We've seen such behavior with ubuntu default OpenMPI - but have no idea why this happens or if we can work around it.
Last I checked - the same version of openmpi - when installed separately did not exhibit such issues.. Satish On Tue, 30 Jul 2019, Fabian.Jakub via petsc-dev wrote: > Dear Petsc Team, > Our cluster recently switched to Ubuntu 18.04 which has gcc 7.4 and > (Open MPI) 2.1.1 - with this I ended up with segfault and valgrind > errors in DMDAGlobalToNatural. > > This is evident in a minimal fortran example such as the attached > example petsc_ex.F90 > > with the following error: > > ==22616== Conditional jump or move depends on uninitialised value(s) > ==22616== at 0x4FA5CDB: PetscTrMallocDefault (mtr.c:185) > ==22616== by 0x4FA4DAC: PetscMallocA (mal.c:413) > ==22616== by 0x5090E94: VecScatterSetUp_SF (vscatsf.c:652) > ==22616== by 0x50A1104: VecScatterSetUp (vscatfce.c:209) > ==22616== by 0x509EE3B: VecScatterCreate (vscreate.c:280) > ==22616== by 0x577B48B: DMDAGlobalToNatural_Create (dagtol.c:108) > ==22616== by 0x577BB6D: DMDAGlobalToNaturalBegin (dagtol.c:155) > ==22616== by 0x5798446: VecView_MPI_DA (gr2.c:720) > ==22616== by 0x51BC7D8: VecView (vector.c:574) > ==22616== by 0x4F4ECA1: PetscObjectView (destroy.c:90) > ==22616== by 0x4F4F05E: PetscObjectViewFromOptions (destroy.c:126) > > and consequently wrong results in the natural vec > > > I was looking at the fortran example if I did forget something but I can > also see the same error, i.e. not being valgrind clean, in pure C - PETSc: > > cd $PETSC_DIR/src/dm/examples/tests && make ex14 && mpirun > --allow-run-as-root -np 2 valgrind ./ex14 > > I then tried various docker/podman linux distributions to make sure that > my setup is clean and to me it seems that this error is confined to the > particular gcc version 7.4 and (Open MPI) 2.1.1 from the ubuntu:latest repo. > > I tried other images from dockerhub including > > gcc:7.4.0 :: where I could neither install openmpi nor mpich through > apt, however works with --download-openmpi and --download-mpich > > ubuntu:rolling(19.04) <-- work > > debian:latest & :stable <-- works > > ubuntu:latest(18.04) <-- fails in case of openmpi, but works with mpich > or with petsc-configure --download-openmpi or --download-mpich > > > Is this error with (Open MPI) 2.1.1 a known issue? In the meantime, I > guess I'll go with a custom mpi install but given that ubuntu:latest is > widely spread, do you think there is an easy solution to the error? > > I guess you are not eager to delve into this issue with old mpi versions > but in case you find some spare time, maybe you find the root cause > and/or a workaround. > > Many thanks, > Fabian >