==69159== Memcheck, a memory error detector ==69159== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==69159== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==69159== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/linalg/test/TestChebyshevIteration -malloc_debug -malloc_dump -memory_info ==69159== Parent PID: 68882 ==69159== ==69159== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==69159== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==69159== ==69159== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==69159== at 0x60F379E: getsockopt_syscall (getsockopt.c:29) ==69159== by 0x60F379E: getsockopt (getsockopt.c:94) ==69159== by 0xB935157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB93CA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB943DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB8433C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB7BCE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==69159== by 0xAF7BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==69159== by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==69159== by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x4AD7D38: PetscInitialize (pinit.c:924) ==69159== by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==69159== by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==69159== by 0x11EA40: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==69159== by 0x11886F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==69159== by 0x11B326: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==69159== by 0x11B1C6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==69159== by 0x11B85D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==69159== by 0x116BA0: main (TestChebyshevIteration.cpp:19) ==69159== Address 0x1ffeffdfac is on thread 1's stack ==69159== in frame #2, created by pmix_ptl_base_make_connection (???:) ==69159== { 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 } ==69159== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==69159== at 0x60F379E: getsockopt_syscall (getsockopt.c:29) ==69159== by 0x60F379E: getsockopt (getsockopt.c:94) ==69159== by 0xB935157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB93CA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB943DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB8433C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB7BCE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==69159== by 0xAF7BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==69159== by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==69159== by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x4AD7D38: PetscInitialize (pinit.c:924) ==69159== by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==69159== by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==69159== by 0x11EA40: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==69159== by 0x11886F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==69159== by 0x11B326: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==69159== by 0x11B1C6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==69159== by 0x11B85D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==69159== by 0x116BA0: main (TestChebyshevIteration.cpp:19) ==69159== Address 0x1ffeffdfac is on thread 1's stack ==69159== in frame #2, created by pmix_ptl_base_make_connection (???:) ==69159== { 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 } ==69159== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==69159== at 0x60F3C7E: setsockopt_syscall (setsockopt.c:29) ==69159== by 0x60F3C7E: setsockopt (setsockopt.c:95) ==69159== by 0xB93CBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB943DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB8433C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==69159== by 0xB7BCE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==69159== by 0xAF7BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==69159== by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==69159== by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x4AD7D38: PetscInitialize (pinit.c:924) ==69159== by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==69159== by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==69159== by 0x11EA40: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==69159== by 0x11886F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==69159== by 0x11B326: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==69159== by 0x11B1C6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==69159== by 0x11B85D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==69159== by 0x116BA0: main (TestChebyshevIteration.cpp:19) ==69159== { 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 } ==69159== ==69159== FILE DESCRIPTORS: 9 open (3 std) at exit. ==69159== Open file descriptor 12: ==69159== at 0x60E122D: pipe (pipe.c:29) ==69159== by 0xAF7C07D: ??? ==69159== by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==69159== by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x4AD7D38: PetscInitialize (pinit.c:924) ==69159== by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==69159== by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==69159== by 0x11EA40: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==69159== by 0x11886F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==69159== by 0x11B326: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==69159== by 0x11B1C6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==69159== by 0x11B85D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==69159== by 0x116BA0: main (TestChebyshevIteration.cpp:19) ==69159== ==69159== Open file descriptor 8: /dev/shm/open_mpi.0000 ==69159== at 0x60E5BCC: __open_nocancel (open64_nocancel.c:39) ==69159== by 0x6069C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==69159== by 0x5D61822: ??? ==69159== by 0x5D6196F: ??? ==69159== by 0x8B316DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==69159== by 0x8B31938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==69159== by 0x8AE7922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==69159== by 0x8A8C2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==69159== by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x4AD7D38: PetscInitialize (pinit.c:924) ==69159== by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==69159== by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==69159== by 0x11EA40: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==69159== by 0x11886F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==69159== by 0x11B326: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==69159== by 0x11B1C6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==69159== by 0x11B85D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==69159== by 0x116BA0: main (TestChebyshevIteration.cpp:19) ==69159== ==69159== Open file descriptor 115: ==69159== ==69159== ==69159== Open file descriptor 110: ==69159== ==69159== ==69159== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestChebyshevIteration_valgrind.txt ==69159== ==69159== ==69159== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==69159== ==69159== ==69159== ==69159== HEAP SUMMARY: ==69159== in use at exit: 700,285 bytes in 9,377 blocks ==69159== total heap usage: 51,439 allocs, 42,062 frees, 1,372,754,820 bytes allocated ==69159== ==69159== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==69159== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==69159== by 0xB84AC13: ??? ==69159== by 0xB84B22C: ??? ==69159== by 0xB7BE4B7: ??? ==69159== by 0x638C15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x6426A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x4AD7D38: PetscInitialize (pinit.c:924) ==69159== by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==69159== by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==69159== by 0x11EA40: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==69159== by 0x11886F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==69159== by 0x11B326: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==69159== by 0x11B1C6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==69159== by 0x11B85D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==69159== by 0x116BA0: main (TestChebyshevIteration.cpp:19) ==69159== { 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 } ==69159== 666,808 (136 direct, 666,672 indirect) bytes in 1 blocks are definitely lost in loss record 65 of 65 ==69159== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==69159== by 0xCA5F74E: ??? ==69159== by 0xCA5FE0B: ??? ==69159== by 0xCA62F56: ??? ==69159== by 0xCA5865D: ??? ==69159== by 0xCA58FA3: ??? ==69159== by 0x8B9DF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==69159== by 0x8B79AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==69159== by 0x8B2ACB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==69159== by 0x8A57EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==69159== by 0xAF7CF03: ??? ==69159== by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==69159== by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==69159== by 0x4AD7D38: PetscInitialize (pinit.c:924) ==69159== by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==69159== by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==69159== by 0x11EA40: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==69159== by 0x11886F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==69159== by 0x11B326: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==69159== by 0x11B1C6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==69159== by 0x11B85D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==69159== by 0x116BA0: main (TestChebyshevIteration.cpp:19) ==69159== { 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 } ==69159== LEAK SUMMARY: ==69159== definitely lost: 688 bytes in 2 blocks ==69159== indirectly lost: 1,760 bytes in 16 blocks ==69159== possibly lost: 0 bytes in 0 blocks ==69159== still reachable: 1,531 bytes in 6 blocks ==69159== suppressed: 696,306 bytes in 9,353 blocks ==69159== Reachable blocks (those to which a pointer was found) are not shown. ==69159== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==69159== ==69159== Use --track-origins=yes to see where uninitialised values come from ==69159== For lists of detected and suppressed errors, rerun with: -s ==69159== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 32 from 32)