I'm running i NEURON in Python 2.6.6 on OSX 10.6.5, importing neuron.h in a Python class object, 'cell', where cell.h = neuron.h, together with some custom hoc-codes and some mechanisms loaded by the cell-class (A bit too much to show here, unfortunately). I want to run some simulation for some time, and save the state to use it as initial condition in succeeding simulations. To my understanding, the following python-code should not end up with a segmentation fault, as it does now, after running the NEURON simulation;
Code: Select all
In [3]: run my_sim.py #ultimately creating the cell object
....
In [4]: svstate = cell.h.SaveState()
In [5]: svstate.save()
Segmentation fault
Chrash report (if it makes any sense):
Code: Select all
Process: Python [17425]
Path: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python
Identifier: org.python.python
Version: 2.6.6 (2.6.6)
Code Type: X86-64 (Native)
Parent Process: bash [2422]
Date/Time: 2010-12-10 13:00:52.763 +0100
OS Version: Mac OS X 10.6.5 (10H574)
Report Version: 6
Interval Since Last Report: 81828 sec
Crashes Since Last Report: 11
Per-App Interval Since Last Report: 283547 sec
Per-App Crashes Since Last Report: 13
Anonymous UUID: A3F8257C-4692-4B4D-8FDF-310344C7B972
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000379
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 libnrniv.0.dylib 0x0000000103ae1a86 SaveState::SaveState() + 214
1 libnrniv.0.dylib 0x0000000103af18d8 TQueue::forall_callback(void (*)(TQItem const*, int)) + 88
2 libnrniv.0.dylib 0x0000000103ae3348 SaveState::savenet() + 328
3 libnrniv.0.dylib 0x0000000103ae097a SaveState::tqsave(TQItem const*, int) + 106
4 libnrnoc.0.dylib 0x0000000103a5bd1d call_ob_proc + 733
5 libnrnoc.0.dylib 0x0000000103a5c253 hoc_object_component + 1139
6 libnrnpython.0.dylib 0x0000000103a1b6a7 nrnpy_hoc_pop + 775
7 libnrniv.0.dylib 0x0000000103ae5eec OcJumpImpl::fpycall(void* (*)(void*, void*), void*, void*) + 556
8 libnrnpython.0.dylib 0x0000000103a1ba6b nrnpy_hoc_pop + 1739
9 org.python.python 0x000000010000b902 PyObject_Call + 98
10 org.python.python 0x00000001000b4fee PyEval_EvalFrameEx + 12990
11 org.python.python 0x00000001000b9af5 PyEval_EvalCodeEx + 2197
12 org.python.python 0x00000001000b8229 PyEval_EvalFrameEx + 25849
13 org.python.python 0x00000001000b9af5 PyEval_EvalCodeEx + 2197
14 org.python.python 0x00000001000b7a8d PyEval_EvalFrameEx + 23901
15 org.python.python 0x00000001000b9af5 PyEval_EvalCodeEx + 2197
16 org.python.python 0x00000001000b7a8d PyEval_EvalFrameEx + 23901
17 org.python.python 0x00000001000b7eea PyEval_EvalFrameEx + 25018
18 org.python.python 0x00000001000b9af5 PyEval_EvalCodeEx + 2197
19 org.python.python 0x00000001000b7a8d PyEval_EvalFrameEx + 23901
20 org.python.python 0x00000001000b9af5 PyEval_EvalCodeEx + 2197
21 org.python.python 0x00000001000b7a8d PyEval_EvalFrameEx + 23901
22 org.python.python 0x00000001000b9af5 PyEval_EvalCodeEx + 2197
23 org.python.python 0x00000001000b7a8d PyEval_EvalFrameEx + 23901
24 org.python.python 0x00000001000b9af5 PyEval_EvalCodeEx + 2197
25 org.python.python 0x00000001000b9c16 PyEval_EvalCode + 54
26 org.python.python 0x00000001000dea6e PyRun_FileExFlags + 174
27 org.python.python 0x00000001000ded29 PyRun_SimpleFileExFlags + 489
28 org.python.python 0x00000001000ee40c Py_Main + 2764
29 org.python.python 0x0000000100000f14 0x100000000 + 3860
Thread 1:
0 libSystem.B.dylib 0x00007fff8235efca __semwait_signal + 10
1 libSystem.B.dylib 0x00007fff82362de1 _pthread_cond_wait + 1286
2 interpreter.so 0x0000000105f552ea th_worker + 122
3 libSystem.B.dylib 0x00007fff8235d536 _pthread_start + 331
4 libSystem.B.dylib 0x00007fff8235d3e9 thread_start + 13
Thread 2:
0 libSystem.B.dylib 0x00007fff8235efca __semwait_signal + 10
1 libSystem.B.dylib 0x00007fff82362de1 _pthread_cond_wait + 1286
2 interpreter.so 0x0000000105f552ea th_worker + 122
3 libSystem.B.dylib 0x00007fff8235d536 _pthread_start + 331
4 libSystem.B.dylib 0x00007fff8235d3e9 thread_start + 13
Thread 3: Dispatch queue: com.apple.libdispatch-manager
0 libSystem.B.dylib 0x00007fff8233d16a kevent + 10
1 libSystem.B.dylib 0x00007fff8233f03d _dispatch_mgr_invoke + 154
2 libSystem.B.dylib 0x00007fff8233ed14 _dispatch_queue_invoke + 185
3 libSystem.B.dylib 0x00007fff8233e83e _dispatch_worker_thread2 + 252
4 libSystem.B.dylib 0x00007fff8233e168 _pthread_wqthread + 353
5 libSystem.B.dylib 0x00007fff8233e005 start_wqthread + 13
Thread 4: com.apple.CFSocket.private
0 libSystem.B.dylib 0x00007fff82367e92 select$DARWIN_EXTSN + 10
1 com.apple.CoreFoundation 0x00007fff81689498 __CFSocketManager + 824
2 libSystem.B.dylib 0x00007fff8235d536 _pthread_start + 331
3 libSystem.B.dylib 0x00007fff8235d3e9 thread_start + 13
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000321 rbx: 0x000000012e3f7b60 rcx: 0x000000000000012c rdx: 0x000000012e3fc000
rdi: 0x000000012b6859d0 rsi: 0x0000000104a7f688 rbp: 0x00007fff5fbfcac0 rsp: 0x00007fff5fbfcab0
r8: 0x0000000000080000 r9: 0x0000000010dba5d3 r10: 0x0000000000000001 r11: 0x0000000000000001
r12: 0x0000000129705650 r13: 0x0000000106638ff0 r14: 0x0000000103a81778 r15: 0x0000000000000000
rip: 0x0000000103ae1a86 rfl: 0x0000000000010206 cr2: 0x0000000000000379
Binary Images:
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0x7fff88251000 - 0x7fff88c47fff com.apple.AppKit 6.6.7 (1038.35) <9F4DF818-9DB9-98DA-490C-EF29EA757A97> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
0x7fff88c5f000 - 0x7fff88e1dfff libicucore.A.dylib 40.0.0 (compatibility 1.0.0) <781E7B63-2AD0-E9BA-927C-4521DB616D02> /usr/lib/libicucore.A.dylib
0x7fff88e66000 - 0x7fff890ecfef com.apple.security 6.1.1 (37594) <17CF7858-52D9-9665-3AE8-23F07CC8BEA1> /System/Library/Frameworks/Security.framework/Versions/A/Security
0x7fff890ed000 - 0x7fff8916bfff com.apple.CoreText 3.5.0 (???) <4D5C7932-293B-17FF-7309-B580BB1953EA> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/Versions/A/CoreText
0x7fffffe00000 - 0x7fffffe01fff libSystem.B.dylib ??? (???) <71E6D4C9-F945-6EC2-998C-D61AD590DAB6> /usr/lib/libSystem.B.dylib
Model: MacBookPro5,3, BootROM MBP53.00AC.B03, 2 processors, Intel Core 2 Duo, 2.66 GHz, 4 GB, SMC 1.48f2
Graphics: NVIDIA GeForce 9600M GT, NVIDIA GeForce 9600M GT, PCIe, 256 MB
Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.10.131.36.1)
Bluetooth: Version 2.3.8f7, 2 service, 19 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: AirPort, AirPort, en1
Serial ATA Device: ST9320423ASG, 298,09 GB
Serial ATA Device: MATSHITADVD-R UJ-868
USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0x24400000
USB Device: My Book 1110, 0x1058 (Western Digital Technologies, Inc.), 0x1110, 0x26200000
USB Device: Internal Memory Card Reader, 0x05ac (Apple Inc.), 0x8403, 0x26500000
USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x06100000
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8213, 0x06110000
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0237, 0x04600000
USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0x04500000