==1603966== Memcheck, a memory error detector ==1603966== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1603966== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1603966== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestRunningPottsBasedSimulationsTutorial -malloc_debug -malloc_dump -memory_info ==1603966== Parent PID: 1586025 ==1603966== ==1603966== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==1603966== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==1603966== ==1603966== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==1603966== at 0xC6CE79E: getsockopt_syscall (getsockopt.c:29) ==1603966== by 0xC6CE79E: getsockopt (getsockopt.c:94) ==1603966== by 0x184C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x184CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1603966== by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1603966== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1603966== by 0xF8D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xF86DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xE564D38: PetscInitialize (pinit.c:924) ==1603966== by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1603966== by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1603966== by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1603966== by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1603966== by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1603966== by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1603966== by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1603966== by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19) ==1603966== Address 0x1ffeffdf7c is on thread 1's stack ==1603966== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1603966== { 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 } ==1603966== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==1603966== at 0xC6CE79E: getsockopt_syscall (getsockopt.c:29) ==1603966== by 0xC6CE79E: getsockopt (getsockopt.c:94) ==1603966== by 0x184C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x184CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1603966== by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1603966== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1603966== by 0xF8D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xF86DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xE564D38: PetscInitialize (pinit.c:924) ==1603966== by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1603966== by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1603966== by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1603966== by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1603966== by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1603966== by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1603966== by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1603966== by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19) ==1603966== Address 0x1ffeffdf7c is on thread 1's stack ==1603966== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1603966== { 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 } ==1603966== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==1603966== at 0xC6CEC7E: setsockopt_syscall (setsockopt.c:29) ==1603966== by 0xC6CEC7E: setsockopt (setsockopt.c:95) ==1603966== by 0x184CEBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1603966== by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1603966== by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1603966== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1603966== by 0xF8D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xF86DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xE564D38: PetscInitialize (pinit.c:924) ==1603966== by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1603966== by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1603966== by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1603966== by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1603966== by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1603966== by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1603966== by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1603966== by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19) ==1603966== { 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 } ==1603966== ==1603966== FILE DESCRIPTORS: 9 open (3 std) at exit. ==1603966== Open file descriptor 12: ==1603966== at 0xC6BC22D: pipe (pipe.c:29) ==1603966== by 0x17B0E07D: ??? ==1603966== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1603966== by 0xF8D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xF86DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xE564D38: PetscInitialize (pinit.c:924) ==1603966== by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1603966== by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1603966== by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1603966== by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1603966== by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1603966== by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1603966== by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1603966== by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19) ==1603966== ==1603966== Open file descriptor 8: /dev/shm/open_mpi.0000 ==1603966== at 0xC6C0BCC: __open_nocancel (open64_nocancel.c:39) ==1603966== by 0xC644C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==1603966== by 0xBFF7822: ??? ==1603966== by 0xBFF796F: ??? ==1603966== by 0x131B36DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1603966== by 0x131B3938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1603966== by 0x13169922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1603966== by 0x1310E2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1603966== by 0xF8D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xF86DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xE564D38: PetscInitialize (pinit.c:924) ==1603966== by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1603966== by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1603966== by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1603966== by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1603966== by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1603966== by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1603966== by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1603966== by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19) ==1603966== ==1603966== Open file descriptor 117: ==1603966== ==1603966== ==1603966== Open file descriptor 110: ==1603966== ==1603966== ==1603966== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestRunningPottsBasedSimulationsTutorial_valgrind.txt ==1603966== ==1603966== ==1603966== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==1603966== ==1603966== ==1603966== ==1603966== HEAP SUMMARY: ==1603966== in use at exit: 700,704 bytes in 9,374 blocks ==1603966== total heap usage: 39,441,459 allocs, 39,432,085 frees, 3,793,234,024 bytes allocated ==1603966== ==1603966== 552 bytes in 1 blocks are definitely lost in loss record 36 of 62 ==1603966== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1603966== by 0x183DCC13: ??? ==1603966== by 0x183DD22C: ??? ==1603966== by 0x183504B7: ??? ==1603966== by 0xF83A15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xF8D4A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xF86DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xE564D38: PetscInitialize (pinit.c:924) ==1603966== by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1603966== by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1603966== by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1603966== by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1603966== by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1603966== by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1603966== by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1603966== by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19) ==1603966== { 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 } ==1603966== 23,323 (136 direct, 23,187 indirect) bytes in 1 blocks are definitely lost in loss record 59 of 62 ==1603966== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1603966== by 0x1994F74E: ??? ==1603966== by 0x1994FE0B: ??? ==1603966== by 0x19952F56: ??? ==1603966== by 0x1994865D: ??? ==1603966== by 0x19948FA3: ??? ==1603966== by 0x13221F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1603966== by 0x131FDAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1603966== by 0x131ACCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1603966== by 0x130D9EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1603966== by 0x17B0EF03: ??? ==1603966== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1603966== by 0xF8D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xF86DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1603966== by 0xE564D38: PetscInitialize (pinit.c:924) ==1603966== by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1603966== by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1603966== by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1603966== by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1603966== by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1603966== by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1603966== by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1603966== by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19) ==1603966== { 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 } ==1603966== LEAK SUMMARY: ==1603966== definitely lost: 688 bytes in 2 blocks ==1603966== indirectly lost: 1,760 bytes in 16 blocks ==1603966== possibly lost: 0 bytes in 0 blocks ==1603966== still reachable: 1,563 bytes in 7 blocks ==1603966== suppressed: 696,693 bytes in 9,349 blocks ==1603966== Reachable blocks (those to which a pointer was found) are not shown. ==1603966== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1603966== ==1603966== Use --track-origins=yes to see where uninitialised values come from ==1603966== For lists of detected and suppressed errors, rerun with: -s ==1603966== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 28 from 28)