==2285718== Memcheck, a memory error detector ==2285718== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2285718== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2285718== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestPeriodicNodeBasedCellPopulationParallelMethods -malloc_debug -malloc_dump -memory_info ==2285718== Parent PID: 2283975 ==2285718== ==2285718== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2285718== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2285718== ==2285718== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2285718== at 0xDCEE79E: getsockopt_syscall (getsockopt.c:29) ==2285718== by 0xDCEE79E: getsockopt (getsockopt.c:94) ==2285718== by 0x184C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x184CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2285718== by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2285718== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2285718== by 0xF9BC418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xF955D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xE64CD38: PetscInitialize (pinit.c:924) ==2285718== by 0xD4FA66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2285718== by 0xD4FA6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2285718== by 0x136C08: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2285718== by 0x13073D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2285718== by 0x132EE8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2285718== by 0x132DE4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2285718== by 0x1333F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2285718== by 0x12EF40: main (TestPeriodicNodeBasedCellPopulationParallelMethods.cpp:18) ==2285718== Address 0x1ffeffdf6c is on thread 1's stack ==2285718== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2285718== { 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 } ==2285718== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2285718== at 0xDCEE79E: getsockopt_syscall (getsockopt.c:29) ==2285718== by 0xDCEE79E: getsockopt (getsockopt.c:94) ==2285718== by 0x184C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x184CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2285718== by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2285718== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2285718== by 0xF9BC418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xF955D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xE64CD38: PetscInitialize (pinit.c:924) ==2285718== by 0xD4FA66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2285718== by 0xD4FA6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2285718== by 0x136C08: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2285718== by 0x13073D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2285718== by 0x132EE8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2285718== by 0x132DE4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2285718== by 0x1333F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2285718== by 0x12EF40: main (TestPeriodicNodeBasedCellPopulationParallelMethods.cpp:18) ==2285718== Address 0x1ffeffdf6c is on thread 1's stack ==2285718== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2285718== { 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 } ==2285718== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2285718== at 0xDCEEC7E: setsockopt_syscall (setsockopt.c:29) ==2285718== by 0xDCEEC7E: setsockopt (setsockopt.c:95) ==2285718== by 0x184CEBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2285718== by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2285718== by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2285718== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2285718== by 0xF9BC418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xF955D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xE64CD38: PetscInitialize (pinit.c:924) ==2285718== by 0xD4FA66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2285718== by 0xD4FA6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2285718== by 0x136C08: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2285718== by 0x13073D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2285718== by 0x132EE8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2285718== by 0x132DE4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2285718== by 0x1333F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2285718== by 0x12EF40: main (TestPeriodicNodeBasedCellPopulationParallelMethods.cpp:18) ==2285718== { 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 } ==2285718== ==2285718== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2285718== Open file descriptor 12: ==2285718== at 0xDCDC22D: pipe (pipe.c:29) ==2285718== by 0x17B0E07D: ??? ==2285718== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2285718== by 0xF9BC418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xF955D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xE64CD38: PetscInitialize (pinit.c:924) ==2285718== by 0xD4FA66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2285718== by 0xD4FA6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2285718== by 0x136C08: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2285718== by 0x13073D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2285718== by 0x132EE8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2285718== by 0x132DE4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2285718== by 0x1333F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2285718== by 0x12EF40: main (TestPeriodicNodeBasedCellPopulationParallelMethods.cpp:18) ==2285718== ==2285718== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2285718== at 0xDCE0BCC: __open_nocancel (open64_nocancel.c:39) ==2285718== by 0xDC64C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2285718== by 0xD532822: ??? ==2285718== by 0xD53296F: ??? ==2285718== by 0x131B36DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2285718== by 0x131B3938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2285718== by 0x13169922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2285718== by 0x1310E2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2285718== by 0xF9BC418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xF955D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xE64CD38: PetscInitialize (pinit.c:924) ==2285718== by 0xD4FA66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2285718== by 0xD4FA6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2285718== by 0x136C08: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2285718== by 0x13073D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2285718== by 0x132EE8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2285718== by 0x132DE4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2285718== by 0x1333F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2285718== by 0x12EF40: main (TestPeriodicNodeBasedCellPopulationParallelMethods.cpp:18) ==2285718== ==2285718== Open file descriptor 117: ==2285718== ==2285718== ==2285718== Open file descriptor 110: ==2285718== ==2285718== ==2285718== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestPeriodicNodeBasedCellPopulationParallelMethods_valgrind.txt ==2285718== ==2285718== ==2285718== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2285718== ==2285718== ==2285718== ==2285718== HEAP SUMMARY: ==2285718== in use at exit: 700,775 bytes in 9,378 blocks ==2285718== total heap usage: 54,387 allocs, 45,009 frees, 1,353,827,486 bytes allocated ==2285718== ==2285718== 552 bytes in 1 blocks are definitely lost in loss record 40 of 66 ==2285718== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2285718== by 0x183DCC13: ??? ==2285718== by 0x183DD22C: ??? ==2285718== by 0x183504B7: ??? ==2285718== by 0xF92215A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xF9BCA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xF955D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xE64CD38: PetscInitialize (pinit.c:924) ==2285718== by 0xD4FA66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2285718== by 0xD4FA6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2285718== by 0x136C08: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2285718== by 0x13073D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2285718== by 0x132EE8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2285718== by 0x132DE4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2285718== by 0x1333F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2285718== by 0x12EF40: main (TestPeriodicNodeBasedCellPopulationParallelMethods.cpp:18) ==2285718== { 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 } ==2285718== 23,323 (136 direct, 23,187 indirect) bytes in 1 blocks are definitely lost in loss record 63 of 66 ==2285718== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2285718== by 0x1994F74E: ??? ==2285718== by 0x1994FE0B: ??? ==2285718== by 0x19952F56: ??? ==2285718== by 0x1994865D: ??? ==2285718== by 0x19948FA3: ??? ==2285718== by 0x1321FF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2285718== by 0x131FBAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2285718== by 0x131ACCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2285718== by 0x130D9EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2285718== by 0x17B0EF03: ??? ==2285718== by 0x1310E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2285718== by 0xF9BC418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xF955D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2285718== by 0xE64CD38: PetscInitialize (pinit.c:924) ==2285718== by 0xD4FA66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2285718== by 0xD4FA6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2285718== by 0x136C08: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2285718== by 0x13073D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2285718== by 0x132EE8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2285718== by 0x132DE4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2285718== by 0x1333F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2285718== by 0x12EF40: main (TestPeriodicNodeBasedCellPopulationParallelMethods.cpp:18) ==2285718== { 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 } ==2285718== LEAK SUMMARY: ==2285718== definitely lost: 688 bytes in 2 blocks ==2285718== indirectly lost: 1,760 bytes in 16 blocks ==2285718== possibly lost: 0 bytes in 0 blocks ==2285718== still reachable: 1,563 bytes in 7 blocks ==2285718== suppressed: 696,764 bytes in 9,353 blocks ==2285718== Reachable blocks (those to which a pointer was found) are not shown. ==2285718== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2285718== ==2285718== Use --track-origins=yes to see where uninitialised values come from ==2285718== For lists of detected and suppressed errors, rerun with: -s ==2285718== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 32 from 32)