Re: SIGSEGV indexing jcc-compiled module in IDEA PyCharm

Wed, 29 May 2013 13:51:53 -0700 


On Wed, 29 May 2013, Barry Wark wrote:


On Wed, May 29, 2013 at 1:53 PM, Andi Vajda <va...@apache.org> wrote:



On Tue, 28 May 2013, Barry Wark wrote:

 On Tue, May 28, 2013 at 11:09 PM, Andi Vajda <va...@apache.org> wrote:




On Tue, 28 May 2013, Barry Wark wrote:

 Hi all,



This is an edge case, I realize, but thought I'd throw it out there in
case
anyone has come across a solution.

I'm using IDEA's PyCharm IDE (v2.7). The project virtualenv contains a
jcc-compiled module (which the project uses). PyCharm's indexer crashes



Which project ? yours or PyCharm-the-project ?
What version of JCC was this module compiled with ?




The project is mine, a python wrapper around Physion's Ovation API. We're
using JCC 2.16. PyCharm is IDEA's Python IDE (
http://www.jetbrains.com/**pycharm/ <http://www.jetbrains.com/pycharm/>).





 when indexing this module with the crash report below. When running the


project's unit tests in PyCharm, this jcc-compiled module is imported
(and
functions) without issue. PyCharm is a Java app, and I'm sure it's doing
some Java-Python bridging as well



If PyCharm is a Java app, what kind of python bridging is it doing ? And
how does that involve JCC ? I'm assuming that if PyCharm is a Java
module,
its indexing would be implemented in Java too ?




I don't really know how PyCharm handles Java/Python bridging. PyCharm is
built on IDEA's (Java) IDE framework, and it works with Python code. It's
purely speculation on my part that PyCharm's Java/Python bridging (if any)
is involved here.





 , so it's possible there's a conflict that


is the root of this crash. If so, I'll gladly file this as a PyCharm
issue,
but though I'd run this by the JCC gurus in case they recognize what's
going on. I've never seen the PyCharm indexer crash before on modules
that
don't use jcc.



What version(s) of JCC are involved here ?




2.16 on OS X 10.8, Python 2.7.



So, to paraphrase to make sure I understand this correctly:
  - PyCharm is a Java program that can spawn Python processes



Yes. In particular, it spawns a python process to "index" a python module
for code completion



  - Your python project uses JCC and runs fine by itself



Yes



  - Your python project crashes when run under PyCharm



Almost. My project *runs* fine when spawned under PyCharm, but the PyCharm
"indexer" crashes when attempting to index my module built with jcc.




One possibility here is that there is a clash of Java VMs. There can only
be one Java VM in a given process. JCC can be embedding a Java VM (the
default case) and it controls and initializes it or JCC can be embedded
inside a existing Java VM (when run inside Tomcat, for example). This
latter feature is not well documented but works fine (see the PythonVM.java
file in the JCC sources for more information).



Interesting. The process that crashes is a python child process spawned by
PyCharm. I don't know whether there is a JavaVM running in this child
process. I looked at the source of PythonVM.java and I don't see any
comments/docs about the various embedding options. Can you give me a bit
more information?


See "Embedding a Python VM in a Java VM" at:
  http://lucene.apache.org/pylucene/jcc/features.html

Andi..







I don't know how PyCharm controls Python programs, does it embed a Python
VM ? does it spawn a sub-process ? There could be an issue here.



It's not transparent to me how PyCharm handles python VMs either. From the
crash log, it appears that in this particular case it is spawning a child
process.

Thank you,
Barry




Andi..



Thanks,
Barry





Andi..



 Thanks,

Barry


The Crash Log:

Process:         python [85552]
Path:            /Users/USER/*/python
Identifier:      python
Version:         60.3
Code Type:       X86-64 (Native)
Parent Process:  pycharm [85481]
User ID:         501

Date/Time:       2013-05-28 13:35:21.728 -0400
OS Version:      Mac OS X 10.8.3 (12D78)
Report Version:  10
Sleep/Wake UUID: 45FF7EDE-FE31-4248-B03D-****1EE79118E02F


Interval Since Last Report:          36408 sec
Crashes Since Last Report:           3
Per-App Crashes Since Last Report:   3
Anonymous UUID:                      5340B35B-8410-1D7A-63C1-**

2E05A95E2522

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

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000544857bc

VM Regions Near 0x544857bc:
-->
   __TEXT                 0000000104484000-****0000000104485000 [
 4K]

r-x/rwx SM=COW  /Users/USER/*

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   _ovation_api.so               0x000000010509e6c5 JArray<unsigned
char>::JArray(long) + 37
1   _ovation_api.so               0x0000000105095250 _jclass*
initializeClass<unsigned char>(bool) + 42
2   _ovation_api.so               0x00000001050a290e
JCCEnv::getClass(_jclass* (*)(bool)) const + 18
3   _ovation_api.so               0x00000001050a6dd9
t_descriptor___get__(t_****descriptor*, _object*, _object*) + 66

4   org.python.python             0x00000001044a13b1 0x10448f000 + 74673
5   org.python.python             0x00000001044a85a9 PyEval_EvalFrameEx
+
9244
6   org.python.python             0x00000001044a6147 PyEval_EvalCodeEx +
1934
7   org.python.python             0x00000001044ac8df 0x10448f000 +
121055
8   org.python.python             0x00000001044a863a PyEval_EvalFrameEx
+
9389
9   org.python.python             0x00000001044ac869 0x10448f000 +
120937
10  org.python.python             0x00000001044a863a PyEval_EvalFrameEx
+
9389
11  org.python.python             0x00000001044ac869 0x10448f000 +
120937
12  org.python.python             0x00000001044a863a PyEval_EvalFrameEx
+
9389
13  org.python.python             0x00000001044a6147 PyEval_EvalCodeEx +
1934
14  org.python.python             0x00000001044ac8df 0x10448f000 +
121055
15  org.python.python             0x00000001044a863a PyEval_EvalFrameEx
+
9389
16  org.python.python             0x00000001044a6147 PyEval_EvalCodeEx +
1934
17  org.python.python             0x00000001044a59b3 PyEval_EvalCode +
54
18  org.python.python             0x00000001044e1c70 0x10448f000 +
339056
19  org.python.python             0x00000001044e1d3c PyRun_FileExFlags +
165
20  org.python.python             0x00000001044e1726
PyRun_SimpleFileExFlags + 410
21  org.python.python             0x0000000104505e27 Py_Main + 2715
22  libdyld.dylib                 0x00007fff907047e1 start + 1

Thread 0 crashed with X86 Thread State (64-bit):
 rax: 0x00007fff78dee180  rbx: 0x00007fff5b77a768  rcx:
0x0000000054485244
rdx: 0x00000001053c55b0
 rdi: 0x00007fff78dee180  rsi: 0x0000000000000000  rbp:
0x00007fff5b77a750
rsp: 0x00007fff5b77a740
  r8: 0x00007fff5b77a838   r9: 0x00007fff5b77a828  r10:
0x0000000000000002
r11: 0x0000000000000003
 r12: 0x000000010465c320  r13: 0x0000000104bd37a0  r14:
0x0000000000000000
r15: 0x00007fea32eb2880
 rip: 0x000000010509e6c5  rfl: 0x0000000000010246  cr2:
0x00000000544857bc
Logical CPU: 1

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707.5) <4140B1F6-7D73-33C7-B3F2-****4DB349C31AE9>
/System/Library/Frameworks/****CoreServices.framework/**
Versions/A/Frameworks/****Metadata.framework/Versions/A/****Metadata

   0x7fff918a4000 -     0x7fff91970ff7  libsystem_c.dylib (825.26)
<4C9EB006-FE1F-3F8F-8074-****DFD94CF2CE7B>
/usr/lib/system/libsystem_c.**

dylib
   0x7fff91cd2000 -     0x7fff91e47fff  com.apple.CFNetwork (596.3.3 -
596.3.3) <3739DC8D-8610-3740-80EC-****43E130779CB8>
/System/Library/Frameworks/****CFNetwork.framework/Versions/***
*A/CFNetwork

   0x7fff9288e000 -     0x7fff928a3ff7  libdispatch.dylib (228.23)
<D26996BF-FC57-39EB-8829-****F63585561E09>
/usr/lib/system/libdispatch.**

dylib
   0x7fff92c2f000 -     0x7fff92c2ffff  libOpenScriptingUtil.dylib
(148.3)
<F8681222-0969-3B10-8BCE-****C55A4B9C520C>
/usr/lib/libOpenScriptingUtil.****

dylib
   0x7fff92f8a000 -     0x7fff93087ff7  libxml2.2.dylib (22.3)
<47B09CB2-C636-3024-8B55-****6040F7829B4C> /usr/lib/libxml2.2.dylib

   0x7fff93a97000 -     0x7fff93a9fff7  libsystem_dnssd.dylib (379.37)
<616FC901-151E-38BF-B2C4-****24A351C5FAAD> /usr/lib/system/libsystem_**

dnssd.dylib
   0x7fff93aa0000 -     0x7fff93aafff7  libxar.1.dylib (105)
<370ED355-E516-311E-BAFD-****D80633A84BE1> /usr/lib/libxar.1.dylib

   0x7fff93ab0000 -     0x7fff93ae6fff  libsystem_info.dylib (406.17)
<4FFCA242-7F04-365F-87A6-****D4EFB89503C1> /usr/lib/system/libsystem_**

info.dylib
   0x7fff93b14000 -     0x7fff93b18fff  libpam.2.dylib (20)
<C8F45864-5B58-3237-87E1-****2C258A1D73B8> /usr/lib/libpam.2.dylib

   0x7fff93ba4000 -     0x7fff93c12fff  com.apple.framework.IOKit
(2.0.1 -
755.22.5) <1547DA6F-9793-30A2-8E92-****7368DE84D46C>
/System/Library/Frameworks/****IOKit.framework/Versions/A/****IOKit

   0x7fff9400b000 -     0x7fff94011fff  libmacho.dylib (829)
<BF332AD9-E89F-387E-92A4-****6E1AB74BD4D9>
/usr/lib/system/libmacho.dylib

   0x7fff94012000 -     0x7fff9401fff7  com.apple.NetAuth (4.0 - 4.0)
<F5BC7D7D-AF28-3C83-A674-****DADA48FF7810>
/System/Library/****PrivateFrameworks/NetAuth.**

framework/Versions/A/NetAuth
   0x7fff941cf000 -     0x7fff941d3ff7  com.apple.TCC (1.0 - 1)
<F2F3B753-FC73-3543-8BBE-****859FDBB4D6A6>
/System/Library/****PrivateFrameworks/TCC.****framework/Versions/A/TCC

   0x7fff941d4000 -     0x7fff941d5fff  libsystem_blocks.dylib (59)
<D92DCBC3-541C-37BD-AADE-****ACC75A0C59C8>
/usr/lib/system/libsystem_****blocks.dylib

   0x7fff941f4000 -     0x7fff941fffff  libsystem_notify.dylib (98.5)
<C49275CC-835A-3207-AFBA-****8C01374927B6>
/usr/lib/system/libsystem_****notify.dylib
   0x7fff9471e000 -     0x7fff9471ffff  libDiagnosticMessagesClient.**
dylib
(8) <8548E0DC-0D2F-30B6-B045-****FE8A038E76D8>
/usr/lib/****libDiagnosticMessagesClient.****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: 10466
   thread_create: 1
   thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=90.9M resident=34.5M(38%)
swapped_out_or_unallocated=56.****3M(62%)

Writable regions: Total=26.2M written=9932K(37%) resident=11.6M(44%)
swapped_out=0K(0%) unallocated=14.6M(56%)

REGION TYPE                      VIRTUAL
===========                      =======
MALLOC                             17.3M
MALLOC guard page                    32K
STACK GUARD                        56.0M
Stack                              8192K
VM_ALLOCATE                           4K
__DATA                             4188K
__LINKEDIT                         55.4M
__TEXT                             35.5M
__UNICODE                           544K
shared memory                        12K
===========                      =======
TOTAL                             176.8M

Model: MacBookPro5,5, BootROM MBP55.00AC.B03, 2 processors, Intel Core 2
Duo, 2.26 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, 0x802C,
0x31364A53463235363634485A2D31****47314631

Memory Module: BANK 1/DIMM0, 2 GB, DDR3, 1067 MHz, 0x802C,
0x31364A53463235363634485A2D31****47314631
AirPort: spairport_wireless_card_type_****airport_extreme (0x14E4,
0x8D),

Broadcom BCM43xx 1.0 (5.106.98.100.16)
Bluetooth: Version 4.1.3f3 11349, 2 service, 18 devices, 1 incoming
serial
ports
Network Service: AirPort, AirPort, en1
Serial ATA Device: APPLE SSD TS256A, 251 GB
Serial ATA Device: HL-DT-ST DVDRW  GS23N
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

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