On Tue, Aug 1, 2017 at 7:03 PM, Barry Smith <[email protected]> wrote:
> > Reported to MPICH folks https://github.com/pmodels/mpich/issues/2437 > and ignored. > If you guys cannot walk down the hall and get them to consider these bugs, we should just stop using MPICH and recommending it to unsuspecting people. This is development malpractice. Matt > What about using Gnu compilers and OpenMPI (allegedly OpenMPI has fixed > up many of their ongoing bugs). > > Barry > > > On Aug 1, 2017, at 6:58 PM, Dave May <[email protected]> wrote: > > > > > > > > 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/ > documentation/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/ > vec/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/ > 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/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/ > externalpackages/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 > > > > -- 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 http://www.caam.rice.edu/~mk51/
