#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 Carsten 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
Binary Images:
0x10d4ed000 - 0x10d4eefff +org.python.python (2.7.6 - 2.7.6) <9EAA7EA7-0461-3548-A192-07D38564031C> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
0x10d4f2000 - 0x10d608ff7 +org.python.python (2.7.6, [c] 2004-2013 Python Software Foundation. - 2.7.6) <980B2D89-E75B-3026-B8F3-CFFA635C4792> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python
0x10d8e1000 - 0x10d8e5fff +math.so (0) <7402006C-C00D-393A-9A6E-7240B2EFAAC4> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/math.so
0x10d8ec000 - 0x10d9d6fff +multiarray.so (0) <030DF069-55B2-31B4-A242-75A0E20C188E> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so
0x10da7c000 - 0x10da88fff +datetime.so (0) <14C3C837-ACA0-3F99-9BF8-368E32EE6E24> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/datetime.so
0x10da94000 - 0x10dad9ff7 +umath.so (0) <4840927E-47BA-3354-AB5B-22BF4FCD4E1B> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/umath.so
0x10db05000 - 0x10db08ff7 +_collections.so (0) <DDDAB77F-A531-3E13-BB63-240398C3E7C7> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_collections.so
0x10db0e000 - 0x10db11fff +operator.so (0) <95D19C2D-417E-3A67-A1BB-97F6234BD4A4> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/operator.so
0x10db58000 - 0x10db5dff7 +itertools.so (0) <A3DA6CBE-61F7-3D0D-9251-22F54CFA6CB8> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/itertools.so
0x10db68000 - 0x10db69fff +_heapq.so (0) <DB5A22ED-B9F3-39EF-A83B-8726F4F8A7E3> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_heapq.so
0x10db6d000 - 0x10db7afff +cPickle.so (0) <2CD483B1-CE6C-3BE8-BD5F-B0A20F477DBD> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/cPickle.so
0x10db82000 - 0x10db83fff +cStringIO.so (0) <EF9551C2-2514-3767-9447-9BA101184349> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/cStringIO.so
0x10db88000 - 0x10db8cfff +_dotblas.so (0) <8F9FAB93-80F6-32F9-A406-89A6A06E8B19> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so
0x10db90000 - 0x10db91ff7 +_functools.so (0) <B36EA2D6-B7DF-3592-93C3-0001BDFB4FEC> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_functools.so
0x10dbd5000 - 0x10dbf1ff7 +scalarmath.so (0) <36D6FDF0-0B2A-316C-A655-5B8021B957F5> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so
0x10dd03000 - 0x10dd05fff +time.so (0) <7B313687-32FF-34C2-ACD8-C7A1790A3343> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/time.so
0x10dd4b000 - 0x10dd4fff7 +_compiled_base.so (0) <72B98C02-BC6F-32F2-B2FF-A875DF946BC0> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so
0x10dd93000 - 0x10dd97fff +lapack_lite.so (0) <FAEA05CA-20B8-3FE2-8EB0-B3E76545EA42> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
0x10dd9b000 - 0x10dda8ff7 +_umath_linalg.so (0) <BEE109CC-BB44-393E-B04D-AAB0A1A9643D> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/_umath_linalg.so
0x10ddb4000 - 0x10ddb5fff +grp.so (0) <B1468245-66CD-364E-B04F-8A63C1A8BAE0> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/grp.so
0x10ddb8000 - 0x10ddb8fff +future_builtins.so (0) <84110E0D-0171-3A3F-B660-70CE6B14442A> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/future_builtins.so
0x10ddfb000 - 0x10de03fff +fftpack_lite.so (0) <CF47109B-BC1E-3AEB-A324-EE416B40DA4A> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
0x10de07000 - 0x10de0afff +strop.so (0) <D4149B0D-D369-37B1-88AB-E54B00955B29> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/strop.so
0x10df0f000 - 0x10df46ff7 +mtrand.so (0) <F09EE7AD-C5B9-3702-9FFB-A7768E164D18> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/random/mtrand.so
0x10df94000 - 0x10dfa4fff +_ctypes.so (0) <2B4B6460-0913-3E02-AB47-B705EDA9D98B> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so
0x10dfb5000 - 0x10dfb8ff7 +_struct.so (0) <82587028-EEA5-3914-A170-AE64F1DE5B17> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_struct.so
0x10dff8000 - 0x10dffbfff +binascii.so (0) <348F9879-1F59-35F6-9432-C30EB2FF50B9> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/binascii.so
0x10dfff000 - 0x10e00eff7 +libz.1.dylib (0) <EE52BDB8-6083-3F10-A193-2E52AAF555E7> /opt/local/lib/libz.1.dylib
0x10e012000 - 0x10e13cfe7 +_ufuncs.so (0) <83F9337A-6EF4-37ED-A051-9FBCE7932EA2> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/_ufuncs.so
0x10e19e000 - 0x10e260ff7 +libgfortran.3.dylib (0) <3DF49470-4342-38EA-BFAC-4ED0485E7941> /opt/local/lib/*/libgfortran.3.dylib
0x10e278000 - 0x10e287fff +libgcc_s.1.dylib (0) <CB5989C5-40C1-3981-AAD9-749821C91651> /opt/local/lib/*/libgcc_s.1.dylib
0x10e28c000 - 0x10e2b6fff +libquadmath.0.dylib (0) <56ABAFC4-2CC4-374E-9653-6953DBA9BD21> /opt/local/lib/*/libquadmath.0.dylib
0x10e2ba000 - 0x10e2c9fff +_ufuncs_cxx.so (0) <2EB8B813-CBDE-3E86-A1BA-E8AF4D4232BE> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/_ufuncs_cxx.so
0x10e314000 - 0x10e3d9fef +specfun.so (0) <148ECDDB-B9C5-3158-9124-897CCDA2CA32> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/specfun.so
0x10e3ea000 - 0x10e41bff7 +_fblas.so (0) <04383174-F37C-3475-A7A7-F932DEDBBB1C> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_fblas.so
0x10e43d000 - 0x10e448fff +_flinalg.so (0) <4FF07CFF-6172-377D-B66D-966E1BC72C08> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flinalg.so
0x10e450000 - 0x10e4affff +_flapack.so (0) <D6F77E6E-322E-3A73-BA6F-CAF0C621458D> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flapack.so
0x10e4f1000 - 0x10e4f8ff7 +calc_lwork.so (0) <DD2F7868-CC98-3FD8-A9AE-FE1AF72FA136> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/calc_lwork.so
0x10e53e000 - 0x10e541fff +futil.so (0) <00314ED1-DEBF-38BC-9FF2-4FA34433507F> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/futil.so
0x10e5c5000 - 0x10e5cbff7 +minpack2.so (0) <5FF1DAD0-FE20-35E4-9458-B74E837BABC0> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/minpack2.so
0x10e5d0000 - 0x10e5edfff +_lbfgsb.so (0) <DD0BCBCB-99B1-37CA-924D-2FB7BF34C703> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_lbfgsb.so
0x10e5f2000 - 0x10e5f8ff7 +moduleTNC.so (0) <4820B6DE-8E71-36DF-8E6D-EF2F391A8F76> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/moduleTNC.so
0x10e63b000 - 0x10e656fff +_cobyla.so (0) <01955553-92B8-3EE8-8067-4C637036DA17> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_cobyla.so
0x10e65b000 - 0x10e674fff +_slsqp.so (0) <F58A5C29-13CD-32C3-9B30-D5C3A42ABB5B> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_slsqp.so
0x10e679000 - 0x10e695fef +_minpack.so (0) <3B3E0207-B017-3AA0-A507-5CB830D59003> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_minpack.so
0x10e6d9000 - 0x10e830ff7 +_csr.so (0) <0ADDE689-D747-35EB-B360-50A6FAB7E3D4> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_csr.so
0x10e87f000 - 0x10e97cff7 +_csc.so (0) <C5841F58-99AB-3F9A-91EB-2BD465DBF007> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_csc.so
0x10e9b9000 - 0x10e9e5ff7 +_coo.so (0) <B9250078-BF24-3C94-A4BD-2667B03D3F52> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so
0x10e9ec000 - 0x10e9fafff +_dia.so (0) <EF67E52F-5E07-383D-9093-E0C72035AD49> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_dia.so
0x10ea00000 - 0x10ebb1fff +_bsr.so (0) <CFC722AA-BE10-33B2-9BF2-1A22364ED188> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_bsr.so
0x10ec37000 - 0x10ec3bfff +_csgraph.so (0) <78A2EAEE-4236-3DDF-ACE3-D25BB9944BEA> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_csgraph.so
0x10ec41000 - 0x10ec42ff7 +_bisect.so (0) <04B6B830-1DE2-3229-9744-99F1610129A4> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_bisect.so
0x10ec85000 - 0x10eca7ff7 +_shortest_path.so (0) <0CFE14D3-AACA-30A7-AF2E-56143ECBA4D9> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/csgraph/_shortest_path.so
0x10ecb8000 - 0x10eccbfff +_tools.so (0) <84414952-4E20-37C3-AE2D-4488B792216A> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/csgraph/_tools.so
0x10ecd9000 - 0x10ecebff7 +_traversal.so (0) <658429E6-2E50-371F-BEF3-6FFE9F734BA7> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/csgraph/_traversal.so
0x10ecf9000 - 0x10ed02ff7 +_min_spanning_tree.so (0) <9C5A57A3-DF1F-35BC-AE28-3805BE42C0B5> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/csgraph/_min_spanning_tree.so
0x10ed0b000 - 0x10ed3bff7 +_iterative.so (0) <331E4835-0901-3852-B1BF-44AF208AADAD> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/_iterative.so
0x10ed91000 - 0x10edd2ff7 +_superlu.so (0) <1E849C9F-F67C-3742-BCF4-21AB8B89E384> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/dsolve/_superlu.so
0x10edee000 - 0x10ee0aff7 +__umfpack.so (0) <EA624B2E-4E42-36E1-B9FF-DA1F64128E6D> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/dsolve/umfpack/__umfpack.so
0x10ee14000 - 0x10efeffff +libSuiteSparse.4.2.1.dylib (0) <731C7366-6C3F-35BB-BBF9-8B7FD33EC2A7> /opt/local/lib/libSuiteSparse.4.2.1.dylib
0x10f04a000 - 0x10f0ddfff +_arpack.so (0) <184584DC-D049-3854-B7FB-D1ECA346E826> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
0x10f0f6000 - 0x10f0f7ff7 +_zeros.so (0) <A7265B28-6C82-305A-BAA2-F663DA52E03C> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_zeros.so
0x10f0fb000 - 0x10f102ff7 +_nnls.so (0) <7C98C9F4-6D92-353E-89E0-633D3555BEA9> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_nnls.so
0x10f106000 - 0x10f14ffef +_odepack.so (0) <F1235CFB-7DAF-3F77-8B12-24C1CC146393> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/_odepack.so
0x10f154000 - 0x10f16cff7 +_quadpack.so (0) <37CB9FD2-69D6-3120-9904-1AC2C4F507D9> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/_quadpack.so
0x10f1b0000 - 0x10f1e8fff +vode.so (0) <3C056C6D-E352-3FCB-9457-46CFFBA6C5D2> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/vode.so
0x10f1ef000 - 0x10f213fff +_dop.so (0) <C1A26ACE-163C-3FE3-89B0-BF01E064E0FE> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/_dop.so
0x10f219000 - 0x10f265fe7 +lsoda.so (0) <6B3EE564-444F-35A4-BE7E-E0631E39D038> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/integrate/lsoda.so
0x10f26c000 - 0x10f277ff7 +vonmises_cython.so (0) <0081DB6A-1906-38D7-B4EF-F024327AD559> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/vonmises_cython.so
0x10f300000 - 0x10f30dfff +_rank.so (0) <E8E216E1-623D-3475-96D2-B28509DD5E8A> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/_rank.so
0x10f318000 - 0x10f324ff7 +statlib.so (0) <45906AE5-59FA-3C6F-A92B-F68D543FE19A> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/statlib.so
0x10f32a000 - 0x10f339fff +mvn.so (0) <CB610F96-678C-31E1-832B-48E917631A22> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/mvn.so
0x10f436000 - 0x11146dff7 +libgraph_tool_core.so (0) <E2893849-72D6-3884-8950-5548CFFA054A> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
0x113f6c000 - 0x113f78fff +libboost_iostreams.dylib (0) <50598239-332B-3A4C-BA01-94278B4CEFFA> /usr/local/lib/libboost_iostreams.dylib
0x113f97000 - 0x113fc7ff6 +libboost_python.dylib (0) <2C2D4A38-F1A0-34BE-ACC8-FA41441F0D74> /usr/local/lib/libboost_python.dylib
0x11400b000 - 0x11409ffff +libboost_regex.dylib (0) <B81820A7-4B73-36BE-A092-46C40F1772B4> /usr/local/lib/libboost_regex.dylib
0x114140000 - 0x11415bfff +libCGAL.10.dylib (0) <F3C41131-CFB3-3D6E-869A-1EB6AAABC7EE> /opt/local/lib/libCGAL.10.dylib
0x114178000 - 0x114191ff7 +libexpat.1.dylib (0) <FC0B6E54-ED80-3460-B2AC-C8B5041957F3> /opt/local/lib/libexpat.1.dylib
0x114198000 - 0x1141a6fff +libbz2.1.0.dylib (0) <57564CB0-AD8D-35AD-A8BE-EAF844A6005C> /opt/local/lib/libbz2.1.0.dylib
0x1141aa000 - 0x114294fff org.python.python (2.7.5 - 2.7.5) <0202C38E-0354-34FA-9996-8D2ADCE353D8> /System/Library/Frameworks/Python.framework/Versions/2.7/Python
0x1142fa000 - 0x11433ffff +libmpfr.4.dylib (0) <94D50580-60B2-3DB1-B273-1482CCE49204> /opt/local/lib/libmpfr.4.dylib
0x11434a000 - 0x1143a7fc7 +libgmp.10.dylib (0) <98B78A55-7635-3C8E-8584-468AFBD4967A> /opt/local/lib/libgmp.10.dylib
0x1143b5000 - 0x1143c2ffb +libboost_thread-mt.dylib (0) <57DDD8D7-9001-345B-91E4-E5ED3E7121EF> /opt/local/lib/libboost_thread-mt.dylib
0x1143e0000 - 0x1143e2ff3 +libboost_system-mt.dylib (0) <D119E92C-749B-311B-90AB-4A070B60CDBE> /opt/local/lib/libboost_system-mt.dylib
0x7fff64c66000 - 0x7fff64c99817 dyld (239.3) <D1DFCF3F-0B0C-332A-BCC0-87A851B570FF> /usr/lib/dyld
0x7fff88e24000 - 0x7fff88e72fff libcorecrypto.dylib (161.1) <F3973C28-14B6-3006-BB2B-00DD7F09ABC7> /usr/lib/system/libcorecrypto.dylib
0x7fff88f38000 - 0x7fff8911dff7 com.apple.CoreFoundation (6.9 - 855.11) <E22C6A1F-8996-349C-905E-96C3BBE07C2F> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff892ff000 - 0x7fff89328ff7 libc++abi.dylib (48) <8C16158F-CBF8-3BD7-BEF4-022704B2A326> /usr/lib/libc++abi.dylib
0x7fff8950b000 - 0x7fff89532ffb libsystem_info.dylib (449.1.3) <7D41A156-D285-3849-A2C3-C04ADE797D98> /usr/lib/system/libsystem_info.dylib
0x7fff89670000 - 0x7fff8968afff libdispatch.dylib (339.1.9) <46878A5B-4248-3057-962C-6D4A235EEF31> /usr/lib/system/libdispatch.dylib
0x7fff8982e000 - 0x7fff8999cff7 libBLAS.dylib (1094.5) <DE93A590-5FA5-32A2-A16C-5D7D7361769F> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x7fff8a027000 - 0x7fff8a04bfff libxpc.dylib (300.1.17) <4554927A-9467-365C-91F1-5A116989DD7F> /usr/lib/system/libxpc.dylib
0x7fff8a2ee000 - 0x7fff8a2efff7 libsystem_blocks.dylib (63) <FB856CD1-2AEA-3907-8E9B-1E54B6827F82> /usr/lib/system/libsystem_blocks.dylib
0x7fff8a386000 - 0x7fff8a38bff7 libunwind.dylib (35.3) <78DCC358-2FC1-302E-B395-0155B47CB547> /usr/lib/system/libunwind.dylib
0x7fff8b1bf000 - 0x7fff8b1c6ff7 liblaunch.dylib (842.1.4) <FCBF0A02-0B06-3F97-9248-5062A9DEB32C> /usr/lib/system/liblaunch.dylib
0x7fff8bd15000 - 0x7fff8bd15fff com.apple.Accelerate (1.9 - Accelerate 1.9) <509BB27A-AE62-366D-86D8-0B06D217CF56> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
0x7fff8bde7000 - 0x7fff8be29ff7 libauto.dylib (185.5) <F45C36E8-B606-3886-B5B1-B6745E757CA8> /usr/lib/libauto.dylib
0x7fff8bf77000 - 0x7fff8bf92ff7 libsystem_malloc.dylib (23.1.10) <FFE5C472-B23A-318A-85BF-77CDE61900D1> /usr/lib/system/libsystem_malloc.dylib
0x7fff8c15e000 - 0x7fff8c165ff7 libsystem_pthread.dylib (53.1.4) <AB498556-B555-310E-9041-F67EC9E00E2C> /usr/lib/system/libsystem_pthread.dylib
0x7fff8c32f000 - 0x7fff8c330ff7 libSystem.B.dylib (1197.1.1) <BFC0DC97-46C6-3BE0-9983-54A98734897A> /usr/lib/libSystem.B.dylib
0x7fff8c49d000 - 0x7fff8c526ff7 libsystem_c.dylib (997.1.1) <61833FAA-7281-3FF9-937F-686B6F20427C> /usr/lib/system/libsystem_c.dylib
0x7fff8f5d8000 - 0x7fff8f5ddfff libmacho.dylib (845) <1D2910DF-C036-3A82-A3FD-44FF73B5FF9B> /usr/lib/system/libmacho.dylib
0x7fff8f5de000 - 0x7fff8f5e6fff libsystem_dnssd.dylib (522.1.11) <270DCF6C-502D-389A-AA9F-DE4624A36FF7> /usr/lib/system/libsystem_dnssd.dylib
0x7fff8f5e7000 - 0x7fff8f603ff7 libsystem_kernel.dylib (2422.1.72) <D14913DB-47F1-3591-8DAF-D4B4EF5F8818> /usr/lib/system/libsystem_kernel.dylib
0x7fff8f613000 - 0x7fff8f615ff3 libsystem_configuration.dylib (596.12) <C4F633D9-94C8-35D9-BB2D-84C5122533C7> /usr/lib/system/libsystem_configuration.dylib
0x7fff8f693000 - 0x7fff8f697fff libsystem_stats.dylib (93.1.26) <B9E26A9E-FBBC-3938-B8B7-6CF7CA8C99AD> /usr/lib/system/libsystem_stats.dylib
0x7fff8f6c9000 - 0x7fff8f6cdff7 libcache.dylib (62) <BDC1E65B-72A1-3DA3-A57C-B23159CAAD0B> /usr/lib/system/libcache.dylib
0x7fff8f6ce000 - 0x7fff8f6ceff7 libkeymgr.dylib (28) <3AA8D85D-CF00-3BD3-A5A0-E28E1A32A6D8> /usr/lib/system/libkeymgr.dylib
0x7fff8f6d4000 - 0x7fff8f703fd2 libsystem_m.dylib (3047.16) <B7F0E2E4-2777-33FC-A787-D6430B630D54> /usr/lib/system/libsystem_m.dylib
0x7fff8fee0000 - 0x7fff8fef1ff7 libz.1.dylib (53) <42E0C8C6-CA38-3CA4-8619-D24ED5DD492E> /usr/lib/libz.1.dylib
0x7fff8ff30000 - 0x7fff8ff3dff0 libbz2.1.0.dylib (29) <0B98AC35-B138-349C-8063-2B987A75D24C> /usr/lib/libbz2.1.0.dylib
0x7fff9013a000 - 0x7fff9013cff7 libquarantine.dylib (71) <7A1A2BCB-C03D-3A25-BFA4-3E569B2D2C38> /usr/lib/system/libquarantine.dylib
0x7fff9013d000 - 0x7fff901edff7 libvMisc.dylib (423.32) <049C0735-1808-39B9-943F-76CB8021744F> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
0x7fff905d0000 - 0x7fff905d7fff libcompiler_rt.dylib (35) <4CD916B2-1B17-362A-B403-EF24A1DAC141> /usr/lib/system/libcompiler_rt.dylib
0x7fff905f5000 - 0x7fff906c0fff libvDSP.dylib (423.32) <3BF732BE-DDE0-38EB-8C54-E4E3C64F77A7> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
0x7fff9070d000 - 0x7fff9070eff7 libsystem_sandbox.dylib (278.10) <A47E7E11-3C76-318E-B67D-98972B86F094> /usr/lib/system/libsystem_sandbox.dylib
0x7fff9071f000 - 0x7fff90729fff libcommonCrypto.dylib (60049) <8C4F0CA0-389C-3EDC-B155-E62DD2187E1D> /usr/lib/system/libcommonCrypto.dylib
0x7fff90af4000 - 0x7fff90afbff3 libcopyfile.dylib (103) <5A881779-D0D6-3029-B371-E3021C2DDA5E> /usr/lib/system/libcopyfile.dylib
0x7fff90b41000 - 0x7fff90b47ff7 libsystem_platform.dylib (24.1.4) <331BA4A5-55CE-3B95-99EB-44E0C89D7FB8> /usr/lib/system/libsystem_platform.dylib
0x7fff9136e000 - 0x7fff913c0fff libc++.1.dylib (120) <4F68DFC5-2077-39A8-A449-CAC5FDEE7BDE> /usr/lib/libc++.1.dylib
0x7fff91691000 - 0x7fff91692fff libunc.dylib (28) <62682455-1862-36FE-8A04-7A6B91256438> /usr/lib/system/libunc.dylib
0x7fff9175c000 - 0x7fff91765ff3 libsystem_notify.dylib (121) <52571EC3-6894-37E4-946E-064B021ED44E> /usr/lib/system/libsystem_notify.dylib
0x7fff9235a000 - 0x7fff92381ff7 libsystem_network.dylib (241.3) <8B1E1F1D-A5CC-3BAE-8B1E-ABC84337A364> /usr/lib/system/libsystem_network.dylib
0x7fff92bf1000 - 0x7fff92bf2ffb libremovefile.dylib (33) <3543F917-928E-3DB2-A2F4-7AB73B4970EF> /usr/lib/system/libremovefile.dylib
0x7fff93118000 - 0x7fff934f9ffe libLAPACK.dylib (1094.5) <7E7A9B8D-1638-3914-BAE0-663B69865986> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x7fff935bb000 - 0x7fff93768f27 libobjc.A.dylib (551.1) <AD7FD984-271E-30F4-A361-6B20319EC73B> /usr/lib/libobjc.A.dylib
0x7fff93d74000 - 0x7fff94048fc7 com.apple.vImage (7.0 - 7.0) <D241DBFA-AC49-31E2-893D-EAAC31890C90> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x7fff94049000 - 0x7fff94201ff3 libicucore.A.dylib (511.25) <3ED7B656-416E-3071-AEC8-E85C90232F78> /usr/lib/libicucore.A.dylib
0x7fff94202000 - 0x7fff94213ff7 libsystem_asl.dylib (217.1.4) <655FB343-52CF-3E2F-B14D-BEBF5AAEF94D> /usr/lib/system/libsystem_asl.dylib
0x7fff95b97000 - 0x7fff95b98ff7 libDiagnosticMessagesClient.dylib (100) <4CDB0F7B-C0AF-3424-BC39-495696F0DB1E> /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff96712000 - 0x7fff96712fff com.apple.Accelerate.vecLib (3.9 - vecLib 3.9) <F8D0CC77-98AC-3B58-9FE6-0C25421827B6> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x7fff96730000 - 0x7fff96733ff7 libdyld.dylib (239.3) <62F4D752-4089-31A8-8B73-B95A68893B3C> /usr/lib/system/libdyld.dylib
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 11 years ago by ryandesign (Ryan Carsten 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 thread → python27: Fatal Python error: PyThreadState_Get: no current thread |
comment:2 Changed 11 years ago by mamoll (Mark Moll)
comment:3 Changed 11 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 *
comment:4 Changed 11 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 11 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 11 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 11 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)
comment:9 follow-up: 11 Changed 11 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 Changed 11 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.
comment:11 Changed 11 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 11 years ago by fredotan@…
Could it be Homebrew or Boost which I installed with Homebrew?
comment:13 Changed 11 years ago by mamoll (Mark Moll)
Possibly. Can you post the output of this command?:
env
comment:14 Changed 11 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
comment:15 Changed 11 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 11 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 11 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 follow-ups: 19 20 Changed 11 years ago by mamoll (Mark Moll)
| Resolution: | → invalid |
|---|---|
| Status: | new → closed |
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 Changed 11 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 Changed 11 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 10 years ago by ryandesign (Ryan Carsten 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.
Note: See
TracTickets for help on using
tickets.
Can you elaborate on this a bit more? Do you have a minimal code example that produces a crash?