[petsc-dev] PETSc OpenMPI library test interminable

[Antonio Trande]

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:

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/