Some updates for this OpenMPI bug: 1) It appears to OpenMPI 2.1.x when configured with --enable-heterogeneous, which is not a default option and is not commonly used. But Ubuntu somehow used that. 2) OpenMPI fixed it in 3.x 3) It was reported to Ubuntu two years ago but is still unassigned. https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/1731938. A user's comment from last year, "We have just spent today hunting down a user bug report for Xyce (which uses Trilinos, and its Zoltan library) that turn out to be exactly this issue "
--Junchao Zhang On Wed, Jul 31, 2019 at 2:17 PM Junchao Zhang <[email protected]<mailto:[email protected]>> wrote: Hi, Fabian, I found it is an OpenMPI bug w.r.t self-to-self MPI_Send/Recv using MPI_ANY_SOURCE for message matching. OpenMPI does not put correct value in recv buffer. I have a workaround jczhang/fix-ubuntu-openmpi-anysource<https://bitbucket.org/petsc/petsc/branch/jczhang/fix-ubuntu-openmpi-anysource>. I tested with your petsc_ex.F90 and $PETSC_DIR/src/dm/examples/tests/ex14. The majority of valgrind errors disappeared. A few left are in ompi_mpi_init and we can ignore them. I filed a bug report to OpenMPI https://www.mail-archive.com/[email protected]//msg33383.html and hope they can fix it in Ubuntu. Thanks. --Junchao Zhang On Tue, Jul 30, 2019 at 9:47 AM Fabian.Jakub via petsc-dev <[email protected]<mailto:[email protected]>> 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
