R crashes when using -qopenmp flag

silverman__justin · ‎12-17-2018

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

silverman__justin · ‎12-18-2018

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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0x10e5a9000 - 0x10e6dbfcf +libiomp5.dylib (0) <C3D4CDB2-0006-3A95-818F-06231E1D3657> /opt/intel/*/libiomp5.dylib
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0x7fff79d5f000 - 0x7fff79ef2ff7 libsqlite3.dylib (274.8.1) <FCAD6A57-829E-3701-B16E-1833D620E0E8> /usr/lib/libsqlite3.dylib
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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
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Calls made by this process:
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Calls made by all processes on this machine:
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thread_set_state: 0
VM Region Summary:
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Viet_H_Intel · ‎12-21-2018

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 · ‎12-21-2018

>>
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 · ‎12-21-2018

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

silverman__justin · ‎12-21-2018

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 · ‎12-21-2018

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