On 2 August 2017 at 00:39, Richard Tran Mills <[email protected]> wrote:
> Hi Folks, > > I am seeing a lot of errors when I run the full test suite (with latest > master) on my MacBook, related to SEGVs inside (or thereabouts) > PetscCommBuildTwoSided_Ibarrier. Do I have something mis-configured or > ... ? > Nope - I have exactly the same issue since moving to El Capitan. I posted a message to maint some time earlier this year / late last year about MatZeroRows being broken. The only way I know around this issue is to simply "avoid the fancy shit" (Barry) via the option -build_twosided allreduce > > Sample error message below: > > > [2]PETSC ERROR: ------------------------------ > ------------------------------------------ > > [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [2]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > [2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d > ocumentation/faq.html#valgrind > > [2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac > OS X to find memory corruption errors > > [2]PETSC ERROR: likely location of problem given in stack below > > [2]PETSC ERROR: --------------------- Stack Frames > ---------------------> [3]PETSC ERROR: Note: The EXACT line numbers in the > stack are not available, > > [3]PETSC ERROR: INSTEAD the line number of the start of the > function > > [3]PETSC ERROR: is given. > > [3]PETSC ERROR: [3] PetscCommBuildTwoSided_Ibarrier line 97 > /Users/rmills/proj/petsc/src/sys/utils/mpits.c > > [3]PETSC ERROR: [3] PetscCommBuildTwoSided line 279 > /Users/rmills/proj/petsc/src/sys/utils/mpits.c > > [3]PETSC ERROR: [3] PetscSFSetUp_Basic line 539 > /Users/rmills/proj/petsc/src/vec/is/sf/impls/basic/sfbasic.c > > [3]PETSC ERROR: [3] PetscSFSetUp line 179 /Users/rmills/proj/petsc/src/v > ec/is/sf/interface/sf.c > > [3]PETSC ERROR: [3] PetscSFBcastBegin line 925 > /Users/rmills/proj/petsc/src/vec/is/sf/interface/sf.c > > [3]PETSC ERROR: [3] MatISSetPreallocation_IS line 1018 > /Users/rmills/proj/petsc/src/mat/impls/is/matis.c > > [3]PETSC ERROR: [3] MatISSetPreallocation line 1005 > /Users/rmills/proj/petsc/src/mat/impls/is/matis.c > > And I'm using MPICH downloaded/built by PETSc: > > rmills@Richards-MBP:mat(master=)arch-osx-gcc7-debug$ > /Users/rmills/proj/petsc/arch-osx-gcc7-debug/bin/mpirun --version > HYDRA build details: > Version: 3.2 > Release Date: Wed Nov 11 22:06:48 CST 2015 > CC: gcc-7 -fstack-protector -g > CXX: g++-7 -fstack-protector -g > F77: gfortran -ffree-line-length-0 -g > F90: gfortran -ffree-line-length-0 -g > Configure options: '--disable-option-checking' > '--prefix=/Users/rmills/proj/petsc/arch-osx-gcc7-debug' > 'MAKE=/usr/bin/make' > '--libdir=/Users/rmills/proj/petsc/arch-osx-gcc7-debug/lib' > 'CC=gcc-7' 'CFLAGS=-fstack-protector -g -O0' 'AR=/usr/bin/ar' 'ARFLAGS=cr' > 'CXX=g++-7' 'CXXFLAGS=-fstack-protector -g ' 'F77=gfortran' > 'FFLAGS=-ffree-line-length-0 -g ' 'FC=gfortran' > 'FCFLAGS=-ffree-line-length-0 -g ' '--enable-shared' > '--with-device=ch3:sock' '--with-pm=hydra' '--enable-fast=no' > '--enable-g=meminit' '--cache-file=/dev/null' '--srcdir=.' 'LDFLAGS=' > 'LIBS=-lpthread ' 'CPPFLAGS= -I/Users/rmills/proj/petsc/arc > h-osx-gcc7-debug/externalpackages/mpich-3.2/src/mpl/include > -I/Users/rmills/proj/petsc/arch-osx-gcc7-debug/externalpackages/mpich-3.2/src/mpl/include > -I/Users/rmills/proj/petsc/arch-osx-gcc7-debug/externalpackages/mpich-3.2/src/openpa/src > -I/Users/rmills/proj/petsc/arch-osx-gcc7-debug/externalpackages/mpich-3.2/src/openpa/src > -D_REENTRANT -I/Users/rmills/proj/petsc/arch-osx-gcc7-debug/externalpacka > ges/mpich-3.2/src/mpi/romio/include' > Process Manager: pmi > Launchers available: ssh rsh fork slurm ll lsf sge > manual persist > Topology libraries available: hwloc > Resource management kernels available: user slurm ll lsf sge pbs > cobalt > Checkpointing libraries available: > Demux engines available: poll select > > --Richard >
