==3589957== Memcheck, a memory error detector ==3589957== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3589957== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3589957== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/pde/test/TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver -malloc_debug -malloc_dump -memory_info ==3589957== Parent PID: 3589102 ==3589957== ==3589957== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3589957== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3589957== ==3589957== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3589957== at 0x851E79E: getsockopt_syscall (getsockopt.c:29) ==3589957== by 0x851E79E: getsockopt (getsockopt.c:94) ==3589957== by 0x10F37157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10F3EA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10F45DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10E453C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10DBEE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3589957== by 0x1057DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3589957== by 0xC38F4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3589957== by 0x8AFF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x8A98D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x6ABCD38: PetscInitialize (pinit.c:924) ==3589957== by 0x699058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3589957== by 0x69905D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3589957== by 0x1A5680: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3589957== by 0x19B5F3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3589957== by 0x19EB44: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3589957== by 0x19E9E4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3589957== by 0x19F07B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3589957== by 0x199620: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3589957== Address 0x1ffeffdf6c is on thread 1's stack ==3589957== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3589957== { 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 } ==3589957== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3589957== at 0x851E79E: getsockopt_syscall (getsockopt.c:29) ==3589957== by 0x851E79E: getsockopt (getsockopt.c:94) ==3589957== by 0x10F37157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10F3EA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10F45DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10E453C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10DBEE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3589957== by 0x1057DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3589957== by 0xC38F4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3589957== by 0x8AFF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x8A98D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x6ABCD38: PetscInitialize (pinit.c:924) ==3589957== by 0x699058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3589957== by 0x69905D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3589957== by 0x1A5680: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3589957== by 0x19B5F3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3589957== by 0x19EB44: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3589957== by 0x19E9E4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3589957== by 0x19F07B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3589957== by 0x199620: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3589957== Address 0x1ffeffdf6c is on thread 1's stack ==3589957== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3589957== { 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 } ==3589957== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3589957== at 0x851EC7E: setsockopt_syscall (setsockopt.c:29) ==3589957== by 0x851EC7E: setsockopt (setsockopt.c:95) ==3589957== by 0x10F3EBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10F45DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10E453C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3589957== by 0x10DBEE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3589957== by 0x1057DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3589957== by 0xC38F4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3589957== by 0x8AFF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x8A98D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x6ABCD38: PetscInitialize (pinit.c:924) ==3589957== by 0x699058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3589957== by 0x69905D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3589957== by 0x1A5680: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3589957== by 0x19B5F3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3589957== by 0x19EB44: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3589957== by 0x19E9E4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3589957== by 0x19F07B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3589957== by 0x199620: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3589957== { 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 } ==3589957== ==3589957== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3589957== Open file descriptor 12: ==3589957== at 0x850C22D: pipe (pipe.c:29) ==3589957== by 0x1057E07D: ??? ==3589957== by 0xC38F4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3589957== by 0x8AFF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x8A98D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x6ABCD38: PetscInitialize (pinit.c:924) ==3589957== by 0x699058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3589957== by 0x69905D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3589957== by 0x1A5680: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3589957== by 0x19B5F3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3589957== by 0x19EB44: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3589957== by 0x19E9E4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3589957== by 0x19F07B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3589957== by 0x199620: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3589957== ==3589957== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3589957== at 0x8510BCC: __open_nocancel (open64_nocancel.c:39) ==3589957== by 0x8494C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3589957== by 0x7D46822: ??? ==3589957== by 0x7D4696F: ??? ==3589957== by 0xC4346DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3589957== by 0xC434938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3589957== by 0xC3EA922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3589957== by 0xC38F2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3589957== by 0x8AFF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x8A98D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x6ABCD38: PetscInitialize (pinit.c:924) ==3589957== by 0x699058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3589957== by 0x69905D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3589957== by 0x1A5680: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3589957== by 0x19B5F3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3589957== by 0x19EB44: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3589957== by 0x19E9E4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3589957== by 0x19F07B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3589957== by 0x199620: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3589957== ==3589957== Open file descriptor 117: ==3589957== ==3589957== ==3589957== Open file descriptor 110: ==3589957== ==3589957== ==3589957== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver_valgrind.txt ==3589957== ==3589957== ==3589957== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3589957== ==3589957== ==3589957== ==3589957== HEAP SUMMARY: ==3589957== in use at exit: 703,208 bytes in 9,374 blocks ==3589957== total heap usage: 2,556,445 allocs, 2,547,071 frees, 1,592,557,696 bytes allocated ==3589957== ==3589957== 552 bytes in 1 blocks are definitely lost in loss record 35 of 62 ==3589957== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3589957== by 0x10E4CC13: ??? ==3589957== by 0x10E4D22C: ??? ==3589957== by 0x10DC04B7: ??? ==3589957== by 0x8A6515A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x8AFFA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x8A98D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x6ABCD38: PetscInitialize (pinit.c:924) ==3589957== by 0x699058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3589957== by 0x69905D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3589957== by 0x1A5680: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3589957== by 0x19B5F3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3589957== by 0x19EB44: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3589957== by 0x19E9E4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3589957== by 0x19F07B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3589957== by 0x199620: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3589957== { 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 } ==3589957== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 59 of 62 ==3589957== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3589957== by 0x11FBF74E: ??? ==3589957== by 0x11FBFE0B: ??? ==3589957== by 0x11FC2F56: ??? ==3589957== by 0x11FB865D: ??? ==3589957== by 0x11FB8FA3: ??? ==3589957== by 0xC4A0F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3589957== by 0xC47CAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3589957== by 0xC42DCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3589957== by 0xC35AEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3589957== by 0x1057EF03: ??? ==3589957== by 0xC38F4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3589957== by 0x8AFF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x8A98D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3589957== by 0x6ABCD38: PetscInitialize (pinit.c:924) ==3589957== by 0x699058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3589957== by 0x69905D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3589957== by 0x1A5680: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3589957== by 0x19B5F3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3589957== by 0x19EB44: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3589957== by 0x19E9E4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3589957== by 0x19F07B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3589957== by 0x199620: main (TestLinearParabolicPdeSystemWithCoupledOdeSystemSolver.cpp:19) ==3589957== { 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 } ==3589957== LEAK SUMMARY: ==3589957== definitely lost: 688 bytes in 2 blocks ==3589957== indirectly lost: 1,760 bytes in 16 blocks ==3589957== possibly lost: 0 bytes in 0 blocks ==3589957== still reachable: 4,083 bytes in 7 blocks ==3589957== suppressed: 696,677 bytes in 9,349 blocks ==3589957== Reachable blocks (those to which a pointer was found) are not shown. ==3589957== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3589957== ==3589957== Use --track-origins=yes to see where uninitialised values come from ==3589957== For lists of detected and suppressed errors, rerun with: -s ==3589957== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 28 from 28)