Reported to MPICH folks https://github.com/pmodels/mpich/issues/2437 and
ignored.
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
>
