[petsc-users] make check failed with intel 2019 compilers

Wed May 13 15:33:51 CDT 2020

Alexander,
   I reproduced the error with Intel MPI 2019.3.199 and I can confirm it is
because Intel MPI_Type_get_envelope() is wrong.

--Junchao Zhang

On Tue, May 12, 2020 at 3:45 PM Alexander Lindsay <alexlindsay239 at gmail.com>
wrote:

> Ok, this is good to know. Yea we'll probably just roll back then. Thanks!
>
> On Tue, May 12, 2020 at 12:45 PM Satish Balay <balay at mcs.anl.gov> wrote:
>
>> On Tue, 12 May 2020, Matthew Knepley wrote:
>>
>> > On Tue, May 12, 2020 at 3:13 PM Alexander Lindsay <
>> alexlindsay239 at gmail.com>
>> > wrote:
>> >
>> > > The parallel make check target (ex19) fails with the error below after
>> > > configuring/building with intel 2019 mpi compilers
>> > > (mpiicc,mpiicpc,mpiifort). Any attempt to run valgrind or to attach
>> to a
>> > > debugger fails with `mpiexec: Error: unknown option "-pmi_args"`. I've
>> > > attached configure.log. Does anyone have any ideas off the top of
>> their
>> > > head? We're trying to link MOOSE with a project that refuses to use a
>> > > toolchain other than intel's. I'm currently trying to figure out
>> whether
>> > > the MPI implementation matters (e.g. can I use mpich/openmpi), but
>> for now
>> > > I'm operating under the assumption that I need to use the intel MPI
>> > > implementation.
>> > >
>> >
>> > There have been a _lot_ of bugs in the 2019 MPI for some reason. Is it
>> at
>> > all possible to rollback?
>> >
>> > If not, is this somewhere we can run?
>>
>> We have this compiler/mpi [19u3] on our KNL box. I've had weird issues
>> with it - so we still use 18u2 on it.
>>
>> Satish
>>
>> >
>> >   Thanks,
>> >
>> >     Matt
>> >
>> >
>> > > lindad at lemhi2
>> :/scratch/lindad/moose/petsc/src/snes/examples/tutorials((detached
>> > > from 7c25e2d))$ mpiexec -np 2 ./ex19
>> > > lid velocity = 0.0625, prandtl # = 1., grashof # = 1.
>> > > [0]PETSC ERROR:
>> > >
>> ------------------------------------------------------------------------
>> > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> > > probably memory access out of range
>> > > [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > > [0]PETSC ERROR: or see
>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> > > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
>> Mac OS
>> > > X to find memory corruption errors
>> > > [0]PETSC ERROR: likely location of problem given in stack below
>> > > [0]PETSC ERROR: ---------------------  Stack Frames
>> > > ------------------------------------
>> > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>> > > available,
>> > > [0]PETSC ERROR:       INSTEAD the line number of the start of the
>> function
>> > > [0]PETSC ERROR:       is given.
>> > > [0]PETSC ERROR: [0] MPIPetsc_Type_unwrap line 38
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/interface/sftype.c
>> > > [0]PETSC ERROR: [1]PETSC ERROR:
>> > >
>> ------------------------------------------------------------------------
>> > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> > > probably memory access out of range
>> > > [1]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > > [1]PETSC ERROR: or see
>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> > > [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
>> Mac OS
>> > > X to find memory corruption errors
>> > > [1]PETSC ERROR: likely location of problem given in stack below
>> > > [1]PETSC ERROR: ---------------------  Stack Frames
>> > > ------------------------------------
>> > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>> > > available,
>> > > [1]PETSC ERROR:       INSTEAD the line number of the start of the
>> function
>> > > [1]PETSC ERROR:       is given.
>> > > [1]PETSC ERROR: [1] MPIPetsc_Type_unwrap line 38
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/interface/sftype.c
>> > > [1]PETSC ERROR: [0] MPIPetsc_Type_compare line 71
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/interface/sftype.c
>> > > [0]PETSC ERROR: [0] PetscSFPackGetInUse line 514
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/impls/basic/sfpack.c
>> > > [0]PETSC ERROR: [0] PetscSFBcastAndOpEnd_Basic line 305
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/impls/basic/sfbasic.c
>> > > [0]PETSC ERROR: [0] PetscSFBcastAndOpEnd line 1335
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/interface/sf.c
>> > > [0]PETSC ERROR: [0] VecScatterEnd_SF line 83
>> > > /scratch/lindad/moose/petsc/src/vec/vscat/impls/sf/vscatsf.c
>> > > [0]PETSC ERROR: [1] MPIPetsc_Type_compare line 71
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/interface/sftype.c
>> > > [1]PETSC ERROR: [1] PetscSFPackGetInUse line 514
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/impls/basic/sfpack.c
>> > > [0] VecScatterEnd line 145
>> > > /scratch/lindad/moose/petsc/src/vec/vscat/interface/vscatfce.c
>> > > [0]PETSC ERROR: [0] DMGlobalToLocalEnd_DA line 25
>> > > /scratch/lindad/moose/petsc/src/dm/impls/da/dagtol.c
>> > > [0]PETSC ERROR: [1]PETSC ERROR: [1] PetscSFBcastAndOpEnd_Basic line
>> 305
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/impls/basic/sfbasic.c
>> > > [1]PETSC ERROR: [1] PetscSFBcastAndOpEnd line 1335
>> > > /scratch/lindad/moose/petsc/src/vec/is/sf/interface/sf.c
>> > > [0] DMGlobalToLocalEnd line 2368
>> > > /scratch/lindad/moose/petsc/src/dm/interface/dm.c
>> > > [0]PETSC ERROR: [0] SNESComputeFunction_DMDA line 67
>> > > /scratch/lindad/moose/petsc/src/snes/utils/dmdasnes.c
>> > > [0]PETSC ERROR: [1]PETSC ERROR: [1] VecScatterEnd_SF line 83
>> > > /scratch/lindad/moose/petsc/src/vec/vscat/impls/sf/vscatsf.c
>> > > [0] MatFDColoringApply_AIJ line 180
>> > > /scratch/lindad/moose/petsc/src/mat/impls/aij/mpi/fdmpiaij.c
>> > > [0]PETSC ERROR: [0] MatFDColoringApply line 610
>> > > /scratch/lindad/moose/petsc/src/mat/matfd/fdmatrix.c
>> > > [0]PETSC ERROR: [1]PETSC ERROR: [1] VecScatterEnd line 145
>> > > /scratch/lindad/moose/petsc/src/vec/vscat/interface/vscatfce.c
>> > > [1]PETSC ERROR: [1] DMGlobalToLocalEnd_DA line 25
>> > > /scratch/lindad/moose/petsc/src/dm/impls/da/dagtol.c
>> > > [0] SNESComputeJacobian_DMDA line 153
>> > > /scratch/lindad/moose/petsc/src/snes/utils/dmdasnes.c
>> > > [0]PETSC ERROR: [0] SNES user Jacobian function line 2678
>> > > /scratch/lindad/moose/petsc/src/snes/interface/snes.c
>> > > [0]PETSC ERROR: [1]PETSC ERROR: [1] DMGlobalToLocalEnd line 2368
>> > > /scratch/lindad/moose/petsc/src/dm/interface/dm.c
>> > > [1]PETSC ERROR: [1] SNESComputeFunction_DMDA line 67
>> > > /scratch/lindad/moose/petsc/src/snes/utils/dmdasnes.c
>> > > [0] SNESComputeJacobian line 2637
>> > > /scratch/lindad/moose/petsc/src/snes/interface/snes.c
>> > > [0]PETSC ERROR: [0] SNESSolve_NEWTONLS line 144
>> > > /scratch/lindad/moose/petsc/src/snes/impls/ls/ls.c
>> > > [0]PETSC ERROR: [1]PETSC ERROR: [1] MatFDColoringApply_AIJ line 180
>> > > /scratch/lindad/moose/petsc/src/mat/impls/aij/mpi/fdmpiaij.c
>> > > [1]PETSC ERROR: [1] MatFDColoringApply line 610
>> > > /scratch/lindad/moose/petsc/src/mat/matfd/fdmatrix.c
>> > > [1]PETSC ERROR: [1] SNESComputeJacobian_DMDA line 153
>> > > /scratch/lindad/moose/petsc/src/snes/utils/dmdasnes.c
>> > > [1]PETSC ERROR: [0] SNESSolve line 4366
>> > > /scratch/lindad/moose/petsc/src/snes/interface/snes.c
>> > > [0]PETSC ERROR: [0] main line 108 ex19.c
>> > > [1] SNES user Jacobian function line 2678
>> > > /scratch/lindad/moose/petsc/src/snes/interface/snes.c
>> > > [1]PETSC ERROR: [0]PETSC ERROR: --------------------- Error Message
>> > > --------------------------------------------------------------
>> > > [1] SNESComputeJacobian line 2637
>> > > /scratch/lindad/moose/petsc/src/snes/interface/snes.c
>> > > [1]PETSC ERROR: [1] SNESSolve_NEWTONLS line 144
>> > > /scratch/lindad/moose/petsc/src/snes/impls/ls/ls.c
>> > > [1]PETSC ERROR: [0]PETSC ERROR: Signal received
>> > > [0]PETSC ERROR: See
>> https://www.mcs.anl.gov/petsc/documentation/faq.html
>> > > for trouble shooting.
>> > > [0]PETSC ERROR: [1] SNESSolve line 4366
>> > > /scratch/lindad/moose/petsc/src/snes/interface/snes.c
>> > > [1]PETSC ERROR: [1] main line 108 ex19.c
>> > > Petsc Release Version 3.12.4, unknown
>> > > [0]PETSC ERROR: ./ex19 on a arch-moose named lemhi2 by lindad Tue May
>> 12
>> > > 12:54:11 2020
>> > > [0]PETSC ERROR: [1]PETSC ERROR: Configure options --download-hypre=1
>> > > --with-debugging=no --with-shared-libraries=1 --download-fblaslapack=1
>> > > --download-metis=1 --download-ptscotch=1 --download-parmetis=1
>> > > --download-superlu_dist=1 --download-mumps=1 --download-scalapack=1
>> > > --download-slepc=git://https://gitlab.com/slepc/slepc.git
>> > > --download-slepc-commit= 59ff81b --with-mpi=1 --with-cxx-dialect=C++11
>> > > --with-fortran-bindings=0 --with-sowing=0 --with-cc=mpiicc
>> > > --with-cxx=mpiicpc --with-fc=mpiifort --with-debugging=yes
>> > > [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>> > > --------------------- Error Message
>> > > --------------------------------------------------------------
>> > > [1]PETSC ERROR: Signal received
>> > > [1]PETSC ERROR: See
>> https://www.mcs.anl.gov/petsc/documentation/faq.html
>> > > for trouble shooting.
>> > > [1]PETSC ERROR: Petsc Release Version 3.12.4, unknown
>> > > [1]PETSC ERROR: Abort(59) on node 0 (rank 0 in comm 0): application
>> called
>> > > MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> > > ./ex19 on a arch-moose named lemhi2 by lindad Tue May 12 12:54:11 2020
>> > > [1]PETSC ERROR: Configure options --download-hypre=1
>> --with-debugging=no
>> > > --with-shared-libraries=1 --download-fblaslapack=1 --download-metis=1
>> > > --download-ptscotch=1 --download-parmetis=1 --download-superlu_dist=1
>> > > --download-mumps=1 --download-scalapack=1 --download-slepc=git://
>> > > https://gitlab.com/slepc/slepc.git --download-slepc-commit= 59ff81b
>> > > --with-mpi=1 --with-cxx-dialect=C++11 --with-fortran-bindings=0
>> > > --with-sowing=0 --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort
>> > > --with-debugging=yes
>> > > [1]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>> > > [0]PETSC ERROR:
>> > >
>> ------------------------------------------------------------------------
>> > > [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or
>> the
>> > > batch system) has told this process to end
>> > > [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > > [0]PETSC ERROR: Abort(59) on node 1 (rank 1 in comm 0): application
>> called
>> > > MPI_Abort(MPI_COMM_WORLD, 59) - process 1
>> > > [1]PETSC ERROR:
>> > >
>> ------------------------------------------------------------------------
>> > > [1]PETSC ERROR: Caught signal number 15 Terminate: Some process (or
>> the
>> > > batch system) has told this process to end
>> > > [1]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > > [1]PETSC ERROR: or see
>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> > > [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
>> Mac OS
>> > > X to find memory corruption errors
>> > > [1]PETSC ERROR: likely location of problem given in stack below
>> > > [1]PETSC ERROR: or see
>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> > > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
>> Mac OS
>> > > X to find memory corruption errors
>> > > [0]PETSC ERROR: likely location of problem given in stack below
>> > > [0]PETSC ERROR: ---------------------  Stack Frames
>> > > ------------------------------------
>> > >
>> >
>> >
>> >
>>
>>
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