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

Tue May 12 14:45:21 CDT 2020

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
> > ------------------------------------
> >
> 
> 
> 