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

Tue May 12 14:11:19 CDT 2020

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.

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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