==1713010== Memcheck, a memory error detector ==1713010== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1713010== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1713010== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestOnLatticeSimulationWithPottsBasedCellPopulation -malloc_debug -malloc_dump -memory_info ==1713010== Parent PID: 1705792 ==1713010== ==1713010== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==1713010== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==1713010== ==1713010== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==1713010== at 0xDD3179E: getsockopt_syscall (getsockopt.c:29) ==1713010== by 0xDD3179E: getsockopt (getsockopt.c:94) ==1713010== by 0x184C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x184CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1713010== by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1713010== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1713010== by 0xF9BB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xF954D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xE64BD38: PetscInitialize (pinit.c:924) ==1713010== by 0xD4F958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1713010== by 0xD4F95D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1713010== by 0x1E6038: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1713010== by 0x1DC313: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1713010== by 0x1DFC4E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1713010== by 0x1DFAEE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1713010== by 0x1E0185: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1713010== by 0x1DA600: main (TestOnLatticeSimulationWithPottsBasedCellPopulation.cpp:19) ==1713010== Address 0x1ffeffdf6c is on thread 1's stack ==1713010== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1713010== { 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 } ==1713010== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==1713010== at 0xDD3179E: getsockopt_syscall (getsockopt.c:29) ==1713010== by 0xDD3179E: getsockopt (getsockopt.c:94) ==1713010== by 0x184C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x184CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1713010== by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1713010== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1713010== by 0xF9BB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xF954D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xE64BD38: PetscInitialize (pinit.c:924) ==1713010== by 0xD4F958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1713010== by 0xD4F95D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1713010== by 0x1E6038: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1713010== by 0x1DC313: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1713010== by 0x1DFC4E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1713010== by 0x1DFAEE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1713010== by 0x1E0185: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1713010== by 0x1DA600: main (TestOnLatticeSimulationWithPottsBasedCellPopulation.cpp:19) ==1713010== Address 0x1ffeffdf6c is on thread 1's stack ==1713010== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1713010== { 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 } ==1713010== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==1713010== at 0xDD31C7E: setsockopt_syscall (setsockopt.c:29) ==1713010== by 0xDD31C7E: setsockopt (setsockopt.c:95) ==1713010== by 0x184CEBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1713010== by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1713010== by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1713010== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1713010== by 0xF9BB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xF954D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xE64BD38: PetscInitialize (pinit.c:924) ==1713010== by 0xD4F958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1713010== by 0xD4F95D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1713010== by 0x1E6038: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1713010== by 0x1DC313: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1713010== by 0x1DFC4E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1713010== by 0x1DFAEE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1713010== by 0x1E0185: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1713010== by 0x1DA600: main (TestOnLatticeSimulationWithPottsBasedCellPopulation.cpp:19) ==1713010== { 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 } ==1713010== ==1713010== FILE DESCRIPTORS: 9 open (3 std) at exit. ==1713010== Open file descriptor 12: ==1713010== at 0xDD1F22D: pipe (pipe.c:29) ==1713010== by 0x17B0E07D: ??? ==1713010== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1713010== by 0xF9BB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xF954D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xE64BD38: PetscInitialize (pinit.c:924) ==1713010== by 0xD4F958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1713010== by 0xD4F95D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1713010== by 0x1E6038: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1713010== by 0x1DC313: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1713010== by 0x1DFC4E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1713010== by 0x1DFAEE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1713010== by 0x1E0185: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1713010== by 0x1DA600: main (TestOnLatticeSimulationWithPottsBasedCellPopulation.cpp:19) ==1713010== ==1713010== Open file descriptor 8: /dev/shm/open_mpi.0000 ==1713010== at 0xDD23BCC: __open_nocancel (open64_nocancel.c:39) ==1713010== by 0xDCA7C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==1713010== by 0xD531822: ??? ==1713010== by 0xD53196F: ??? ==1713010== by 0x131B36DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1713010== by 0x131B3938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1713010== by 0x13169922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1713010== by 0x1310E2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1713010== by 0xF9BB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xF954D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xE64BD38: PetscInitialize (pinit.c:924) ==1713010== by 0xD4F958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1713010== by 0xD4F95D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1713010== by 0x1E6038: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1713010== by 0x1DC313: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1713010== by 0x1DFC4E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1713010== by 0x1DFAEE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1713010== by 0x1E0185: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1713010== by 0x1DA600: main (TestOnLatticeSimulationWithPottsBasedCellPopulation.cpp:19) ==1713010== ==1713010== Open file descriptor 117: ==1713010== ==1713010== ==1713010== Open file descriptor 110: ==1713010== ==1713010== ==1713010== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestOnLatticeSimulationWithPottsBasedCellPopulation_valgrind.txt ==1713010== ==1713010== ==1713010== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==1713010== ==1713010== ==1713010== ==1713010== HEAP SUMMARY: ==1713010== in use at exit: 700,720 bytes in 9,375 blocks ==1713010== total heap usage: 11,367,824 allocs, 11,358,449 frees, 2,209,007,249 bytes allocated ==1713010== ==1713010== 552 bytes in 1 blocks are definitely lost in loss record 38 of 64 ==1713010== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1713010== by 0x183DCC13: ??? ==1713010== by 0x183DD22C: ??? ==1713010== by 0x183504B7: ??? ==1713010== by 0xF92115A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xF9BBA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xF954D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xE64BD38: PetscInitialize (pinit.c:924) ==1713010== by 0xD4F958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1713010== by 0xD4F95D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1713010== by 0x1E6038: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1713010== by 0x1DC313: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1713010== by 0x1DFC4E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1713010== by 0x1DFAEE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1713010== by 0x1E0185: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1713010== by 0x1DA600: main (TestOnLatticeSimulationWithPottsBasedCellPopulation.cpp:19) ==1713010== { 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 } ==1713010== 84,417 (136 direct, 84,281 indirect) bytes in 1 blocks are definitely lost in loss record 61 of 64 ==1713010== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1713010== by 0x1994F74E: ??? ==1713010== by 0x1994FE0B: ??? ==1713010== by 0x19952F56: ??? ==1713010== by 0x1994865D: ??? ==1713010== by 0x19948FA3: ??? ==1713010== by 0x1321FF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1713010== by 0x131FBAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1713010== by 0x131ACCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1713010== by 0x130D9EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1713010== by 0x17B0EF03: ??? ==1713010== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1713010== by 0xF9BB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xF954D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1713010== by 0xE64BD38: PetscInitialize (pinit.c:924) ==1713010== by 0xD4F958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1713010== by 0xD4F95D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1713010== by 0x1E6038: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1713010== by 0x1DC313: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1713010== by 0x1DFC4E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1713010== by 0x1DFAEE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1713010== by 0x1E0185: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1713010== by 0x1DA600: main (TestOnLatticeSimulationWithPottsBasedCellPopulation.cpp:19) ==1713010== { 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 } ==1713010== LEAK SUMMARY: ==1713010== definitely lost: 688 bytes in 2 blocks ==1713010== indirectly lost: 1,760 bytes in 16 blocks ==1713010== possibly lost: 0 bytes in 0 blocks ==1713010== still reachable: 1,579 bytes in 8 blocks ==1713010== suppressed: 696,693 bytes in 9,349 blocks ==1713010== Reachable blocks (those to which a pointer was found) are not shown. ==1713010== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1713010== ==1713010== Use --track-origins=yes to see where uninitialised values come from ==1713010== For lists of detected and suppressed errors, rerun with: -s ==1713010== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 28 from 28)