#42454 closed defect (invalid)
Fatal error dolfin import
| Reported by: | mwathen@… | Owned by: | seanfarley (Sean Farley) |
|---|---|---|---|
| Priority: | Normal | Milestone: | |
| Component: | ports | Version: | 2.2.1 |
| Keywords: | Cc: | ||
| Port: |
Description (last modified by seanfarley (Sean Farley))
I managed to install dolfin using macport but when I try and run an example program using this package I get the following error Fatal Python error: PyThreadState_Get: no current thread
[1] 23196 abort python programs/demo_poisson.py
I have attached the python error I get as well.
Process: Python [23196]
Path: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.6 (2.7.6)
Code Type: X86-64 (Native)
Parent Process: zsh [23168]
Responsible: Terminal [22736]
User ID: 501
Date/Time: 2014-02-10 10:06:43.935 -0800
OS Version: Mac OS X 10.9.1 (13B3116)
Report Version: 11
Anonymous UUID: EFA00D8E-20FE-A2F9-8079-313E6DB02242
Sleep/Wake UUID: 9ABD15B3-FD31-46CD-81E5-6BC27015C37C
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 0x00007fff9896d866 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff8ee6e35c pthread_kill + 92
2 libsystem_c.dylib 0x00007fff8d54cbba abort + 125
3 org.python.python 0x0000000110ca9ec1 Py_FatalError + 49
4 org.python.python 0x0000000110ca9411 PyThreadState_Get + 28
5 org.python.python 0x0000000110ca6476 Py_InitModule4_64 + 58
6 _ffc_form_fca4b6ffb2fc6e2e2de21f0bd1c9de03ea2f593c.so 0x00000001077c5b40 init_ffc_form_fca4b6ffb2fc6e2e2de21f0bd1c9de03ea2f593c + 784
7 org.python.python 0x00000001075e9d86 _PyImport_LoadDynamicModule + 150
8 org.python.python 0x00000001075e849c imp_load_module + 284
9 org.python.python 0x00000001075ce010 PyEval_EvalFrameEx + 7712
10 org.python.python 0x00000001075d2ed2 fast_function + 194
11 org.python.python 0x00000001075cf28b PyEval_EvalFrameEx + 12443
12 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
13 org.python.python 0x00000001075cb9a6 PyEval_EvalCode + 54
14 org.python.python 0x00000001075e5f57 PyImport_ExecCodeModuleEx + 247
15 org.python.python 0x00000001075e8e77 load_source_module + 935
16 org.python.python 0x00000001075e9a87 import_submodule + 279
17 org.python.python 0x00000001075e951f load_next + 271
18 org.python.python 0x00000001075e74b1 PyImport_ImportModuleLevel + 1153
19 org.python.python 0x00000001075c7304 builtin___import__ + 132
20 org.python.python 0x000000010753b665 PyObject_Call + 101
21 org.python.python 0x00000001075cf763 PyEval_EvalFrameEx + 13683
22 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
23 org.python.python 0x00000001075cb9a6 PyEval_EvalCode + 54
24 org.python.python 0x00000001075e5f57 PyImport_ExecCodeModuleEx + 247
25 org.python.python 0x00000001075e8e77 load_source_module + 935
26 org.python.python 0x00000001075e916a load_package + 298
27 org.python.python 0x00000001075e9a87 import_submodule + 279
28 org.python.python 0x00000001075e951f load_next + 271
29 org.python.python 0x00000001075e74b1 PyImport_ImportModuleLevel + 1153
30 org.python.python 0x00000001075c7304 builtin___import__ + 132
31 org.python.python 0x00000001075ce010 PyEval_EvalFrameEx + 7712
32 org.python.python 0x00000001075d2ed2 fast_function + 194
33 org.python.python 0x00000001075cf28b PyEval_EvalFrameEx + 12443
34 org.python.python 0x00000001075d2ed2 fast_function + 194
35 org.python.python 0x00000001075cf28b PyEval_EvalFrameEx + 12443
36 org.python.python 0x00000001075d2ed2 fast_function + 194
37 org.python.python 0x00000001075cf28b PyEval_EvalFrameEx + 12443
38 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
39 org.python.python 0x00000001075d2f36 fast_function + 294
40 org.python.python 0x00000001075cf28b PyEval_EvalFrameEx + 12443
41 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
42 org.python.python 0x00000001075d2f36 fast_function + 294
43 org.python.python 0x00000001075cf28b PyEval_EvalFrameEx + 12443
44 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
45 org.python.python 0x00000001075d2f36 fast_function + 294
46 org.python.python 0x00000001075cf28b PyEval_EvalFrameEx + 12443
47 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
48 org.python.python 0x00000001075d2f36 fast_function + 294
49 org.python.python 0x00000001075cf28b PyEval_EvalFrameEx + 12443
50 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
51 org.python.python 0x000000010755f0c6 function_call + 342
52 org.python.python 0x000000010753b665 PyObject_Call + 101
53 org.python.python 0x00000001075d04e6 PyEval_EvalFrameEx + 17142
54 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
55 org.python.python 0x00000001075d2f36 fast_function + 294
56 org.python.python 0x00000001075cf28b PyEval_EvalFrameEx + 12443
57 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
58 org.python.python 0x000000010755f0c6 function_call + 342
59 org.python.python 0x000000010753b665 PyObject_Call + 101
60 org.python.python 0x00000001075477b6 instancemethod_call + 182
61 org.python.python 0x000000010753b665 PyObject_Call + 101
62 org.python.python 0x00000001075d00b4 PyEval_EvalFrameEx + 16068
63 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
64 org.python.python 0x000000010755f0c6 function_call + 342
65 org.python.python 0x000000010753b665 PyObject_Call + 101
66 org.python.python 0x00000001075477b6 instancemethod_call + 182
67 org.python.python 0x000000010753b665 PyObject_Call + 101
68 org.python.python 0x00000001075929fd slot_tp_init + 141
69 org.python.python 0x000000010758cfe2 type_call + 338
70 org.python.python 0x000000010753b665 PyObject_Call + 101
71 org.python.python 0x00000001075d00b4 PyEval_EvalFrameEx + 16068
72 org.python.python 0x00000001075cc076 PyEval_EvalCodeEx + 1734
73 org.python.python 0x00000001075cb9a6 PyEval_EvalCode + 54
74 org.python.python 0x00000001075f3611 PyRun_FileExFlags + 161
75 org.python.python 0x00000001075f315e PyRun_SimpleFileExFlags + 718
76 org.python.python 0x0000000107607002 Py_Main + 3314
77 libdyld.dylib 0x00007fff927395fd start + 1
Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff9896e662 kevent64 + 10
1 libdispatch.dylib 0x00007fff9634243d _dispatch_mgr_invoke + 239
2 libdispatch.dylib 0x00007fff96342152 _dispatch_mgr_thread + 52
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00007fff7c396310 rcx: 0x00007fff586d4508 rdx: 0x0000000000000000
rdi: 0x0000000000000d07 rsi: 0x0000000000000006 rbp: 0x00007fff586d4530 rsp: 0x00007fff586d4508
r8: 0x0000000000000040 r9: 0x00007fff586d4500 r10: 0x0000000008000000 r11: 0x0000000000000206
r12: 0x0000000000000000 r13: 0x00000001077c5830 r14: 0x0000000000000006 r15: 0x00000000000003f5
rip: 0x00007fff9896d866 rfl: 0x0000000000000206 cr2: 0x00007fff7c167760
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff9770a000 - 0x7fff9775bff3 com.apple.audio.CoreAudio (4.2.0 - 4.2.0) <EAC1821B-CD20-30E3-BF95-C1839CA97BF7> /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
0x7fff97a64000 - 0x7fff97b53fff libFontParser.dylib (111.1) <835A8253-6AB9-3AAB-9CBF-171440DEC486> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
0x7fff97ebc000 - 0x7fff97ec7fff libGL.dylib (9.3.1) <D643A325-3257-373A-A8C1-035E9F0484B0> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff97ec8000 - 0x7fff97f2cff3 com.apple.datadetectorscore (5.0 - 354.0) <25525311-E3A2-3D06-9010-DDB12A936E88> /System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsCore
0x7fff97ff5000 - 0x7fff9801aff7 com.apple.ChunkingLibrary (2.0 - 155.1) <B49408CD-ECE8-3785-84A4-45B03882574A> /System/Library/PrivateFrameworks/ChunkingLibrary.framework/Versions/A/ChunkingLibrary
0x7fff9802e000 - 0x7fff980f0ff1 com.apple.CoreText (352.0 - 367.15) <ACA9E85D-275D-3388-A2E3-1B15FD1A0A39> /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText
0x7fff980f5000 - 0x7fff980f7ff3 libsystem_configuration.dylib (596.12) <9883100A-4D35-3D84-99B7-1CE999AE110A> /usr/lib/system/libsystem_configuration.dylib
0x7fff980f8000 - 0x7fff98102ff7 com.apple.bsd.ServiceManagement (2.0 - 2.0) <9556885C-22DD-3392-ACCB-2B413434D8D3> /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement
0x7fff9892d000 - 0x7fff9892dfff com.apple.ApplicationServices (48 - 48) <F250170A-8805-3731-9097-78CAD04481F0> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x7fff98958000 - 0x7fff98974ff7 libsystem_kernel.dylib (2422.75.4) <F5C190DA-A845-3ADE-9B50-161A881BC136> /usr/lib/system/libsystem_kernel.dylib
0x7fff98ba5000 - 0x7fff98ba6ffb libremovefile.dylib (33) <26266E3F-FDDC-3CFC-B27F-78B49BDC9BDC> /usr/lib/system/libremovefile.dylib
0x7fff98bb5000 - 0x7fff98bc2ff7 libxar.1.dylib (202) <5572AA71-E98D-3FE1-9402-BB4A84E0E71E> /usr/lib/libxar.1.dylib
0x7fff98bc3000 - 0x7fff98fa4ffe libLAPACK.dylib (1094.5) <7E7A9B8D-1638-3914-BAE0-663B69865986> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x7fff9902a000 - 0x7fff9902afff com.apple.Carbon (154 - 157) <14069023-0BBB-3925-9BA9-EB2C9E9B8C75> /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
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: 25494
thread_create: 1
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=264.8M resident=162.5M(61%) swapped_out_or_unallocated=102.3M(39%)
Writable regions: Total=76.4M written=17.0M(22%) resident=31.3M(41%) swapped_out=0K(0%) unallocated=45.1M(59%)
REGION TYPE VIRTUAL
=========== =======
Dispatch continuations 8192K
Kernel Alloc Once 4K
MALLOC 53.1M
MALLOC (admin) 32K
STACK GUARD 56.0M
Stack 8264K
VM_ALLOCATE 28K
__DATA 28.6M
__IMAGE 528K
__LINKEDIT 103.3M
__TEXT 161.5M
__UNICODE 544K
shared memory 4K
=========== =======
TOTAL 419.6M
Model: MacBookPro11,1, BootROM MBP111.0138.B03, 2 processors, Intel Core i5, 2.6 GHz, 16 GB, SMC 2.16f58
Graphics: Intel Iris, Intel Iris, Built-In, 1024 MB
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x112), Broadcom BCM43xx 1.0 (6.30.223.154.49)
Bluetooth: Version 4.2.1f2 12982, 3 services, 23 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
Serial ATA Device: APPLE SSD SD0256F, 251 GB
USB Device: Internal Memory Card Reader
USB Device: Apple Internal Keyboard / Trackpad
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 17.2
Change History (37)
comment:1 Changed 11 years ago by seanfarley (Sean Farley)
| Owner: | changed from macports-tickets@… to sean@… |
|---|---|
| Status: | new → assigned |
comment:2 Changed 11 years ago by seanfarley (Sean Farley)
comment:3 follow-up: 4 Changed 11 years ago by mwathen@…
I saw the previous post and I removed all paths that point to the systems python and reinstalled dolfin but still get the same error message.
comment:4 Changed 11 years ago by seanfarley (Sean Farley)
Replying to mwathen@…:
I saw the previous post and I removed all paths that point to the systems python and reinstalled dolfin but still get the same error message.
Can you post the output of:
$ port contents ufc | grep so$ | xargs otool -L
comment:5 Changed 11 years ago by seanfarley (Sean Farley)
| Description: | modified (diff) |
|---|
comment:6 follow-up: 7 Changed 11 years ago by mwathen@…
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ufc/_ufc.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
comment:7 follow-up: 8 Changed 11 years ago by seanfarley (Sean Farley)
Replying to mwathen@…:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ufc/_ufc.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
Damn, well, what about the output of:
$ port contents dolfin | grep so$ | xargs otool -L | grep Python
comment:8 follow-up: 9 Changed 11 years ago by mwathen@…
Replying to sean@…:
Replying to mwathen@…:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ufc/_ufc.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
Damn, well, what about the output of:
$ port contents dolfin | grep so$ | xargs otool -L | grep Python
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_common.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_fem.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_function.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_io.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_la.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_mesh.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
comment:9 follow-up: 10 Changed 11 years ago by seanfarley (Sean Farley)
Replying to mwathen@…:
Replying to sean@…:
Replying to mwathen@…:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ufc/_ufc.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
Damn, well, what about the output of:
$ port contents dolfin | grep so$ | xargs otool -L | grep Python/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_common.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_fem.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_function.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_io.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_la.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_mesh.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
Ok, we might as well just check every port that dolfin is using:
$ port echo rdepof:dolfin | xargs port contents | grep -E 'so$|dylib$' | xargs otool -L | grep Python
comment:10 Changed 11 years ago by mwathen@…
Replying to sean@…:
Replying to mwathen@…:
Replying to sean@…:
Replying to mwathen@…:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ufc/_ufc.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
Damn, well, what about the output of:
$ port contents dolfin | grep so$ | xargs otool -L | grep Python/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_common.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_fem.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_function.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_io.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_la.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_mesh.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
Ok, we might as well just check every port that dolfin is using:
$ port echo rdepof:dolfin | xargs port contents | grep -E 'so$|dylib$' | xargs otool -L | grep Python
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/boost/mpi.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/boost/mpi.so (compatibility version 0.0.0, current version 0.0.0) /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0) /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0) /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/time_elements_ext.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/_dummy.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray_tests.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/operand_flag_tests.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/struct_ufunc_test.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/test_rational.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/umath.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/umath_tests.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/_umath_linalg.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/numarray/_capi.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/random/mtrand.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Scientific/darwin/Scientific_affinitypropagation.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Scientific/darwin/Scientific_interpolation.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Scientific/darwin/Scientific_netcdf.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Scientific/darwin/Scientific_numerics_package_id.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Scientific/darwin/Scientific_vector.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/ColorPicker.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/MacOS.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/Nav.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/OSATerminology.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_AE.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_AH.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_App.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_CF.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_CG.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_CarbonEvt.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Cm.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Ctl.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Dlg.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Drag.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Evt.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_File.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Fm.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Folder.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Help.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_IBCarbon.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Icn.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Launch.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_List.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Menu.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Mlte.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_OSA.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Qd.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Qdoffs.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Qt.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Res.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Scrap.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Snd.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_TE.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_Win.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_bisect.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_bsddb.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_codecs_cn.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_codecs_hk.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_codecs_iso2022.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_codecs_jp.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_codecs_kr.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_codecs_tw.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_collections.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_csv.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes_test.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_curses.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_curses_panel.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_elementtree.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_functools.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_hashlib.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_heapq.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_hotshot.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_json.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_locale.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_lsprof.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_multibytecodec.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_multiprocessing.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_random.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_scproxy.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_socket.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_sqlite3.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ssl.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_struct.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_testcapi.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/array.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/audioop.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/autoGIL.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/binascii.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/bz2.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/cPickle.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/cStringIO.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/cmath.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/crypt.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/datetime.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/dbm.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/fcntl.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/future_builtins.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/gestalt.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/grp.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/icglue.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/itertools.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/math.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/mmap.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/nis.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/operator.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/parser.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/pyexpat.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/readline.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/resource.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/select.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/strop.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/syslog.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/termios.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/time.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/unicodedata.so: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/zlib.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ufc/_ufc.so:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
comment:11 follow-up: 12 Changed 11 years ago by seanfarley (Sean Farley)
This is turning out to be difficult to pin down :-( Let's check all your shared libraries in MacPorts:
$ otool -L /opt/local/lib/*.dylib | grep -i pyt
and in python 2.7
$ otool -L /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/* | grep -i pyt $ find /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -name \*.so -or -name \*.dylib | xargs otool -L | grep -i system/
I'm hoping something there will tell us that a package is linking to the system python.
comment:12 follow-up: 13 Changed 11 years ago by mwathen@…
Replying to sean@…:
This is turning out to be difficult to pin down :-( Let's check all your shared libraries in MacPorts:
$ otool -L /opt/local/lib/*.dylib | grep -i pytand in python 2.7
$ otool -L /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/* | grep -i pyt $ find /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -name \*.so -or -name \*.dylib | xargs otool -L | grep -i system/I'm hoping something there will tell us that a package is linking to the system python.
$ otool -L /opt/local/lib/*.dylib | grep -i pyt
gives:
/opt/local/lib/libboost_mpi_python-mt.dylib:
/opt/local/lib/libboost_mpi_python-mt.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/local/lib/libboost_python-mt.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/lib/libboost_python-mt.dylib:
/opt/local/lib/libboost_python-mt.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/opt/local/lib/libpython2.7.dylib:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
$ otool -L /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/* | grep -i pyt $ find /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -name \*.so -or -name \*.dylib | xargs otool -L | grep -i system/
gives:
otool: can't map file: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/pkgconfig (Invalid argument) otool: can't map file: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 (Invalid argument) /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
and
otool: one of -fahlLtdoOrTMRIHGScis must be specified Usage: otool [-arch arch_type] [-fahlLDtdorSTMRIHGvVcXmqQ] [-mcpu=arg] <object file> ...
-f print the fat headers -a print the archive header -h print the mach header -l print the load commands -L print shared libraries used -D print shared library id name -t print the text section (disassemble with -v) -p <routine name> start dissassemble from routine name -s <segname> <sectname> print contents of section -d print the data section -o print the Objective-C segment -r print the relocation entries -S print the table of contents of a library -T print the table of contents of a dynamic shared library -M print the module table of a dynamic shared library -R print the reference table of a dynamic shared library -I print the indirect symbol table -H print the two-level hints table -G print the data in code table -v print verbosely (symbolically) when possible -V print disassembled operands symbolically -c print argument strings of a core file -X print no leading addresses or headers -m don't use archive(member) syntax -B force Thumb disassembly (ARM objects only) -q use llvm's disassembler (the default) -Q use otool(1)'s disassembler -mcpu=arg use `arg' as the cpu for disassembly
comment:13 follow-up: 14 Changed 11 years ago by seanfarley (Sean Farley)
Replying to mwathen@…:
otool: one of -fahlLtdoOrTMRIHGScis must be specified Usage: otool [-arch arch_type] [-fahlLDtdorSTMRIHGvVcXmqQ] [-mcpu=arg] <object file> ...
-f print the fat headers -a print the archive header -h print the mach header -l print the load commands -L print shared libraries used -D print shared library id name -t print the text section (disassemble with -v) -p <routine name> start dissassemble from routine name -s <segname> <sectname> print contents of section -d print the data section -o print the Objective-C segment -r print the relocation entries -S print the table of contents of a library -T print the table of contents of a dynamic shared library -M print the module table of a dynamic shared library -R print the reference table of a dynamic shared library -I print the indirect symbol table -H print the two-level hints table -G print the data in code table -v print verbosely (symbolically) when possible -V print disassembled operands symbolically -c print argument strings of a core file -X print no leading addresses or headers -m don't use archive(member) syntax -B force Thumb disassembly (ARM objects only) -q use llvm's disassembler (the default) -Q use otool(1)'s disassembler -mcpu=arg use `arg' as the cpu for disassembly
Did you paste the command correctly? It should be (without the dollar sign):
$ find /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -name \*.so -or -name \*.dylib | xargs otool -L | grep -i system/
comment:14 Changed 11 years ago by mwathen@…
Replying to sean@…:
Replying to mwathen@…:
otool: one of -fahlLtdoOrTMRIHGScis must be specified Usage: otool [-arch arch_type] [-fahlLDtdorSTMRIHGvVcXmqQ] [-mcpu=arg] <object file> ...
-f print the fat headers -a print the archive header -h print the mach header -l print the load commands -L print shared libraries used -D print shared library id name -t print the text section (disassemble with -v) -p <routine name> start dissassemble from routine name -s <segname> <sectname> print contents of section -d print the data section -o print the Objective-C segment -r print the relocation entries -S print the table of contents of a library -T print the table of contents of a dynamic shared library -M print the module table of a dynamic shared library -R print the reference table of a dynamic shared library -I print the indirect symbol table -H print the two-level hints table -G print the data in code table -v print verbosely (symbolically) when possible -V print disassembled operands symbolically -c print argument strings of a core file -X print no leading addresses or headers -m don't use archive(member) syntax -B force Thumb disassembly (ARM objects only) -q use llvm's disassembler (the default) -Q use otool(1)'s disassembler -mcpu=arg use `arg' as the cpu for disassembly
Did you paste the command correctly? It should be (without the dollar sign):
$ find /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib -name \*.so -or -name \*.dylib | xargs otool -L | grep -i system/
Opps, missed out a bit at the end
/System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0)
/System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.11.0) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 48.0.0) /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics (compatibility version 64.0.0, current version 600.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 48.0.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.11.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0) /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration (compatibility version 1.0.0, current version 596.12.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.11.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.11.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 48.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 48.0.0) /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics (compatibility version 64.0.0, current version 600.0.0) /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 157.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0) /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)
comment:15 follow-up: 16 Changed 11 years ago by seanfarley (Sean Farley)
It looks like everything is linking together properly. Let's try something else. Do you get the same error when you run:
$ python2.7 /opt/local/share/dolfin/demo/documented/poisson/python/demo_poisson.py
While we're at it, what is the output of:
$ port select --list python
comment:16 Changed 11 years ago by mwathen@…
Replying to sean@…:
It looks like everything is linking together properly. Let's try something else. Do you get the same error when you run:
$ python2.7 /opt/local/share/dolfin/demo/documented/poisson/python/demo_poisson.pyWhile we're at it, what is the output of:
$ port select --list python
I get the same error when trying to run
$ python2.7 /opt/local/share/dolfin/demo/documented/poisson/python/demo_poisson.py
Here is the python list that I get from port
Available versions for python: none python25-apple python26-apple python27 (active) python27-apple
comment:17 follow-up: 18 Changed 11 years ago by seanfarley (Sean Farley)
Ok, I see an error in one of the files in dolfin but let's see what you have for:
$ port contents dolfin | xargs -I{} grep '#!' /dev/null {} 2>/dev/null | grep -i python
Also, did you happen to set your python after installing dolfin?
comment:18 Changed 11 years ago by mwathen@…
Replying to sean@…:
Ok, I see an error in one of the files in dolfin but let's see what you have for:
$ port contents dolfin | xargs -I{} grep '#!' /dev/null {} 2>/dev/null | grep -i pythonAlso, did you happen to set your python after installing dolfin?
So I installed python using port then selected that version then installed dolfin.
$ port contents dolfin | xargs -I{} grep '#!' /dev/null {} 2>/dev/null | grep -i python
Binary file /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_fem.so matches Binary file /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_function.so matches Binary file /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_la.so matches Binary file /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/cpp/_mesh.so matches /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.py:#!/usr/bin/python /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/pjobs/pjobs.py:#!/opt/local/bin/python2.7 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/pjobs/sge.py:#!/opt/local/bin/python2.7 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/pjobs/sge.py:template = """#!/bin/sh /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/pjobs/slurm.py:#!/opt/local/bin/python2.7 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/pjobs/slurm.py:template = """#!/bin/bash /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/pjobs/torque.py:#!/opt/local/bin/python2.7 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/pjobs/torque.py:template = """#!/bin/bash /opt/local/bin/dolfin-convert:#!/opt/local/bin/python2.7 /opt/local/bin/dolfin-order:#!/opt/local/bin/python2.7 /opt/local/bin/dolfin-plot:#!/opt/local/bin/python2.7
comment:19 follow-up: 20 Changed 11 years ago by seanfarley (Sean Farley)
You could try changing the header of /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.py to see if that helps (might have to delete the ~/.instant cache). Let me know if that works.
comment:20 follow-up: 21 Changed 11 years ago by mwathen@…
Replying to sean@…:
You could try changing the header of
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.pyto see if that helps (might have to delete the ~/.instant cache). Let me know if that works.
What do you mean by changing /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.py?
comment:21 follow-up: 22 Changed 11 years ago by seanfarley (Sean Farley)
Replying to mwathen@…:
Replying to sean@…:
You could try changing the header of
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.pyto see if that helps (might have to delete the ~/.instant cache). Let me know if that works.What do you mean by changing
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.py?
I mean change #!/usr/bin/python to #!/opt/local/bin/python2.7
comment:22 follow-up: 23 Changed 11 years ago by mwathen@…
Replying to sean@…:
Replying to mwathen@…:
Replying to sean@…:
You could try changing the header of
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.pyto see if that helps (might have to delete the ~/.instant cache). Let me know if that works.What do you mean by changing
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.py?I mean change
#!/usr/bin/pythonto#!/opt/local/bin/python2.7
I changed the header and deleted ~/.instant/cache but I still get the same errors. It seems to fail when Calling FFC just-in-time (JIT) compiler, this may take some time.
comment:23 follow-up: 24 Changed 11 years ago by seanfarley (Sean Farley)
Replying to mwathen@…:
Replying to sean@…:
Replying to mwathen@…:
Replying to sean@…:
You could try changing the header of
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.pyto see if that helps (might have to delete the ~/.instant cache). Let me know if that works.What do you mean by changing
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.py?I mean change
#!/usr/bin/pythonto#!/opt/local/bin/python2.7I changed the header and deleted ~/.instant/cache but I still get the same errors. It seems to fail when
Calling FFC just-in-time (JIT) compiler, this may take some time.
You might have to delete all of ~/.instant actually. What is the error? Are you calling the python program in a directory you have permission to write to?
comment:24 Changed 11 years ago by mwathen@…
Replying to sean@…:
Replying to mwathen@…:
Replying to sean@…:
Replying to mwathen@…:
Replying to sean@…:
You could try changing the header of
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.pyto see if that helps (might have to delete the ~/.instant cache). Let me know if that works.What do you mean by changing
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin_utils/cppparser/CppHeaderParser.py?I mean change
#!/usr/bin/pythonto#!/opt/local/bin/python2.7I changed the header and deleted ~/.instant/cache but I still get the same errors. It seems to fail when
Calling FFC just-in-time (JIT) compiler, this may take some time.You might have to delete all of
~/.instantactually. What is the error? Are you calling the python program in a directory you have permission to write to?
I just deleted ~/.instant and I still get the same error. I can write to the director so thats fine.
comment:25 follow-up: 26 Changed 11 years ago by seanfarley (Sean Farley)
Ok, let's see what is getting linked in ~/.instant
$ find ~/.instant -name '*.so' -or -name '*.dylib' | xargs otool -L | grep -i python
comment:26 follow-up: 27 Changed 11 years ago by mwathen@…
Replying to sean@…:
Ok, let's see what is getting linked in
~/.instant$ find ~/.instant -name '*.so' -or -name '*.dylib' | xargs otool -L | grep -i python
I get:
/System/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.5)
comment:27 follow-up: 28 Changed 11 years ago by seanfarley (Sean Farley)
Replying to mwathen@…:
Replying to sean@…:
Ok, let's see what is getting linked in
~/.instant$ find ~/.instant -name '*.so' -or -name '*.dylib' | xargs otool -L | grep -i pythonI get:
/System/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.5)
Ah, finally! For my system, I get /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Python so now we just need to figure out where it's grabbing the system python. Let's see if FFC or Instant are at fault:
$ port contents py27-{ffc,instant} | xargs -I{} grep '#!' /dev/null {} 2>/dev/null | grep -i python
comment:28 Changed 11 years ago by mwathen@…
Replying to sean@…:
Replying to mwathen@…:
Replying to sean@…:
Ok, let's see what is getting linked in
~/.instant$ find ~/.instant -name '*.so' -or -name '*.dylib' | xargs otool -L | grep -i pythonI get:
/System/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.5)
Ah, finally! For my system, I get
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Pythonso now we just need to figure out where it's grabbing the system python. Let's see if FFC or Instant are at fault:$ port contents py27-{ffc,instant} | xargs -I{} grep '#!' /dev/null {} 2>/dev/null | grep -i python
I get
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/ffc:#!/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python /opt/local/bin/ffc:#!/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/instant-clean:#!/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/instant-showcache:#!/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Pytho.app/Contents/MacOS/Python /opt/local/bin/instant-clean:#!/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python /opt/local/bin/instant-showcache:#!/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Thanks for all the help by the way!!
comment:29 follow-up: 30 Changed 11 years ago by seanfarley (Sean Farley)
Those look ok, hmm… let's try all of them:
$ port contents ufc py27-{ufl,fiat,ffc,instant} | xargs -I{} grep '#!' /dev/null {} 2>/dev/null | grep -i usr
For any files that have /usr/bin/env try changing them to the full path to python as we did before.
comment:30 Changed 11 years ago by mwathen@…
Replying to sean@…:
Those look ok, hmm… let's try all of them:
$ port contents ufc py27-{ufl,fiat,ffc,instant} | xargs -I{} grep '#!' /dev/null {} 2>/dev/null | grep -i usrFor any files that have
/usr/bin/envtry changing them to the full path to python as we did before.
I changed all the /usr/bin/env to /opt/local/bin/python2.7 so when I run
$ port contents ufc py27-{ufl,fiat,ffc,instant} | xargs -I{} grep '#!' /dev/null {} 2>/dev/null | grep -i usr
I get no output but I still get a fatal error.
comment:31 follow-up: 32 Changed 11 years ago by seanfarley (Sean Farley)
Did you remove ~/.instant before trying again? Also, a few questions I should have started with, what's the output of:
$ which python $ ls /usr/local
comment:32 follow-up: 33 Changed 11 years ago by mwathen@…
Replying to sean@…:
Did you remove ~/.instant before trying again? Also, a few questions I should have started with, what's the output of:
$ which python $ ls /usr/local
I did remove ~/.instant before trying again but it still failed....
I get
/opt/local/bin/python
and
Library bin etc gfortran include lib opt share texlive
comment:33 follow-up: 34 Changed 11 years ago by seanfarley (Sean Farley)
Replying to mwathen@…:
Replying to sean@…:
Did you remove ~/.instant before trying again? Also, a few questions I should have started with, what's the output of:
$ which python $ ls /usr/localI did remove ~/.instant before trying again but it still failed....
I get
/opt/local/bin/pythonand
Library bin etc gfortran include lib opt share texlive
Can you temporarily move /usr/local to something like ~/Desktop/backup-local? Then remove ~/.instant, run hash -rf, and then try again? As a reminder, putting things in /usr/local causes headaches and is against the MacPorts guidelines.
comment:34 follow-up: 35 Changed 11 years ago by mwathen@…
Replying to sean@…:
Replying to mwathen@…:
Replying to sean@…:
Did you remove ~/.instant before trying again? Also, a few questions I should have started with, what's the output of:
$ which python $ ls /usr/localI did remove ~/.instant before trying again but it still failed....
I get
/opt/local/bin/pythonand
Library bin etc gfortran include lib opt share texliveCan you temporarily move
/usr/localto something like~/Desktop/backup-local? Then remove~/.instant, runhash -rf, and then try again? As a reminder, putting things in/usr/localcauses headaches and is against the MacPorts guidelines.
That made it run fine. How do I make sure MacPorts does not install stuff to /usr/local?
comment:35 Changed 11 years ago by seanfarley (Sean Farley)
| Resolution: | → invalid |
|---|---|
| Status: | assigned → closed |
Replying to mwathen@…:
Replying to sean@…:
Replying to mwathen@…:
Replying to sean@…:
Did you remove ~/.instant before trying again? Also, a few questions I should have started with, what's the output of:
$ which python $ ls /usr/localI did remove ~/.instant before trying again but it still failed....
I get
/opt/local/bin/pythonand
Library bin etc gfortran include lib opt share texliveCan you temporarily move
/usr/localto something like~/Desktop/backup-local? Then remove~/.instant, runhash -rf, and then try again? As a reminder, putting things in/usr/localcauses headaches and is against the MacPorts guidelines.That made it run fine. How do I make sure MacPorts does not install stuff to
/usr/local?
Aw yeah! MacPorts never installs anything into /usr/local. HomeBrew does install stuff there. Also, if you've installed TeXLive or HPC gfortran from a .pkg file (not MacPorts) then that would also put stuff there. I would recommend installing the equivalent software you had in /usr/local with MacPorts. For example, to install gfortran, you'll need
$ sudo port install gcc48
And for texlive, I usually install most everything,
$ sudo port install texlive-bibtex-extra texlive-math-extra texlive-formats-extra texlive-latex-extra texlive-plain-extra texlive-bin-extra
comment:36 follow-up: 37 Changed 11 years ago by mwathen@…
Thanks for all your help! It is now working on my mac. I just had one more question, is it possible to enable dolfin with petsc4py using macports? I installed petsc4py from source.
comment:37 Changed 11 years ago by seanfarley (Sean Farley)
Replying to mwathen@…:
Thanks for all your help! It is now working on my mac. I just had one more question, is it possible to enable dolfin with petsc4py using macports? I installed petsc4py from source.
Why are you installing this from source? You're just going to make more headaches for yourself in the future. If you want to install petsc4py, just run:
$ sudo port install py27-petsc4py
As for getting dolfin to use this, I tried but there was an error in the build last time I tried (about a month ago). I could try again but it will probably have to wait until a new release of FEniCS. If you can get it to work you can email the macports mailing list and cc me letting me know.
So, this error usually happens when there is a package that accidentally links to the system python. Looking at the stack trace it seems like that is the case:
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 0x7fff6398b000 - 0x7fff639be817 dyld (239.3) <D1DFCF3F-0B0C-332A-BCC0-87A851B570FF> /usr/lib/dyld 0x7fff8b67d000 - 0x7fff8b6acfd2 libsystem_m.dylib (3047.16) <9D96AACD-5870-3A5C-B849-7F9C0F6EBB09> /usr/lib/system/libsystem_m.dylib 0x7fff8b6ad000 - 0x7fff8b6fffff libc++.1.dylib (120) <2CB96D10-1E3E-39B1-B90D-C56C3818321E> /usr/lib/libc++.1.dylib 0x7fff8b700000 - 0x7fff8b703ffc com.apple.IOSurface (91 - 91) <812F4D48-6FD4-3DCB-8691-B077EBF981D7>I fixed a similar error in r116593 for ticket #42306 so, first, could you update your macports tree and perhaps uninstall and reinstall dolfin?