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mike-lawrence/rstanSegafult.log

Created March 3, 2014 16:02
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segfault in rstan
Raw
rstanSegafult.log
> library(rstan)
Loading required package: Rcpp
Loading required package: inline
Attaching package: ‘inline’
The following object is masked from ‘package:Rcpp’:
registerPlugin
rstan (Version 2.2.0, packaged: 2014-02-14 04:29:17 UTC, GitRev: 52d7b230aaa0)
> set_cppo('debug')
mode debug without NDEBUG for compiling C++ code has been set already
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rstan_2.2.0 inline_0.3.13 Rcpp_0.11.0
loaded via a namespace (and not attached):
[1] stats4_3.0.2
> schools_code <- '
+ data {
+ int<lower=0> J; // number of schools
+ real y[J]; // estimated treatment effects
+ real<lower=0> sigma[J]; // s.e. of effect estimates
+ }
+ parameters {
+ real mu;
+ real<lower=0> tau;
+ real eta[J];
+ }
+ transformed parameters {
+ real theta[J];
+ for (j in 1:J)
+ theta[j] <- mu + tau * eta[j];
+ }
+ model {
+ eta ~ normal(0, 1);
+ y ~ normal(theta, sigma);
+ }
+ '
>
> schools_dat <- list(J = 8,
+ y = c(28, 8, -3, 7, -1, 1, 18, 12),
+ sigma = c(15, 10, 16, 11, 9, 11, 10, 18))
>
> fit <- stan(model_code = schools_code, data = schools_dat,
+ iter = 1000, chains = 4)
TRANSLATING MODEL 'schools_code' FROM Stan CODE TO C++ CODE NOW.
COMPILING THE C++ CODE FOR MODEL 'schools_code' NOW.
*** caught segfault ***
address 0x20, cause 'memory not mapped'
Traceback:
1: Module(module, mustStart = TRUE)
2: .getModulePointer(x)
3: <S4 object of class "Module">$stan_fit4model256a256e3533_schools_code
4: <S4 object of class "Module">$stan_fit4model256a256e3533_schools_code
5: eval(expr, envir, enclos)
6: eval(call("$", mod, paste("stan_fit4", model_cppname, sep = "")))
7: .local(object, ...)
8: sampling(sm, data, pars, chains, iter, warmup, thin, seed, init, check_data = TRUE, sample_file = sample_file, diagnostic_file = diagnostic_file, verbose = verbose, algorithm = match.arg(algorithm), control = control, ...)
9: sampling(sm, data, pars, chains, iter, warmup, thin, seed, init, check_data = TRUE, sample_file = sample_file, diagnostic_file = diagnostic_file, verbose = verbose, algorithm = match.arg(algorithm), control = control, ...)
10: stan(model_code = schools_code, data = schools_dat, iter = 1000, chains = 4)
Process: R [9578]
Path: /Applications/R.app/Contents/MacOS/R
Identifier: org.R-project.R
Version: R 3.0.2 GUI 1.62 Snow Leopard build (6558)
Code Type: X86-64 (Native)
Parent Process: launchd [152]
Responsible: R [9578]
User ID: 501
Date/Time: 2014-03-03 11:50:52.035 -0400
OS Version: Mac OS X 10.9.2 (13C64)
Report Version: 11
Anonymous UUID: 81EAA116-CC89-6656-3A72-FEE828864BC0
Sleep/Wake UUID: 5E7F617C-2B92-4F34-945B-34B5FAAD2E68
Crashed Thread: 1 Dispatch queue: com.apple.libdispatch-manager
Exception Type: EXC_CRASH (SIGSEGV)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Thread 0:: Dispatch queue: com.apple.main-thread
0 Rcpp.so 0x0000000109ced0c4 Rcpp::Module::functions_names() + 100
1 Rcpp.so 0x0000000109ceb396 Module__functions_names(SEXPREC*) + 54
2 libR.dylib 0x0000000100182ed5 do_dotcall + 469 (dotcode.c:581)
3 libR.dylib 0x00000001001ad94e bcEval + 9358 (eval.c:4627)
4 libR.dylib 0x00000001001aaf06 Rf_eval + 246 (eval.c:545)
5 libR.dylib 0x00000001001b535e Rf_applyClosure + 1422 (eval.c:1019)
6 libR.dylib 0x00000001001ad77e bcEval + 8894 (eval.c:4597)
7 libR.dylib 0x00000001001aaf06 Rf_eval + 246 (eval.c:545)
8 libR.dylib 0x00000001001b535e Rf_applyClosure + 1422 (eval.c:1019)
9 libR.dylib 0x00000001001ad77e bcEval + 8894 (eval.c:4597)
10 libR.dylib 0x00000001001aaf06 Rf_eval + 246 (eval.c:545)
11 libR.dylib 0x00000001001b8636 R_execMethod + 1398 (eval.c:1115)
12 methods.so 0x00000001099fa520 R_dispatchGeneric + 1856
13 libR.dylib 0x00000001001e5555 do_standardGeneric + 533 (objects.c:1167)
14 libR.dylib 0x00000001001ad60c bcEval + 8524 (eval.c:4587)
15 libR.dylib 0x00000001001aaf06 Rf_eval + 246 (eval.c:545)
16 libR.dylib 0x00000001001b535e Rf_applyClosure + 1422 (eval.c:1019)
17 libR.dylib 0x00000001001e4f94 R_possible_dispatch + 1460 (objects.c:1495)
18 libR.dylib 0x00000001001b67e3 Rf_DispatchOrEval + 515 (eval.c:2474)
19 libR.dylib 0x000000010023b939 do_subset3 + 201 (subset.c:1100)
20 libR.dylib 0x00000001001ab11f Rf_eval + 783 (eval.c:614)
21 libR.dylib 0x00000001001b5c65 do_eval + 597 (eval.c:2254)
22 libR.dylib 0x00000001001ad94e bcEval + 9358 (eval.c:4627)
23 libR.dylib 0x00000001001aaf06 Rf_eval + 246 (eval.c:545)
24 libR.dylib 0x00000001001b535e Rf_applyClosure + 1422 (eval.c:1019)
25 libR.dylib 0x00000001001ab34e Rf_eval + 1342 (eval.c:661)
26 libR.dylib 0x00000001001b7717 do_set + 343 (eval.c:1902)
27 libR.dylib 0x00000001001ab11f Rf_eval + 783 (eval.c:614)
28 libR.dylib 0x00000001001b7a70 do_begin + 384 (eval.c:1573)
29 libR.dylib 0x00000001001ab11f Rf_eval + 783 (eval.c:614)
30 libR.dylib 0x00000001001b535e Rf_applyClosure + 1422 (eval.c:1019)
31 libR.dylib 0x00000001001ad77e bcEval + 8894 (eval.c:4597)
32 libR.dylib 0x00000001001aaf06 Rf_eval + 246 (eval.c:545)
33 libR.dylib 0x00000001001b8636 R_execMethod + 1398 (eval.c:1115)
34 methods.so 0x00000001099fa520 R_dispatchGeneric + 1856
35 libR.dylib 0x00000001001e5555 do_standardGeneric + 533 (objects.c:1167)
36 libR.dylib 0x00000001001ad94e bcEval + 9358 (eval.c:4627)
37 libR.dylib 0x00000001001aaf06 Rf_eval + 246 (eval.c:545)
38 libR.dylib 0x00000001001b535e Rf_applyClosure + 1422 (eval.c:1019)
39 libR.dylib 0x00000001001ad77e bcEval + 8894 (eval.c:4597)
40 libR.dylib 0x00000001001aaf06 Rf_eval + 246 (eval.c:545)
41 libR.dylib 0x00000001001b535e Rf_applyClosure + 1422 (eval.c:1019)
42 libR.dylib 0x00000001001ab34e Rf_eval + 1342 (eval.c:661)
43 libR.dylib 0x00000001001b7717 do_set + 343 (eval.c:1902)
44 libR.dylib 0x00000001001ab11f Rf_eval + 783 (eval.c:614)
45 libR.dylib 0x00000001001d8b9a R_ReplDLLdo1 + 458 (main.c:363)
46 org.R-project.R 0x000000010001f38e run_REngineRmainloop + 302
47 org.R-project.R 0x000000010001379c -[REngine runREPL] + 124
48 org.R-project.R 0x0000000100001b7e main + 910
49 org.R-project.R 0x00000001000017e4 start + 52
Thread 1 Crashed:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff882ab662 kevent64 + 10
1 libdispatch.dylib 0x00007fff85ae343d _dispatch_mgr_invoke + 239
2 libdispatch.dylib 0x00007fff85ae3152 _dispatch_mgr_thread + 52
Thread 2:
0 libsystem_kernel.dylib 0x00007fff882aa9aa __select + 10
1 org.R-project.R 0x000000010000ddf4 -[RController readThread:] + 548
2 com.apple.Foundation 0x00007fff84b7376b __NSThread__main__ + 1318
3 libsystem_pthread.dylib 0x00007fff893f1899 _pthread_body + 138
4 libsystem_pthread.dylib 0x00007fff893f172a _pthread_start + 137
5 libsystem_pthread.dylib 0x00007fff893f5fc9 thread_start + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff882a6a1a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff882a5d18 mach_msg + 64
2 com.apple.CoreFoundation 0x00007fff8b8c6155 __CFRunLoopServiceMachPort + 181
3 com.apple.CoreFoundation 0x00007fff8b8c5779 __CFRunLoopRun + 1161
4 com.apple.CoreFoundation 0x00007fff8b8c50b5 CFRunLoopRunSpecific + 309
5 com.apple.AppKit 0x00007fff8848216e _NSEventThread + 144
6 libsystem_pthread.dylib 0x00007fff893f1899 _pthread_body + 138
7 libsystem_pthread.dylib 0x00007fff893f172a _pthread_start + 137
8 libsystem_pthread.dylib 0x00007fff893f5fc9 thread_start + 13
Thread 4:: com.apple.appkit-heartbeat
0 libsystem_kernel.dylib 0x00007fff882aaa3a __semwait_signal + 10
1 libsystem_c.dylib 0x00007fff8a4a8dc0 nanosleep + 200
2 libsystem_c.dylib 0x00007fff8a4a8cb2 usleep + 54
3 com.apple.AppKit 0x00007fff8854621d -[NSUIHeartBeat _heartBeatThread:] + 2132
4 com.apple.Foundation 0x00007fff84b7376b __NSThread__main__ + 1318
5 libsystem_pthread.dylib 0x00007fff893f1899 _pthread_body + 138
6 libsystem_pthread.dylib 0x00007fff893f172a _pthread_start + 137
7 libsystem_pthread.dylib 0x00007fff893f5fc9 thread_start + 13
Thread 5:
0 libsystem_kernel.dylib 0x00007fff882aae6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff893f2f08 _pthread_wqthread + 330
2 libsystem_pthread.dylib 0x00007fff893f5fb9 start_wqthread + 13
Thread 6:
0 libsystem_kernel.dylib 0x00007fff882aae6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff893f2f08 _pthread_wqthread + 330
2 libsystem_pthread.dylib 0x00007fff893f5fb9 start_wqthread + 13
Thread 7:
0 libsystem_kernel.dylib 0x00007fff882aae6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff893f2f08 _pthread_wqthread + 330
2 libsystem_pthread.dylib 0x00007fff893f5fb9 start_wqthread + 13
Thread 1 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000004 rbx: 0x00007fff710cc900 rcx: 0x0000000101a105c8 rdx: 0x0000000000000000
rdi: 0x0000000000000003 rsi: 0x0000000000000000 rbp: 0x0000000101a10650 rsp: 0x0000000101a105c8
r8: 0x0000000000000001 r9: 0x0000000000000000 r10: 0x0000000101a105e0 r11: 0x0000000000000246
r12: 0x00007fff710cc9c0 r13: 0x0000000101a10610 r14: 0x0000000101a105e0 r15: 0x00007fff85af5c10
rip: 0x00007fff882ab662 rfl: 0x0000000000000247 cr2: 0x0000000106026010
Logical CPU: 0
Error Code: 0x02000171
Trap Number: 133
Binary Images:
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0x100117000 - 0x100380fef +libR.dylib (3.0.2) <3FE96BB2-BC53-3212-8062-3CF47D50413C> /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libR.dylib
0x1004a1000 - 0x1004caff7 +libRblas.dylib (0) <10C1D4A9-CD7F-30B2-8330-EA63EFC82FD1> /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libRblas.dylib
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0x10b57d000 - 0x10b5b9fff +grDevices.so (0) <B1F051BB-A7C3-3CB8-BE82-85CC3C1EBCC8> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/grDevices/libs/grDevices.so
0x10b5d5000 - 0x10b65ffff +stats.so (0) <8C4A196D-CEB0-327C-9BDE-E665FA32C60C> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/libs/stats.so
0x10c800000 - 0x10c97efff +libRlapack.dylib (3.0.2) <AD18949B-10A1-3FCA-A727-A1648D161C06> /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libRlapack.dylib
0x10cfa3000 - 0x10d11bfff +rstan.so (0) <43F1AF34-0AC2-33BE-99F7-C63F048A428C> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/rstan/libs/rstan.so
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0x7fff8d61e000 - 0x7fff8d627ff7 libcldcpuengine.dylib (2.3.58) <C8785704-6195-3129-86CA-20F0F3C20F15> /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libcldcpuengine.dylib
0x7fff8d628000 - 0x7fff8d62aff7 com.apple.securityhi (9.0 - 55005) <405E2BC6-2B6F-3B6B-B48E-2FD39214F052> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
0x7fff8d66a000 - 0x7fff8d8c3ff9 com.apple.security (7.0 - 55471.14) <3F7100A0-FE46-333D-9A4B-396580F1B4FE> /System/Library/Frameworks/Security.framework/Versions/A/Security
0x7fff8d8c4000 - 0x7fff8d8c6ff7 libquarantine.dylib (71) <973BE51D-6465-392F-9099-D4AB21BF0D25> /usr/lib/system/libquarantine.dylib
0x7fff8ddef000 - 0x7fff8ddf0ff7 libsystem_blocks.dylib (63) <FB856CD1-2AEA-3907-8E9B-1E54B6827F82> /usr/lib/system/libsystem_blocks.dylib
0x7fff8ddf1000 - 0x7fff8dec2fff com.apple.QuickLookUIFramework (5.0 - 622.7) <13841701-34C2-353D-868D-3E08D020C90F> /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuickLookUI.framework/Versions/A/QuickLookUI
0x7fff8df4b000 - 0x7fff8df59fff com.apple.opengl (9.6.0 - 9.6.0) <709F4A02-73A0-303C-86B5-85C596C8B707> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff8df5a000 - 0x7fff8df5afff com.apple.ApplicationServices (48 - 48) <F250170A-8805-3731-9097-78CAD04481F0> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x7fff8df5b000 - 0x7fff8df5effc com.apple.IOSurface (91 - 91) <812F4D48-6FD4-3DCB-8691-B077EBF981D7> /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
0x7fff8df5f000 - 0x7fff8df63ff7 libGIF.dylib (1042) <C57840F6-1C11-3273-B4FC-956950B94034> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
0x7fff8e029000 - 0x7fff8e058fff com.apple.DebugSymbols (106 - 106) <9F66640E-277C-317E-A01E-A1E5B13E2592> /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols
0x7fff8e1ae000 - 0x7fff8e1ddfd2 libsystem_m.dylib (3047.16) <9D96AACD-5870-3A5C-B849-7F9C0F6EBB09> /usr/lib/system/libsystem_m.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 3
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: 38786
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=226.2M resident=97.4M(43%) swapped_out_or_unallocated=128.9M(57%)
Writable regions: Total=3.4G written=51.1M(1%) resident=2.2G(66%) swapped_out=4K(0%) unallocated=1.2G(34%)
REGION TYPE VIRTUAL
=========== =======
CG backing stores 18.2M
CG image 648K
CG raster data 524K
CG shared images 244K
CoreAnimation 3224K
CoreImage 32K
Foundation 4K
Image IO 360K
JS JIT generated code 8K
JS JIT generated code (reserved) 1.0G reserved VM address space (unallocated)
Kernel Alloc Once 8K
MALLOC 2.4G
MALLOC (admin) 32K
Memory Tag 242 12K
Memory Tag 251 24K
OpenCL 60K
SQLite page cache 256K
STACK GUARD 56.0M
Stack 11.1M
VM_ALLOCATE 16.4M
WebKit Malloc 1232K
__DATA 28.5M
__IMAGE 528K
__LINKEDIT 71.1M
__TEXT 155.1M
__UNICODE 544K
mapped file 63.5M
shared memory 4K
=========== =======
TOTAL 3.8G
TOTAL, minus reserved VM space 2.8G
Model: MacBookPro11,3, BootROM MBP112.0138.B02, 4 processors, Intel Core i7, 2.6 GHz, 16 GB, SMC 2.19f3
Graphics: Intel Iris Pro, Intel Iris Pro, Built-In, 1024 MB
Graphics: NVIDIA GeForce GT 750M, NVIDIA GeForce GT 750M, PCIe, 2048 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, 0x134), Broadcom BCM43xx 1.0 (6.30.223.154.63)
Bluetooth: Version 4.2.3f10 13477, 3 services, 15 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
Serial ATA Device: APPLE SSD SM0512F, 500.28 GB
USB Device: Internal Memory Card Reader
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
USB Device: Apple Internal Keyboard / Trackpad
Thunderbolt Bus: MacBook Pro, Apple Inc., 17.1
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