Re: [R-SIG-Mac] [External] Re: problem with Rprof

Tomas Kalibera Tue, 08 Nov 2022 13:04:32 -0800


On 11/7/22 01:58, luke-tier...@uiowa.edu wrote:

On Sun, 6 Nov 2022, Simon Urbanek wrote:
Carl,
first, setting such low interval won't work anyway - the overhead isbigger than the sampled time, so we should really not allow it tobegin with (on my machine the timer signals arrive before anythingcan be done so you have to kill R and you get no output).
That said, it crashes in doprof() which is called on all threads -the main R one is ok, but one of the other threads crashes inpthread_self(). At that time R is trying to propagate the signal fromall threads to the main thread which seems odd to me (since the mainthread already got the signal), I'm CCing Luke in the hope that hehas any ideas. This may fall in the category of "don't do this" andthe fix may be to set a lower bound on the interval.
I can't reproduce this on Linux or macOS.

On Linux only one thread receives a signal sent to a process, but the
kernel picks which one if multiple threads have the signal unblocked,
so we make sure the signal gets relayed to the main thread. If macOS
behaves differently then someone who knows how signals and threads
interact there would have to adjust this code.

From my reading this is the same on macOS. The profiling signal isasynchronous, sent to the process, it will be served by one thread whichis picked by the OS. POSIX doesn't say which thread is preferred. Whilesome OSes prefer the main thread (I read macOS and Linux do, but fromnon-authoritative sources), R may also be embedded and not run on themain thread.

We have to do something to ensure the R thread is not running while wesample its R stack, anyway. On Windows we suspend the R thread for that.On Unix we do the relaying. We could in principle suspend the R threadon macOS as well, but would have to use Mach calls directly.

Disallowing such a low interval is reasonable, but if there is a real
issue on macOS then it would only mask the problem.

Yes. The key question is why pthread_self() crashed. Otherwise, from thestack trace, the behavior looks ok. The main thread (also R thread) isserving the signal, hence the signal is blocked, but it is receivedagain, so another thread is picked to serve it, and it is relaying it tothe main thread. One more thread is picked to serve it, and it crasheswhile calling pthread_self(). There is also one more thread not involvedin the signal handling.

POSIX statest that pthread_self() is async-signal-safe. macOS 12.6manuals (sigaction) however doesn't include any pthread function in thelist of async-signal-functions.

We could do some work-around (hiding the problem a bit more) like exitfrom the handler if the signal is being served by another thread. Wecould also report such situation to indicate that the interval isunreasonable. But it would be good first to know for sure what causedthe problem.


Best
Tomas

Best,

luke
Cheers,
Simon
On Nov 6, 2022, at 6:46 AM, Carl Witthoft <c...@witthoft.com> wrote:
Wondering if this is a hiccup in R-mac 4.2.1 (running under 11.6.8Big Sur), or a bug in Rprof:
If I try to set a very small time interval,
 Rprof(interval = 0.000001)  ,
R crashes.

Crash report follows:

Process:               R [54439]
Path:                  /Applications/R.app/Contents/MacOS/R
Identifier:            org.R-project.R
Version:               R 4.2.1 GUI 1.79 High Sierra build (8095)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           R [54439]
User ID:               502

Date/Time:             2022-11-05 13:37:36.003 -0400
OS Version:            macOS 11.6.8 (20G730)
Report Version:        12
Anonymous UUID:        B755C094-C366-46AB-8EEA-9D3B8E7B388D

Sleep/Wake UUID:       6135D492-FF9D-4ED1-AF9F-C0F790F64110

Time Awake Since Boot: 1500000 seconds
Time Since Wake:       7200 seconds

System Integrity Protection: enabled

Crashed Thread:        6

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Segmentation fault: 11
Termination Reason:    Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [54439]

VM Regions Near 0:
-->
__TEXT 103034000-1030bc000 [ 544K]r-x/r-x SM=COW /Applications/R.app/Contents/MacOS/R
Thread 0:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff208cdf4a __sigaction+ 101 libsystem_platform.dylib 0x00007fff2094367c__platform_sigaction + 103
2   libsystem_c.dylib                 0x00007fff207fe689 signal__ + 66
3 libR.dylib 0x000000010323a23c doprof +1676 (eval.c:345)
4   libsystem_platform.dylib          0x00007fff20943d7d _sigtramp + 29
5 ??? 0x8000000000000000 0 +92233720368547758086 libsystem_malloc.dylib 0x00007fff207255ednanov2_allocate + 3677 libsystem_malloc.dylib 0x00007fff2072754dnanov2_calloc + 1238 libsystem_malloc.dylib 0x00007fff2073fff4_malloc_zone_calloc + 599 libobjc.A.dylib 0x00007fff2079c5faclass_createInstance + 6510 com.apple.CoreFoundation 0x00007fff2097a335__CFAllocateObject + 1511 com.apple.CoreFoundation 0x00007fff20980f04__NSDictionaryI_new + 12612 com.apple.CoreFoundation 0x00007fff20980d48+[NSDictionary dictionaryWithObjects:forKeys:count:] + 4913 com.apple.AppKit 0x00007fff23a5dddd-[_NSToolbarButtonCell _symbolImageHints] + 21314 com.apple.AppKit 0x00007fff2326659a-[NSButtonCell _currentImageInView:] + 40115 com.apple.AppKit 0x00007fff232c0992-[NSButtonCell _effectiveContentStyleForImageInView:] + 18416 com.apple.AppKit 0x00007fff232646c4-[NSButtonCell _updateImageViewImageInView:] + 9317 com.apple.AppKit 0x00007fff232645a4__60-[NSButtonCell_updateSubviewsInView:includeTitleTextField:]_block_invoke + 13418 com.apple.AppKit 0x00007fff231ea835+[NSAppearance _performWithCurrentAppearance:usingBlock:] + 6619 com.apple.AppKit 0x00007fff23231321-[NSButtonCell _updateSubviewsInView:includeTitleTextField:] + 13120 com.apple.AppKit 0x00007fff232310eb -[NSButtonupdateCell:] + 8721 com.apple.AppKit 0x00007fff23230a84 -[NSCellsetEnabled:] + 15622 com.apple.AppKit 0x00007fff23230d0f -[NSControlsetEnabled:] + 12023 com.apple.AppKit 0x00007fff2330af46-[NSToolbarItem _reallySetEnabled:] + 124
24  org.R-project.R                   0x000000010304542b Re_RBusy + 59
25 libR.dylib 0x00000001032694bfR_ReplDLLdo1 + 559 (main.c:408)26 org.R-project.R 0x0000000103052e15run_REngineRmainloop + 26127 org.R-project.R 0x000000010304798f -[REnginerunREPL] + 143
28  org.R-project.R                   0x0000000103037288 main + 792
29  libdyld.dylib                     0x00007fff20919f3d start + 1

Thread 1:: JavaScriptCore bmalloc scavenger
0 libsystem_kernel.dylib 0x00007fff208cf91e__pthread_kill + 101 libsystem_pthread.dylib 0x00007fff208fe5bdpthread_kill + 2632 libR.dylib 0x000000010323a24d doprof +1693 (eval.c:231)
3   libsystem_platform.dylib          0x00007fff20943d7d _sigtramp + 29
4   ???                               000000000000000000 0 + 0
5 libc++.1.dylib 0x00007fff20867d72std::__1::condition_variable::wait(std::__1::unique_lock<std::__1::mutex>&)+ 186 com.apple.JavaScriptCore 0x00007fff379f0894 voidstd::__1::condition_variable_any::wait<std::__1::unique_lock<bmalloc::Mutex>>(std::__1::unique_lock<bmalloc::Mutex>&) + 847 com.apple.JavaScriptCore 0x00007fff379f535bbmalloc::Scavenger::threadRunLoop() + 3318 com.apple.JavaScriptCore 0x00007fff379f4ee9bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) + 99 com.apple.JavaScriptCore 0x00007fff379f7a77 void*std::__1::__thread_proxy<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct,std::__1::default_delete<std::__1::__thread_struct> >, void(*)(bmalloc::Scavenger*), bmalloc::Scavenger*> >(void*) + 3910 libsystem_pthread.dylib 0x00007fff208fe8fc_pthread_start + 22411 libsystem_pthread.dylib 0x00007fff208fa443thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff208cf91e__pthread_kill + 101 libsystem_pthread.dylib 0x00007fff208fe5bdpthread_kill + 2632 libR.dylib 0x000000010323a24d doprof +1693 (eval.c:231)
3   libsystem_platform.dylib          0x00007fff20943d7d _sigtramp + 29
4 ??? 0x00007000032c6c18 0 +1231453555538165 com.apple.Foundation 0x00007fff2177f447__NSThread__start__ + 10686 libsystem_pthread.dylib 0x00007fff208fe8fc_pthread_start + 2247 libsystem_pthread.dylib 0x00007fff208fa443thread_start + 15
Thread 3:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff208c92aamach_msg_trap + 10
1   libsystem_kernel.dylib            0x00007fff208c96a9 mach_msg + 201
2 com.apple.CoreFoundation 0x00007fff209f6ecf__CFRunLoopServiceMachPort + 3163 com.apple.CoreFoundation 0x00007fff209f55af__CFRunLoopRun + 13284 com.apple.CoreFoundation 0x00007fff209f49bcCFRunLoopRunSpecific + 5635 com.apple.AppKit 0x00007fff23383bba_NSEventThread + 1246 libsystem_pthread.dylib 0x00007fff208fe8fc_pthread_start + 2247 libsystem_pthread.dylib 0x00007fff208fa443thread_start + 15
Thread 4:
0 libsystem_pthread.dylib 0x00007fff208fa420start_wqthread + 0
Thread 5:: LocalStorage
0 com.apple.JavaScriptCore 0x00007fff3799e468WTF::TimeWithDynamicClockType::nowWithSameClock() const + 1361 com.apple.JavaScriptCore 0x00007fff3797bdedWTF::ParkingLot::parkConditionallyImpl(void const*,WTF::ScopedLambda<bool ()> const&, WTF::ScopedLambda<void ()>const&, WTF::TimeWithDynamicClockType const&) + 36452 com.apple.WebKitLegacy 0x00007fff351643ea boolWTF::Condition::waitUntil<WTF::Lock>(WTF::Lock&,WTF::TimeWithDynamicClockType const&) + 1543 com.apple.WebKitLegacy 0x00007fff35167443std::__1::unique_ptr<WTF::Function<void ()>,std::__1::default_delete<WTF::Function<void ()> > >WTF::MessageQueue<WTF::Function<void ()>>::waitForMessageFilteredWithTimeout<WTF::MessageQueue<WTF::Function<void()> >::waitForMessage()::'lambda'(WTF::Function<void ()>const&)>(WTF::MessageQueueWaitResult&,WTF::MessageQueue<WTF::Function<void ()>>::waitForMessage()::'lambda'(WTF::Function<void ()> const&)&&,WTF::Seconds) + 1474 com.apple.WebKitLegacy 0x00007fff35166ab6WebCore::StorageThread::threadEntryPoint() + 865 com.apple.JavaScriptCore 0x00007fff3799acefWTF::Thread::entryPoint(WTF::Thread::NewThreadContext*) + 2236 com.apple.JavaScriptCore 0x00007fff3691faf9WTF::wtfThreadEntryPoint(void*) + 97 libsystem_pthread.dylib 0x00007fff208fe8fc_pthread_start + 2248 libsystem_pthread.dylib 0x00007fff208fa443thread_start + 15
Thread 6 Crashed:
0 libsystem_pthread.dylib 0x00007fff208fad58pthread_self + 201 libR.dylib 0x0000000103239be8 doprof + 56(eval.c:230)
2   libsystem_platform.dylib          0x00007fff20943d7d _sigtramp + 29

Thread 6 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000000 rcx:0xb42f27cc422d1008 rdx: 0x0000700003243ab8 rdi: 0x000000000000001b rsi: 0x0000700003243a50 rbp:0x00007000032408a0 rsp: 0x00007000032408a0 r8: 0x0000700003243ab8 r9: 0xe1411a080670e3cc r10:0x0000000000000000 r11: 0x0000000000000000 r12: 0xe1411a080670e3cc r13: 0x0000000000000000 r14:0x000000000000001b r15: 0x0000000000000000 rip: 0x00007fff208fad58 rfl: 0x0000000000010202 cr2:0x0000000000000000
Logical CPU:     3
Error Code:      0x00000004 (no mapping for user data read)
Trap Number:     14

Thread 6 instruction stream:
 ff 48 c7 47 28 ff ff ff-ff 31 c0 48 89 06 48 89 .H.G(....1.H..H.
 02 eb 1a 48 c7 c0 ff ff-ff ff 48 89 47 18 48 89 ...H......H.G.H.
 47 28 48 89 47 20 c7 47-18 00 00 00 00 48 89 f8  G(H.G .G.....H..
 48 f7 d0 48 89 47 30 89-4f 38 89 4f 3c 89 4f 14 H..H.G0.O8.O<.O.
 c7 47 04 00 00 00 00 89-0f 31 c0 c3 55 48 89 e5 .G.......1..UH..
 65 48 8b 04 25 00 00 00-00 48 8b 0d 80 dd 2f 60 eH..%....H..../`
[48]33 08 48 39 c8 75 02-5d c3 e8 53 6c 00 00 55 H3.H9.u.]..Sl..U <==
 48 89 e5 41 56 53 48 89-fb 65 48 39 3c 25 00 00 H..AVSH..eH9<%..
 00 00 74 30 45 31 f6 48-85 db 74 62 48 8d 3d 29 ..t0E1.H..tbH.=)
 dd 2f 60 be 00 00 05 00-e8 e5 6d 00 00 48 8b 05 ./`.......m..H..
 d4 dc 2f 60 48 85 c0 74-39 48 39 d8 74 1e 48 8b ../`H..t9H9.t.H.
 40 10 eb f0 48 8b 05 25-dd 2f 60 48 33 03 48 39 @...H..%./`H3.H9

Thread 6 last branch register state not available.


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0x7fff40ed8fffcom.apple.CaptiveNetworkSupport (13.0 - 1)<240BA909-E91B-3F24-A2EC-8D6A02931F5D>/System/Library/PrivateFrameworks/CaptiveNetwork.framework/Versions/A/CaptiveNetwork 0x7fff41290000 - 0x7fff412bffff libncurses.5.4.dylib (57)<FA01E50C-EF52-31C7-99DA-66855588EADC> /usr/lib/libncurses.5.4.dylib 0x7fff412c0000 - 0x7fff412c9fff com.apple.IOAccelMemoryInfo(1.0 - 1) <08AAEF20-40F5-3E42-8A12-B057F6B19622>/System/Library/PrivateFrameworks/IOAccelMemoryInfo.framework/Versions/A/IOAccelMemoryInfo 0x7fff41324000 - 0x7fff41327fff com.apple.quartzframework(1.5 - 25) <2FA7F7A0-15D1-30F2-A17E-98EB732C4310>/System/Library/Frameworks/Quartz.framework/Versions/A/Quartz 0x7fff4174c000 - 0x7fff4176afff libCGInterfaces.dylib(544.5) <10657BC7-3A0C-32CA-A5AC-E2A3A6F49D95>/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib 0x7fff43cf9000 - 0x7fff43f6cfff com.apple.RawCamera.bundle(9.10.0 - 1450.3) <9CF8B9F4-AA5E-335B-A17F-BBBFDC66E9C5>/System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera 0x7fff4402b000 - 0x7fff440a3fff com.apple.ShareKit (668 -668) <5802F889-D618-38F4-9566-247EE7F5FB9F>/System/Library/PrivateFrameworks/ShareKit.framework/Versions/A/ShareKit 0x7fff47e75000 - 0x7fff47eb6fffcom.apple.osanalytics.OSAnalytics (1.0 - 1)<0866BE79-2765-3533-B7A5-905869A2799F>/System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics 0x7fff4bbda000 - 0x7fff4bbddfff com.apple.FinderSyncPriv(1.7.1 - 1350.7.1) <37F01F1D-DFF1-3609-B7B9-F39CC19DB991>/System/Library/PrivateFrameworks/FinderSyncPriv.framework/Versions/A/FinderSyncPriv 0x7fff51946000 - 0x7fff519e5fff com.apple.Symbolication (12.5- 64544.70.1) <6D9C8333-6369-3964-A972-5BF99B0AC549>/System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication 0x7fff69993000 - 0x7fff69997fff libmetal_timestamp.dylib(31001.192.1) <B3C388EA-0FE0-3F19-A575-59A2ACA1428E>/System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib 0x7fff6bdde000 - 0x7fff6bde4fff libCoreFSCache.dylib(200.12) <0E7443EE-D778-3B2E-9973-F825BCA0E0D6>/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib 0x7fff6bde5000 - 0x7fff6bde9fff libCoreVMClient.dylib(200.12) <93679C5E-92E3-3C6A-A585-C603F4AD399A>/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib 0x7fff6bdea000 - 0x7fff6bdf9fff com.apple.opengl (18.5.9 -18.5.9) <2A421CC5-4D60-339C-9772-3AC991232BD8>/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x7fff6bdfa000 - 0x7fff6bdfcfff libCVMSPluginSupport.dylib(18.5.9) <BF44FEB3-FB8E-3FD8-8988-AD56AD53CFD4>/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib 0x7fff6bdfd000 - 0x7fff6be05fff libGFXShared.dylib (18.5.9)<C4751529-359A-3ECC-84B2-74A23EFAD42A>/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib 0x7fff6be06000 - 0x7fff6be39fff libGLImage.dylib (18.5.9)<C153E192-20A3-3F7D-A897-533DACE748EC>/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x7fff6be3a000 - 0x7fff6be76fff libGLU.dylib (18.5.9)<8275A6AB-AAD5-3222-A80B-411C0FAFCA63>/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x7fff6c00b000 - 0x7fff6c015fff libGL.dylib (18.5.9)<C6BE589B-CD26-3142-BD18-10C13D404904>/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x7fff6d455000 - 0x7fff6d4adfff com.apple.opencl (4.6 - 4.6)<79DA4138-12AB-3561-9967-D49EFB14B437>/System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x7fff6dfd7000 - 0x7fff6e1f2fff com.apple.AMDMTLBronzeDriver(4.6.21 - 4.0.6) <4FABB9FE-AA27-38FA-8D8C-11D4F41D95A2>/System/Library/Extensions/AMDMTLBronzeDriver.bundle/Contents/MacOS/AMDMTLBronzeDriver 0x7fff6e55f000 - 0x7fff6e646fff com.apple.audio.AVFAudio (1.0- 477.88) <B2C8331B-60D4-3651-B9A0-B9914A230C36>/System/Library/Frameworks/AVFAudio.framework/Versions/A/AVFAudio 0x7fff6f7da000 - 0x7fff6f7e4fffcom.apple.AccessibilityBundles (1.0 - 174)<02426063-0FDE-340D-9129-25FFEAD81CD0>/System/Library/PrivateFrameworks/AccessibilityBundles.framework/Versions/A/AccessibilityBundles 0x7fff6fbc8000 - 0x7fff6fbdafff com.apple.CMImaging (1.0 -82.6) <F60EEDA0-C221-3B51-B537-EE2FE48E19E9>/System/Library/PrivateFrameworks/CMImaging.framework/Versions/A/CMImaging 0x7fff77a41000 - 0x7fff77a48fff libRosetta.dylib (203.58)<26D08622-69F5-32DB-80D2-9B4651A9F0CC> /usr/lib/libRosetta.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: 0
   thread_create: 0
   thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=906.4M resident=0K(0%)swapped_out_or_unallocated=906.4M(100%)Writable regions: Total=2.0G written=0K(0%) resident=0K(0%)swapped_out=0K(0%) unallocated=2.0G(100%)
                               VIRTUAL   REGION
REGION TYPE                        SIZE    COUNT (non-coalesced)
===========                     =======  =======
Accelerate framework               512K        4
Activity Tracing                   256K        1
CG backing stores                 4608K        6
CG image                          1632K       32
CG raster data                     176K       10
CoreAnimation                    375.9M      159
CoreGraphics                        12K        2
CoreImage                          304K       15
CoreUI image data                 3092K       26
Foundation                          60K        2
IOKit                             7940K        1
Image IO                           500K       20
JS JIT generated code              1.0G        3
JS VM Isolated Heap                708K       17
Kernel Alloc Once                    8K        1
MALLOC                           251.3M       93
MALLOC guard page                   32K        8
MALLOC_NANO (reserved) 384.0M 1 reserved VM addressspace (unallocated)
SQLite page cache                  192K        3
STACK GUARD                       56.0M        7
Stack                             11.0M        7
VM_ALLOCATE                        140K       32
WebKit Malloc                     15.2M       17
__DATA                            22.2M      497
__DATA_CONST                      28.0M      300
__DATA_DIRTY                      1705K      210
__FONT_DATA                          4K        1
__LINKEDIT                       502.9M       39
__OBJC_RO                         70.3M        1
__OBJC_RW                         2496K        2
__TEXT                           403.7M      490
__UNICODE                          588K        1
mapped file                      274.2M       68
shared memory                      744K       13
===========                     =======  =======
TOTAL                              3.4G     2089
TOTAL, minus reserved VM space     3.0G     2089


--
Carl Witthoft
personal: c...@witthoft.com
The Witthoft Group, Consulting
https://witthoftgroup.weebly.com/

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Re: [R-SIG-Mac] [External] Re: problem with Rprof

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