[petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
zeyu xia
xiazeyu01 at gmail.com
Fri Mar 29 13:30:23 CDT 2024
Hi! I am grateful for your prompt response.
I follow your suggestions, and however, it still does not work. For the
related information please find the files 'make check2.txt' and
'configure.log' in the attachment.
If possible, please do me a favor again. Thanks for your patience.
Best wishes,
Zeyu Xia
Satish Balay <balay at mcs.anl.gov> 于2024年3月29日周五 23:48写道：
> Could you:
>
> - reinstall brew after the xcode upgrade (not just update)
> https://urldefense.us/v3/__https://petsc.org/main/install/install/*installing-on-macos__;Iw!!G_uCfscf7eWS!dGItos-D58VSJn4kOlKy2TEX-PWhflbWfNuM0zqhEXbGniD5S13iWCxgBmg9wYk4OrSwaP6jjzANIHN1ZHATKXE$
> - not use --LDFLAGS=-Wl,-ld_classic
>
> And see if the problem persists?
>
> Satish
>
> On Fri, 29 Mar 2024, zeyu xia wrote:
>
> > Dear PETSc team:
> >
> > Recently I installed firedrake on MacOS (arm64) with the latest
> > Xcode, and there seems some error with mumps. I ran two times of the
> > command `make check`. The first time it just output wrong results, and
> the
> > second time it raised an error with Segmentation Violation. Please see
> the
> > files “make check.txt” and “configure.log” in the attachment.
> >
> > I will certainly be happy and grateful if you can take some time
> to
> > deal with this problem. Thanks for your patience.
> >
> > Best wishes,
> > Zeyu Xia
> >
>
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xiazeyu at 192 ~ % cd opt/firedrake/firedrake-real-int32-debug/src/petsc
xiazeyu at 192 petsc % ls
CODE_OF_CONDUCT.md configure lib
CONTRIBUTING configure.log make.log
GNUmakefile default makefile
LICENSE doc petscdir.mk
RDict.log gmakefile setup.py
README.md gmakefile.test share
config include src
configtest.mod interfaces systems
xiazeyu at 192 petsc % make check
Running PETSc check examples to verify correct installation
Using PETSC_DIR=/Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc and PETSC_ARCH=default
C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes
C/C++ example src/snes/tutorials/ex19 run successfully with HYPRE
3c3
< 0 KSP Residual norm 0.235858
---
> 0 KSP Residual norm 0.0348072
5,9c5,8
< 1 SNES Function norm 6.81968e-05
< 0 KSP Residual norm 2.30906e-05
< 1 KSP Residual norm < 1.e-11
< 2 SNES Function norm < 1.e-11
< Number of SNES iterations = 2
---
> 1 SNES Function norm 0.211774
> 0 KSP Residual norm 1.45097e-06
> Internal error 1 in MUMPS_SOL_GET_NPIV_LIELL_IPOS 3
> application called MPI_Abort(MPI_COMM_WORLD, -99) - process 0
/Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/snes/tutorials
Possible problem with ex19 running with MUMPS, diffs above
=========================================
C/C++ example src/snes/tutorials/ex19 run successfully with SuiteSparse
C/C++ example src/snes/tutorials/ex19 run successfully with SuperLU_DIST
C/C++ example src/vec/vec/tests/ex47 run successfully with HDF5
Running SLEPc check examples to verify correct installation
Using SLEPC_DIR=/Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/default/externalpackages/git.slepc, PETSC_DIR=/Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc, and PETSC_ARCH=default
C/C++ example src/eps/tests/test10 run successfully with 1 MPI process
C/C++ example src/eps/tests/test10 run successfully with 2 MPI processes
Completed SLEPc check examples
Completed PETSc check examples
Error while running make check
make[1]: *** [check] Error 1
make: *** [check] Error 2
xiazeyu at 192 petsc % make check
Running PETSc check examples to verify correct installation
Using PETSC_DIR=/Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc and PETSC_ARCH=default
C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes
C/C++ example src/snes/tutorials/ex19 run successfully with HYPRE
3c3
< 0 KSP Residual norm 0.235858
---
> 0 KSP Residual norm 0.0348072
5,9c5,30
< 1 SNES Function norm 6.81968e-05
< 0 KSP Residual norm 2.30906e-05
< 1 KSP Residual norm < 1.e-11
< 2 SNES Function norm < 1.e-11
< Number of SNES iterations = 2
---
> 1 SNES Function norm 0.211774
> [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://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
> [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> [0]PETSC ERROR: The line numbers in the error traceback are not always exact.
> [0]PETSC ERROR: #1 dmumps_c()
> [0]PETSC ERROR: #2 MatFactorNumeric_MUMPS() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/mat/impls/aij/mpi/mumps/mumps.c:2012
> [0]PETSC ERROR: #3 MatLUFactorNumeric() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/mat/interface/matrix.c:3253
> [0]PETSC ERROR: #4 PCSetUp_LU() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/pc/impls/factor/lu/lu.c:121
> [0]PETSC ERROR: #5 PCSetUp() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/pc/interface/precon.c:1079
> [0]PETSC ERROR: #6 KSPSetUp() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/ksp/interface/itfunc.c:415
> [0]PETSC ERROR: #7 KSPSolve_Private() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/ksp/interface/itfunc.c:831
> [0]PETSC ERROR: #8 KSPSolve() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/ksp/interface/itfunc.c:1078
> [0]PETSC ERROR: #9 PCApply_FieldSplit_Schur() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/pc/impls/fieldsplit/fieldsplit.c:1187
> [0]PETSC ERROR: #10 PCApply() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/pc/interface/precon.c:497
> [0]PETSC ERROR: #11 KSP_PCApply() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/include/petsc/private/kspimpl.h:409
> [0]PETSC ERROR: #12 KSPInitialResidual() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/ksp/interface/itres.c:64
> [0]PETSC ERROR: #13 KSPSolve_GMRES() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/ksp/impls/gmres/gmres.c:226
> [0]PETSC ERROR: #14 KSPSolve_Private() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/ksp/interface/itfunc.c:905
> [0]PETSC ERROR: #15 KSPSolve() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/ksp/ksp/interface/itfunc.c:1078
> [0]PETSC ERROR: #16 SNESSolve_NEWTONLS() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/snes/impls/ls/ls.c:220
> [0]PETSC ERROR: #17 SNESSolve() at /Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/snes/interface/snes.c:4738
> [0]PETSC ERROR: #18 main() at ex19.c:152
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
/Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/src/snes/tutorials
Possible problem with ex19 running with MUMPS, diffs above
=========================================
C/C++ example src/snes/tutorials/ex19 run successfully with SuiteSparse
C/C++ example src/snes/tutorials/ex19 run successfully with SuperLU_DIST
C/C++ example src/vec/vec/tests/ex47 run successfully with HDF5
Running SLEPc check examples to verify correct installation
Using SLEPC_DIR=/Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc/default/externalpackages/git.slepc, PETSC_DIR=/Users/xiazeyu/opt/firedrake/firedrake-real-int32-debug/src/petsc, and PETSC_ARCH=default
C/C++ example src/eps/tests/test10 run successfully with 1 MPI process
C/C++ example src/eps/tests/test10 run successfully with 2 MPI processes
Completed SLEPc check examples
Completed PETSc check examples
Error while running make check
make[1]: *** [check] Error 1
make: *** [check] Error 2
xiazeyu at 192 petsc %
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