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segfault on Python 3.5 #66

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ExpandingMan opened this issue Oct 6, 2016 · 8 comments
Closed

segfault on Python 3.5 #66

ExpandingMan opened this issue Oct 6, 2016 · 8 comments

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@ExpandingMan
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I get the following segfault when I do j = julia.Julia() on Python 3.5.

WARNING: redefining constant JULIA_HOME
InitError(:PyCall,PyError (:PyImport_ImportModule) <class 'SystemError'>
SystemError('initialization of _opcode did not return an extension module',)

signal (11): Segmentation fault
while loading no file, in expression starting on line 0
PyObject_Call at /usr/bin/../lib/x86_64-linux-gnu/libpython3.5m.so (unknown line)
macro expansion at /home/savastio/.julia/v0.5/PyCall/src/exception.jl:78 [inlined]
#_pycall#62 at /home/savastio/.julia/v0.5/PyCall/src/PyCall.jl:546
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
jl_apply at /build/julia-0ecDfF/julia-0.5.0/src/julia.h:1392 [inlined]
jl_f__apply at /build/julia-0ecDfF/julia-0.5.0/src/builtins.c:547
_pycall at /home/savastio/.julia/v0.5/PyCall/src/PyCall.jl:534
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
jl_apply at /build/julia-0ecDfF/julia-0.5.0/src/julia.h:1392 [inlined]
jl_f__apply at /build/julia-0ecDfF/julia-0.5.0/src/builtins.c:547
#pycall#65 at /home/savastio/.julia/v0.5/PyCall/src/PyCall.jl:565
show at /home/savastio/.julia/v0.5/PyCall/src/exception.jl:39
unknown function (ip: 0x7f7f98d931f6)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
show_default at ./show.jl:130
unknown function (ip: 0x7f7f98d91c06)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
show at ./show.jl:116
unknown function (ip: 0x7f7f98d91686)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
jl_apply at /build/julia-0ecDfF/julia-0.5.0/src/julia.h:1392 [inlined]
jl_show at /build/julia-0ecDfF/julia-0.5.0/src/builtins.c:972
ffi_call_unix64 at /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so (unknown line)
ffi_call at /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so (unknown line)
_ctypes_callproc at /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so (unknown line)
unknown function (ip: 0x7f81dfd4cfca)
PyObject_Call at python3 (unknown line)
PyEval_EvalFrameEx at python3 (unknown line)
unknown function (ip: 0x523de6)
PyEval_EvalFrameEx at python3 (unknown line)
PyEval_EvalFrameEx at python3 (unknown line)
PyEval_EvalCodeEx at python3 (unknown line)
unknown function (ip: 0x4e3827)
PyObject_Call at python3 (unknown line)
unknown function (ip: 0x4f498d)
PyObject_Call at python3 (unknown line)
unknown function (ip: 0x54e948)
unknown function (ip: 0x5586ab)
PyObject_Call at python3 (unknown line)
PyEval_EvalFrameEx at python3 (unknown line)
unknown function (ip: 0x523de6)
PyEval_EvalCode at python3 (unknown line)
unknown function (ip: 0x5fd5f1)
PyRun_InteractiveOneObject at python3 (unknown line)
PyRun_InteractiveLoopFlags at python3 (unknown line)
unknown function (ip: 0x458aef)
unknown function (ip: 0x4cf513)
main at python3 (unknown line)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at python3 (unknown line)
Allocations: 2217234 (Pool: 2216298; Big: 936); GC: 1
[1]    89582 segmentation fault (core dumped)  python3

My PyCall package has been successfully compiled for Python 3.5.
@ExpandingMan
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ExpandingMan commented Oct 10, 2016 •
edited
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Fixed by re-installing. Still no idea what was causing the problem.

I'm still getting segfaults if I do j.using("PackageX") where "PackageX" is (apparently) any package that has using PyCall.

@stevengj
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Pkg.build("PyCall")?

@ExpandingMan
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ExpandingMan commented Oct 11, 2016 •
edited
Loading

Yes, PyCall has been built successfully.

I haven't been able to reproduce that error since I reinstalled (but PyCall was definitely built when it was thrown), so I really have no idea what happened.

Ok, I am still rather confused but at least now I can consistently reproduce the errors I am getting. I'm pretty sure these errors are only occurring for packages which use PyCall but I'm not certain (it's certainly not every package).

I get the following error

could not spawn `/usr/local/lib/python3.5/dist-packages/julia-0.1.1-py3.5.egg/julia/../fake-julia/julia -Cx86-64 -J/usr/lib/x86_64-linux-gnu/julia/sys.so --compile=yes --depwarn=yes -O0 --output-ji /home/savastio/.julia/lib/pyjulia3-v0.5/DatasToolbox.ji --output-incremental=yes --startup-file=no --history-file=no --color=no --eval 'while !eof(STDIN)
    eval(Main, deserialize(STDIN))
end
'`: no such file or directory (ENOENT)Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.5/dist-packages/julia-0.1.1-py3.5.egg/julia/core.py", line 447, in using
    self.eval("using %s" % module)
  File "/usr/local/lib/python3.5/dist-packages/julia-0.1.1-py3.5.egg/julia/core.py", line 429, in eval
    ans = self._call(src)
  File "/usr/local/lib/python3.5/dist-packages/julia-0.1.1-py3.5.egg/julia/core.py", line 392, in _call
    self.check_exception(src)
  File "/usr/local/lib/python3.5/dist-packages/julia-0.1.1-py3.5.egg/julia/core.py", line 412, in check_exception
    .format(exception_type, src))
julia.core.JuliaError: Exception 'UVError' occurred while calling julia code:
using DatasToolbox

However, if I am in the home directory of pyjulia I instead get

signal (11): Segmentation fault
while loading /home/savastio/.julia/v0.5/DatasToolbox/src/DatasToolbox.jl, in expression starting on line 9
PyEval_GetFrame at /usr/bin/python3 (unknown line)
PyEval_GetGlobals at /usr/bin/python3 (unknown line)
PyImport_Import at /usr/bin/python3 (unknown line)
PyImport_ImportModule at /usr/bin/python3 (unknown line)
macro expansion at /home/savastio/.julia/v0.5/PyCall/src/exception.jl:78 [inlined]
pyimport at /home/savastio/.julia/v0.5/PyCall/src/PyCall.jl:387
__init__ at /home/savastio/.julia/v0.5/PyCall/src/pyinit.jl:58
unknown function (ip: 0x7fa7a18925be)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
jl_apply at /build/julia-0ecDfF/julia-0.5.0/src/julia.h:1392 [inlined]
jl_module_run_initializer at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:83
jl_init_restored_modules at /build/julia-0ecDfF/julia-0.5.0/src/dump.c:1994 [inlined]
_jl_restore_incremental at /build/julia-0ecDfF/julia-0.5.0/src/dump.c:2560
_jl_restore_incremental at /build/julia-0ecDfF/julia-0.5.0/src/dump.c:2498 [inlined]
jl_restore_incremental at /build/julia-0ecDfF/julia-0.5.0/src/dump.c:2580
_include_from_serialized at ./loading.jl:150
_require_from_serialized at ./loading.jl:187
_require_search_from_serialized at ./loading.jl:217
unknown function (ip: 0x7fa9bb281ad0)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
require at ./loading.jl:371
unknown function (ip: 0x7fa9bb179eeb)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
jl_apply at /build/julia-0ecDfF/julia-0.5.0/src/julia.h:1392 [inlined]
eval_import_path_ at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:402
eval_import_path at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:429 [inlined]
jl_toplevel_eval_flex at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:480
jl_eval_module_expr at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:196
jl_toplevel_eval_flex at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:465
jl_parse_eval_all at /build/julia-0ecDfF/julia-0.5.0/src/ast.c:717
jl_load at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:596
jl_load_ at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:605
include_from_node1 at ./loading.jl:488
unknown function (ip: 0x7fa9bb13f16b)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
do_call at /build/julia-0ecDfF/julia-0.5.0/src/interpreter.c:66
eval at /build/julia-0ecDfF/julia-0.5.0/src/interpreter.c:190
jl_toplevel_eval_flex at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:558 [inlined]
jl_toplevel_eval at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:580
jl_toplevel_eval_in_warn at /build/julia-0ecDfF/julia-0.5.0/src/builtins.c:590
macro expansion; at ./none:2 [inlined]
anonymous at ./<missing> (unknown line)
unknown function (ip: 0x7fa7a187b681)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_toplevel_eval_flex at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:569 [inlined]
jl_toplevel_eval at /build/julia-0ecDfF/julia-0.5.0/src/toplevel.c:580
jl_toplevel_eval_in_warn at /build/julia-0ecDfF/julia-0.5.0/src/builtins.c:590
eval at ./boot.jl:234
unknown function (ip: 0x7fa9bb12a81f)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
process_options at ./client.jl:239
_start at ./client.jl:318
unknown function (ip: 0x7fa9bb164708)
jl_call_method_internal at /build/julia-0ecDfF/julia-0.5.0/src/julia_internal.h:189 [inlined]
jl_apply_generic at /build/julia-0ecDfF/julia-0.5.0/src/gf.c:1942
ffi_call_unix64 at /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so (unknown line)
ffi_call at /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so (unknown line)
_ctypes_callproc at /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so (unknown line)
unknown function (ip: 0x7fa9bfca2fca)
PyObject_Call at /usr/bin/python3 (unknown line)
PyEval_EvalFrameEx at /usr/bin/python3 (unknown line)
unknown function (ip: 0x523de6)
PyEval_EvalCode at /usr/bin/python3 (unknown line)
unknown function (ip: 0x5fd5f1)
PyRun_FileExFlags at /usr/bin/python3 (unknown line)
PyRun_SimpleFileExFlags at /usr/bin/python3 (unknown line)
Py_Main at /usr/bin/python3 (unknown line)
main at /usr/bin/python3 (unknown line)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /usr/bin/python3 (unknown line)
Allocations: 3101149 (Pool: 3100144; Big: 1005); GC: 3
ErrorException("Failed to precompile DatasToolbox to /home/savastio/.julia/lib/pyjulia3-v0.5/DatasToolbox.ji.")Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/savastio/pyjulia/julia/julia/core.py", line 447, in using
    self.eval("using %s" % module)
  File "/home/savastio/pyjulia/julia/julia/core.py", line 429, in eval
    ans = self._call(src)
  File "/home/savastio/pyjulia/julia/julia/core.py", line 392, in _call
    self.check_exception(src)
  File "/home/savastio/pyjulia/julia/julia/core.py", line 412, in check_exception
    .format(exception_type, src))
julia.core.JuliaError: Exception 'ErrorException' occurred while calling julia code:
using DatasToolbox

@stevengj
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@Keno, this seems like a conflict between your "fake-julia" precompilation trick and precompilation of packages with PyCall. Does precompilation using fake-julia load the correct (pyjulia) version of PyCall? It doesn't seem like julia.py has the stuff from core.py to grab the correct PyCall version (the one built for the in-process libpython).

@goretkin
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I'm experiencing what I think is the same issue, using Julia v0.0.5 ( binary release), Python 2.7.6, Ubuntu 14.04

�[0;34mIn [�[1;34m1�[0;34m]: �[0mimport julia

�[0;34mIn [�[1;34m2�[0;34m]: �[0mjulia.Julia()
WARNING: redefining constant JULIA_HOME
InitError(:PyCall,PyError (:PyImport_ImportModule) <type 'exceptions.SystemError'>
SystemError('dynamic module not initialized properly',)

signal (11): Segmentation fault
while loading no file, in expression starting on line 0
PyObject_Call at /usr/lib/x86_64-linux-gnu/libpython2.7.so (unknown line)
macro expansion at /home/goretkin/.julia/v0.5/PyCall/src/exception.jl:78 [inlined]
#_pycall#62 at /home/goretkin/.julia/v0.5/PyCall/src/PyCall.jl:546
jl_call_method_internal at /home/centos/buildbot/slave/package_tarball64/build/src/julia_internal.h:189 [inlined]
jl_apply_generic at /home/centos/buildbot/slave/package_tarball64/build/src/gf.c:1942
jl_apply at /home/centos/buildbot/slave/package_tarball64/build/src/julia.h:1392 [inlined]
jl_f__apply at /home/centos/buildbot/slave/package_tarball64/build/src/builtins.c:547
_pycall at /home/goretkin/.julia/v0.5/PyCall/src/PyCall.jl:534
jl_call_method_internal at /home/centos/buildbot/slave/package_tarball64/build/src/julia_internal.h:189 [inlined]
jl_apply_generic at /home/centos/buildbot/slave/package_tarball64/build/src/gf.c:1942
jl_apply at /home/centos/buildbot/slave/package_tarball64/build/src/julia.h:1392 [inlined]
jl_f__apply at /home/centos/buildbot/slave/package_tarball64/build/src/builtins.c:547
#pycall#65 at /home/goretkin/.julia/v0.5/PyCall/src/PyCall.jl:565
show at /home/goretkin/.julia/v0.5/PyCall/src/exception.jl:39
unknown function (ip: 0x7fadbb1476f6)
jl_call_method_internal at /home/centos/buildbot/slave/package_tarball64/build/src/julia_internal.h:189 [inlined]
jl_apply_generic at /home/centos/buildbot/slave/package_tarball64/build/src/gf.c:1942
show_default at ./show.jl:130
unknown function (ip: 0x7fadbb1460a6)
jl_call_method_internal at /home/centos/buildbot/slave/package_tarball64/build/src/julia_internal.h:189 [inlined]
jl_apply_generic at /home/centos/buildbot/slave/package_tarball64/build/src/gf.c:1942
show at ./show.jl:116
unknown function (ip: 0x7fadbb145b06)
jl_call_method_internal at /home/centos/buildbot/slave/package_tarball64/build/src/julia_internal.h:189 [inlined]
jl_apply_generic at /home/centos/buildbot/slave/package_tarball64/build/src/gf.c:1942
jl_apply at /home/centos/buildbot/slave/package_tarball64/build/src/julia.h:1392 [inlined]
jl_show at /home/centos/buildbot/slave/package_tarball64/build/src/builtins.c:972
ffi_call_unix64 at /usr/lib/x86_64-linux-gnu/libffi.so.6 (unknown line)
ffi_call at /usr/lib/x86_64-linux-gnu/libffi.so.6 (unknown line)
_ctypes_callproc at /usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so (unknown line)
unknown function (ip: 0x7fafdd49ef9d)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
unknown function (ip: 0x56d0a9)
unknown function (ip: 0x4d9853)
unknown function (ip: 0x4d8378)
unknown function (ip: 0x4f5d0a)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalCode at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
unknown function (ip: 0x56d0a9)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalFrameEx at /usr/bin/python (unknown line)
PyEval_EvalCodeEx at /usr/bin/python (unknown line)
PyEval_EvalCode at /usr/bin/python (unknown line)
unknown function (ip: 0x469662)
PyRun_FileExFlags at /usr/bin/python (unknown line)
PyRun_SimpleFileExFlags at /usr/bin/python (unknown line)
Py_Main at /usr/bin/python (unknown line)
__libc_start_main at /build/buildd/eglibc-2.19/csu/libc-start.c:287
unknown function (ip: 0x57497d)
Allocations: 2235728 (Pool: 2234774; Big: 954); GC: 1
Segmentation fault (core dumped)

@Certhas
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Certhas commented Oct 24, 2016

Also seeing such an error, on multiple machines, Linux and OSX:
julia-error.txt

The minimal python test case looks like this. The hack makes no difference, in my private copy of the bugfixed package I get the same segmentation fault:

import julia

def f(t, x, dx):
    return x - dx

j = julia.Julia()
j.using("DASSL")

# Hack that is needed to massage the types when using the unmodified DASSL.jl
fwrap = j.eval('f -> (args...) -> f(args...)')
r = j.dasslSolve(fwrap, 1., [0., 10.])

@GunnarFarneback GunnarFarneback mentioned this issue Nov 30, 2016
Closed
@Alexander-Barth
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I had the same issue on Julia v0.5.0, (binary release), Python 2.7.6, Ubuntu 14.04, but a Pkg.rebuild("PyCall") after installing pyjulia solved this issue.

@ExpandingMan
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Sorry all. I had completely forgotten about this and have recently reposted it as #92. I'll close this in favor of that one.

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@goretkin @stevengj @Certhas @Alexander-Barth @ExpandingMan