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 I have experience the segfault from several code paths but they all have the same stack trace. I use conda to run python and numpy. The dump of the packages version is: conda 3.18.9 py27_0 geos 3.3.3 0 matplotlib 1.4.3 np19py27_2 networkx 1.10 py27_0 numpy 1.9.2 py27_2 openblas 0.2.14 3 pandas 0.16.2 np19py27_0 python 2.7.10 2 scikit-image 0.11.3 np19py27_0 scipy 0.15.1 np19py27_0 shapely 1.5.7 py27_0 system 5.8 1 Cheers, Jacopo
On Thu, Dec 10, 2015 at 4:05 PM, Jacopo Sabbatini <jacopo.sabbatini@roames.com.au> wrote:
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
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@pobox.com> wrote:
-- *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 Observe | Model | Simulate This email transmission is confidential and may contain proprietary information for the exclusive use of the intended recipient. Any use, distribution or copying of this transmission, other than by the intended recipient, is strictly prohibited. If you are not the intended recipient, please notify the sender and delete all copies. Electronic media is susceptible to unauthorized modification, deterioration, and incompatibility. Accordingly, the electronic media version of any work product may not be relied upon. Any advice provided in or attached to this email is subject to limitations. Please consider the environment before printing this email.
Hi, On Fri, 11 Dec 2015 10:05:59 +1000 Jacopo Sabbatini <jacopo.sabbatini@roames.com.au> wrote:
In addition to openblas, you should also submit a bug to Anaconda so that they know of problems with that particular openblas version: https://github.com/ContinuumIO/anaconda-issues Regards Antoine.
On Thu, Dec 10, 2015 at 4:05 PM, Jacopo Sabbatini <jacopo.sabbatini@roames.com.au> wrote:
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
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@pobox.com> wrote:
-- *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 Observe | Model | Simulate This email transmission is confidential and may contain proprietary information for the exclusive use of the intended recipient. Any use, distribution or copying of this transmission, other than by the intended recipient, is strictly prohibited. If you are not the intended recipient, please notify the sender and delete all copies. Electronic media is susceptible to unauthorized modification, deterioration, and incompatibility. Accordingly, the electronic media version of any work product may not be relied upon. Any advice provided in or attached to this email is subject to limitations. Please consider the environment before printing this email.
Hi, On Fri, 11 Dec 2015 10:05:59 +1000 Jacopo Sabbatini <jacopo.sabbatini@roames.com.au> wrote:
In addition to openblas, you should also submit a bug to Anaconda so that they know of problems with that particular openblas version: https://github.com/ContinuumIO/anaconda-issues Regards Antoine.
participants (3)
-
Antoine Pitrou -
Jacopo Sabbatini -
Nathaniel Smith