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networkdynamics / zenlib

The Zero Effort Network Library for Python
http://zen.networkdynamics.org
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compact() fails on linux for zen.DiGraph #5

Closed mmisiewicz closed 12 years ago

mmisiewicz commented 12 years ago

Compact function fails to run on a zen.DiGraph (with or without edges in the graph) following random deletion of a number of nodes.

Python 2.7.1, GCC 4.4.3, Cyton 0.15.1, Ubuntu 10.04.4 LTS

Code to reproduce problem:

import zen
import random
net = zen.DiGraph()

for i in range(100):
    data = {1:"Item1", 2:"Item2", 3:random.uniform(5,25)}
    net.add_node(nobj=i, data=data)

for i in net.nodes():
    print i, net.node_data(i)

for i in random.sample(range(100), 50):
    net.rm_node(i)

print "After sampling:"
for i in net.nodes():
    print i, net.node_data(i)
# segfault here
net.compact()

print "After compacting:"
for i in net.nodes():
    print i, net.node_data(i)
mmisiewicz commented 12 years ago

This problem is also reproduced on OS 10.7.4, Python 2.7.1, Cyton 0.16, GCC 4.2.1. The same code causes the issue.


Process:         Python [99583]
Path:            /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier:      Python
Version:         ??? (???)
Code Type:       X86-64 (Native)
Parent Process:  bash [66574]

Date/Time:       2012-07-10 16:42:56.580 -0400
OS Version:      Mac OS X 10.7.4 (11E53)
Report Version:  9

Interval Since Last Report:          513378 sec
Crashes Since Last Report:           9
Per-App Crashes Since Last Report:   1
Anonymous UUID:                      724DC832-FA1E-4893-8E71-065AD26DF7F6

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

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x000000028316f15c

VM Regions Near 0x28316f15c:
    MALLOC_LARGE           0000000101b60000-0000000101be0000 [  512K] rw-/rwx SM=PRV  
--> 
    STACK GUARD            00007fff5bc00000-00007fff5f400000 [ 56.0M] ---/rwx SM=NUL  stack guard for thread 0

Application Specific Information:
objc[99583]: garbage collection is OFF

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   digraph.so                      0x0000000101552651 __pyx_f_3zen_7digraph_7DiGraph_compact + 433 (digraph.c:6658)
1   digraph.so                      0x0000000101537f70 __pyx_pw_3zen_7digraph_7DiGraph_21compact + 16 (digraph.c:7002)
2   org.python.python               0x00000001000c13aa PyEval_EvalFrameEx + 22746
3   org.python.python               0x00000001000c2f49 PyEval_EvalCodeEx + 2137
4   org.python.python               0x00000001000c3066 PyEval_EvalCode + 54
5   org.python.python               0x00000001000e7b2e PyRun_FileExFlags + 174
6   org.python.python               0x00000001000e7de9 PyRun_SimpleFileExFlags + 489
7   org.python.python               0x00000001000fe75c Py_Main + 2940
8   org.python.python               0x0000000100000f14 0x100000000 + 3860

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x000000010158b6e0  rbx: 0x0000000000000000  rcx: 0x0000000100b5f800  rdx: 0x00000000000001d6
  rdi: 0x000000010197b960  rsi: 0x00000001003138c8  rbp: 0x00007fff5fbff410  rsp: 0x00007fff5fbff3a0
   r8: 0x0000000000000000   r9: 0x0000000000000000  r10: 0x0000000000000001  r11: 0x000000010003eb10
  r12: 0x0000000101a5e890  r13: 0x000000010030a180  r14: 0x0000000010195fb9  r15: 0x00000000304c1f2b
  rip: 0x0000000101552651  rfl: 0x0000000000010297  cr2: 0x000000028316f15c
Logical CPU: 0

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    0x7fff8fa9c000 -     0x7fff8faa1ff7  libsystem_network.dylib (??? - ???) <5DE7024E-1D2D-34A2-80F4-08326331A75B> /usr/lib/system/libsystem_network.dylib
    0x7fff8fecd000 -     0x7fff8fedfff7  libz.1.dylib (1.2.5 - compatibility 1.0.0) <30CBEF15-4978-3DED-8629-7109880A19D4> /usr/lib/libz.1.dylib
    0x7fff8fee0000 -     0x7fff8fee1ff7  libremovefile.dylib (21.1.0 - compatibility 1.0.0) <739E6C83-AA52-3C6C-A680-B37FE2888A04> /usr/lib/system/libremovefile.dylib
    0x7fff902fd000 -     0x7fff90308ff7  libc++abi.dylib (14.0.0 - compatibility 1.0.0) <8FF3D766-D678-36F6-84AC-423C878E6D14> /usr/lib/libc++abi.dylib
    0x7fff904c0000 -     0x7fff904c2fff  libquarantine.dylib (36.6.0 - compatibility 1.0.0) <0EBF714B-4B69-3E1F-9A7D-6BBC2AACB310> /usr/lib/system/libquarantine.dylib
    0x7fff907bc000 -     0x7fff907cafff  libdispatch.dylib (187.9.0 - compatibility 1.0.0) <1D5BE322-A9B9-3BCE-8FAC-076FB07CF54A> /usr/lib/system/libdispatch.dylib
    0x7fff90ceb000 -     0x7fff90df7fff  libcrypto.0.9.8.dylib (44.0.0 - compatibility 0.9.8) <3A8E1F89-5E26-3C8B-B538-81F5D61DBF8A> /usr/lib/libcrypto.0.9.8.dylib
    0x7fff90f2a000 -     0x7fff90f2bfff  libdnsinfo.dylib (395.11.0 - compatibility 1.0.0) <853BAAA5-270F-3FDC-B025-D448DB72E1C3> /usr/lib/system/libdnsinfo.dylib
    0x7fff9105c000 -     0x7fff9105efff  com.apple.TrustEvaluationAgent (2.0 - 1) <1F31CAFF-C1C6-33D3-94E9-11B721761DDF> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
    0x7fff91552000 -     0x7fff91552fff  libkeymgr.dylib (23.0.0 - compatibility 1.0.0) <61EFED6A-A407-301E-B454-CD18314F0075> /usr/lib/system/libkeymgr.dylib
    0x7fff9159c000 -     0x7fff9159cfff  com.apple.Accelerate.vecLib (3.7 - vecLib 3.7) <C06A140F-6114-3B8B-B080-E509303145B8> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
    0x7fff9161c000 -     0x7fff91621fff  libcompiler_rt.dylib (6.0.0 - compatibility 1.0.0) <98ECD5F6-E85C-32A5-98CD-8911230CB66A> /usr/lib/system/libcompiler_rt.dylib
    0x7fff9165e000 -     0x7fff9173bfef  libsystem_c.dylib (763.13.0 - compatibility 1.0.0) <41B43515-2806-3FBC-ACF1-A16F35B7E290> /usr/lib/system/libsystem_c.dylib
    0x7fff92476000 -     0x7fff928a3fff  libLAPACK.dylib (??? - ???) <4F2E1055-2207-340B-BB45-E4F16171EE0D> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
    0x7fff928aa000 -     0x7fff928aafff  com.apple.Accelerate (1.7 - Accelerate 1.7) <82DDF6F5-FBC3-323D-B71D-CF7ABC5CF568> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
    0x7fff93a0c000 -     0x7fff93a39fe7  libSystem.B.dylib (159.1.0 - compatibility 1.0.0) <095FDD3C-3961-3865-A59B-A5B0A4B8B923> /usr/lib/libSystem.B.dylib
    0x7fff94154000 -     0x7fff9415afff  libmacho.dylib (800.0.0 - compatibility 1.0.0) <D86F63EC-D2BD-32E0-8955-08B5EAFAD2CC> /usr/lib/system/libmacho.dylib
    0x7fff941c2000 -     0x7fff941c9fff  libcopyfile.dylib (85.1.0 - compatibility 1.0.0) <172B1985-F24A-34E9-8D8B-A2403C9A0399> /usr/lib/system/libcopyfile.dylib
    0x7fff9421f000 -     0x7fff94220fff  libDiagnosticMessagesClient.dylib (??? - ???) <3DCF577B-F126-302B-BCE2-4DB9A95B8598> /usr/lib/libDiagnosticMessagesClient.dylib
    0x7fff94260000 -     0x7fff94844fff  libBLAS.dylib (??? - ???) <C34F6D88-187F-33DC-8A68-C0C9D1FA36DF> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    0x7fff949ee000 -     0x7fff94b24fff  com.apple.vImage (5.1 - 5.1) <A08B7582-67BC-3EED-813A-4833645964A7> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
    0x7fff94bf7000 -     0x7fff94bfffff  libsystem_dnssd.dylib (??? - ???) <D9BB1F87-A42B-3CBC-9DC2-FC07FCEF0016> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff94f25000 -     0x7fff94f42fff  libxpc.dylib (77.19.0 - compatibility 1.0.0) <9F57891B-D7EF-3050-BEDD-21E7C6668248> /usr/lib/system/libxpc.dylib
    0x7fff9661f000 -     0x7fff9667ffff  libvDSP.dylib (325.4.0 - compatibility 1.0.0) <3A7521E6-5510-3FA7-AB65-79693A7A5839> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
    0x7fff96fd7000 -     0x7fff96ff7fff  libsystem_kernel.dylib (1699.26.8 - compatibility 1.0.0) <1DDC0B0F-DB2A-34D6-895D-E5B2B5618946> /usr/lib/system/libsystem_kernel.dylib
    0x7fff9779f000 -     0x7fff977a4fff  libcache.dylib (47.0.0 - compatibility 1.0.0) <B7757E2E-5A7D-362E-AB71-785FE79E1527> /usr/lib/system/libcache.dylib
    0x7fff9782b000 -     0x7fff9782bfff  com.apple.vecLib (3.7 - vecLib 3.7) <9A58105C-B36E-35B5-812C-4ED693F2618F> /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
    0x7fff97ccc000 -     0x7fff97d1afff  libauto.dylib (??? - ???) <D8AC8458-DDD0-3939-8B96-B6CED81613EF> /usr/lib/libauto.dylib
    0x7fff97db4000 -     0x7fff97e2afff  libc++.1.dylib (28.1.0 - compatibility 1.0.0) <DA22E4D6-7F20-3BEA-9B89-2FBA735C2EE1> /usr/lib/libc++.1.dylib
    0x7fff97ee7000 -     0x7fff97eedff7  libunwind.dylib (30.0.0 - compatibility 1.0.0) <1E9C6C8C-CBE8-3F4B-A5B5-E03E3AB53231> /usr/lib/system/libunwind.dylib
    0x7fff97eee000 -     0x7fff97ef2fff  libdyld.dylib (195.5.0 - compatibility 1.0.0) <F1903B7A-D3FF-3390-909A-B24E09BAD1A5> /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: 277689
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=77.6M resident=28.6M(37%) swapped_out_or_unallocated=49.0M(63%)
Writable regions: Total=28.2M written=11.2M(40%) resident=14.0M(50%) swapped_out=0K(0%) unallocated=14.1M(50%)

REGION TYPE                      VIRTUAL
===========                      =======
MALLOC                             19.5M
MALLOC guard page                    32K
STACK GUARD                        56.0M
Stack                              8192K
VM_ALLOCATE                           8K
__DATA                             2228K
__LINKEDIT                         49.9M
__TEXT                             27.6M
__UNICODE                           544K
shared memory                        12K
===========                      =======
TOTAL                             163.8M

Model: MacBookPro5,5, BootROM MBP55.00AC.B03, 2 processors, Intel Core 2 Duo, 2.53 GHz, 4 GB, SMC 1.47f2
Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB
Memory Module: BANK 0/DIMM0, 2 GB, DDR3, 1067 MHz, 0x80CE, 0x4D34373142353637334548312D4346382020
Memory Module: BANK 1/DIMM0, 2 GB, DDR3, 1067 MHz, 0x80CE, 0x4D34373142353637334548312D4346382020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.106.198.4.20)
Bluetooth: Version 4.0.5f11, 2 service, 18 devices, 1 incoming serial ports
Network Service: AirPort, AirPort, en1
Serial ATA Device: TOSHIBA MK2555GSXF, 250.06 GB
Serial ATA Device: OPTIARC  DVD RW AD-5960S
USB Device: Keyboard Hub, apple_vendor_id, 0x1006, 0x24100000 / 3
USB Device: Apple Keyboard, apple_vendor_id, 0x0220, 0x24120000 / 4
USB Device: Built-in iSight, apple_vendor_id, 0x8507, 0x24400000 / 2
USB Device: Internal Memory Card Reader, apple_vendor_id, 0x8403, 0x26500000 / 2
USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, 0x0236, 0x04600000 / 3
USB Device: IR Receiver, apple_vendor_id, 0x8242, 0x04500000 / 2
USB Device: BRCM2046 Hub, 0x0a5c  (Broadcom Corp.), 0x4500, 0x06100000 / 2
USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x8213, 0x06110000 / 3
mmisiewicz commented 12 years ago

Fixed in latest versions of zen.