Opened 7 years ago

Closed 7 years ago

Last modified 6 years ago

#41761 closed defect (invalid)

python27: Fatal Python error: PyThreadState_Get: no current thread

Reported by: fredotan@… Owned by: jyrkiwahlstedt
Priority: Normal Milestone:
Component: ports Version: 2.2.1
Keywords: Cc: count0 (Tiago de Paula Peixoto), mamoll (Mark Moll)
Port: python27, py27-graph-tool

Description (last modified by ryandesign (Ryan Schmidt))

So, I figured in order to call the Macports python version you have to use:

/opt/local/bin/python2.7 

However I get this error now using /opt/local/bin/python2.7 SIR.py:

Fatal Python error: PyThreadState_Get: no current thread 
Abort trap: 6 

The report says:

Crashed Thread:  0  Dispatch queue: com.apple.main-thread 

Exception Type:  EXC_CRASH (SIGABRT) 
Exception Codes: 0x0000000000000000, 0x0000000000000000 

Application Specific Information: 
abort() called 

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 
0   libsystem_kernel.dylib        	0x00007fff8f5fc866 __pthread_kill + 10 
1   libsystem_pthread.dylib       0x00007fff8c16035c pthread_kill + 92 
2   libsystem_c.dylib             0x00007fff8c4f9bba abort + 125 
3   org.python.python             0x0000000114247ec1 Py_FatalError + 49 
4   org.python.python             0x0000000114247411 PyThreadState_Get + 28 
5   org.python.python             0x0000000114244476 Py_InitModule4_64 + 58 
6   libboost_python.dylib         0x0000000113fb1ef8 boost::python::detail::init_module(char const*, void (*)()) + 40 
7   org.python.python             0x000000010d5add86 _PyImport_LoadDynamicModule + 150 
8   org.python.python             0x000000010d5ada87 import_submodule + 279 
9   org.python.python             0x000000010d5ad854 ensure_fromlist + 532 
10  org.python.python             0x000000010d5ab573 PyImport_ImportModuleLevel + 1347 
11  org.python.python             0x000000010d58b304 builtin___import__ + 132 
12  org.python.python             0x000000010d4ff665 PyObject_Call + 101 
13  org.python.python             0x000000010d593763 PyEval_EvalFrameEx + 13683 
14  org.python.python             0x000000010d590076 PyEval_EvalCodeEx + 1734 
15  org.python.python             0x000000010d58f9a6 PyEval_EvalCode + 54 
16  org.python.python             0x000000010d5b775d PyRun_StringFlags + 125 
17  org.python.python             0x000000010d594985 PyEval_EvalFrameEx + 18325 
18  org.python.python             0x000000010d590076 PyEval_EvalCodeEx + 1734 
19  org.python.python             0x000000010d596f36 fast_function + 294 
20  org.python.python             0x000000010d59328b PyEval_EvalFrameEx + 12443 
21  org.python.python             0x000000010d590076 PyEval_EvalCodeEx + 1734 
22  org.python.python             0x000000010d58f9a6 PyEval_EvalCode + 54 
23  org.python.python             0x000000010d5a9f57 PyImport_ExecCodeModuleEx + 247 
24  org.python.python             0x000000010d5ace77 load_source_module + 935 
25  org.python.python             0x000000010d5ad16a load_package + 298 
26  org.python.python             0x000000010d5ada87 import_submodule + 279 
27  org.python.python             0x000000010d5ad51f load_next + 271 
28  org.python.python             0x000000010d5ab4b1 PyImport_ImportModuleLevel + 1153 
29  org.python.python             0x000000010d58b304 builtin___import__ + 132 
30  org.python.python             0x000000010d4ff665 PyObject_Call + 101 
31  org.python.python             0x000000010d593763 PyEval_EvalFrameEx + 13683 
32  org.python.python             0x000000010d590076 PyEval_EvalCodeEx + 1734 
33  org.python.python             0x000000010d58f9a6 PyEval_EvalCode + 54 
34  org.python.python             0x000000010d5b7611 PyRun_FileExFlags + 161 
35  org.python.python             0x000000010d5b715e PyRun_SimpleFileExFlags + 718 
36  org.python.python             0x000000010d5cb002 Py_Main + 3314 
37  libdyld.dylib                 0x00007fff967335fd start + 1 

Thread 0 crashed with X86 Thread State (64-bit): 
  rax: 0x0000000000000000  rbx: 0x00007fff79527310  rcx: 0x00007fff52711708  rdx: 0x0000000000000000 
  rdi: 0x0000000000000d07  rsi: 0x0000000000000006  rbp: 0x00007fff52711730  rsp: 0x00007fff52711708 
   r8: 0x0000000000000040   r9: 0x00007fff52711700  r10: 0x0000000008000000  r11: 0x0000000000000206 
  r12: 0x0000000000000000  r13: 0x000000010f44ba60  r14: 0x0000000000000006  r15: 0x00000000000003f5 
  rip: 0x00007fff8f5fc866  rfl: 0x0000000000000206  cr2: 0x0000000114280d5c 
  
Logical CPU:     0 
Error Code:      0x02000148 
Trap Number:     133 


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    0x7fff8bf77000 -     0x7fff8bf92ff7  libsystem_malloc.dylib (23.1.10) <FFE5C472-B23A-318A-85BF-77CDE61900D1> /usr/lib/system/libsystem_malloc.dylib 
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    0x7fff8c49d000 -     0x7fff8c526ff7  libsystem_c.dylib (997.1.1) <61833FAA-7281-3FF9-937F-686B6F20427C> /usr/lib/system/libsystem_c.dylib 
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External Modification Summary: 
  Calls made by other processes targeting this process: 
    task_for_pid: 0 
    thread_create: 0 
    thread_set_state: 0 
  Calls made by this process: 
    task_for_pid: 0 
    thread_create: 0 
    thread_set_state: 0 
  Calls made by all processes on this machine: 
    task_for_pid: 330445 
    thread_create: 2 
    thread_set_state: 0 

I installed graph-tool using macports. But it doesn't seem to work.

Change History (20)

comment:1 Changed 7 years ago by ryandesign (Ryan Schmidt)

Cc: tiago@… mmoll@… added
Description: modified (diff)
Owner: changed from macports-tickets@… to jwa@…
Port: python27 py27-graph-tool added
Summary: Fatal Python error: PyThreadState_Get: no current threadpython27: Fatal Python error: PyThreadState_Get: no current thread

comment:2 Changed 7 years ago by mamoll (Mark Moll)

Can you elaborate on this a bit more? Do you have a minimal code example that produces a crash?

comment:3 Changed 7 years ago by fredotan@…

from graph_tool.all import *
from random import *
import smallthings

def create_network():
  g = smallthings.triumph_strength(50, 2, 0.0)

I think the first line already produces a crash: from graph_tool.all import *

Last edited 6 years ago by ryandesign (Ryan Schmidt) (previous) (diff)

comment:4 Changed 7 years ago by mamoll (Mark Moll)

Which version of OS X? I don't have a module called smallthings, but the first line works for me on 10.9 with latest Xcode. I have the python33 variant installed, though.

comment:5 Changed 7 years ago by fredotan@…

I have OS X 10.9 with Python 2.7

Well, smallthings.py is a python file that I created, which I am importing.

comment:6 Changed 7 years ago by mamoll (Mark Moll)

I am guessing that somehow a wrong dynamic library is picked up. What is the output of this command?:

otool -L /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so

I am installing py27-graph-tool now to see if I can reproduce the error.

comment:7 Changed 7 years ago by fredotan@…

This is the output, sir:

	/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
	/usr/local/lib/libboost_iostreams.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/lib/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/lib/libboost_regex.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/local/lib/libCGAL.10.dylib (compatibility version 10.0.0, current version 10.0.2)
	/opt/local/lib/libexpat.1.dylib (compatibility version 8.0.0, current version 8.0.0)
	/opt/local/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.6)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)
Last edited 6 years ago by ryandesign (Ryan Schmidt) (previous) (diff)

comment:9 Changed 7 years ago by mamoll (Mark Moll)

This is the same for me. I just confirmed that this does not crash /opt/local/bin/python2.7 for me:

from graph_tool.all import *

Do you have any dependencies installed with non-default variants? I have no idea why it crashes for you.

comment:10 in reply to:  8 Changed 7 years ago by seanfarley (Sean Farley)

Replying to fredotan@…:

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)

/usr/local/lib/libboost_iostreams.dylib (compatibility version 0.0.0, current version 0.0.0)

/usr/local/lib/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0)

/usr/local/lib/libboost_regex.dylib (compatibility version 0.0.0, current version 0.0.0)

I would wager a bet that something you installed manually in /usr/local is causing linking grief.

Version 0, edited 7 years ago by seanfarley (Sean Farley) (next)

comment:11 in reply to:  9 Changed 7 years ago by fredotan@…

Replying to mmoll@…:

This is the same for me. I just confirmed that this does not crash /opt/local/bin/python2.7 for me:

from graph_tool.all import *

Do you have any dependencies installed with non-default variants? I have no idea why it crashes for you.

Not that I know of, is there a way I can check that with a cmd?

comment:12 Changed 7 years ago by fredotan@…

Could it be Homebrew or Boost which I installed with Homebrew?

comment:13 Changed 7 years ago by mamoll (Mark Moll)

Possibly. Can you post the output of this command?:

env

comment:14 Changed 7 years ago by fredotan@…

TERM_PROGRAM=Apple_Terminal
SHELL=/bin/bash
TERM=xterm-256color
TMPDIR=/var/folders/ln/xvd5c_qd5nj2ptb6b0_8sssr0000gn/T/
Apple_PubSub_Socket_Render=/tmp/launch-hEvgyI/Render
TERM_PROGRAM_VERSION=326
OLDPWD=/Users
TERM_SESSION_ID=B61F1E5F-3AC5-4208-A4DC-58A73C58C3FD
USER=user
SSH_AUTH_SOCK=/tmp/launch-6b8DMK/Listeners
__CF_USER_TEXT_ENCODING=0x1F5:0:5
PATH=/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
__CHECKFIX1436934=1
PWD=/
LANG=nl_NL.UTF-8
SHLVL=1
HOME=/Users/user
PYTHONPATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool
LOGNAME=user
_=/usr/bin/env
Last edited 6 years ago by ryandesign (Ryan Schmidt) (previous) (diff)

comment:15 Changed 7 years ago by mamoll (Mark Moll)

This doesn't show anything suspicious (e.g., odd DYLD_* or PYTHONPATH variable settings). Without further leads I cannot help you.

comment:16 Changed 7 years ago by ned-deily (Ned Deily)

All those /usr/local/lib library references in the otool -L output are suspicious, e.g. /usr/local/lib/libboost_iostreams.dylib , /usr/local/lib/libboost_python.dylib, et al. Try removing them from /usr/local, installing the appropriate boost ports, and rebuilding.

comment:17 Changed 7 years ago by t.m.isele@…

Hi, could this be resolved in the meantime? I have a similar problem.. See also ticket #43086

comment:18 Changed 7 years ago by mamoll (Mark Moll)

Resolution: invalid
Status: newclosed

This problem is likely caused by having another version of Boost installed in /usr/local. This is not a MacPorts problem. The person reporting the bug can probably work around this problem by setting the environment variable DYLD_LIBRARY_PATH to /opt/local.

comment:19 in reply to:  18 Changed 7 years ago by sophiaqhsw@…

Replying to mmoll@…:

This problem is likely caused by having another version of Boost installed in /usr/local. This is not a MacPorts problem. The person reporting the bug can probably work around this problem by setting the environment variable DYLD_LIBRARY_PATH to /opt/local.

I have encountered with the same problem. As you suggested, I have set DYLD_LIBRARY_PATH to /opt/local. But it seems not work. As you pointed, it maybe caused by having another version of Boost installed in /usr/local. How do I check that? Is there a way I can check with cmd? I am new to this. Could you give me further suggestions? Thanks.

comment:20 in reply to:  18 Changed 7 years ago by sophiaqhsw@…

Replying to mmoll@…:

This problem is likely caused by having another version of Boost installed in /usr/local. This is not a MacPorts problem. The person reporting the bug can probably work around this problem by setting the environment variable DYLD_LIBRARY_PATH to /opt/local.

I find this problem is so common, but I didn't find the solution on the Internet. It seems the person who encountered the problem also don't show how they fix that.

comment:21 Changed 6 years ago by ryandesign (Ryan Schmidt)

Setting DYLD_LIBRARY_PATH is usually inadvisable.

The problem is that /usr/local is a special location; the compiler will look there without being told to. The solution is to remove what you have installed in /usr/local, then rebuild the broken port, and don't install anything else in /usr/local in the future.

And don't try to use two different package managers on the same system; they will interfere with one another. Pick which one you want to use and uninstall the other.

MacPorts trace mode (the -t flag) should prevent this kind of problem from happening. We may make trace mode the default in a future release of MacPorts.

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