Things work fine when I use clang, but I'd really like to be able to use GCC as well.
I updated the ignored issue to reflect that the bug is still present when using GCC 7.1.0. I suppose I will give OpenMPI a try when I get a chance. --Richard On Tue, Aug 1, 2017 at 5:15 PM, Matthew Knepley <[email protected]> wrote: > 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/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/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/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 >> > >> >> > > > -- > 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/ >
