[petsc-dev] PETSc OpenMPI library test interminable
Matthew Knepley
knepley at gmail.com
Mon Oct 15 07:33:01 CDT 2018
On Mon, Oct 15, 2018 at 6:21 AM Antonio Trande <anto.trande at gmail.com>
wrote:
> Hi all.
>
> PETSc-3.10.2 compiled with OpenMPI-2.1.5 on Fedora 30 (devel branch) (or
> with OpenMPI-2.1.1 on Fedora 28), on x86 architectures only:
>
This looks like an OpenMPI bug. Does it work with MPICH?
Thanks,
Matt
> the 'src/snes/examples/tutorials/ex19' test has no end with the
> following output:
>
> + export
>
> LD_LIBRARY_PATH=/builddir/build/BUILD/petsc-3.10.2/buildopenmpi_dir/i386/lib
> +
>
> LD_LIBRARY_PATH=/builddir/build/BUILD/petsc-3.10.2/buildopenmpi_dir/i386/lib
> + export PETSC_DIR=/builddir/build/BUILD/petsc-3.10.2/buildopenmpi_dir
> + PETSC_DIR=/builddir/build/BUILD/petsc-3.10.2/buildopenmpi_dir
> + export PETSC_ARCH=i386
> + PETSC_ARCH=i386
> + export MPI_INTERFACE_HOSTNAME=localhost
> + MPI_INTERFACE_HOSTNAME=localhost
> + export 'PETSCVALGRIND_OPTIONS= --tool=memcheck --leak-check=yes
> --track-origins=yes'
> + PETSCVALGRIND_OPTIONS=' --tool=memcheck --leak-check=yes
> --track-origins=yes'
> + export 'CFLAGS=-O0 -g -Wl,-z,now -fPIC'
> + CFLAGS='-O0 -g -Wl,-z,now -fPIC'
> + export 'CXXFLAGS=-O0 -g -Wl,-z,now -fPIC'
> + CXXFLAGS='-O0 -g -Wl,-z,now -fPIC'
> + export 'FFLAGS=-O0 -g -Wl,-z,now -fPIC -I/usr/lib/gfortran/modules'
> + FFLAGS='-O0 -g -Wl,-z,now -fPIC -I/usr/lib/gfortran/modules'
> + make -C buildopenmpi_dir test
>
> 'MPIEXEC=/builddir/build/BUILD/petsc-3.10.2/buildopenmpi_dir/lib/petsc/bin/petscmpiexec
> -valgrind'
> make: Entering directory
> '/builddir/build/BUILD/petsc-3.10.2/buildopenmpi_dir'
> Running test examples to verify correct installation
> Using PETSC_DIR=/builddir/build/BUILD/petsc-3.10.2/buildopenmpi_dir and
> PETSC_ARCH=i386
> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI
> process
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> ==25868== Conditional jump or move depends on uninitialised value(s)
> ==25868== at 0x8E2CCA3: opal_value_unload (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x6088607: ompi_proc_complete_init (in
> /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868== by 0x608C845: ompi_mpi_init (in
> /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868== by 0x60B2A97: PMPI_Init_thread (in
> /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868== by 0x49E0B0F: PetscInitialize (pinit.c:875)
> ==25868== by 0x8049643: main (ex19.c:106)
> ==25868== Uninitialised value was created by a stack allocation
> ==25868== at 0x6088593: ompi_proc_complete_init (in
> /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868==
> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
> Number of SNES iterations = 2
> ==25868== 10 bytes in 1 blocks are definitely lost in loss record 11 of 189
> ==25868== at 0x40356A4: malloc (vg_replace_malloc.c:299)
> ==25868== by 0xA890F6F: ??? (in
> /usr/lib/openmpi/lib/openmpi/mca_pmix_pmix112.so)
> ==25868== by 0xA88FEFD: pmix_bfrop_unpack_buffer (in
> /usr/lib/openmpi/lib/openmpi/mca_pmix_pmix112.so)
> ==25868== by 0xA8901D0: ??? (in
> /usr/lib/openmpi/lib/openmpi/mca_pmix_pmix112.so)
> ==25868== by 0xA89BED4: ??? (in
> /usr/lib/openmpi/lib/openmpi/mca_pmix_pmix112.so)
> ==25868== by 0xA899C7C: ??? (in
> /usr/lib/openmpi/lib/openmpi/mca_pmix_pmix112.so)
> ==25868== by 0x8E63AFD: opal_libevent2022_event_base_loop (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0xA897C32: ??? (in
> /usr/lib/openmpi/lib/openmpi/mca_pmix_pmix112.so)
> ==25868== by 0x61635DD: start_thread (in
> /usr/lib/libpthread-2.28.9000.so)
> ==25868== by 0x626A699: clone (in /usr/lib/libc-2.28.9000.so)
> ==25868==
> ==25868== 10 bytes in 1 blocks are definitely lost in loss record 12 of 189
> ==25868== at 0x40356A4: malloc (vg_replace_malloc.c:299)
> ==25868== by 0x6201519: strdup (in /usr/lib/libc-2.28.9000.so)
> ==25868== by 0x8E4B0FE: mca_base_var_enum_create_flag (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x8E5DDA5: ??? (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x8E4CC34: mca_base_framework_register (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x8E4CCE0: mca_base_framework_open (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x60DD028: ??? (in /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868== by 0x8E4CD68: mca_base_framework_open (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x608C410: ompi_mpi_init (in
> /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868== by 0x60B2A97: PMPI_Init_thread (in
> /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868== by 0x49E0B0F: PetscInitialize (pinit.c:875)
> ==25868== by 0x8049643: main (ex19.c:106)
> ==25868==
> ==25868== 17 bytes in 1 blocks are definitely lost in loss record 79 of 189
> ==25868== at 0x40356A4: malloc (vg_replace_malloc.c:299)
> ==25868== by 0x6201519: strdup (in /usr/lib/libc-2.28.9000.so)
> ==25868== by 0x8E4B0FE: mca_base_var_enum_create_flag (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x8E5DDC0: ??? (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x8E4CC34: mca_base_framework_register (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x8E4CCE0: mca_base_framework_open (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x60DD028: ??? (in /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868== by 0x8E4CD68: mca_base_framework_open (in
> /usr/lib/openmpi/lib/libopen-pal.so.20.10.4)
> ==25868== by 0x608C410: ompi_mpi_init (in
> /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868== by 0x60B2A97: PMPI_Init_thread (in
> /usr/lib/openmpi/lib/libmpi.so.20.10.3)
> ==25868== by 0x49E0B0F: PetscInitialize (pinit.c:875)
> ==25868== by 0x8049643: main (ex19.c:106)
> ...
>
>
>
> --
> ---
> Antonio Trande
> Fedora Project
> mailto 'sagitter at fedoraproject dot org'
> GPG key: 0x5E212EE1D35568BE
> GPG key server: https://keys.fedoraproject.org/
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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