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R crashes when using -qopenmp flag

I have an R package available here: https://github.com/jsilve24/mongrel/tree/develop

I have started linking this to MKL using  following R makevars parameters:

PKG_CPPFLAGS =  -I../inst/include/ -DMONGREL_USE_MKL
PKG_CXXFLAGS = -I/opt/intel/compilers_and_libraries_2019.1.144/mac/mkl/include -qopenmp
PKG_LIBS = -L/opt/intel/compilers_and_libraries_2019.1.144/mac/mkl/lib -Wl,-rpath,/opt/intel/compilers_and_libraries_2019.1.144/mac/mkl/lib -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl 

However whenever I add the -qopenmp flag as I do above everything compiles but R crashes whenever I try to run the program. This never happened when I was using Clang. I am now using  icc (ICC) 19.0.1.144 20181018. 

 

I don't know where to even begin debugging this problem. I would like to use my own omp pragmas but without that flag I don't believe I can (unless I am mistaken). 

 

Thank you!

Justin

 

0 Kudos
6 Replies
135 Views

UPDATE: This is the Error report I get when R crashes

 

Process:               R [36630]
Path:                  /Applications/R.app/Contents/MacOS/R
Identifier:            org.R-project.R
Version:               R 3.5.1 GUI 1.70 El Capitan build (7543)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           R [36630]
User ID:               503

Date/Time:             2018-12-18 07:57:25.771 -0500
OS Version:            Mac OS X 10.13.6 (17G3025)
Report Version:        12
Anonymous UUID:        F525F1A1-4041-0A71-F177-D2BD72A18D32

Sleep/Wake UUID:       343BFF89-35E8-44E9-A5F5-CA409188B65D

Time Awake Since Boot: 78000 seconds
Time Since Wake:       320 seconds

System Integrity Protection: enabled

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

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

Application Specific Information:
abort() called

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib            0x00007fff7a5b5b66 __pthread_kill + 10
1   libsystem_pthread.dylib           0x00007fff7a780080 pthread_kill + 333
2   libsystem_c.dylib                 0x00007fff7a5111ae abort + 127
3   libomp.dylib                      0x000000010e48a712 __kmp_abort_process + 43
4   libomp.dylib                      0x000000010e489251 __kmp_fatal + 150
5   libomp.dylib                      0x000000010e49053e __kmp_register_library_startup() + 621
6   libomp.dylib                      0x000000010e4897b3 __kmp_do_serial_initialize() + 29
7   libomp.dylib                      0x000000010e4905f3 __kmp_do_middle_initialize() + 27
8   libomp.dylib                      0x000000010e4905c1 __kmp_middle_initialize + 52
9   libomp.dylib                      0x000000010e4bd5b0 omp_get_max_threads + 21
10  mongrel.so                        0x000000010e3252a8 void Eigen::internal::parallelize_gemm<true, Eigen::internal::gemm_functor<double, long, Eigen::internal::general_matrix_matrix_product<long, double, 0, false, double, 0, false, 0>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::internal::gemm_blocking_space<0, double, double, -1, -1, -1, 1, false> >, long>(Eigen::internal::gemm_functor<double, long, Eigen::internal::general_matrix_matrix_product<long, double, 0, false, double, 0, false, 0>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::internal::gemm_blocking_space<0, double, double, -1, -1, -1, 1, false> > const&, long, long, long, bool) + 2344
11  mongrel.so                        0x000000010e323fe5 void Eigen::internal::generic_product_impl<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::DenseShape, Eigen::DenseShape, 8>::evalTo<Eigen::Matrix<double, -1, -1, 0, -1, -1> >(Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&) + 405
12  mongrel.so                        0x000000010e352a2d void Eigen::internal::generic_product_impl<Eigen::Product<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::DenseShape, Eigen::DenseShape, 8>::scaleAndAddTo<Eigen::Matrix<double, -1, -1, 0, -1, -1> >(Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Product<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, double const&) + 621
13  mongrel.so                        0x000000010e351d04 void Eigen::internal::generic_product_impl<Eigen::Product<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::DenseShape, Eigen::DenseShape, 8>::evalTo<Eigen::Matrix<double, -1, -1, 0, -1, -1> >(Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Product<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&) + 260
14  mongrel.so                        0x000000010e35190a void Eigen::internal::generic_product_impl<Eigen::Product<Eigen::Product<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0>, Eigen::Transpose<Eigen::Matrix<double, -1, -1, 0, -1, -1> >, Eigen::DenseShape, Eigen::DenseShape, 8>::scaleAndAddTo<Eigen::Matrix<double, -1, -1, 0, -1, -1> >(Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Product<Eigen::Product<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0> const&, Eigen::Transpose<Eigen::Matrix<double, -1, -1, 0, -1, -1> > const&, double const&) + 586
15  mongrel.so                        0x000000010e350bc7 void Eigen::internal::generic_product_impl<Eigen::Product<Eigen::Product<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0>, Eigen::Transpose<Eigen::Matrix<double, -1, -1, 0, -1, -1> >, Eigen::DenseShape, Eigen::DenseShape, 8>::evalTo<Eigen::Matrix<double, -1, -1, 0, -1, -1> >(Eigen::Matrix<double, -1, -1, 0, -1, -1>&, Eigen::Product<Eigen::Product<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0> const&, Eigen::Transpose<Eigen::Matrix<double, -1, -1, 0, -1, -1> > const&) + 263
16  mongrel.so                        0x000000010e36ccff MongrelCollapsed::updateWithEtaLL(Eigen::Ref<Eigen::Matrix<double, -1, 1, 0, -1, 1> const, 0, Eigen::InnerStride<1> > const&) + 1919
17  mongrel.so                        0x000000010e36f526 MongrelCollapsed::f_grad(Eigen::Ref<Eigen::Matrix<double, -1, 1, 0, -1, 1> const, 0, Eigen::InnerStride<1> > const&, Eigen::Ref<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::InnerStride<1> >) + 38
18  mongrel.so                        0x000000010e37912e Numer::LBFGSFun::operator()(Eigen::Matrix<double, -1, 1, 0, -1, 1> const&, Eigen::Matrix<double, -1, 1, 0, -1, 1>&) + 62
19  mongrel.so                        0x000000010e37444c int LBFGSpp::LBFGSSolver<double>::minimize<Numer::LBFGSFun>(Numer::LBFGSFun&, Eigen::Matrix<double, -1, 1, 0, -1, 1>&, double&) + 92
20  mongrel.so                        0x000000010e373ca3 Numer::optim_lbfgs(Numer::MFuncGrad&, Eigen::Ref<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::InnerStride<1> >, double&, int, double const&, double const&) + 915
21  mongrel.so                        0x000000010e37083e optimMongrelCollapsed(Eigen::Array<double, -1, -1, 0, -1, -1>, double, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, -1, 0, -1, -1>, int, bool, double, double, double, double, double, double, int, bool, int, Rcpp::String, Rcpp::String, double, double, bool, double, bool, int) + 878
22  mongrel.so                        0x000000010e3925a1 _mongrel_optimMongrelCollapsed + 1473
23  libR.dylib                        0x0000000106c559bd R_doDotCall + 6365
24  libR.dylib                        0x0000000106c56333 do_dotcall + 323 (dotcode.c:1252)
25  libR.dylib                        0x0000000106c84c9a Rf_eval + 1658 (eval.c:727)
26  libR.dylib                        0x0000000106c99580 do_begin + 432 (eval.c:2404)
27  libR.dylib                        0x0000000106c849ce Rf_eval + 942 (eval.c:699)
28  libR.dylib                        0x0000000106c9714c R_execClosure + 3004
29  libR.dylib                        0x0000000106c84d0c Rf_eval + 1772 (eval.c:747)
30  libR.dylib                        0x0000000106c9a169 do_set + 2201 (eval.c:2787)
31  libR.dylib                        0x0000000106c849ce Rf_eval + 942 (eval.c:699)
32  libR.dylib                        0x0000000106c99580 do_begin + 432 (eval.c:2404)
33  libR.dylib                        0x0000000106c849ce Rf_eval + 942 (eval.c:699)
34  libR.dylib                        0x0000000106c9714c R_execClosure + 3004
35  libR.dylib                        0x0000000106c84d0c Rf_eval + 1772 (eval.c:747)
36  libR.dylib                        0x0000000106c9a169 do_set + 2201 (eval.c:2787)
37  libR.dylib                        0x0000000106c849ce Rf_eval + 942 (eval.c:699)
38  libR.dylib                        0x0000000106cc81f8 R_ReplDLLdo1 + 360 (main.c:391)
39  org.R-project.R                   0x0000000106adcddf run_REngineRmainloop + 287
40  org.R-project.R                   0x0000000106ad0e31 -[REngine runREPL] + 225
41  org.R-project.R                   0x0000000106abfba1 main + 817
42  libdyld.dylib                     0x00007fff7a465015 start + 1

Thread 1:
0   libsystem_kernel.dylib            0x00007fff7a5b5a16 __psynch_cvwait + 10
1   libsystem_pthread.dylib           0x00007fff7a77e589 _pthread_cond_wait + 732
2   libc++.1.dylib                    0x00007fff783b9cb0 std::__1::condition_variable::wait(std::__1::unique_lock<std::__1::mutex>&) + 18
3   com.apple.JavaScriptCore          0x00007fff561aa8a6 void std::__1::condition_variable_any::wait<std::__1::unique_lock<bmalloc::Mutex> >(std::__1::unique_lock<bmalloc::Mutex>&) + 86
4   com.apple.JavaScriptCore          0x00007fff561aa55b bmalloc::Scavenger::threadRunLoop() + 251
5   com.apple.JavaScriptCore          0x00007fff561aa359 bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) + 9
6   com.apple.JavaScriptCore          0x00007fff561aa698 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*) + 40
7   libsystem_pthread.dylib           0x00007fff7a77d661 _pthread_body + 340
8   libsystem_pthread.dylib           0x00007fff7a77d50d _pthread_start + 377
9   libsystem_pthread.dylib           0x00007fff7a77cbf9 thread_start + 13

Thread 2:
0   libobjc.A.dylib                   0x00007fff7983dea1 objc_msgSend + 33
1   com.apple.Foundation              0x00007fff5469d599 lastConversationInfo + 58
2   com.apple.Foundation              0x00007fff5469c7ca -[NSConnection sendInvocation:internal:] + 355
3   com.apple.CoreFoundation          0x00007fff5252f43c ___forwarding___ + 748
4   com.apple.CoreFoundation          0x00007fff5252f0c8 _CF_forwarding_prep_0 + 120
5   org.R-project.R                   0x0000000106ac2c9a -[RController readThread:] + 1722
6   com.apple.Foundation              0x00007fff5463f148 __NSThread__start__ + 1197
7   libsystem_pthread.dylib           0x00007fff7a77d661 _pthread_body + 340
8   libsystem_pthread.dylib           0x00007fff7a77d50d _pthread_start + 377
9   libsystem_pthread.dylib           0x00007fff7a77cbf9 thread_start + 13

Thread 3:: com.apple.NSEventThread
0   libsystem_kernel.dylib            0x00007fff7a5ac20a mach_msg_trap + 10
1   libsystem_kernel.dylib            0x00007fff7a5ab724 mach_msg + 60
2   com.apple.CoreFoundation          0x00007fff52534665 __CFRunLoopServiceMachPort + 341
3   com.apple.CoreFoundation          0x00007fff525339b7 __CFRunLoopRun + 1783
4   com.apple.CoreFoundation          0x00007fff52533033 CFRunLoopRunSpecific + 483
5   com.apple.AppKit                  0x00007fff4fc0afc4 _NSEventThread + 184
6   libsystem_pthread.dylib           0x00007fff7a77d661 _pthread_body + 340
7   libsystem_pthread.dylib           0x00007fff7a77d50d _pthread_start + 377
8   libsystem_pthread.dylib           0x00007fff7a77cbf9 thread_start + 13

Thread 4:
0   libsystem_kernel.dylib            0x00007fff7a5b628a __workq_kernreturn + 10
1   libsystem_pthread.dylib           0x00007fff7a77d009 _pthread_wqthread + 1035
2   libsystem_pthread.dylib           0x00007fff7a77cbe9 start_wqthread + 13

Thread 5:
0   libsystem_kernel.dylib            0x00007fff7a5b628a __workq_kernreturn + 10
1   libsystem_pthread.dylib           0x00007fff7a77d009 _pthread_wqthread + 1035
2   libsystem_pthread.dylib           0x00007fff7a77cbe9 start_wqthread + 13

Thread 6:
0   libsystem_pthread.dylib           0x00007fff7a77cbdc start_wqthread + 0
1   ???                               0x00006040001f6610 0 + 105827996231184

Thread 7:
0   libsystem_kernel.dylib            0x00007fff7a5b628a __workq_kernreturn + 10
1   libsystem_pthread.dylib           0x00007fff7a77d009 _pthread_wqthread + 1035
2   libsystem_pthread.dylib           0x00007fff7a77cbe9 start_wqthread + 13

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x00007fffb2eab380  rcx: 0x00007ffee913e0e8  rdx: 0x0000000000000000
  rdi: 0x0000000000000307  rsi: 0x0000000000000006  rbp: 0x00007ffee913e120  rsp: 0x00007ffee913e0e8
   r8: 0x00007f8d34e29600   r9: 0x0000000000008002  r10: 0x0000000000000000  r11: 0x0000000000000206
  r12: 0x0000000000000307  r13: 0x00007ffee913e310  r14: 0x0000000000000006  r15: 0x000000000000002d
  rip: 0x00007fff7a5b5b66  rfl: 0x0000000000000206  cr2: 0x00007fffb2e88168
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133


Binary Images:
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       0x106bd1000 -        0x106e8cfff +libR.dylib (0) <6BF8385C-D0BA-38DB-AC62-60C673E5DC71> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib
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    0x7fff761b0000 -     0x7fff7635ffff  com.apple.UIFoundation (1.0 - 547.5) <86A2FBA7-2709-3894-A3D5-A00C19BAC48D> /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
    0x7fff77034000 -     0x7fff77103ff7  com.apple.ViewBridge (343.2 - 343.2) <5519FCED-1F88-3BE6-9BE1-69992086B01B> /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
    0x7fff77adb000 -     0x7fff77addffb  com.apple.loginsupport (1.0 - 1) <D1232C1B-80EA-3DF8-9466-013695D0846E> /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
    0x7fff77ade000 -     0x7fff77af3fff  com.apple.login (3.0 - 3.0) <79189BF9-70D4-3839-9E2F-B3990B673A3E> /System/Library/PrivateFrameworks/login.framework/Versions/A/login
    0x7fff77b1e000 -     0x7fff77b4bfff  com.apple.contacts.vCard (1.0 - 2330.3) <02AB9DF0-0471-3FDA-8EC6-27C72E00DD75> /System/Library/PrivateFrameworks/vCard.framework/Versions/A/vCard
    0x7fff77c44000 -     0x7fff77c77ff7  libclosured.dylib (551.5) <112BC241-6626-3848-8DD8-B34B5B6F7ABC> /usr/lib/closure/libclosured.dylib
    0x7fff77d31000 -     0x7fff77d6aff7  libCRFSuite.dylib (41) <FE5EDB68-2593-3C2E-BBAF-1C52D206F296> /usr/lib/libCRFSuite.dylib
    0x7fff77d6b000 -     0x7fff77d76fff  libChineseTokenizer.dylib (28) <53633C9B-A3A8-36F7-A53C-432D802F4BB8> /usr/lib/libChineseTokenizer.dylib
    0x7fff77e08000 -     0x7fff77e09ff3  libDiagnosticMessagesClient.dylib (104) <9712E980-76EE-3A89-AEA6-DF4BAF5C0574> /usr/lib/libDiagnosticMessagesClient.dylib
    0x7fff77e40000 -     0x7fff7800aff3  libFosl_dynamic.dylib (17.8) <C58ED77A-4986-31C2-994C-34DDFB8106F0> /usr/lib/libFosl_dynamic.dylib
    0x7fff78042000 -     0x7fff78042fff  libOpenScriptingUtil.dylib (174) <610F0242-7CE5-3C86-951B-B646562694AF> /usr/lib/libOpenScriptingUtil.dylib
    0x7fff78179000 -     0x7fff7817dffb  libScreenReader.dylib (562.18.4) <E239923D-54C9-3BBF-852F-87C09DEF4091> /usr/lib/libScreenReader.dylib
    0x7fff7817e000 -     0x7fff7817fffb  libSystem.B.dylib (1252.50.4) <5BDEB632-6CFD-30E4-B917-F6EE581DB4F2> /usr/lib/libSystem.B.dylib
    0x7fff781fe000 -     0x7fff781fffff  libThaiTokenizer.dylib (2.2) <6F416F41-BF77-3078-A05C-AFF5DA5AB008> /usr/lib/libThaiTokenizer.dylib
    0x7fff78212000 -     0x7fff78212fff  libapple_crypto.dylib (109.50.14) <48BA2E76-BF2F-3522-A54E-D7FB7EAF7A57> /usr/lib/libapple_crypto.dylib
    0x7fff78213000 -     0x7fff78229ff7  libapple_nghttp2.dylib (1.24) <01402BC4-4822-3676-9C80-50D83F816424> /usr/lib/libapple_nghttp2.dylib
    0x7fff7822a000 -     0x7fff78254ff3  libarchive.2.dylib (54) <8FC28DD8-E315-3C3E-95FE-D1D2CBE49888> /usr/lib/libarchive.2.dylib
    0x7fff78255000 -     0x7fff782d6fdf  libate.dylib (1.13.1) <178ACDAD-DE7E-346C-A613-1CBF7929AC07> /usr/lib/libate.dylib
    0x7fff782da000 -     0x7fff782daff3  libauto.dylib (187) <A05C7900-F8C7-3E75-8D3F-909B40C19717> /usr/lib/libauto.dylib
    0x7fff782db000 -     0x7fff78393ff3  libboringssl.dylib (109.50.14) <E6813F87-B5E4-3F7F-A725-E6A7F2BD02EC> /usr/lib/libboringssl.dylib
    0x7fff78394000 -     0x7fff783a4ff3  libbsm.0.dylib (39) <6BC96A72-AFBE-34FD-91B1-748A530D8AE6> /usr/lib/libbsm.0.dylib
    0x7fff783a5000 -     0x7fff783b2ffb  libbz2.1.0.dylib (38) <0A5086BB-4724-3C14-979D-5AD4F26B5B45> /usr/lib/libbz2.1.0.dylib
    0x7fff783b3000 -     0x7fff78409fff  libc++.1.dylib (400.9) <7D3DACCC-3804-393C-ABC1-1A580FD00CB6> /usr/lib/libc++.1.dylib
    0x7fff7840a000 -     0x7fff7842eff7  libc++abi.dylib (400.8.2) <EF5E37D7-11D9-3530-BE45-B986612D13E2> /usr/lib/libc++abi.dylib
    0x7fff78430000 -     0x7fff78440fff  libcmph.dylib (6) <890DEC4C-4334-393C-8B56-7C8560BBED9D> /usr/lib/libcmph.dylib
    0x7fff78441000 -     0x7fff78458fcf  libcompression.dylib (47.60.2) <543F07BF-2F2F-37D5-9866-E84BF659885B> /usr/lib/libcompression.dylib
    0x7fff78703000 -     0x7fff7871bff7  libcoretls.dylib (155.50.1) <D350052E-DC4D-3185-ADBA-BA48EDCEE955> /usr/lib/libcoretls.dylib
    0x7fff7871c000 -     0x7fff7871dff3  libcoretls_cfhelpers.dylib (155.50.1) <B297F5D8-F2FE-3566-A752-E9D998B9C039> /usr/lib/libcoretls_cfhelpers.dylib
    0x7fff78bee000 -     0x7fff78c44ff3  libcups.2.dylib (462.2.5) <EA944DD1-0B60-32E9-8FB4-BE642D2E7352> /usr/lib/libcups.2.dylib
    0x7fff78d84000 -     0x7fff78d84fff  libenergytrace.dylib (16) <A92AB8B8-B986-3CE6-980D-D55090FEF387> /usr/lib/libenergytrace.dylib
    0x7fff78db6000 -     0x7fff78dbaff7  libgermantok.dylib (17) <37C1C061-5214-3050-9C3A-783A784435A8> /usr/lib/libgermantok.dylib
    0x7fff78dbb000 -     0x7fff78dc0ff3  libheimdal-asn1.dylib (520.50.7) <BC22EC07-A701-3B8F-B075-E29BB437E6CF> /usr/lib/libheimdal-asn1.dylib
    0x7fff78dec000 -     0x7fff78eddff7  libiconv.2.dylib (51.50.1) <2FEC9707-3FAF-3828-A50D-8605086D060F> /usr/lib/libiconv.2.dylib
    0x7fff78ede000 -     0x7fff79105ffb  libicucore.A.dylib (59181.0.1) <2CE6205F-D375-3BF5-AA0A-3254BC4773D0> /usr/lib/libicucore.A.dylib
    0x7fff79152000 -     0x7fff79153fff  liblangid.dylib (128) <39C39393-0D05-301D-93B2-F224FC4949AA> /usr/lib/liblangid.dylib
    0x7fff79154000 -     0x7fff7916dffb  liblzma.5.dylib (10) <3D419A50-961F-37D2-8A01-3DC7AB7B8D18> /usr/lib/liblzma.5.dylib
    0x7fff7916e000 -     0x7fff79184ff7  libmarisa.dylib (9) <D6D2D55D-1D2E-3442-B152-B18803C0ABB4> /usr/lib/libmarisa.dylib
    0x7fff79185000 -     0x7fff79234fff  libmecab.1.0.0.dylib (779.7.6) <334D4742-BDDD-3C2D-BBEB-85B32643BFA0> /usr/lib/libmecab.1.0.0.dylib
    0x7fff79235000 -     0x7fff7945dff7  libmecabra.dylib (779.7.6) <F462F170-E872-3D09-B219-973D5E99C09F> /usr/lib/libmecabra.dylib
    0x7fff79462000 -     0x7fff79492ffb  libncurses.5.4.dylib (53) <030DF747-F71B-367A-83EE-2F30B7947929> /usr/lib/libncurses.5.4.dylib
    0x7fff79635000 -     0x7fff797b0fff  libnetwork.dylib (1229.70.2) <E185D902-AC7F-3044-87C0-AE2887C59CE7> /usr/lib/libnetwork.dylib
    0x7fff79837000 -     0x7fff79c257e7  libobjc.A.dylib (723) <DD9E5EC5-B507-3249-B700-93433E2D5EDF> /usr/lib/libobjc.A.dylib
    0x7fff79c38000 -     0x7fff79c3cfff  libpam.2.dylib (22) <7B4D2CE2-1438-387A-9802-5CEEFBF26F86> /usr/lib/libpam.2.dylib
    0x7fff79c3f000 -     0x7fff79c73fff  libpcap.A.dylib (79.20.1) <FA13918B-A247-3181-B256-9B852C7BA316> /usr/lib/libpcap.A.dylib
    0x7fff79cf2000 -     0x7fff79d0effb  libresolv.9.dylib (65) <E8F3415B-4472-3202-8901-41FD87981DB2> /usr/lib/libresolv.9.dylib
    0x7fff79d4a000 -     0x7fff79d5cfff  libsasl2.2.dylib (211) <04EF3F61-12EC-3319-A649-851999F4C7A4> /usr/lib/libsasl2.2.dylib
    0x7fff79d5d000 -     0x7fff79d5eff3  libspindump.dylib (252) <D8E27057-E3CC-3D7F-A010-4A87830F6A83> /usr/lib/libspindump.dylib
    0x7fff79d5f000 -     0x7fff79ef2ff7  libsqlite3.dylib (274.8.1) <FCAD6A57-829E-3701-B16E-1833D620E0E8> /usr/lib/libsqlite3.dylib
    0x7fff7a079000 -     0x7fff7a0aefff  libtidy.A.dylib (15.18.1) <D1FF31AF-3000-366D-8714-09B2330007B5> /usr/lib/libtidy.A.dylib
    0x7fff7a0c6000 -     0x7fff7a126ff3  libusrtcp.dylib (1229.70.2) <1E065228-D0E3-3808-9405-894056C6BEC0> /usr/lib/libusrtcp.dylib
    0x7fff7a127000 -     0x7fff7a12affb  libutil.dylib (51.20.1) <216D18E5-0BAF-3EAF-A38E-F6AC37CBABD9> /usr/lib/libutil.dylib
    0x7fff7a12b000 -     0x7fff7a138fff  libxar.1.dylib (400) <0316128D-3B47-3052-995D-97B4FE5491DC> /usr/lib/libxar.1.dylib
    0x7fff7a13c000 -     0x7fff7a223fff  libxml2.2.dylib (31.13) <8C12B82A-66FD-330C-9BEA-AAC090C7076A> /usr/lib/libxml2.2.dylib
    0x7fff7a224000 -     0x7fff7a24cfff  libxslt.1.dylib (15.12) <4A5E011D-8B29-3135-A52B-9A9070ABD752> /usr/lib/libxslt.1.dylib
    0x7fff7a24d000 -     0x7fff7a25fffb  libz.1.dylib (70) <48C67CFC-940D-3857-8DAD-857774605352> /usr/lib/libz.1.dylib
    0x7fff7a2fb000 -     0x7fff7a2ffff7  libcache.dylib (80) <092479CB-1008-3A83-BECF-E115F24D13C1> /usr/lib/system/libcache.dylib
    0x7fff7a300000 -     0x7fff7a30aff3  libcommonCrypto.dylib (60118.50.1) <029F5985-9B6E-3DCB-9B96-FD007678C6A7> /usr/lib/system/libcommonCrypto.dylib
    0x7fff7a30b000 -     0x7fff7a312fff  libcompiler_rt.dylib (62) <968B8E3F-3681-3230-9D78-BB8732024F6E> /usr/lib/system/libcompiler_rt.dylib
    0x7fff7a313000 -     0x7fff7a31cffb  libcopyfile.dylib (146.50.5) <3885083D-50D8-3EEC-B481-B2E605180D7F> /usr/lib/system/libcopyfile.dylib
    0x7fff7a31d000 -     0x7fff7a3a2ffb  libcorecrypto.dylib (562.70.2) <495BACA2-67D7-369D-ABB1-FE67FAF63A6A> /usr/lib/system/libcorecrypto.dylib
    0x7fff7a42a000 -     0x7fff7a463ff7  libdispatch.dylib (913.60.3) <BF368549-2DFB-3530-B4CB-31D5EDAC4F2F> /usr/lib/system/libdispatch.dylib
    0x7fff7a464000 -     0x7fff7a481ff7  libdyld.dylib (551.5) <49BF9E96-8297-30CF-8AA6-128CC14054B2> /usr/lib/system/libdyld.dylib
    0x7fff7a482000 -     0x7fff7a482ffb  libkeymgr.dylib (28) <E34E283E-90FA-3C59-B48E-1277CDB9CDCE> /usr/lib/system/libkeymgr.dylib
    0x7fff7a483000 -     0x7fff7a48fff3  libkxld.dylib (4570.71.13) <8B5CF013-E6D0-385D-B648-1153FCF3EAB3> /usr/lib/system/libkxld.dylib
    0x7fff7a490000 -     0x7fff7a490ff7  liblaunch.dylib (1205.70.9) <B184B521-FF24-3142-AFAF-23D170CF918C> /usr/lib/system/liblaunch.dylib
    0x7fff7a491000 -     0x7fff7a495ffb  libmacho.dylib (906) <1902A611-081A-3452-B11E-EBD1B166E831> /usr/lib/system/libmacho.dylib
    0x7fff7a496000 -     0x7fff7a498ff3  libquarantine.dylib (86) <26C0BA22-8F93-3A07-9A4E-C8D53D2CE42E> /usr/lib/system/libquarantine.dylib
    0x7fff7a499000 -     0x7fff7a49aff3  libremovefile.dylib (45) <711E18B2-5BBE-3211-A916-56740C27D17A> /usr/lib/system/libremovefile.dylib
    0x7fff7a49b000 -     0x7fff7a4b2fff  libsystem_asl.dylib (356.70.1) <39E46A6F-B228-3E78-B83E-1779F9707A39> /usr/lib/system/libsystem_asl.dylib
    0x7fff7a4b3000 -     0x7fff7a4b3fff  libsystem_blocks.dylib (67) <17303FDF-0D2D-3963-B05E-B4DF63052D47> /usr/lib/system/libsystem_blocks.dylib
    0x7fff7a4b4000 -     0x7fff7a53dff7  libsystem_c.dylib (1244.50.9) <1187BFE8-4576-3247-8177-481554E1F9E7> /usr/lib/system/libsystem_c.dylib
    0x7fff7a53e000 -     0x7fff7a541ffb  libsystem_configuration.dylib (963.50.8) <DF6B5287-203E-30CB-9947-78DF446C72B8> /usr/lib/system/libsystem_configuration.dylib
    0x7fff7a542000 -     0x7fff7a545ffb  libsystem_coreservices.dylib (51) <486000D3-D8CB-3BE7-8EE5-8BF380DE6DF7> /usr/lib/system/libsystem_coreservices.dylib
    0x7fff7a546000 -     0x7fff7a547fff  libsystem_darwin.dylib (1244.50.9) <09C21A4A-9EE0-388B-A9D9-DFF8F6758791> /usr/lib/system/libsystem_darwin.dylib
    0x7fff7a548000 -     0x7fff7a54eff7  libsystem_dnssd.dylib (878.70.2) <976168E4-0F95-3725-800F-CEC6166C9E76> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff7a54f000 -     0x7fff7a598ff7  libsystem_info.dylib (517.30.1) <AB634A98-B8AA-3804-8436-38261FC8EC4D> /usr/lib/system/libsystem_info.dylib
    0x7fff7a599000 -     0x7fff7a5bfff7  libsystem_kernel.dylib (4570.71.13) <7601E31F-FC69-3FD9-B2F4-1BA00E0E4381> /usr/lib/system/libsystem_kernel.dylib
    0x7fff7a5c0000 -     0x7fff7a60bfcb  libsystem_m.dylib (3147.50.1) <17570F46-566C-39FC-BEF6-635A355DD549> /usr/lib/system/libsystem_m.dylib
    0x7fff7a60c000 -     0x7fff7a62bfff  libsystem_malloc.dylib (140.50.6) <7FD43735-9DDD-300E-8C4A-F909A74BDF49> /usr/lib/system/libsystem_malloc.dylib
    0x7fff7a62c000 -     0x7fff7a75cff7  libsystem_network.dylib (1229.70.2) <5E86B2DE-9E15-3354-8714-4094ED5F698D> /usr/lib/system/libsystem_network.dylib
    0x7fff7a75d000 -     0x7fff7a767ffb  libsystem_networkextension.dylib (767.70.2) <9DC03712-552D-3AEE-9519-B5ED70980B70> /usr/lib/system/libsystem_networkextension.dylib
    0x7fff7a768000 -     0x7fff7a771ff3  libsystem_notify.dylib (172) <08012EC0-2CD2-34BE-BF93-E7F56491299A> /usr/lib/system/libsystem_notify.dylib
    0x7fff7a772000 -     0x7fff7a779ff7  libsystem_platform.dylib (161.50.1) <6355EE2D-5456-3CA8-A227-B96E8F1E2AF8> /usr/lib/system/libsystem_platform.dylib
    0x7fff7a77a000 -     0x7fff7a785fff  libsystem_pthread.dylib (301.50.1) <0E51CCBA-91F2-34E1-BF2A-FEEFD3D321E4> /usr/lib/system/libsystem_pthread.dylib
    0x7fff7a786000 -     0x7fff7a789fff  libsystem_sandbox.dylib (765.70.1) <553DFCC6-9D31-3B9C-AB7C-30F6F265786D> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff7a78a000 -     0x7fff7a78bff3  libsystem_secinit.dylib (30) <DE8D14E8-A276-3FF8-AE13-77F7040F33C1> /usr/lib/system/libsystem_secinit.dylib
    0x7fff7a78c000 -     0x7fff7a793ff7  libsystem_symptoms.dylib (820.60.3) <441C6CA0-5711-3BB1-8420-DDAC3D5272E1> /usr/lib/system/libsystem_symptoms.dylib
    0x7fff7a794000 -     0x7fff7a7a7fff  libsystem_trace.dylib (829.70.1) <3A6CB706-8CA6-3616-8AFC-14AAD7FAF187> /usr/lib/system/libsystem_trace.dylib
    0x7fff7a7a9000 -     0x7fff7a7aeff7  libunwind.dylib (35.3) <BEF3FB49-5604-3B5F-82B5-332B80023AC3> /usr/lib/system/libunwind.dylib
    0x7fff7a7af000 -     0x7fff7a7dcff7  libxpc.dylib (1205.70.9) <0BC7AD67-671D-31D4-8B88-C317B8379598> /usr/lib/system/libxpc.dylib

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 1
    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: 2901548
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=583.3M resident=0K(0%) swapped_out_or_unallocated=583.3M(100%)
Writable regions: Total=1.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.5G(100%)
 
                                  VIRTUAL   REGION 
REGION TYPE                          SIZE    COUNT (non-coalesced) 
===========                       =======  ======= 
Accelerate framework                 256K        3 
Activity Tracing                     256K        2 
CG backing stores                   18.2M        4 
CG image                             720K       14 
CoreAnimation                       50.8M       31 
CoreGraphics                           8K        2 
CoreImage                             40K        4 
CoreUI image data                   3220K       18 
CoreUI image file                    208K        3 
Foundation                            32K        3 
Image IO                             364K       14 
JS JIT generated code              128.0M        4 
JS JIT generated code (reserved)   896.0M        2         reserved VM address space (unallocated)
Kernel Alloc Once                      8K        2 
MALLOC                             382.5M       65 
MALLOC guard page                     48K       11 
MALLOC_LARGE (reserved)              228K        2         reserved VM address space (unallocated)
Memory Tag 242                        12K        2 
Memory Tag 251                        52K        2 
SQLite page cache                     64K        2 
STACK GUARD                         56.0M        9 
Stack                               11.6M        9 
VM_ALLOCATE                          128K       19 
WebKit Malloc                       12.1M        6 
__DATA                              39.9M      388 
__FONT_DATA                            4K        2 
__LINKEDIT                         214.2M       55 
__TEXT                             369.1M      363 
__UNICODE                            560K        2 
mapped file                        108.2M       47 
shared memory                        632K       12 
===========                       =======  ======= 
TOTAL                                2.2G     1071 
TOTAL, minus reserved VM space       1.4G     1071 

Model: MacBookPro11,3, BootROM 149.0.0.0.0, 4 processors, Intel Core i7, 2.5 GHz, 16 GB, SMC 2.19f12
Graphics: Intel Iris Pro, Intel Iris Pro, Built-In
Graphics: NVIDIA GeForce GT 750M, NVIDIA GeForce GT 750M, PCIe
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 (7.77.37.31.1a9)
Bluetooth: Version 6.0.7f11, 3 services, 18 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
Serial ATA Device: APPLE SSD SM0512F, 500.28 GB
USB Device: USB 3.0 Bus
USB Device: Apple Internal Keyboard / Trackpad
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 17.1

Viet_H_Intel
Moderator
135 Views

It's not clear if you used icc to build R or still using clang? You can add -g to the command line, then run under a debugger to debug R.

Thanks,

Viet

jimdempseyatthecove
Black Belt
135 Views

>>
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib            0x00007fff7a5b5b66 __pthread_kill + 10
1   libsystem_pthread.dylib           0x00007fff7a780080 pthread_kill + 333
2   libsystem_c.dylib                 0x00007fff7a5111ae abort + 127
3   libomp.dylib                      0x000000010e48a712 __kmp_abort_process + 43
4   libomp.dylib                      0x000000010e489251 __kmp_fatal + 150
5   libomp.dylib                      0x000000010e49053e __kmp_register_library_startup() + 621
6   libomp.dylib                      0x000000010e4897b3 __kmp_do_serial_initialize() + 29
7   libomp.dylib                      0x000000010e4905f3 __kmp_do_middle_initialize() + 27
8   libomp.dylib                      0x000000010e4905c1 __kmp_middle_initialize + 52
9   libomp.dylib                      0x000000010e4bd5b0 omp_get_max_threads + 21
10  mongrel.so                        0x000000010e3252a8 void Eigen::internal::parallelize_gemm<true,
<<

Intel's OpenMP library is libiomp5.so on Linux (or perhaps libiomp5.dylib on Mac).

There may be a library compatibility issue.

note, the "crash" is caused by an explicit all to abort(); from inside __kmp_register_library_startup().
IOW __kmp_register_library_startup() detected something wrong.
I don't know why an accompanying error message was not emitted (likely a NULL console window).

Jim Dempsey

 

jimdempseyatthecove
Black Belt
135 Views

Additional info:

>>
63430374B31A> /Library/Frameworks/R.framework/Versions/3.5/Resources/library/MASS/libs/MASS.so
       0x10e2ec000 -        0x10e409fe7 +mongrel.so (0) <E5DA8C3E-EBC0-3F8F-8A1F-89B0250EEB75> /Users/USER/*/mongrel.so
       0x10e473000 -        0x10e4c8fff +libomp.dylib (0) <7AEB9F1D-3F05-352B-A39F-16A867E0A606> /usr/local/opt/llvm/lib/libomp.dylib
       0x10e4f7000 -        0x10e54efff +libc++.1.dylib (0) <77256C53-F8EE-3568-9482-7974E105FF3B> /usr/local/opt/llvm/lib/libc++.1.dylib
       0x10e5a9000 -        0x10e6dbfcf +libiomp5.dylib (0) <C3D4CDB2-0006-3A95-818F-06231E1D3657> /opt/intel/*/libiomp5.dylib
       0x10e74d000 -        0x10e798fff +testthat.so (0) <C2304E54-E70B-3464-943A-
<<

It appears that both libomp.dylib and libiomp5.dylib are loaded

*** two different OpenMP libraries - not good.

Jim Dempsey

135 Views

Hmmm thanks for pointing that out... I wonder where that second OpenMP library is coming from... Any Ideas on how to find out? Those are all the compiler flags I was passing...

jimdempseyatthecove
Black Belt
135 Views

I am not familiar with building on MAC nor with Mongre, however I suspect the vanilla make file (without MKL) includes GCC OpenMP library (libomp). I suggest when building with MKL that you substitute libiomp5 for libomp (as opposed to adding it).

Jim Dempsey

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