==2060377== Memcheck, a memory error detector ==2060377== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2060377== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2060377== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/crypt/test/TestVanLeeuwen2009WntSwatCellCycleOdeSystem -malloc_debug -malloc_dump -memory_info ==2060377== Parent PID: 2040441 ==2060377== ==2060377== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2060377== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2060377== ==2060377== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2060377== at 0x10C2C79E: getsockopt_syscall (getsockopt.c:29) ==2060377== by 0x10C2C79E: getsockopt (getsockopt.c:94) ==2060377== by 0x19DA8157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19DAFA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19DB6DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19CB63C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19C2FE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2060377== by 0x193EEE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2060377== by 0x149A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2060377== by 0x10526418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0x104BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0xF1B4D38: PetscInitialize (pinit.c:924) ==2060377== by 0xF02658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2060377== by 0xF0265D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2060377== by 0x1412CF: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==2060377== by 0x13A4FF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2060377== by 0x13D44E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2060377== by 0x13D2EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2060377== by 0x13D985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2060377== by 0x138830: main (TestVanLeeuwen2009WntSwatCellCycleOdeSystem.cpp:19) ==2060377== Address 0x1ffeffdf8c is on thread 1's stack ==2060377== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2060377== { Memcheck:Param socketcall.getsockopt(optlen) fun:getsockopt_syscall fun:getsockopt fun:pmix_ptl_base_set_timeout fun:pmix_ptl_base_make_connection obj:/usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2 fun:PMIx_Init fun:ext3x_client_init obj:/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so fun:orte_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2060377== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2060377== at 0x10C2C79E: getsockopt_syscall (getsockopt.c:29) ==2060377== by 0x10C2C79E: getsockopt (getsockopt.c:94) ==2060377== by 0x19DA8157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19DAFA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19DB6DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19CB63C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19C2FE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2060377== by 0x193EEE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2060377== by 0x149A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2060377== by 0x10526418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0x104BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0xF1B4D38: PetscInitialize (pinit.c:924) ==2060377== by 0xF02658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2060377== by 0xF0265D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2060377== by 0x1412CF: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==2060377== by 0x13A4FF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2060377== by 0x13D44E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2060377== by 0x13D2EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2060377== by 0x13D985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2060377== by 0x138830: main (TestVanLeeuwen2009WntSwatCellCycleOdeSystem.cpp:19) ==2060377== Address 0x1ffeffdf8c is on thread 1's stack ==2060377== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2060377== { Memcheck:Param socketcall.getsockopt(optlen_out) fun:getsockopt_syscall fun:getsockopt fun:pmix_ptl_base_set_timeout fun:pmix_ptl_base_make_connection obj:/usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2 fun:PMIx_Init fun:ext3x_client_init obj:/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so fun:orte_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2060377== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2060377== at 0x10C2CC7E: setsockopt_syscall (setsockopt.c:29) ==2060377== by 0x10C2CC7E: setsockopt (setsockopt.c:95) ==2060377== by 0x19DAFBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19DB6DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19CB63C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2060377== by 0x19C2FE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2060377== by 0x193EEE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2060377== by 0x149A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2060377== by 0x10526418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0x104BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0xF1B4D38: PetscInitialize (pinit.c:924) ==2060377== by 0xF02658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2060377== by 0xF0265D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2060377== by 0x1412CF: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==2060377== by 0x13A4FF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2060377== by 0x13D44E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2060377== by 0x13D2EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2060377== by 0x13D985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2060377== by 0x138830: main (TestVanLeeuwen2009WntSwatCellCycleOdeSystem.cpp:19) ==2060377== { Memcheck:Param setsockopt(optlen) fun:setsockopt_syscall fun:setsockopt fun:pmix_ptl_base_make_connection obj:/usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2 fun:PMIx_Init fun:ext3x_client_init obj:/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so fun:orte_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2060377== ==2060377== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2060377== Open file descriptor 12: ==2060377== at 0x10C1A22D: pipe (pipe.c:29) ==2060377== by 0x193EF07D: ??? ==2060377== by 0x149A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2060377== by 0x10526418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0x104BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0xF1B4D38: PetscInitialize (pinit.c:924) ==2060377== by 0xF02658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2060377== by 0xF0265D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2060377== by 0x1412CF: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==2060377== by 0x13A4FF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2060377== by 0x13D44E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2060377== by 0x13D2EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2060377== by 0x13D985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2060377== by 0x138830: main (TestVanLeeuwen2009WntSwatCellCycleOdeSystem.cpp:19) ==2060377== ==2060377== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2060377== at 0x10C1EBCC: __open_nocancel (open64_nocancel.c:39) ==2060377== by 0x10BA2C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2060377== by 0xF05E822: ??? ==2060377== by 0xF05E96F: ??? ==2060377== by 0x14A476DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2060377== by 0x14A47938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2060377== by 0x149FD922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2060377== by 0x149A22DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2060377== by 0x10526418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0x104BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0xF1B4D38: PetscInitialize (pinit.c:924) ==2060377== by 0xF02658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2060377== by 0xF0265D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2060377== by 0x1412CF: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==2060377== by 0x13A4FF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2060377== by 0x13D44E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2060377== by 0x13D2EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2060377== by 0x13D985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2060377== by 0x138830: main (TestVanLeeuwen2009WntSwatCellCycleOdeSystem.cpp:19) ==2060377== ==2060377== Open file descriptor 117: ==2060377== ==2060377== ==2060377== Open file descriptor 110: ==2060377== ==2060377== ==2060377== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestVanLeeuwen2009WntSwatCellCycleOdeSystem_valgrind.txt ==2060377== ==2060377== ==2060377== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2060377== ==2060377== ==2060377== ==2060377== HEAP SUMMARY: ==2060377== in use at exit: 700,759 bytes in 9,377 blocks ==2060377== total heap usage: 520,102 allocs, 510,725 frees, 1,561,954,758 bytes allocated ==2060377== ==2060377== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==2060377== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2060377== by 0x19CBDC13: ??? ==2060377== by 0x19CBE22C: ??? ==2060377== by 0x19C314B7: ??? ==2060377== by 0x1048C15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0x10526A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0x104BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0xF1B4D38: PetscInitialize (pinit.c:924) ==2060377== by 0xF02658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2060377== by 0xF0265D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2060377== by 0x1412CF: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==2060377== by 0x13A4FF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2060377== by 0x13D44E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2060377== by 0x13D2EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2060377== by 0x13D985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2060377== by 0x138830: main (TestVanLeeuwen2009WntSwatCellCycleOdeSystem.cpp:19) ==2060377== { Memcheck:Leak match-leak-kinds: definite fun:calloc obj:* obj:* obj:* fun:ompi_proc_complete_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2060377== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65 ==2060377== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2060377== by 0x1B23074E: ??? ==2060377== by 0x1B230E0B: ??? ==2060377== by 0x1B233F56: ??? ==2060377== by 0x1B22965D: ??? ==2060377== by 0x1B229FA3: ??? ==2060377== by 0x14AB5F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2060377== by 0x14A91AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2060377== by 0x14A40CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2060377== by 0x1496DEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2060377== by 0x193EFF03: ??? ==2060377== by 0x149A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2060377== by 0x10526418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0x104BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2060377== by 0xF1B4D38: PetscInitialize (pinit.c:924) ==2060377== by 0xF02658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2060377== by 0xF0265D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2060377== by 0x1412CF: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==2060377== by 0x13A4FF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2060377== by 0x13D44E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2060377== by 0x13D2EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2060377== by 0x13D985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2060377== by 0x138830: main (TestVanLeeuwen2009WntSwatCellCycleOdeSystem.cpp:19) ==2060377== { Memcheck:Leak match-leak-kinds: definite fun:calloc obj:* obj:* obj:* obj:* obj:* obj:/usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2 fun:hwloc_topology_load fun:opal_hwloc_base_get_topology fun:orte_ess_base_proc_binding obj:* fun:orte_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2060377== LEAK SUMMARY: ==2060377== definitely lost: 688 bytes in 2 blocks ==2060377== indirectly lost: 1,760 bytes in 16 blocks ==2060377== possibly lost: 0 bytes in 0 blocks ==2060377== still reachable: 1,531 bytes in 6 blocks ==2060377== suppressed: 696,780 bytes in 9,353 blocks ==2060377== Reachable blocks (those to which a pointer was found) are not shown. ==2060377== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2060377== ==2060377== Use --track-origins=yes to see where uninitialised values come from ==2060377== For lists of detected and suppressed errors, rerun with: -s ==2060377== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 32 from 32)