R crashes with mxCI

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bverhulst's picture
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Joined: 03/08/2010

So I am technically not a beta tester, but I think that this issue fits with this section, as the script is using the new mxExpectationNormal(), but I don't think that that has any impact on the crashing problem

# This script seems to crash R on my computer (MacBook Pro) but it seems to run fine on our cluster at VIPBG (light).
# I have two versions of the script analysis, one that uses the new style of mxExpectationNormal() statements and an old style mxAlgebraObjective version appended to the end of the script. The problem arises when I try and add the mxCI statments into the model and shuts down R completely.

Data is generated within the script.
Any suggestions would be most helpful.
(and I know that the script is a little clunky)

Brad

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Crash.R23.09 KB
bverhulst's picture
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Joined: 03/08/2010
Sorry, I hit upload before I

Sorry, I hit upload before I had saved the final version.
Brad

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Crash.R 23.33 KB
tbates's picture
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Joined: 07/31/2009
parallel

hi brad,
Cis run parallel, so might be hitting the lack of default parallel support on os x.

Might try compiling/installing again, ensuring parallel /OpenMP is disabled?

bverhulst's picture
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Joined: 03/08/2010
fixed?

Okay, I got it to run fine with the single threaded version binary release.
Thanks for your suggestions.
B

jpritikin's picture
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Joined: 05/23/2012
crash

Thank you for your report.

I tried running your code with svn trunk and could not reproduce a crash. However, the current code is not robust to R's garbage collection. I test suite fails with GC torture enabled.

Can you re-run your test against the code at https://gitorious.org/openmx/openmx/commits/proposed ?

bverhulst's picture
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Joined: 03/08/2010
Another mxCI Crash Issue

I am having another crashing issue with OpenMx. Mike urged me to post the script and the data so, I am attaching simulated data file and a parts of a script for the a meta analysis.

Again, the script crashes when CIs are added, but this might be just on my computer again (so below I am including the crash report - I don't know how to read it, but perhaps you do and it would be helpful in identifying the issue).

Process: R [3640]
Path: /Applications/R.app/Contents/MacOS/R
Identifier: org.R-project.R
Version: R 2.15.2 GUI 1.53 Leopard build 32-bit (6335)
Code Type: X86 (Native)
Parent Process: launchd [150]
User ID: 502

Date/Time: 2013-04-25 11:49:24.155 -0400
OS Version: Mac OS X 10.8.3 (12D78)
Report Version: 10

Interval Since Last Report: 10469 sec
Crashes Since Last Report: 13
Per-App Interval Since Last Report: 4579 sec
Per-App Crashes Since Last Report: 13
Anonymous UUID: A6CDB7F9-C6E1-E34B-A3F8-D06ABE4CDBEE

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

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x9077f8e2 __psynch_cvwait + 10
1 libsystem_c.dylib 0x98cfd2e9 _pthread_cond_wait + 938
2 libsystem_c.dylib 0x98d8aaf0 pthread_cond_wait + 48
3 OpenMx.so 0x0f3e30cc gomp_sem_wait + 76
4 OpenMx.so 0x0f3e31b6 gomp_barrier_wait_end + 102
5 OpenMx.so 0x0f3e3247 gomp_barrier_wait + 55
6 OpenMx.so 0x0f3e2a55 gomp_team_end + 53
7 OpenMx.so 0x0f3f8057 omxCallFIMLOrdinalObjective + 663
8 OpenMx.so 0x0f405580 omxObjectiveCompute + 16
9 OpenMx.so 0x0f3e67fe omxAlgebraRecompute + 46
10 OpenMx.so 0x0f3e67fe omxAlgebraRecompute + 46
11 OpenMx.so 0x0f3e67fe omxAlgebraRecompute + 46
12 OpenMx.so 0x0f3e67fe omxAlgebraRecompute + 46
13 OpenMx.so 0x0f3e67fe omxAlgebraRecompute + 46
14 OpenMx.so 0x0f3e67fe omxAlgebraRecompute + 46
15 OpenMx.so 0x0f3f1b75 omxCallAlgebraObjective + 37
16 OpenMx.so 0x0f405580 omxObjectiveCompute + 16
17 OpenMx.so 0x0f3e3e07 objectiveFunction_ + 151
18 OpenMx.so 0x0f44d114 npfd_ + 1364
19 OpenMx.so 0x0f45afb1 npcore_ + 7441
20 OpenMx.so 0x0f45daf1 npsol_ + 9313
21 OpenMx.so 0x0f3e5f0b callNPSOL + 6491
22 libR.dylib 0x0015bf0d do_dotcall + 1117 (dotcode.c:626)
23 libR.dylib 0x001907b1 Rf_eval + 1777 (eval.c:494)
24 libR.dylib 0x00193a96 do_set + 678 (eval.c:1717)
25 libR.dylib 0x001905b2 Rf_eval + 1266 (eval.c:468)
26 libR.dylib 0x00192432 do_begin + 146 (eval.c:1415)
27 libR.dylib 0x001905b2 Rf_eval + 1266 (eval.c:468)
28 libR.dylib 0x0019598d Rf_applyClosure + 861 (eval.c:861)
29 libR.dylib 0x001904b2 Rf_eval + 1010 (eval.c:512)
30 libR.dylib 0x00192432 do_begin + 146 (eval.c:1415)
31 libR.dylib 0x001905b2 Rf_eval + 1266 (eval.c:468)
32 libR.dylib 0x0019598d Rf_applyClosure + 861 (eval.c:861)
33 libR.dylib 0x001904b2 Rf_eval + 1010 (eval.c:512)
34 libR.dylib 0x00193a96 do_set + 678 (eval.c:1717)
35 libR.dylib 0x001905b2 Rf_eval + 1266 (eval.c:468)
36 libR.dylib 0x001cc0d8 R_ReplDLLdo1 + 504 (main.c:362)
37 org.R-project.R 0x000239fc run_REngineRmainloop + 252
38 org.R-project.R 0x0001721c -[REngine runREPL] + 284
39 org.R-project.R 0x00003334 main + 932
40 org.R-project.R 0x00002cb6 start + 54

Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x907809ae kevent + 10
1 libdispatch.dylib 0x92911c71 _dispatch_mgr_invoke + 993
2 libdispatch.dylib 0x929117a9 _dispatch_mgr_thread + 53

Thread 2:: com.apple.NSURLConnectionLoader
0 libsystem_kernel.dylib 0x9077d7d2 mach_msg_trap + 10
1 libsystem_kernel.dylib 0x9077ccb0 mach_msg + 68
2 com.apple.CoreFoundation 0x97705f89 __CFRunLoopServiceMachPort + 185
3 com.apple.CoreFoundation 0x9770b96f __CFRunLoopRun + 1247
4 com.apple.CoreFoundation 0x9770b02a CFRunLoopRunSpecific + 378
5 com.apple.CoreFoundation 0x9770ae9b CFRunLoopRunInMode + 123
6 com.apple.Foundation 0x9189463a +[NSURLConnection(Loader) _resourceLoadLoop:] + 395
7 com.apple.Foundation 0x918f87c8 -[NSThread main] + 45
8 com.apple.Foundation 0x918f874b __NSThread__main__ + 1396
9 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
10 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 3:
0 libsystem_kernel.dylib 0x907800ee __workq_kernreturn + 10
1 libsystem_c.dylib 0x98cfb0ac _pthread_workq_return + 45
2 libsystem_c.dylib 0x98cfae79 _pthread_wqthread + 448
3 libsystem_c.dylib 0x98ce2d2a start_wqthread + 30

Thread 4:
0 libsystem_kernel.dylib 0x9077fbe6 __select + 10
1 org.R-project.R 0x000135a2 -[RController readThread:] + 674
2 com.apple.Foundation 0x918f87c8 -[NSThread main] + 45
3 com.apple.Foundation 0x918f874b __NSThread__main__ + 1396
4 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
5 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 5:
0 libsystem_kernel.dylib 0x907800ee __workq_kernreturn + 10
1 libsystem_c.dylib 0x98cfb0ac _pthread_workq_return + 45
2 libsystem_c.dylib 0x98cfae79 _pthread_wqthread + 448
3 libsystem_c.dylib 0x98ce2d2a start_wqthread + 30

Thread 6:
0 libsystem_kernel.dylib 0x907800ee __workq_kernreturn + 10
1 libsystem_c.dylib 0x98cfb0ac _pthread_workq_return + 45
2 libsystem_c.dylib 0x98cfae79 _pthread_wqthread + 448
3 libsystem_c.dylib 0x98ce2d2a start_wqthread + 30

Thread 7:: com.apple.appkit-heartbeat
0 libsystem_kernel.dylib 0x9077fc72 __semwait_signal + 10
1 libsystem_c.dylib 0x98d82a55 nanosleep$UNIX2003 + 189
2 libsystem_c.dylib 0x98d8291e usleep$UNIX2003 + 60
3 com.apple.AppKit 0x90c50c9d -[NSUIHeartBeat _heartBeatThread:] + 879
4 com.apple.Foundation 0x918f87c8 -[NSThread main] + 45
5 com.apple.Foundation 0x918f874b __NSThread__main__ + 1396
6 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
7 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 8:
0 libsystem_kernel.dylib 0x9077f8e2 __psynch_cvwait + 10
1 libsystem_c.dylib 0x98cfd2e9 _pthread_cond_wait + 938
2 libsystem_c.dylib 0x98d8aaf0 pthread_cond_wait + 48
3 OpenMx.so 0x0f3e30cc gomp_sem_wait + 76
4 OpenMx.so 0x0f3e31d3 gomp_barrier_wait_end + 131
5 OpenMx.so 0x0f3e3247 gomp_barrier_wait + 55
6 OpenMx.so 0x0f3e2a02 gomp_thread_start + 322
7 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
8 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 9:
0 libsystem_kernel.dylib 0x9077f8e2 __psynch_cvwait + 10
1 libsystem_c.dylib 0x98cfd2e9 _pthread_cond_wait + 938
2 libsystem_c.dylib 0x98d8aaf0 pthread_cond_wait + 48
3 OpenMx.so 0x0f3e30cc gomp_sem_wait + 76
4 OpenMx.so 0x0f3e31d3 gomp_barrier_wait_end + 131
5 OpenMx.so 0x0f3e3247 gomp_barrier_wait + 55
6 OpenMx.so 0x0f3e2a02 gomp_thread_start + 322
7 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
8 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 10:
0 libsystem_kernel.dylib 0x9077f8e2 __psynch_cvwait + 10
1 libsystem_c.dylib 0x98cfd2e9 _pthread_cond_wait + 938
2 libsystem_c.dylib 0x98d8aaf0 pthread_cond_wait + 48
3 OpenMx.so 0x0f3e30cc gomp_sem_wait + 76
4 OpenMx.so 0x0f3e31d3 gomp_barrier_wait_end + 131
5 OpenMx.so 0x0f3e3247 gomp_barrier_wait + 55
6 OpenMx.so 0x0f3e2a02 gomp_thread_start + 322
7 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
8 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 11:
0 libsystem_kernel.dylib 0x9077f8e2 __psynch_cvwait + 10
1 libsystem_c.dylib 0x98cfd2e9 _pthread_cond_wait + 938
2 libsystem_c.dylib 0x98d8aaf0 pthread_cond_wait + 48
3 OpenMx.so 0x0f3e30cc gomp_sem_wait + 76
4 OpenMx.so 0x0f3e31d3 gomp_barrier_wait_end + 131
5 OpenMx.so 0x0f3e3247 gomp_barrier_wait + 55
6 OpenMx.so 0x0f3e2a02 gomp_thread_start + 322
7 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
8 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 12:
0 libsystem_kernel.dylib 0x9077f8e2 __psynch_cvwait + 10
1 libsystem_c.dylib 0x98cfd2e9 _pthread_cond_wait + 938
2 libsystem_c.dylib 0x98d8aaf0 pthread_cond_wait + 48
3 OpenMx.so 0x0f3e30cc gomp_sem_wait + 76
4 OpenMx.so 0x0f3e31d3 gomp_barrier_wait_end + 131
5 OpenMx.so 0x0f3e3247 gomp_barrier_wait + 55
6 OpenMx.so 0x0f3e2a02 gomp_thread_start + 322
7 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
8 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 13:
0 libsystem_kernel.dylib 0x9077f8e2 __psynch_cvwait + 10
1 libsystem_c.dylib 0x98cfd2e9 _pthread_cond_wait + 938
2 libsystem_c.dylib 0x98d8aaf0 pthread_cond_wait + 48
3 OpenMx.so 0x0f3e30cc gomp_sem_wait + 76
4 OpenMx.so 0x0f3e31d3 gomp_barrier_wait_end + 131
5 OpenMx.so 0x0f3e3247 gomp_barrier_wait + 55
6 OpenMx.so 0x0f3e2a02 gomp_thread_start + 322
7 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
8 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 14:
0 libsystem_kernel.dylib 0x9077f8e2 __psynch_cvwait + 10
1 libsystem_c.dylib 0x98cfd2e9 _pthread_cond_wait + 938
2 libsystem_c.dylib 0x98d8aaf0 pthread_cond_wait + 48
3 OpenMx.so 0x0f3e30cc gomp_sem_wait + 76
4 OpenMx.so 0x0f3e31d3 gomp_barrier_wait_end + 131
5 OpenMx.so 0x0f3e3247 gomp_barrier_wait + 55
6 OpenMx.so 0x0f3e2a02 gomp_thread_start + 322
7 libsystem_c.dylib 0x98cf85b7 _pthread_start + 344
8 libsystem_c.dylib 0x98ce2d4e thread_start + 34

Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00000016 ebx: 0x00000100 ecx: 0xbfffcddc edx: 0x9077f8e2
edi: 0x00000101 esi: 0x00000000 ebp: 0xbfffce68 esp: 0xbfffcddc
ss: 0x00000023 efl: 0x00000247 eip: 0x9077f8e2 cs: 0x0000000b
ds: 0x00000023 es: 0x00000023 fs: 0x00000000 gs: 0x0000000f
cr2: 0x63640004
Logical CPU: 0

Binary Images:
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0xe0000 - 0x39eff7 +libR.dylib (2.15.2) <914758AA-B381-1541-666F-D81B9AE9DD0C> /Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libR.dylib
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0xacfa000 - 0xacfaff3 +cl_kernels (???) cl_kernels
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0xdf04000 - 0xdf60fe7 +stats.so (0) <724F25A4-0532-A990-44A6-3BDB119EF3A0> /Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/libs/i386/stats.so
0xdfee000 - 0xdff6fff +lapack.so (0) /Library/Frameworks/R.framework/Resources/modules/i386/lapack.so
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0x90191000 - 0x90272fff libcrypto.0.9.8.dylib (47) <219227B4-75D2-3CCC-B241-4BE8F8E1D4AB> /usr/lib/libcrypto.0.9.8.dylib
0x902bf000 - 0x90319fff com.apple.ImageCaptureCore (5.0.2 - 5.0.2) /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore
0x9031a000 - 0x906d2ffa libLAPACK.dylib (1073.4) <9A6E5EAD-F2F2-3D5C-B655-2B536DB477F2> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x906d3000 - 0x9076aff7 com.apple.ink.framework (10.8.2 - 150) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
0x9076b000 - 0x90785ffc libsystem_kernel.dylib (2050.22.13) <70C520E8-0394-3DFB-823B-FE8C251C169A> /usr/lib/system/libsystem_kernel.dylib
0x90786000 - 0x90786ffd libOpenScriptingUtil.dylib (148.3) <87895E27-88E2-3249-8D0E-B17E76FB00C1> /usr/lib/libOpenScriptingUtil.dylib
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0x91557000 - 0x91599ffb com.apple.RemoteViewServices (2.0 - 80.6) /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 2
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: 24738
thread_create: 1
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=183.4M resident=118.2M(64%) swapped_out_or_unallocated=65.2M(36%)
Writable regions: Total=277.1M written=135.4M(49%) resident=189.2M(68%) swapped_out=0K(0%) unallocated=87.9M(32%)

REGION TYPE VIRTUAL
=========== =======
CG backing stores 20.2M
CG image 1080K
CG raster data 180K
CG shared images 1280K
CoreAnimation 280K
CoreServices 3708K
MALLOC 207.0M
MALLOC guard page 48K
MALLOC_LARGE (reserved) 228K reserved VM address space (unallocated)
Memory tag=240 4K
Memory tag=242 12K
Memory tag=35 4376K
OpenCL 36K
SQLite page cache 192K
Stack 71.1M
VM_ALLOCATE 16.2M
__DATA 22.4M
__DATA/__OBJC 180K
__IMAGE 528K
__IMPORT 52K
__LINKEDIT 39.9M
__OBJC 2716K
__OBJC/__DATA 52K
__PAGEZERO 4K
__TEXT 143.5M
__UNICODE 544K
mapped file 106.0M
shared memory 308K
=========== =======
TOTAL 641.8M
TOTAL, minus reserved VM space 641.5M

Model: MacBookPro10,1, BootROM MBP101.00EE.B02, 4 processors, Intel Core i7, 2.6 GHz, 16 GB, SMC 2.3f35
Graphics: Intel HD Graphics 4000, Intel HD Graphics 4000, Built-In, 512 MB
Graphics: NVIDIA GeForce GT 650M, NVIDIA GeForce GT 650M, PCIe, 1024 MB
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Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D5434314753364D465238432D50422020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xEF), 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: Wi-Fi, AirPort, en0
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USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, 0x1a100000 / 2
USB Device: FaceTime HD Camera (Built-in), apple_vendor_id, 0x8510, 0x1a110000 / 3
USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, 0x1d100000 / 2
USB Device: hub_device, 0x0424 (SMSC), 0x2512, 0x1d180000 / 3
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USB Device: BRCM20702 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x1d181000 / 4
USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x8286, 0x1d181300 / 8

AttachmentSize
Forum.R 49.13 KB
mhunter's picture
Offline
Joined: 07/31/2009
The code you posted runs

The code you posted runs without a problem on my machine. It takes 1.3 hours. This could be a parallelism issue. I have a single-threaded version installed, and your crash report listed 14 threads. You could try to reduce the number of threads used by setting the mxOption.

ciModel <- mxOption(ciModel, "Number of Threads", 4)
ciFit <- mxRun(ciModel, intervals=TRUE)

In the worst case, setting the number of threads to 1 should be slow but effective. Anyone have an idea about why multi-threadef CIs would cause a problem?

tbrick's picture
Offline
Joined: 07/31/2009
OS X's OpenMP is broken

OpenMP on OS X is known to be broken. So the OS X build of OpenMx has problems with any kind of parallelism. I had thought we were detecting and catching the problem without it actually crashing R, but apparently that's not true. It's also possible that 10.8 has a new version that's broken in some sort of new and more exciting way. We'll take a look

If you're using OS X and want to be able to run multithreaded, the instructions are pretty straightforward, and are listed in this comment:
http://openmx.psyc.virginia.edu/thread/2071#comment-4677

I believe you have to compile from source to be sure you're linking against the right OpenMP.

bverhulst's picture
Offline
Joined: 03/08/2010
Thanks for the advice. I was

Thanks for the advice.
I was unaware/neglectful of the number of threads argument, but I will try that out and see if it fixes everything.
Thanks again,
Brad