BOSS_TEST.construction hangs sometimes

Question

BOSS_TEST.construction hangs sometimes

jnalanko opened this issue 2 years ago · 0 comments

GDB backtrace when the hang happens:

#0  0x00007fd7468cbd2d in __GI___pthread_timedjoin_ex (threadid=140562561988352, thread_return=0x0, abstime=0x0, block=<optimized out>) at pthread_join_common.c:89
#1  0x00007fd7463affb3 in std::thread::join() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#2  0x000055e68a3253f6 in CExceptionAwareThread::join (this=0x55e68cf85490) at /usr/include/c++/8/bits/unique_ptr.h:345
#3  CKMC<2u>::ProcessStage2_impl (this=<optimized out>) at /home/niklas/code/Themisto/KMC/kmc_core/kmc.h:1659
#4  0x000055e68a24ec19 in CKMC<2u>::ProcessStage2 (this=<optimized out>) at /home/niklas/code/Themisto/KMC/kmc_core/kmc.h:1802
#5  KMC::CApplication<2u>::ProcessStage2 (stage2Params=..., this=0x55e68ce6c530) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:62
#6  KMC::CApplication<2u>::ProcessStage2 (stage2Params=..., this=0x55e68ce6c530) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:57
#7  KMC::CApplication<3u>::ProcessStage2 (stage2Params=..., this=<optimized out>) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:65
#8  KMC::CApplication<4u>::ProcessStage2 (stage2Params=..., this=<optimized out>) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:65
#9  KMC::CApplication<5u>::ProcessStage2 (stage2Params=..., this=<optimized out>) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:65
#10 KMC::CApplication<6u>::ProcessStage2 (stage2Params=..., this=<optimized out>) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:65
#11 KMC::CApplication<7u>::ProcessStage2 (stage2Params=..., this=<optimized out>) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:65
#12 KMC::CApplication<8u>::ProcessStage2 (stage2Params=..., this=<optimized out>) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:65
#13 KMC::Runner::RunnerImpl::RunStage2 (stage2Params=..., this=<optimized out>) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:424
#14 KMC::Runner::RunStage2 (this=<optimized out>, params=...) at /home/niklas/code/Themisto/KMC/kmc_core/kmc_runner.cpp:439
#15 0x000055e68a1beda8 in run_kmc (input_files=std::vector of length 1, capacity 1 = {...}, k=39, n_threads=2, ram_gigas=2, min_abundance=1, max_abundance=1000000000)
    at /home/niklas/code/Themisto/src/KMC_wrapper.cpp:47
#16 0x000055e68a0be958 in test_construction (tcase=..., reverse_complements=false) at /home/niklas/code/Themisto/include/libwheeler/BOSS_tests.hh:158
#17 0x000055e68a0bef5b in BOSS_TEST_construction_Test::TestBody (this=0x55e68cd88540) at /home/niklas/code/Themisto/include/libwheeler/BOSS_tests.hh:172
#18 0x000055e68a1fc56c in testing::internal::HandleSehExceptionsInMethodIfSupported<testing::Test, void> (object=0x55e68cd88540, method=&virtual testing::Test::TestBody(), 
    location=0x55e68a47a323 "the test body") at /home/niklas/code/Themisto/googletest/googletest/src/gtest.cc:2599
#19 0x000055e68a1f63fb in testing::internal::HandleExceptionsInMethodIfSupported<testing::Test, void> (object=0x55e68cd88540, method=&virtual testing::Test::TestBody(), 
    location=0x55e68a47a323 "the test body") at /home/niklas/code/Themisto/googletest/googletest/src/gtest.cc:2635
#20 0x000055e68a1d5344 in testing::Test::Run (this=0x55e68cd88540) at /home/niklas/code/Themisto/googletest/googletest/src/gtest.cc:2674
#21 0x000055e68a1d5d61 in testing::TestInfo::Run (this=0x55e68cd79d20) at /home/niklas/code/Themisto/googletest/googletest/src/gtest.cc:2853
#22 0x000055e68a1d6648 in testing::TestSuite::Run (this=0x55e68cd798b0) at /home/niklas/code/Themisto/googletest/googletest/src/gtest.cc:3012
#23 0x000055e68a1e5a04 in testing::internal::UnitTestImpl::RunAllTests (this=0x55e68cd750b0) at /home/niklas/code/Themisto/googletest/googletest/src/gtest.cc:5870
#24 0x000055e68a1fd75e in testing::internal::HandleSehExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool> (object=0x55e68cd750b0, 
    method=(bool (testing::internal::UnitTestImpl::*)(class testing::internal::UnitTestImpl * const)) 0x55e68a1e55c2 <testing::internal::UnitTestImpl::RunAllTests()>, 
    location=0x55e68a47ad80 "auxiliary test code (environments or event listeners)") at /home/niklas/code/Themisto/googletest/googletest/src/gtest.cc:2599
#25 0x000055e68a1f730f in testing::internal::HandleExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool> (object=0x55e68cd750b0, 
    method=(bool (testing::internal::UnitTestImpl::*)(class testing::internal::UnitTestImpl * const)) 0x55e68a1e55c2 <testing::internal::UnitTestImpl::RunAllTests()>, 
    location=0x55e68a47ad80 "auxiliary test code (environments or event listeners)") at /home/niklas/code/Themisto/googletest/googletest/src/gtest.cc:2635
#26 0x000055e68a1e40dc in testing::UnitTest::Run (this=0x55e68a7779e0 <testing::UnitTest::GetInstance()::instance>)
    at /home/niklas/code/Themisto/googletest/googletest/src/gtest.cc:5444
#27 0x000055e68a0cc5f6 in RUN_ALL_TESTS () at /home/niklas/code/Themisto/googletest/googletest/include/gtest/gtest.h:2293
#28 0x000055e68a0c43ca in main (argc=2, argv=0x7fffb7f7ca98) at /home/niklas/code/Themisto/tests/test_main.cpp:32