==2305474== Memcheck, a memory error detector ==2305474== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2305474== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2305474== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestHodgkinHuxleySquidAxon1952OriginalOdeSystem -malloc_debug -malloc_dump -memory_info ==2305474== Parent PID: 2283975 ==2305474== ==2305474== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2305474== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2305474== ==2305474== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2305474== at 0x85C279E: getsockopt_syscall (getsockopt.c:29) ==2305474== by 0x85C279E: getsockopt (getsockopt.c:94) ==2305474== by 0x1467B157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x14682A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x14689DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x145893C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x14502E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2305474== by 0x13CC1E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2305474== by 0xE7BA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305474== by 0x9CC3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x9C5CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x8953D38: PetscInitialize (pinit.c:924) ==2305474== by 0x81DE66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305474== by 0x81DE6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305474== by 0x11518A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305474== by 0x110CB3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305474== by 0x112FD2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305474== by 0x112ECD: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305474== by 0x1134E1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305474== by 0x10F4B5: main (TestHodgkinHuxleySquidAxon1952OriginalOdeSystem.cpp:18) ==2305474== Address 0x1ffeffdf7c is on thread 1's stack ==2305474== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2305474== { 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 } ==2305474== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2305474== at 0x85C279E: getsockopt_syscall (getsockopt.c:29) ==2305474== by 0x85C279E: getsockopt (getsockopt.c:94) ==2305474== by 0x1467B157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x14682A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x14689DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x145893C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x14502E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2305474== by 0x13CC1E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2305474== by 0xE7BA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305474== by 0x9CC3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x9C5CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x8953D38: PetscInitialize (pinit.c:924) ==2305474== by 0x81DE66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305474== by 0x81DE6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305474== by 0x11518A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305474== by 0x110CB3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305474== by 0x112FD2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305474== by 0x112ECD: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305474== by 0x1134E1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305474== by 0x10F4B5: main (TestHodgkinHuxleySquidAxon1952OriginalOdeSystem.cpp:18) ==2305474== Address 0x1ffeffdf7c is on thread 1's stack ==2305474== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2305474== { 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 } ==2305474== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2305474== at 0x85C2C7E: setsockopt_syscall (setsockopt.c:29) ==2305474== by 0x85C2C7E: setsockopt (setsockopt.c:95) ==2305474== by 0x14682BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x14689DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x145893C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305474== by 0x14502E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2305474== by 0x13CC1E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2305474== by 0xE7BA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305474== by 0x9CC3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x9C5CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x8953D38: PetscInitialize (pinit.c:924) ==2305474== by 0x81DE66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305474== by 0x81DE6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305474== by 0x11518A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305474== by 0x110CB3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305474== by 0x112FD2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305474== by 0x112ECD: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305474== by 0x1134E1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305474== by 0x10F4B5: main (TestHodgkinHuxleySquidAxon1952OriginalOdeSystem.cpp:18) ==2305474== { 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 } ==2305474== ==2305474== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2305474== Open file descriptor 12: ==2305474== at 0x85B022D: pipe (pipe.c:29) ==2305474== by 0x13CC207D: ??? ==2305474== by 0xE7BA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305474== by 0x9CC3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x9C5CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x8953D38: PetscInitialize (pinit.c:924) ==2305474== by 0x81DE66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305474== by 0x81DE6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305474== by 0x11518A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305474== by 0x110CB3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305474== by 0x112FD2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305474== by 0x112ECD: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305474== by 0x1134E1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305474== by 0x10F4B5: main (TestHodgkinHuxleySquidAxon1952OriginalOdeSystem.cpp:18) ==2305474== ==2305474== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2305474== at 0x85B4BCC: __open_nocancel (open64_nocancel.c:39) ==2305474== by 0x8538C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2305474== by 0x8216822: ??? ==2305474== by 0x821696F: ??? ==2305474== by 0xE85F6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305474== by 0xE85F938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305474== by 0xE815922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305474== by 0xE7BA2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305474== by 0x9CC3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x9C5CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x8953D38: PetscInitialize (pinit.c:924) ==2305474== by 0x81DE66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305474== by 0x81DE6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305474== by 0x11518A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305474== by 0x110CB3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305474== by 0x112FD2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305474== by 0x112ECD: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305474== by 0x1134E1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305474== by 0x10F4B5: main (TestHodgkinHuxleySquidAxon1952OriginalOdeSystem.cpp:18) ==2305474== ==2305474== Open file descriptor 117: ==2305474== ==2305474== ==2305474== Open file descriptor 110: ==2305474== ==2305474== ==2305474== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestHodgkinHuxleySquidAxon1952OriginalOdeSystem_valgrind.txt ==2305474== ==2305474== ==2305474== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2305474== ==2305474== ==2305474== ==2305474== HEAP SUMMARY: ==2305474== in use at exit: 700,759 bytes in 9,377 blocks ==2305474== total heap usage: 51,053 allocs, 41,676 frees, 1,353,527,135 bytes allocated ==2305474== ==2305474== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==2305474== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2305474== by 0x14590C13: ??? ==2305474== by 0x1459122C: ??? ==2305474== by 0x145044B7: ??? ==2305474== by 0x9C2915A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x9CC3A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x9C5CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x8953D38: PetscInitialize (pinit.c:924) ==2305474== by 0x81DE66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305474== by 0x81DE6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305474== by 0x11518A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305474== by 0x110CB3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305474== by 0x112FD2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305474== by 0x112ECD: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305474== by 0x1134E1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305474== by 0x10F4B5: main (TestHodgkinHuxleySquidAxon1952OriginalOdeSystem.cpp:18) ==2305474== { 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 } ==2305474== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65 ==2305474== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2305474== by 0x1570374E: ??? ==2305474== by 0x15703E0B: ??? ==2305474== by 0x15706F56: ??? ==2305474== by 0x156FC65D: ??? ==2305474== by 0x156FCFA3: ??? ==2305474== by 0xE8CBF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2305474== by 0xE8A7AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2305474== by 0xE858CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305474== by 0xE785EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305474== by 0x13CC2F03: ??? ==2305474== by 0xE7BA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305474== by 0x9CC3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x9C5CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305474== by 0x8953D38: PetscInitialize (pinit.c:924) ==2305474== by 0x81DE66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305474== by 0x81DE6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305474== by 0x11518A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305474== by 0x110CB3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305474== by 0x112FD2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305474== by 0x112ECD: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305474== by 0x1134E1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305474== by 0x10F4B5: main (TestHodgkinHuxleySquidAxon1952OriginalOdeSystem.cpp:18) ==2305474== { 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 } ==2305474== LEAK SUMMARY: ==2305474== definitely lost: 688 bytes in 2 blocks ==2305474== indirectly lost: 1,760 bytes in 16 blocks ==2305474== possibly lost: 0 bytes in 0 blocks ==2305474== still reachable: 1,531 bytes in 6 blocks ==2305474== suppressed: 696,780 bytes in 9,353 blocks ==2305474== Reachable blocks (those to which a pointer was found) are not shown. ==2305474== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2305474== ==2305474== Use --track-origins=yes to see where uninitialised values come from ==2305474== For lists of detected and suppressed errors, rerun with: -s ==2305474== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 32 from 32)