[Numpy-discussion] Numpy intermittent seg fault

Jacopo Sabbatini jacopo.sabbatini at roames.com.au
Sun Dec 13 22:34:45 EST 2015


Filed the bug with OpenBlas (https://github.com/xianyi/OpenBLAS/issues/716)
but they seem more inclined to think that something else corrupted the
memory and the problem only shows up in OpenBlas.

I have attached the backtrace for all the threads at the end. From
preliminary investigation it seems that "getenv" is not thread safe.
OpenBlas gets initialised on a separate thread and tries to access the
environment variable "GOTO_BLOCK_FACTOR" and I suspect that something else
on another thread might be calling "setenv".

Backtrace:

Thread 2 (Thread 0x7f3911c4c700 (LWP 27553)):
#0  0x00007f3910d62255 in _xstat () from /lib64/libc.so.6
#1  0x00007f3911766420 in stat (__statbuf=0x7fff271b06a0, __path=0x235a210
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/core/arrayprint")
    at /usr/include/sys/stat.h:436
#2  isdir (path=0x235a210
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/core/arrayprint")
at Python/import.c:133
#3  find_module (fullname=0x23527e0 "numpy.core.arrayprint",
subname=<optimized out>, path=<optimized out>, buf=0x235b220 "arrayprint",
buflen=4097, p_fp=0x7fff271b1750, p_loader=0x7fff271b1758)
    at Python/import.c:1501
#4  0x00007f3911767f48 in import_submodule (mod=0x7f3908bedf68,
subname=0x23527eb "arrayprint", fullname=0x23527e0 "numpy.core.arrayprint")
at Python/import.c:2693
#5  0x00007f39117681f4 in load_next (mod=0x7f3908bedf68,
altmod=0x7f3908bedf68, p_name=<optimized out>, buf=0x23527e0
"numpy.core.arrayprint", p_buflen=0x7fff271b1810) at Python/import.c:2519
#6  0x00007f3911768820 in import_module_level (level=<optimized out>,
fromlist=0x7f3908329960, locals=<optimized out>, globals=<optimized out>,
name=0x0) at Python/import.c:2228
#7  PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3908329960, level=<optimized
out>) at Python/import.c:2292
#8  0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#9  0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#10 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f390832b770, kw=<optimized out>) at
Python/ceval.c:4219
#11 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#12 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f3908345930,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#13 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#14 0x00007f3911764a82 in PyImport_ExecCodeModuleEx (name=0x2327130
"numpy.core.numeric", co=0x7f3908345930,
    pathname=0x23063c0
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/core/numeric.pyc")
at Python/import.c:713
#15 0x00007f39117671ce in load_source_module (name=0x2327130
"numpy.core.numeric",
    pathname=0x23063c0
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/core/numeric.pyc",
fp=<optimized out>) at Python/import.c:1103
#16 0x00007f3911767f81 in import_submodule (mod=0x7f3908bedf68,
subname=0x7f3908c07564 "numeric", fullname=0x2327130 "numpy.core.numeric")
at Python/import.c:2704
#17 0x00007f39117684bc in ensure_fromlist (mod=0x7f3908bedf68,
fromlist=0x7f3908c0f0d0, buf=0x2327130 "numpy.core.numeric", buflen=10,
recursive=0) at Python/import.c:2610
#18 0x00007f391176895c in import_module_level (level=<optimized out>,
fromlist=0x7f3908c0f0d0, locals=<optimized out>, globals=<optimized out>,
name=0x0) at Python/import.c:2273
#19 PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3908c0f0d0, level=<optimized
out>) at Python/import.c:2292
#20 0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#21 0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#22 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f3908e2ed10, kw=<optimized out>) at
Python/ceval.c:4219
#23 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#24 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f3908bebb30,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#25 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#26 0x00007f3911764a82 in PyImport_ExecCodeModuleEx (name=0x23000c0
"numpy.core", co=0x7f3908bebb30,
    pathname=0x23030f0
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/core/__init__.pyc")
at Python/import.c:713
#27 0x00007f39117671ce in load_source_module (name=0x23000c0 "numpy.core",
pathname=0x23030f0
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/core/__init__.pyc",
    fp=<optimized out>) at Python/import.c:1103
#28 0x00007f3911767a2a in load_package (name=0x23000c0 "numpy.core",
pathname=<optimized out>) at Python/import.c:1170
#29 0x00007f3911767f81 in import_submodule (mod=0x7f3908c0e210,
subname=0x23000c6 "core", fullname=0x23000c0 "numpy.core") at
Python/import.c:2704
#30 0x00007f39117681f4 in load_next (mod=0x7f3908c0e210,
altmod=0x7f3908c0e210, p_name=<optimized out>, buf=0x23000c0 "numpy.core",
p_buflen=0x7fff271b23b0) at Python/import.c:2519
#31 0x00007f3911768860 in import_module_level (level=<optimized out>,
fromlist=0x7f3911a05cd0 <_Py_NoneStruct>, locals=<optimized out>,
globals=<optimized out>, name=0x7f3908bedf07 "numeric")
    at Python/import.c:2236
#32 PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3911a05cd0 <_Py_NoneStruct>,
level=<optimized out>) at Python/import.c:2292
#33 0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#34 0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#35 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f3908e2ecb0, kw=<optimized out>) at
Python/ceval.c:4219
#36 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#37 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f3908c0a5b0,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#38 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#39 0x00007f3911764a82 in PyImport_ExecCodeModuleEx (name=0x22f7e50
"numpy.lib.type_check", co=0x7f3908c0a5b0,
    pathname=0x22fbe90
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/lib/type_check.pyc")
at Python/import.c:713
#40 0x00007f39117671ce in load_source_module (name=0x22f7e50
"numpy.lib.type_check",
    pathname=0x22fbe90
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/lib/type_check.pyc",
fp=<optimized out>) at Python/import.c:1103
#41 0x00007f3911767f81 in import_submodule (mod=0x7f3908bed8d8,
subname=0x22f7e5a "type_check", fullname=0x22f7e50 "numpy.lib.type_check")
at Python/import.c:2704
#42 0x00007f39117681f4 in load_next (mod=0x7f3908bed8d8,
altmod=0x7f3908bed8d8, p_name=<optimized out>, buf=0x22f7e50
"numpy.lib.type_check", p_buflen=0x7fff271b2950) at Python/import.c:2519
#43 0x00007f3911768820 in import_module_level (level=<optimized out>,
fromlist=0x7f3908c02790, locals=<optimized out>, globals=<optimized out>,
name=0x0) at Python/import.c:2228
#44 PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3908c02790, level=<optimized
out>) at Python/import.c:2292
#45 0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#46 0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#47 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f3908e2eb30, kw=<optimized out>) at
Python/ceval.c:4219
#48 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#49 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f3908beb530,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#50 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#51 0x00007f3911764a82 in PyImport_ExecCodeModuleEx (name=0x22f3b00
"numpy.lib", co=0x7f3908beb530,
    pathname=0x22f6b30
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/lib/__init__.pyc")
at Python/import.c:713
#52 0x00007f39117671ce in load_source_module (name=0x22f3b00 "numpy.lib",
pathname=0x22f6b30
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/lib/__init__.pyc",
    fp=<optimized out>) at Python/import.c:1103
#53 0x00007f3911767a2a in load_package (name=0x22f3b00 "numpy.lib",
pathname=<optimized out>) at Python/import.c:1170
#54 0x00007f3911767f81 in import_submodule (mod=0x7f3908c0e210,
subname=0x22f3b06 "lib", fullname=0x22f3b00 "numpy.lib") at
Python/import.c:2704
#55 0x00007f39117681f4 in load_next (mod=0x7f3908c0e210,
altmod=0x7f3908c0e210, p_name=<optimized out>, buf=0x22f3b00 "numpy.lib",
p_buflen=0x7fff271b2f40) at Python/import.c:2519
#56 0x00007f3911768860 in import_module_level (level=<optimized out>,
fromlist=0x7f3908c02110, locals=<optimized out>, globals=<optimized out>,
name=0x0) at Python/import.c:2236
#57 PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3908c02110, level=<optimized
out>) at Python/import.c:2292
#58 0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#59 0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#60 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f3908e2e830, kw=<optimized out>) at
Python/ceval.c:4219
#61 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#62 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f3908beb430,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#63 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#64 0x00007f3911764a82 in PyImport_ExecCodeModuleEx (name=0x22b7380
"numpy.add_newdocs", co=0x7f3908beb430,
    pathname=0x2290560
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/add_newdocs.pyc")
at Python/import.c:713
#65 0x00007f39117671ce in load_source_module (name=0x22b7380
"numpy.add_newdocs", pathname=0x2290560
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/add_newdocs.pyc",
    fp=<optimized out>) at Python/import.c:1103
#66 0x00007f3911767f81 in import_submodule (mod=0x7f3908c0e210,
subname=0x7f3908bf5fe4 "add_newdocs", fullname=0x22b7380
"numpy.add_newdocs") at Python/import.c:2704
#67 0x00007f39117684bc in ensure_fromlist (mod=0x7f3908c0e210,
fromlist=0x7f3908be8650, buf=0x22b7380 "numpy.add_newdocs", buflen=5,
recursive=0) at Python/import.c:2610
#68 0x00007f391176895c in import_module_level (level=<optimized out>,
fromlist=0x7f3908be8650, locals=<optimized out>, globals=<optimized out>,
name=0x0) at Python/import.c:2273
#69 PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3908be8650, level=<optimized
out>) at Python/import.c:2292
#70 0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#71 0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#72 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f3911afffb0, kw=<optimized out>) at
Python/ceval.c:4219
#73 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#74 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f3909508230,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#75 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#76 0x00007f3911764a82 in PyImport_ExecCodeModuleEx (name=0x2222130
"numpy", co=0x7f3909508230,
    pathname=0x22b6370
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/__init__.pyc")
at Python/import.c:713
#77 0x00007f39117671ce in load_source_module (name=0x2222130 "numpy",
pathname=0x22b6370
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/__init__.pyc",
    fp=<optimized out>) at Python/import.c:1103
#78 0x00007f3911767a2a in load_package (name=0x2222130 "numpy",
pathname=<optimized out>) at Python/import.c:1170
#79 0x00007f3911767f81 in import_submodule (mod=0x7f3911a05cd0
<_Py_NoneStruct>, subname=0x2222130 "numpy", fullname=0x2222130 "numpy") at
Python/import.c:2704
#80 0x00007f3911768235 in load_next (mod=0x7f39095047f8,
altmod=0x7f3911a05cd0 <_Py_NoneStruct>, p_name=<optimized out>,
buf=0x2222120 "sonar_intensity.numpy", p_buflen=0x7fff271b3ae0)
    at Python/import.c:2523
#81 0x00007f3911768820 in import_module_level (level=<optimized out>,
fromlist=0x7f3911a05cd0 <_Py_NoneStruct>, locals=<optimized out>,
globals=<optimized out>, name=0x0) at Python/import.c:2228
#82 PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3911a05cd0 <_Py_NoneStruct>,
level=<optimized out>) at Python/import.c:2292
#83 0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#84 0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#85 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f39092cb838, kw=<optimized out>) at
Python/ceval.c:4219
#86 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#87 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f39095020b0,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#88 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#89 0x00007f3911764a82 in PyImport_ExecCodeModuleEx (name=0x7f3908e538c4
"sonar_intensity.determine_bins", co=0x7f39095020b0,
    pathname=0x7f3911aeda64
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/sidescananalysis-9.7.1.29-py2.7.egg/sonar_intensity/determine_bins.py")
at Python/import.c:713
#90 0x00007f39117a052e in zipimporter_load_module (obj=<optimized out>,
args=<optimized out>) at ./Modules/zipimport.c:360
#91 0x00007f391169ed23 in PyObject_Call (func=0x7f3908e47d40,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#92 0x00007f391169ee11 in call_function_tail (callable=0x7f3908e47d40,
args=0x7f3908e33090) at Objects/abstract.c:2578
#93 0x00007f39116a31b8 in PyObject_CallMethod (o=<optimized out>,
name=<optimized out>, format=<optimized out>) at Objects/abstract.c:2653
#94 0x00007f3911767f81 in import_submodule (mod=0x7f39095047f8,
subname=0x22259e0 "determine_bins", fullname=0x22259d0
"sonar_intensity.determine_bins") at Python/import.c:2704
#95 0x00007f39117681f4 in load_next (mod=0x7f39095047f8,
altmod=0x7f39095047f8, p_name=<optimized out>, buf=0x22259d0
"sonar_intensity.determine_bins", p_buflen=0x7fff271b4140) at
Python/import.c:2519
#96 0x00007f3911768860 in import_module_level (level=<optimized out>,
fromlist=0x7f3911aa06d0, locals=<optimized out>, globals=<optimized out>,
name=0x0) at Python/import.c:2236
#97 PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3911aa06d0, level=<optimized
out>) at Python/import.c:2292
#98 0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#99 0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#100 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f39092cb7e0, kw=<optimized out>) at
Python/ceval.c:4219
#101 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#102 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f3911a9d0b0,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#103 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#104 0x00007f3911764a82 in PyImport_ExecCodeModuleEx (name=0x7f39094f4fa4
"sonar_intensity", co=0x7f3911a9d0b0,
    pathname=0x7f3911aedd44
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/sidescananalysis-9.7.1.29-py2.7.egg/sonar_intensity/__init__.py")
at Python/import.c:713
#105 0x00007f39117a052e in zipimporter_load_module (obj=<optimized out>,
args=<optimized out>) at ./Modules/zipimport.c:360
#106 0x00007f391169ed23 in PyObject_Call (func=0x7f3908e47d88,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#107 0x00007f391169ee11 in call_function_tail (callable=0x7f3908e47d88,
args=0x7f39094f0350) at Objects/abstract.c:2578
#108 0x00007f39116a31b8 in PyObject_CallMethod (o=<optimized out>,
name=<optimized out>, format=<optimized out>) at Objects/abstract.c:2653
#109 0x00007f3911767f81 in import_submodule (mod=0x7f3911a05cd0
<_Py_NoneStruct>, subname=0x22b98e0 "sonar_intensity", fullname=0x22b98e0
"sonar_intensity") at Python/import.c:2704
#110 0x00007f39117681f4 in load_next (mod=0x7f3911a05cd0 <_Py_NoneStruct>,
altmod=0x7f3911a05cd0 <_Py_NoneStruct>, p_name=<optimized out>,
buf=0x22b98e0 "sonar_intensity", p_buflen=0x7fff271b47a0)
    at Python/import.c:2519
#111 0x00007f3911768820 in import_module_level (level=<optimized out>,
fromlist=0x7f3911b10b10, locals=<optimized out>, globals=<optimized out>,
name=0x0) at Python/import.c:2228
#112 PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3911b10b10, level=<optimized
out>) at Python/import.c:2292
#113 0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#114 0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#115 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f3911b01c58, kw=<optimized out>) at
Python/ceval.c:4219
#116 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#117 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f3911b02030,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#118 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#119 0x00007f3911764a82 in PyImport_ExecCodeModuleEx (name=0x7f3911b1655c
"sonar_signal", co=0x7f3911b02030,
    pathname=0x7f3911af2444
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/sidescananalysis-9.7.1.29-py2.7.egg/sonar_signal.py")
at Python/import.c:713
#120 0x00007f39117a052e in zipimporter_load_module (obj=<optimized out>,
args=<optimized out>) at ./Modules/zipimport.c:360
#121 0x00007f391169ed23 in PyObject_Call (func=0x7f3911b0d560,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#122 0x00007f391169ee11 in call_function_tail (callable=0x7f3911b0d560,
args=0x7f3911af6390) at Objects/abstract.c:2578
#123 0x00007f39116a31b8 in PyObject_CallMethod (o=<optimized out>,
name=<optimized out>, format=<optimized out>) at Objects/abstract.c:2653
#124 0x00007f3911767f81 in import_submodule (mod=0x7f3911a05cd0
<_Py_NoneStruct>, subname=0x22004a0 "sonar_signal", fullname=0x22004a0
"sonar_signal") at Python/import.c:2704
#125 0x00007f39117681f4 in load_next (mod=0x7f3911a05cd0 <_Py_NoneStruct>,
altmod=0x7f3911a05cd0 <_Py_NoneStruct>, p_name=<optimized out>,
buf=0x22004a0 "sonar_signal", p_buflen=0x7fff271b4e00)
    at Python/import.c:2519
#126 0x00007f3911768820 in import_module_level (level=<optimized out>,
fromlist=0x7f3911b52c90, locals=<optimized out>, globals=<optimized out>,
name=0x0) at Python/import.c:2228
#127 PyImport_ImportModuleLevel (name=<optimized out>, globals=<optimized
out>, locals=<optimized out>, fromlist=0x7f3911b52c90, level=<optimized
out>) at Python/import.c:2292
#128 0x00007f391174814f in builtin___import__ (self=<optimized out>,
args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:49
#129 0x00007f391169ed23 in PyObject_Call (func=0x7f3911c3efc8,
arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2546
#130 0x00007f3911748633 in PyEval_CallObjectWithKeywords
(func=0x7f3911c3efc8, arg=0x7f3911b3f788, kw=<optimized out>) at
Python/ceval.c:4219
#131 0x00007f391174d29e in PyEval_EvalFrameEx (f=<optimized out>,
throwflag=<optimized out>) at Python/ceval.c:2622
#132 0x00007f3911752a2e in PyEval_EvalCodeEx (co=0x7f3911afd330,
globals=<optimized out>, locals=<optimized out>, args=<optimized out>,
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at Python/ceval.c:3582
#133 0x00007f3911752b42 in PyEval_EvalCode (co=<optimized out>,
globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#134 0x00007f3911773050 in run_mod (arena=0x2166370, flags=0x7fff271b5320,
locals=0x7f3911be0168, globals=0x7f3911be0168, filename=<optimized out>,
mod=0x2209f20) at Python/pythonrun.c:1370
#135 PyRun_FileExFlags (fp=0x220e8c0, filename=<optimized out>,
start=<optimized out>, globals=0x7f3911be0168, locals=0x7f3911be0168,
closeit=1, flags=0x7fff271b5320) at Python/pythonrun.c:1356
#136 0x00007f391177322f in PyRun_SimpleFileExFlags (fp=0x220e8c0,
filename=0x7fff271b741e
"/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/bin/SonarSignal",
closeit=1, flags=0x7fff271b5320)
    at Python/pythonrun.c:948
#137 0x00007f3911788b74 in Py_Main (argc=<optimized out>, argv=<optimized
out>) at Modules/main.c:645
#138 0x00007f3910cae7d5 in __libc_start_main () from /lib64/libc.so.6
#139 0x0000000000400649 in _start ()

Thread 1 (Thread 0x7f3906922700 (LWP 27554)):
#0  __GI_getenv (name=0x7f3907894dc5 "TO_BLOCK_FACTOR") at getenv.c:89
#1  0x00007f3907059e21 in blas_set_parameter () from
/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/core/../../../../libopenblas.so.0
#2  0x00007f3907058d91 in blas_memory_alloc () from
/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/core/../../../../libopenblas.so.0
#3  0x00007f39070594e5 in blas_thread_server () from
/opt/apps/sidescananalysis-9.7.1-29-gc2e684d+dev/lib/python2.7/site-packages/numpy/core/../../../../libopenblas.so.0
#4  0x00007f3911440f18 in start_thread (arg=0x7f3906922700) at
pthread_create.c:308
#5  0x00007f3910d6fb2d in clone () at
../sysdeps/unix/sysv/linux/x86_64/clone.S:113

On 11 December 2015 at 10:49, Nathaniel Smith <njs at pobox.com> wrote:

> On Thu, Dec 10, 2015 at 4:05 PM, Jacopo Sabbatini
> <jacopo.sabbatini at roames.com.au> wrote:
> > Hi,
> >
> > I'm experiencing random segmentation faults from numpy. I have generated
> a
> > core dumped and extracted a stack trace, the following:
> >
> > #0  0x00007f3a8d921d5d in getenv () from /lib64/libc.so.6
> > #1  0x00007f3a843bde21 in blas_set_parameter () from
> >
> /opt/apps/sidescananalysis-9.7.1-42-gdd3e068+dev/lib/python2.7/site-packages/numpy/core/../../../../libopenblas.so.0
> > #2  0x00007f3a843bcd91 in blas_memory_alloc () from
> >
> /opt/apps/sidescananalysis-9.7.1-42-gdd3e068+dev/lib/python2.7/site-packages/numpy/core/../../../../libopenblas.so.0
> > #3  0x00007f3a843bd4e5 in blas_thread_server () from
> >
> /opt/apps/sidescananalysis-9.7.1-42-gdd3e068+dev/lib/python2.7/site-packages/numpy/core/../../../../libopenblas.so.0
> > #4  0x00007f3a8e09ff18 in start_thread () from /lib64/libpthread.so.0
> > #5  0x00007f3a8d9ceb2d in clone () from /lib64/libc.so.6
>
> Given the backtrace this is almost certainly some sort of bug in
> openblas, and I'd suggest filing a bug with them.
>
> It's possible that we might have accidentally added a workaround in
> 1.10.2 (release candidate currently available, final should be out
> soon). There was some environment variable handling code in numpy 1.9
> through 1.10.1 that triggered problems in some buggy libraries (see
> numpy issues #6460 and 6622); possibly the workaround for those issues
> will also workaround this issue. But if not then I'm not sure what
> else we can do, and it's probably a good idea to file a bug with
> openblas regardless.
>
> -n
>
> --
> Nathaniel J. Smith -- http://vorpus.org
> _______________________________________________
> NumPy-Discussion mailing list
> NumPy-Discussion at scipy.org
> https://mail.scipy.org/mailman/listinfo/numpy-discussion
>



-- 

*Jacopo Sabbatini* | Software & Algorithm Engineer | Fugro ROAMES Pty Ltd
Level 1 | 53 Brandl Street | Eight Mile Plains, QLD, 4113, Australia | ( | P.O.
Box 10, Sunnybank Qld 4109, Australia, Australia)
www.fugroroames.com.au

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