dst_dtype=0xf7adacd4, move_references=0) at numpy/core/src/multiarray/dtype_transfer.c:3865
stransfer = 0xf79b7584 <_aligned_strided_to_strided_size4_srcstride0>
transferdata = 0x0
aligned = 1
needs_api = 0
#2 0xf78f8fd4 in PyArray_AssignRawScalar (dst=0x883ed8, src_dtype=0xf7adacd4, src_data=0x8d3dca "", wheremask=0x883e88, casting=NPY_SAME_KIND_CASTING,
preservena=0 '\000', preservewhichna=0x0) at numpy/core/src/multiarray/array_assign_scalar.c:390
tmp_src_data = 0xffffacc8 "\377\377\255h"
allocated_src_data = 0
dst_has_maskna = 0
scalarbuffer = {-90812779577720, -599647614278287736, 1099511627776, 0}
#3 0xf78faae4 in PyArray_AssignArray (dst=0x883ed8, src=0x883f28, wheremask=0x883e88, casting=NPY_SAME_KIND_CASTING, preservena=0 '\000', preservewhichna=0x0)
at numpy/core/src/multiarray/array_assign_array.c:410
dst_has_maskna = 0
src_has_maskna = 0
copied_src = 0
src_strides = {0, -139730776, 2, 0, 0, 0, -139722760, 2, 4, 5, 2, 0, 0, -139555256, 1, 9481980, 9481896, 7168208, 473795708, 2128, 7, 9333623, -139632288,
4526776, 9481896, -139726632, -139600928, -139616340, -20568, -20704, -140352480, -20652}
src_maskna_strides = {0, 1280, -139614652, -139616340, 2, -20652, 3752016, 0, 3752016, 0, 1, 1, 9256394, 2, 0, 5083832, 8928904, 5083832, 8929144,
-139616340, 12, 12, 0, 0, 8928904, -139614652, 32768, -20720, -20724, -20856, -20728, -20716}
#4 0xf7a264dc in array_copyto (__NPY_UNUSED_TAGGEDignored=0x0, args=0x4512b8, kwds=0x90aea8) at numpy/core/src/multiarray/multiarraymodule.c:1911
kwlist = {0xf7abffe8 "dst", 0xf7abfff0 "src", 0xf7abf4c8 "casting", 0xf7abf900 "where", 0xf7abfff8 "preservena", 0x0}
wheremask_in = 0x883e88
dst = 0x883ed8
src = 0x883f28
wheremask = 0x883e88
casting = NPY_SAME_KIND_CASTING
preservena = 0
#5 0x0023e374 in PyCFunction_Call (func=0x4d0df8, arg=0x4512b8, kw=0x90aea8) at ../Objects/methodobject.c:85
f = 0x4d0df8
meth = 0xf7a26364 <array_copyto>
self = 0x0
size = 8928984
#6 0x00122dbc in do_call (func=0x4d0df8, pp_stack=0xffffb224, na=2, nk=1) at ../Python/ceval.c:3965
tstate = 0x394050
callargs = 0x4512b8
kwdict = 0x90aea8
result = 0x0
#7 0x00121da0 in call_function (pp_stack=0xffffb224, oparg=258) at ../Python/ceval.c:3773
na = 2
nk = 1
n = 4
pfunc = 0x8d427c
func = 0x4d0df8
x = 0x883e38
w = 0x3cf060
#8 0x0011afe8 in PyEval_EvalFrameEx (f=0x8d4120, throwflag=0) at ../Python/ceval.c:2412
sp = 0x8d4280
stack_pointer = 0x8d4290
next_instr = 0x863155 "\001q\023"
opcode = 131
oparg = 258
why = WHY_NOT
err = 0
x = 0x883e88
v = 0x83
w = 0x3cf060
u = 0x0
t = 0x102
stream = 0x0
fastlocals = 0x8d4260
freevars = 0x8d4278
retval = 0x0
tstate = 0x394050
co = 0x865448
instr_ub = -1
instr_lb = 0
instr_prev = -1
first_instr = 0x8630ec "|"
names = 0x8660c8
consts = 0x859db8
filename = 0x864744 "/home/matthew/.virtualenvs/bare-dbg/lib/python2.6/site-packages/numpy/ma/core.py"
__PRETTY_FUNCTION__ = "PyEval_EvalFrameEx"
#9 0x00122158 in fast_function (func=0x8ff458, pp_stack=0xffffb4d4, n=3, na=3, nk=0) at ../Python/ceval.c:3836
retval = 0x0
fastlocals = 0x8d4260
i = 3
f = 0x8d4120
tstate = 0x394050
stack = 0x8d3bdc
co = 0x865448
globals = 0x84de00
argdefs = 0x0
d = 0x0
nd = 0
__PRETTY_FUNCTION__ = "fast_function"
#10 0x00121d78 in call_function (pp_stack=0xffffb4d4, oparg=3) at ../Python/ceval.c:3771
na = 3
nk = 0
n = 3
pfunc = 0x8d3bcc
func = 0x8ff458
x = 0x861458
w = 0x6d60d0
#11 0x0011afe8 in PyEval_EvalFrameEx (f=0x8d3a78, throwflag=0) at ../Python/ceval.c:2412
sp = 0x8d3bdc
stack_pointer = 0x8d3bdc
next_instr = 0x8e6b77 "\001n\346"
opcode = 131
oparg = 3
why = WHY_NOT
err = 0
x = 0x883d48
v = 0x83
w = 0x6d60d0
u = 0x850
t = 0x3
stream = 0x0
fastlocals = 0x8d3bb8
freevars = 0x8d3bcc
retval = 0x0
tstate = 0x394050
co = 0x86e868
instr_ub = -1
instr_lb = 0
instr_prev = -1
first_instr = 0x8e6ae4 "|"
names = 0x7a9d48
consts = 0x8667d0
filename = 0x86adc4 "/home/matthew/.virtualenvs/bare-dbg/lib/python2.6/site-packages/numpy/ma/core.py"
__PRETTY_FUNCTION__ = "PyEval_EvalFrameEx"
#12 0x0011e48c in PyEval_EvalCodeEx (co=0x86e868, globals=0x84de00, locals=0x0, args=0x8d3a40, argcount=2, kws=0x8d3a48, kwcount=0, defs=0x8f9cc4, defcount=1,
closure=0x0) at ../Python/ceval.c:3000
f = 0x8d3a78
retval = 0x0
fastlocals = 0x8d3bb8
freevars = 0x8d3bcc
tstate = 0x394050
x = 0x39ffc8
u = 0x9121a0
__PRETTY_FUNCTION__ = "PyEval_EvalCodeEx"
#13 0x001222b4 in fast_function (func=0x902198, pp_stack=0xffffb86c, n=2, na=2, nk=0) at ../Python/ceval.c:3846
co = 0x86e868
globals = 0x84de00
argdefs = 0x8f9cb0
d = 0x8f9cc4
nd = 1
__PRETTY_FUNCTION__ = "fast_function"
#14 0x00121d78 in call_function (pp_stack=0xffffb86c, oparg=1) at ../Python/ceval.c:3771
na = 2
nk = 0
n = 2
pfunc = 0x8d3a40
func = 0x902198
x = 0x861458
w = 0x7c07d0
#15 0x0011afe8 in PyEval_EvalFrameEx (f=0x8d38f8, throwflag=0) at ../Python/ceval.c:2412
sp = 0x8d3a48
stack_pointer = 0x8d3a48
next_instr = 0x7a9818 "S\001t\002"
opcode = 131
oparg = 1
why = WHY_NOT
err = 0
x = 0x39ffc8
v = 0x83
w = 0x7c07d0
u = 0x0
t = 0x1
stream = 0x0
fastlocals = 0x8d3a38
freevars = 0x8d3a40
retval = 0x0
tstate = 0x394050
co = 0x7bba48
instr_ub = -1
instr_lb = 0
instr_prev = -1
first_instr = 0x7a97fc "t"
names = 0x7bcb28
consts = 0x7be8f0
filename = 0x85b344 "/home/matthew/.virtualenvs/bare-dbg/lib/python2.6/site-packages/numpy/ma/core.py"
__PRETTY_FUNCTION__ = "PyEval_EvalFrameEx"
#16 0x0011e48c in PyEval_EvalCodeEx (co=0x7bba48, globals=0x84de00, locals=0x0, args=0x8d38b0, argcount=2, kws=0x8d38b8, kwcount=0, defs=0x8f904c, defcount=1,
closure=0x0) at ../Python/ceval.c:3000
f = 0x8d38f8
retval = 0x0
fastlocals = 0x8d3a38
freevars = 0x8d3a40
tstate = 0x394050
x = 0x39ffc8
u = 0x9121a0
__PRETTY_FUNCTION__ = "PyEval_EvalCodeEx"
#17 0x001222b4 in fast_function (func=0x8fa140, pp_stack=0xffffbc04, n=2, na=2, nk=0) at ../Python/ceval.c:3846
co = 0x7bba48
globals = 0x84de00
argdefs = 0x8f9038
d = 0x8f904c
nd = 1
__PRETTY_FUNCTION__ = "fast_function"
#18 0x00121d78 in call_function (pp_stack=0xffffbc04, oparg=2) at ../Python/ceval.c:3771
na = 2
nk = 0
n = 2
pfunc = 0x8d38ac
func = 0x8fa140
x = 0x883e38
w = 0x0
#19 0x0011afe8 in PyEval_EvalFrameEx (f=0x8d3740, throwflag=0) at ../Python/ceval.c:2412
sp = 0x8d38b8
stack_pointer = 0x8d38b8
next_instr = 0x8e7c3c "}\004"
opcode = 131
oparg = 2
why = WHY_NOT
err = 0
x = 0x39ffc8
v = 0x83
w = 0x7c07d0
u = 0x4dfc27b8
t = 0x2
stream = 0x0
fastlocals = 0x8d3880
freevars = 0x8d38ac
retval = 0x0
tstate = 0x394050
co = 0x86eb68
instr_ub = -1
instr_lb = 0
instr_prev = -1
first_instr = 0x8e7ba4 "|"
names = 0x855610
consts = 0x85dcb8
filename = 0x86b144 "/home/matthew/.virtualenvs/bare-dbg/lib/python2.6/site-packages/numpy/ma/core.py"
__PRETTY_FUNCTION__ = "PyEval_EvalFrameEx"
#20 0x0011e48c in PyEval_EvalCodeEx (co=0x86eb68, globals=0x84de00, locals=0x0, args=0x76bc0c, argcount=2, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
at ../Python/ceval.c:3000
f = 0x8d3740
retval = 0x0
fastlocals = 0x8d3880
freevars = 0x8d38ac
tstate = 0x394050
x = 0x861458
u = 0x90aea8
__PRETTY_FUNCTION__ = "PyEval_EvalCodeEx"
#21 0x0023d59c in function_call (func=0x902350, arg=0x76bbf8, kw=0x0) at ../Objects/funcobject.c:524
result = 0x907213
argdefs = 0x0
d = 0x0
k = 0x0
nk = 0
nd = 0
#22 0x00035994 in PyObject_Call (func=0x902350, arg=0x76bbf8, kw=0x0) at ../Objects/abstract.c:2492
result = 0x76bbe8
call = 0x23d36c <function_call>
#23 0x00044054 in instancemethod_call (func=0x902350, arg=0x76bbf8, kw=0x0) at ../Objects/classobject.c:2579
self = 0x7a6c38
klass = 0x8b63e8
result = 0x900ef8
#24 0x00035994 in PyObject_Call (func=0x75d6b8, arg=0x44c1f8, kw=0x0) at ../Objects/abstract.c:2492
result = 0x44c20c
call = 0x43d44 <instancemethod_call>
#25 0x000d1a88 in half_richcompare (self=0x7a6c38, other=0x861458, op=2) at ../Objects/typeobject.c:5513
func = 0x75d6b8
args = 0x44c1f8
res = 0x17
op_str = {0x0, 0x0, 0xf7ae3990, 0x0, 0x0, 0x0}
#26 0x000d1bf4 in slot_tp_richcompare (self=0x7a6c38, other=0x861458, op=2) at ../Objects/typeobject.c:5526
res = 0x8812c8
#27 0x00087944 in PyObject_RichCompare (v=0x7a6c38, w=0x861458, op=2) at ../Objects/object.c:958
fcmp = 0
frich = 0xd1bb0 <slot_tp_richcompare>
res = 0xa
__PRETTY_FUNCTION__ = "PyObject_RichCompare"
#28 0x00124424 in cmp_outcome (op=2, v=0x7a6c38, w=0x861458) at ../Python/ceval.c:4255
res = 0
#29 0x00119ce0 in PyEval_EvalFrameEx (f=0x47b5d8, throwflag=0) at ../Python/ceval.c:2113
stack_pointer = 0x47b71c
next_instr = 0xf7b1f628 "\001d\002"
opcode = 8023096
oparg = 2
why = WHY_NOT
err = 0
x = 0x861458
v = 0x7a6c38
w = 0x861458
u = 0x39ffdc
t = 0x2
stream = 0x0
fastlocals = 0x47b718
freevars = 0x47b718
retval = 0x0
tstate = 0x394050
co = 0xf7b15e08
instr_ub = -1
instr_lb = 0
instr_prev = -1
first_instr = 0xf7b1f584 "d"
names = 0x3d70a0
consts = 0x42c9c8
filename = 0x4477b4 "atest.py"
__PRETTY_FUNCTION__ = "PyEval_EvalFrameEx"
#30 0x0011e48c in PyEval_EvalCodeEx (co=0xf7b15e08, globals=0xf7b20ea8, locals=0xf7b20ea8, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at ../Python/ceval.c:3000
f = 0x47b5d8
retval = 0x0
fastlocals = 0x47b718
freevars = 0x47b718
tstate = 0x394050
x = 0x0
u = 0x0
__PRETTY_FUNCTION__ = "PyEval_EvalCodeEx"
#31 0x00111e74 in PyEval_EvalCode (co=0xf7b15e08, globals=0xf7b20ea8, locals=0xf7b20ea8) at ../Python/ceval.c:541
No locals.
#32 0x0015fa90 in run_mod (mod=0x481fe8, filename=0xffffcb80 "atest.py", globals=0xf7b20ea8, locals=0xf7b20ea8, flags=0xffffc888, arena=0x3a28e0)
at ../Python/pythonrun.c:1351
co = 0xf7b15e08
v = 0xf7b17410
#33 0x0015fa00 in PyRun_FileExFlags (fp=0x4217a8, filename=0xffffcb80 "atest.py", start=257, globals=0xf7b20ea8, locals=0xf7b20ea8, closeit=1, flags=0xffffc888)
at ../Python/pythonrun.c:1337
ret = 0x0
mod = 0x481fe8
arena = 0x3a28e0
#34 0x0015d9e8 in PyRun_SimpleFileExFlags (fp=0x4217a8, filename=0xffffcb80 "atest.py", closeit=1, flags=0xffffc888) at ../Python/pythonrun.c:941
m = 0x3afa80
d = 0xf7b20ea8
v = 0x43ed38
ext = 0xffffcb84 "t.py"
set_file_name = 1
ret = 3752016
len = 8
#35 0x0015ccf4 in PyRun_AnyFileExFlags (fp=0x4217a8, filename=0xffffcb80 "atest.py", closeit=1, flags=0xffffc888) at ../Python/pythonrun.c:745
No locals.
#36 0x00026a44 in Py_Main (argc=2, argv=0xffffca04) at ../Modules/main.c:577
c = -1
sts = -1
command = 0x0
filename = 0xffffcb80 "atest.py"
module = 0x0
fp = 0x4217a8
p = 0x0
unbuffered = 0
skipfirstline = 0
stdin_is_interactive = 1
help = 0
version = 0
saw_unbuffered_flag = 0
cf = {cf_flags = 0}
#37 0x00024e1c in main (argc=2, argv=0xffffca04) at ../Modules/python.c:23
No locals.
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