==3283480== Memcheck, a memory error detector ==3283480== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3283480== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3283480== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/pde/test/TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver -malloc_debug -malloc_dump -memory_info ==3283480== Parent PID: 3282641 ==3283480== ==3283480== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3283480== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3283480== ==3283480== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3283480== at 0x80F879E: getsockopt_syscall (getsockopt.c:29) ==3283480== by 0x80F879E: getsockopt (getsockopt.c:94) ==3283480== by 0x10A90157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x10A97A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x10A9EDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x1099E3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x10917E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3283480== by 0x100D6E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3283480== by 0xBF694CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3283480== by 0x86D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x8672D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x6696D38: PetscInitialize (pinit.c:924) ==3283480== by 0x656A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3283480== by 0x656A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3283480== by 0x1A571C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3283480== by 0x19B613: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3283480== by 0x19EB64: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3283480== by 0x19EA04: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3283480== by 0x19F09B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3283480== by 0x199640: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3283480== Address 0x1ffeffdf6c is on thread 1's stack ==3283480== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3283480== { 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 } ==3283480== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3283480== at 0x80F879E: getsockopt_syscall (getsockopt.c:29) ==3283480== by 0x80F879E: getsockopt (getsockopt.c:94) ==3283480== by 0x10A90157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x10A97A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x10A9EDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x1099E3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x10917E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3283480== by 0x100D6E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3283480== by 0xBF694CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3283480== by 0x86D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x8672D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x6696D38: PetscInitialize (pinit.c:924) ==3283480== by 0x656A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3283480== by 0x656A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3283480== by 0x1A571C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3283480== by 0x19B613: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3283480== by 0x19EB64: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3283480== by 0x19EA04: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3283480== by 0x19F09B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3283480== by 0x199640: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3283480== Address 0x1ffeffdf6c is on thread 1's stack ==3283480== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3283480== { 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 } ==3283480== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3283480== at 0x80F8C7E: setsockopt_syscall (setsockopt.c:29) ==3283480== by 0x80F8C7E: setsockopt (setsockopt.c:95) ==3283480== by 0x10A97BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x10A9EDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x1099E3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3283480== by 0x10917E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3283480== by 0x100D6E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3283480== by 0xBF694CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3283480== by 0x86D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x8672D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x6696D38: PetscInitialize (pinit.c:924) ==3283480== by 0x656A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3283480== by 0x656A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3283480== by 0x1A571C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3283480== by 0x19B613: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3283480== by 0x19EB64: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3283480== by 0x19EA04: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3283480== by 0x19F09B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3283480== by 0x199640: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3283480== { 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 } ==3283480== ==3283480== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3283480== Open file descriptor 12: ==3283480== at 0x80E622D: pipe (pipe.c:29) ==3283480== by 0x100D707D: ??? ==3283480== by 0xBF694CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3283480== by 0x86D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x8672D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x6696D38: PetscInitialize (pinit.c:924) ==3283480== by 0x656A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3283480== by 0x656A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3283480== by 0x1A571C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3283480== by 0x19B613: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3283480== by 0x19EB64: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3283480== by 0x19EA04: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3283480== by 0x19F09B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3283480== by 0x199640: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3283480== ==3283480== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3283480== at 0x80EABCC: __open_nocancel (open64_nocancel.c:39) ==3283480== by 0x806EC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3283480== by 0x7920822: ??? ==3283480== by 0x792096F: ??? ==3283480== by 0xC00E6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3283480== by 0xC00E938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3283480== by 0xBFC4922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3283480== by 0xBF692DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3283480== by 0x86D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x8672D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x6696D38: PetscInitialize (pinit.c:924) ==3283480== by 0x656A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3283480== by 0x656A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3283480== by 0x1A571C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3283480== by 0x19B613: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3283480== by 0x19EB64: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3283480== by 0x19EA04: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3283480== by 0x19F09B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3283480== by 0x199640: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3283480== ==3283480== Open file descriptor 117: ==3283480== ==3283480== ==3283480== Open file descriptor 108: ==3283480== ==3283480== ==3283480== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver_valgrind.txt ==3283480== ==3283480== ==3283480== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3283480== ==3283480== ==3283480== ==3283480== HEAP SUMMARY: ==3283480== in use at exit: 703,208 bytes in 9,374 blocks ==3283480== total heap usage: 2,556,389 allocs, 2,547,015 frees, 1,592,385,985 bytes allocated ==3283480== ==3283480== 552 bytes in 1 blocks are definitely lost in loss record 35 of 62 ==3283480== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3283480== by 0x109A5C13: ??? ==3283480== by 0x109A622C: ??? ==3283480== by 0x109194B7: ??? ==3283480== by 0x863F15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x86D9A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x8672D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x6696D38: PetscInitialize (pinit.c:924) ==3283480== by 0x656A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3283480== by 0x656A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3283480== by 0x1A571C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3283480== by 0x19B613: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3283480== by 0x19EB64: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3283480== by 0x19EA04: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3283480== by 0x19F09B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3283480== by 0x199640: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3283480== { 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 } ==3283480== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 59 of 62 ==3283480== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3283480== by 0x11B1874E: ??? ==3283480== by 0x11B18E0B: ??? ==3283480== by 0x11B1BF56: ??? ==3283480== by 0x11B1165D: ??? ==3283480== by 0x11B11FA3: ??? ==3283480== by 0xC07AF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3283480== by 0xC056AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3283480== by 0xC007CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3283480== by 0xBF34EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3283480== by 0x100D7F03: ??? ==3283480== by 0xBF694CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3283480== by 0x86D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x8672D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3283480== by 0x6696D38: PetscInitialize (pinit.c:924) ==3283480== by 0x656A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3283480== by 0x656A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3283480== by 0x1A571C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3283480== by 0x19B613: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3283480== by 0x19EB64: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3283480== by 0x19EA04: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3283480== by 0x19F09B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3283480== by 0x199640: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3283480== { 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 } ==3283480== LEAK SUMMARY: ==3283480== definitely lost: 688 bytes in 2 blocks ==3283480== indirectly lost: 1,760 bytes in 16 blocks ==3283480== possibly lost: 0 bytes in 0 blocks ==3283480== still reachable: 4,083 bytes in 7 blocks ==3283480== suppressed: 696,677 bytes in 9,349 blocks ==3283480== Reachable blocks (those to which a pointer was found) are not shown. ==3283480== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3283480== ==3283480== Use --track-origins=yes to see where uninitialised values come from ==3283480== For lists of detected and suppressed errors, rerun with: -s ==3283480== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 28 from 28)