[petsc-users] [External] Periodic boundary condition
Sepideh Kavousi
kavousi at mines.edu
Thu Nov 3 09:56:35 CDT 2022
Barry,
Even for the case that I am not solving any PDE equations in the FormFunction ( by setting :
aF[j][i].vx=aY[j][i].vx;
aF[j][i].vy=aY[j][i].vy;
aF[j][i].pp=aY[j][i].pp;
aF[j][i].U=aY[j][i].U
aF[j][i].p=aY[j][i].p; )
I will run into segmentation error.
Let me just follow what you suggested in the following link: https://lists.mcs.anl.gov/pipermail/petsc-users/2012-May/013476.html
src/ksp/ksp/tutorials/ex45.c runs perfectly, but when I change bc along x direction from DM_BOUNDARY_NONE to DM_BOUNDARY_PERIODIC and delete (i==0 || i==mx-1) from if (i==0 || j==0 || k==0 || i==mx-1 || j==my-1 || k==mz-1), I run to the following error.
I am not sure how else should I implement periodic bc in a problem.
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Object is in wrong state
[0]PETSC ERROR: Matrix is missing diagonal entry 5
[0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[1]PETSC ERROR: Object is in wrong state
[1]PETSC ERROR: Matrix is missing diagonal entry 5
[1]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[1]PETSC ERROR: [2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[2]PETSC ERROR: Object is in wrong state
[2]PETSC ERROR: Matrix is missing diagonal entry 5
[2]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[2]PETSC ERROR: Petsc Release Version 3.14.2, Dec 03, 2020
[2]PETSC ERROR: /scratch/07065/tg863649/convection/periodic_test/one.out on a skylake named c402-092.stampede2.tacc.utexas.edu by tg863649 Thu Nov 3 09:53:00 2022
[2]PETSC ERROR: [3]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[3]PETSC ERROR: Object is in wrong state
[3]PETSC ERROR: Matrix is missing diagonal entry 5
[3]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[3]PETSC ERROR: Petsc Release Version 3.14.2, Dec 03, 2020
[3]PETSC ERROR: /scratch/07065/tg863649/convection/periodic_test/one.out on a skylake named c402-092.stampede2.tacc.utexas.edu by tg863649 Thu Nov 3 09:53:00 2022
[3]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 3.14.2, Dec 03, 2020
[0]PETSC ERROR: /scratch/07065/tg863649/convection/periodic_test/one.out on a skylake named c402-092.stampede2.tacc.utexas.edu by tg863649 Thu Nov 3 09:53:00 2022
[0]PETSC ERROR: Configure options --with-x=0 -with-pic --with-make-np=12 --download-petsc4py=1 --with-python-exec=/opt/apps/intel18/python2/2.7.16/bin/python2 --with-packages-build-dir=/tmp/petsc-3.14/skylake --with-mpi=1 --with-mpi-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64 --with-scalar-type=real --with-shared-libraries=1 --with-precision=double --with-chaco=1 --download-chaco --with-hypre=1 --download-hypre --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-plapack=1 --download-plapack --with-spai=1 --download-spai --with-sundials=1 --download-sundials --with-elemental=1 --download-elemental --with-cxx-dialect=C++11 --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-fftw=1 --with-fftw-dir=/opt/apps/intel18/impi18_0/fftw3/3.3.8 --with-hdf5=1 --with-hdf5-dir=/opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64 --download-hpddm --download-slepc --with-mumps=1 --download-mumps --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-scalapack=1 --download-scalapack --with-blacs=1 --download-blacs --with-spooles=1 --download-spooles --with-suitesparse=1 --download-suitesparse --with-superlu_dist=1 --download-superlu_dist --with-superlu=1 --download-superlu --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-zoltan=1 --download-zoltan=1 --download-ptscotch=1 --with-debugging=no --LIBS= --with-blaslapack-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl COPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" FOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" CXXOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g"
Petsc Release Version 3.14.2, Dec 03, 2020
[1]PETSC ERROR: /scratch/07065/tg863649/convection/periodic_test/one.out on a skylake named c402-092.stampede2.tacc.utexas.edu by tg863649 Thu Nov 3 09:53:00 2022
[1]PETSC ERROR: [0]PETSC ERROR: #1 MatILUFactorSymbolic_SeqAIJ() line 1686 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/impls/aij/seq/aijfact.c
Configure options --with-x=0 -with-pic --with-make-np=12 --download-petsc4py=1 --with-python-exec=/opt/apps/intel18/python2/2.7.16/bin/python2 --with-packages-build-dir=/tmp/petsc-3.14/skylake --with-mpi=1 --with-mpi-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64 --with-scalar-type=real --with-shared-libraries=1 --with-precision=double --with-chaco=1 --download-chaco --with-hypre=1 --download-hypre --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-plapack=1 --download-plapack --with-spai=1 --download-spai --with-sundials=1 --download-sundials --with-elemental=1 --download-elemental --with-cxx-dialect=C++11 --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-fftw=1 --with-fftw-dir=/opt/apps/intel18/impi18_0/fftw3/3.3.8 --with-hdf5=1 --with-hdf5-dir=/opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64 --download-hpddm --download-slepc --with-mumps=1 --download-mumps --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-scalapack=1 --download-scalapack --with-blacs=1 --download-blacs --with-spooles=1 --download-spooles --with-suitesparse=1 --download-suitesparse --with-superlu_dist=1 --download-superlu_dist --with-superlu=1 --download-superlu --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-zoltan=1 --download-zoltan=1 --download-ptscotch=1 --with-debugging=no --LIBS= --with-blaslapack-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl COPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" FOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" CXXOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g"
[2]PETSC ERROR: #1 MatILUFactorSymbolic_SeqAIJ() line 1686 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/impls/aij/seq/aijfact.c
Configure options --with-x=0 -with-pic --with-make-np=12 --download-petsc4py=1 --with-python-exec=/opt/apps/intel18/python2/2.7.16/bin/python2 --with-packages-build-dir=/tmp/petsc-3.14/skylake --with-mpi=1 --with-mpi-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64 --with-scalar-type=real --with-shared-libraries=1 --with-precision=double --with-chaco=1 --download-chaco --with-hypre=1 --download-hypre --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-plapack=1 --download-plapack --with-spai=1 --download-spai --with-sundials=1 --download-sundials --with-elemental=1 --download-elemental --with-cxx-dialect=C++11 --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-fftw=1 --with-fftw-dir=/opt/apps/intel18/impi18_0/fftw3/3.3.8 --with-hdf5=1 --with-hdf5-dir=/opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64 --download-hpddm --download-slepc --with-mumps=1 --download-mumps --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-scalapack=1 --download-scalapack --with-blacs=1 --download-blacs --with-spooles=1 --download-spooles --with-suitesparse=1 --download-suitesparse --with-superlu_dist=1 --download-superlu_dist --with-superlu=1 --download-superlu --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-zoltan=1 --download-zoltan=1 --download-ptscotch=1 --with-debugging=no --LIBS= --with-blaslapack-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl COPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" FOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" CXXOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g"
[3]PETSC ERROR: #1 MatILUFactorSymbolic_SeqAIJ() line 1686 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/impls/aij/seq/aijfact.c
Configure options --with-x=0 -with-pic --with-make-np=12 --download-petsc4py=1 --with-python-exec=/opt/apps/intel18/python2/2.7.16/bin/python2 --with-packages-build-dir=/tmp/petsc-3.14/skylake --with-mpi=1 --with-mpi-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64 --with-scalar-type=real --with-shared-libraries=1 --with-precision=double --with-chaco=1 --download-chaco --with-hypre=1 --download-hypre --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-plapack=1 --download-plapack --with-spai=1 --download-spai --with-sundials=1 --download-sundials --with-elemental=1 --download-elemental --with-cxx-dialect=C++11 --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-fftw=1 --with-fftw-dir=/opt/apps/intel18/impi18_0/fftw3/3.3.8 --with-hdf5=1 --with-hdf5-dir=/opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64 --download-hpddm --download-slepc --with-mumps=1 --download-mumps --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-scalapack=1 --download-scalapack --with-blacs=1 --download-blacs --with-spooles=1 --download-spooles --with-suitesparse=1 --download-suitesparse --with-superlu_dist=1 --download-superlu_dist --with-superlu=1 --download-superlu --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-zoltan=1 --download-zoltan=1 --download-ptscotch=1 --with-debugging=no --LIBS= --with-blaslapack-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl COPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" FOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" CXXOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g"
[1]PETSC ERROR: #1 MatILUFactorSymbolic_SeqAIJ() line 1686 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/impls/aij/seq/aijfact.c
[0]PETSC ERROR: #2 MatILUFactorSymbolic() line 6710 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/interface/matrix.c
[1]PETSC ERROR: #2 MatILUFactorSymbolic() line 6710 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/interface/matrix.c
[1]PETSC ERROR: #3 PCSetUp_ILU() line 141 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/factor/ilu/ilu.c
[2]PETSC ERROR: #2 MatILUFactorSymbolic() line 6710 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/interface/matrix.c
[2]PETSC ERROR: #3 PCSetUp_ILU() line 141 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/factor/ilu/ilu.c
[2]PETSC ERROR: [3]PETSC ERROR: #2 MatILUFactorSymbolic() line 6710 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/interface/matrix.c
[3]PETSC ERROR: #3 PCSetUp_ILU() line 141 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/factor/ilu/ilu.c
[3]PETSC ERROR: #4 PCSetUp() line 1009 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/interface/precon.c
[3]PETSC ERROR: [0]PETSC ERROR: #3 PCSetUp_ILU() line 141 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/factor/ilu/ilu.c
[0]PETSC ERROR: #4 PCSetUp() line 1009 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: #5 KSPSetUp() line 406 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[1]PETSC ERROR: #4 PCSetUp() line 1009 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/interface/precon.c
[1]PETSC ERROR: #5 KSPSetUp() line 406 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
#4 PCSetUp() line 1009 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/interface/precon.c
[2]PETSC ERROR: #5 KSPSetUp() line 406 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
#5 KSPSetUp() line 406 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: [2]PETSC ERROR: #6 KSPSolve_Private() line 658 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[2]PETSC ERROR: [3]PETSC ERROR: #6 KSPSolve_Private() line 658 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[3]PETSC ERROR: #7 KSPSolve() line 889 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
#6 KSPSolve_Private() line 658 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #7 KSPSolve() line 889 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[1]PETSC ERROR: #6 KSPSolve_Private() line 658 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[1]PETSC ERROR: #7 KSPSolve() line 889 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
#7 KSPSolve() line 889 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[1]PETSC ERROR: [2]PETSC ERROR: #8 DMDAGetFaceInterpolation() line 493 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/wb/wb.c
[2]PETSC ERROR: [0]PETSC ERROR: #8 DMDAGetFaceInterpolation() line 493 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/wb/wb.c
#8 DMDAGetFaceInterpolation() line 493 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/wb/wb.c
[1]PETSC ERROR: #9 PCSetUp_Exotic() line 667 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/wb/wb.c
[1]PETSC ERROR: #10 PCSetUp() line 1009 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/interface/precon.c
#9 PCSetUp_Exotic() line 667 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/wb/wb.c
[2]PETSC ERROR: #10 PCSetUp() line 1009 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/interface/precon.c
[2]PETSC ERROR: #11 KSPSetUp() line 406 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #9 PCSetUp_Exotic() line 667 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/wb/wb.c
[0]PETSC ERROR: #10 PCSetUp() line 1009 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: [1]PETSC ERROR: #11 KSPSetUp() line 406 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[1]PETSC ERROR: #12 KSPSolve_Private() line 658 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[1]PETSC ERROR: #13 KSPSolve() line 889 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[2]PETSC ERROR: #12 KSPSolve_Private() line 658 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[2]PETSC ERROR: #13 KSPSolve() line 889 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[3]PETSC ERROR: #8 DMDAGetFaceInterpolation() line 493 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/wb/wb.c
[3]PETSC ERROR: #9 PCSetUp_Exotic() line 667 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/impls/wb/wb.c
[3]PETSC ERROR: #10 PCSetUp() line 1009 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/pc/interface/precon.c
[3]PETSC ERROR: #11 KSPSetUp() line 406 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[3]PETSC ERROR: #12 KSPSolve_Private() line 658 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
#11 KSPSetUp() line 406 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #12 KSPSolve_Private() line 658 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #13 KSPSolve() line 889 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[3]PETSC ERROR: #13 KSPSolve() line 889 in /home1/apps/intel18/impi18_0/petsc/3.14/src/ksp/ksp/interface/itfunc.c
[1]PETSC ERROR: [0]PETSC ERROR: #14 main() line 51 in /scratch/07065/tg863649/convection/periodic_test/one.c
#14 main() line 51 in /scratch/07065/tg863649/convection/periodic_test/one.c
[1]PETSC ERROR: PETSc Option Table entries:
[1]PETSC ERROR: -ksp_monitor_short
[2]PETSC ERROR: #14 main() line 51 in /scratch/07065/tg863649/convection/periodic_test/one.c
[2]PETSC ERROR: PETSc Option Table entries:
[2]PETSC ERROR: -ksp_monitor_short
[2]PETSC ERROR: [0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -ksp_monitor_short
[0]PETSC ERROR: -ksp_type fgmres
[0]PETSC ERROR: -mg_levels_ksp_max_it 1
[0]PETSC ERROR: -mg_levels_ksp_type gmres
[0]PETSC ERROR: -mg_levels_pc_type bjacobi
[1]PETSC ERROR: -ksp_type fgmres
[1]PETSC ERROR: -mg_levels_ksp_max_it 1
[1]PETSC ERROR: -mg_levels_ksp_type gmres
[1]PETSC ERROR: -mg_levels_pc_type bjacobi
[1]PETSC ERROR: -pc_type exotic
[1]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
-ksp_type fgmres
[2]PETSC ERROR: -mg_levels_ksp_max_it 1
[2]PETSC ERROR: -mg_levels_ksp_type gmres
[2]PETSC ERROR: -mg_levels_pc_type bjacobi
[2]PETSC ERROR: -pc_type exotic
[2]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
[3]PETSC ERROR: #14 main() line 51 in /scratch/07065/tg863649/convection/periodic_test/one.c
[3]PETSC ERROR: PETSc Option Table entries:
[3]PETSC ERROR: -ksp_monitor_short
[3]PETSC ERROR: -ksp_type fgmres
[3]PETSC ERROR: -mg_levels_ksp_max_it 1
[3]PETSC ERROR: -mg_levels_ksp_type gmres
[3]PETSC ERROR: -mg_levels_pc_type bjacobi
[3]PETSC ERROR: -pc_type exotic
[3]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
[0]PETSC ERROR: -pc_type exotic
[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
application called MPI_Abort(MPI_COMM_SELF, 51073) - process 0
application called MPI_Abort(MPI_COMM_SELF, 51073) - process 0
application called MPI_Abort(MPI_COMM_SELF, 51073) - process 0
application called MPI_Abort(MPI_COMM_SELF, 51073) - process 0
TACC: MPI job exited with code: 129
TACC: Shutdown complete. Exiting.
Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
From: Barry Smith<mailto:bsmith at petsc.dev>
Sent: Tuesday, October 25, 2022 7:24 PM
To: Sepideh Kavousi<mailto:kavousi at mines.edu>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
Subject: Re: [External] [petsc-users] Periodic boundary condition
Sorry I was not clear, at this point you need to type c for continue and then when it crashes in the debugger type bt
Barry
On Oct 25, 2022, at 6:37 PM, Sepideh Kavousi <kavousi at mines.edu<mailto:kavousi at mines.edu>> wrote:
Hello Barry,
When I ran with , the error is about PetscInitialize line (Line 333). When I write bt multiple times, it just continues referring to this line.
#0 0x00002b701cfed9fd in nanosleep () from /lib64/libc.so.6
#1 0x00002b701cfed894 in sleep () from /lib64/libc.so.6
#2 0x00002b70035fb4ae in PetscSleep (s=1) at /home1/apps/intel18/impi18_0/petsc/3.14/src/sys/utils/psleep.c:46
#3 0x00002b700364b8bb in PetscAttachDebugger () at /home1/apps/intel18/impi18_0/petsc/3.14/src/sys/error/adebug.c:405
#4 0x00002b700366cfcd in PetscOptionsCheckInitial_Private (help=0x7ffec24c7940 "\t") at /home1/apps/intel18/impi18_0/petsc/3.14/src/sys/objects/init.c:608
#5 0x00002b7003674cd6 in PetscInitialize (argc=0x7ffec24c7940, args=0x7ffec24c7940, file=0x0, help=0xffffffffffffffff <Address 0xffffffffffffffff out of bounds>)
at /home1/apps/intel18/impi18_0/petsc/3.14/src/sys/objects/pinit.c:1025
#6 0x00000000004021ce in main (argc=24, argv=0x7ffec24d14e8) at /scratch/07065/tg863649/convection/test-a9-3-options_small_MAC_pressure_old/one.c:333
Best,
Sepideh
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From: Barry Smith<mailto:bsmith at petsc.dev>
Sent: Friday, October 21, 2022 10:54 AM
To: Sepideh Kavousi<mailto:kavousi at mines.edu>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
Subject: Re: [External] [petsc-users] Periodic boundary condition
The problem with the output below is it is not giving a clear indication where the crash occurred.
#1 User provided function() line 0 in unknown file
Run with the exact same options but also -start_in_debugger noxterm It should then crash in the debugger and you can type bt to see the backtrace of where it crashed, send that output.
Barry
Background: MatFDColoringSetUpBlocked_AIJ_Private() allocates the space that is used when evaluating the function multiple times to get the Jacobian entries. If the FormFunction writes into incorrect locations, then it will corrupt this memory that was allocated in MatFDColoringSetUpBlocked_AIJ_Private() . It does not mean necessarily that there is anything wrong in MatFDColoringSetUpBlocked_AIJ_Private()
On Oct 21, 2022, at 12:32 AM, Sepideh Kavousi <kavousi at mines.edu<mailto:kavousi at mines.edu>> wrote:
Barry,
I ran the code with -malloc_debug and added CHKMEMQ for all the lines inside formfunction. Following is the detail of error.
Best,
Sepideh
[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<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fdocumentation%2Ffaq.html%23valgrind&data=05%7C01%7Ckavousi%40mines.edu%7C69fba9c581cd4ac9adae08dab6e012ed%7C997209e009b346239a4d76afa44a675c%7C0%7C0%7C638023370775173292%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wkYcffHdhDe8THCP%2Fk6%2FyUO0YXOnILQmsGutldFIk%2BI%3D&reserved=0>
[0]PETSC ERROR: or try http://valgrind.org<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvalgrind.org%2F&data=05%7C01%7Ckavousi%40mines.edu%7C69fba9c581cd4ac9adae08dab6e012ed%7C997209e009b346239a4d76afa44a675c%7C0%7C0%7C638023370775173292%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PYWGQpNE8LOn5NSnN%2BlFzp8rLmoIdaLkcxvwsNa%2F9xo%3D&reserved=0> on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: PetscMallocValidate: error detected at PetscError() line 401 in /home1/apps/intel18/impi18_0/petsc/3.14/src/sys/error/err.c
[0]PETSC ERROR: Memory [id=0(73960000)] at address 0x2b5aed6ab050 is corrupted (probably write past end of array)
[0]PETSC ERROR: Memory originally allocated in MatFDColoringSetUpBlocked_AIJ_Private() line 125 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/impls/aij/seq/fdaij.c
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fdocumentation%2Ffaq.html&data=05%7C01%7Ckavousi%40mines.edu%7C69fba9c581cd4ac9adae08dab6e012ed%7C997209e009b346239a4d76afa44a675c%7C0%7C0%7C638023370775173292%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=FBQNgDbFWKb1Qa9cwajS%2B0JNB5PfIqrvbRIFd%2FI8x3I%3D&reserved=0> for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.14.2, Dec 03, 2020
[0]PETSC ERROR: ./one.out on a skylake named c415-063.stampede2.tacc.utexas.edu<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fc415-063.stampede2.tacc.utexas.edu%2F&data=05%7C01%7Ckavousi%40mines.edu%7C69fba9c581cd4ac9adae08dab6e012ed%7C997209e009b346239a4d76afa44a675c%7C0%7C0%7C638023370775173292%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JGr48qlrEtYEaC5NzX9LtVKkHdnPNDK8AbN6pbKUJs0%3D&reserved=0> by tg863649 Thu Oct 20 23:30:05 2022
[0]PETSC ERROR: Configure options --with-x=0 -with-pic --with-make-np=12 --download-petsc4py=1 --with-python-exec=/opt/apps/intel18/python2/2.7.16/bin/python2 --with-packages-build-dir=/tmp/petsc-3.14/skylake --with-mpi=1 --with-mpi-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64 --with-scalar-type=real --with-shared-libraries=1 --with-precision=double --with-chaco=1 --download-chaco --with-hypre=1 --download-hypre --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-plapack=1 --download-plapack --with-spai=1 --download-spai --with-sundials=1 --download-sundials --with-elemental=1 --download-elemental --with-cxx-dialect=C++11 --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-fftw=1 --with-fftw-dir=/opt/apps/intel18/impi18_0/fftw3/3.3.8 --with-hdf5=1 --with-hdf5-dir=/opt/apps/intel18/impi18_0/phdf5/1.10.4/x86_64 --download-hpddm --download-slepc --with-mumps=1 --download-mumps --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-scalapack=1 --download-scalapack --with-blacs=1 --download-blacs --with-spooles=1 --download-spooles --with-suitesparse=1 --download-suitesparse --with-superlu_dist=1 --download-superlu_dist --with-superlu=1 --download-superlu --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-zoltan=1 --download-zoltan=1 --download-ptscotch=1 --with-debugging=no --LIBS= --with-blaslapack-dir=/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl COPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" FOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g" CXXOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,CORE-AVX512 -O2 -g"
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
[0]PETSC ERROR: Checking the memory for corruption.
[0]PETSC ERROR: PetscMallocValidate: error detected at PetscSignalHandlerDefault() line 170 in /home1/apps/intel18/impi18_0/petsc/3.14/src/sys/error/signal.c
[0]PETSC ERROR: Memory [id=0(73960000)] at address 0x2b5aed6ab050 is corrupted (probably write past end of array)
[0]PETSC ERROR: Memory originally allocated in MatFDColoringSetUpBlocked_AIJ_Private() line 125 in /home1/apps/intel18/impi18_0/petsc/3.14/src/mat/impls/aij/seq/fdaij.c
application called MPI_Abort(MPI_COMM_WORLD, 50176059) - process 0
[unset]: readline failed
Sent from Mail<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986&data=05%7C01%7Ckavousi%40mines.edu%7C69fba9c581cd4ac9adae08dab6e012ed%7C997209e009b346239a4d76afa44a675c%7C0%7C0%7C638023370775173292%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3AHsDWTVLXZcgkPccM9Xwmq6a98y2zM3b1fS8FxwTm4%3D&reserved=0> for Windows
From: Barry Smith<mailto:bsmith at petsc.dev>
Sent: Thursday, October 20, 2022 10:27 PM
To: Sepideh Kavousi<mailto:kavousi at mines.edu>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
Subject: [External] Re: [petsc-users] Periodic boundary condition
Some of the valgrind information does not appear to make sense
PetscMemcpy() is not calling SNESSolve() so I suspect there must be some serious corruption of something to this impossible stack trace
==236074== by 0x6FD160F: SNESSolve (snes.c:4569)
==236074== by 0x711917E: PetscMemcpy (bdf.c:223)
From
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x5F10977: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:146)
==236074== by 0x5F10977: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074== by 0x6FD160F: SNESSolve (snes.c:4569)
==236074== by 0x711917E: PetscMemcpy (bdf.c:223)
==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074== by 0x70C363A: TSStep (ts.c:3757)
==236074== by 0x70C1999: TSSolve (ts.c:4154)
==236074== by 0x402594: main (one.c:391)
I suggest you run with -malloc_debug instead of valgrind and see if any errors are reported. If so you can add the macro CHKMEMQ; inside your function evaluation where you write to memory to see if anything is writing to the wrong location. For example wherever you assign aF such as
aF[j][i].vx=(x3+x4+x5+x6+x7+x8+x9-x1-x2)*user->hx;
this can help you determine the exact line number where you are writing to the wrong location and determine what might be the cause.
On Oct 20, 2022, at 6:45 PM, Sepideh Kavousi <kavousi at mines.edu<mailto:kavousi at mines.edu>> wrote:
Hello,
I want to solve my 5 PDEs based on finite difference method using periodic BC in x-direction and non-periodic in y-direction but I run into error (Segmentation Violation, probably memory access out of range).
For this, I discretize my equation in FormFunction function. My PDE discretization in (i,j) node needs data on (i+1,j), (i+2,j), (i-1,j), (i-2,j), (i,j+1), (i,j+2), (i,j-1), (i,j-2) points.
In my previous codes that the x-direction was non-periodic (no flux) boundary condition, I:
i) implemented the no flux BC for i=0 and i=Nx-1,
ii) set i+2= Nx-1 in discretizing (Nx-2,j) and i+2= 0 in discretizing (1,j)
iii) discretized my equation for i=1..Nx-2.
I am not sure how I should do the periodic BC. From the following discussions (https://lists.mcs.anl.gov/pipermail/petsc-users/2012-May/013476.html<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.mcs.anl.gov%2Fpipermail%2Fpetsc-users%2F2012-May%2F013476.html&data=05%7C01%7Ckavousi%40mines.edu%7C69fba9c581cd4ac9adae08dab6e012ed%7C997209e009b346239a4d76afa44a675c%7C0%7C0%7C638023370775173292%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=b8Fmx5UHkTufu0S8IXqMvwObom2wGbMQd0TXySv%2FV2E%3D&reserved=0> andhttps://lists.mcs.anl.gov/pipermail/petsc-users/2016-May/029273.html<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.mcs.anl.gov%2Fpipermail%2Fpetsc-users%2F2016-May%2F029273.html&data=05%7C01%7Ckavousi%40mines.edu%7C69fba9c581cd4ac9adae08dab6e012ed%7C997209e009b346239a4d76afa44a675c%7C0%7C0%7C638023370775173292%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2B%2F9VsgTbaXPiqR8twtCtpSX7EEKpmVdHrm6tKI6HqjI%3D&reserved=0>), I guess I should not do step (i) (stated above) for the x-boundaries and just do step (iii) for i=0..Nx-1. If I just focus on solving 2 of the PDEs which does need data on (i+2,j), (i-2,j), (i,j+2), (i,j-2) points for discretizing equation in (i,j) node, I still run into error:
Running with Valgrind (just 1 processor) gave the following file. I did not find any information which gives me hint on the error source.
Can you please help me to find the error?
Best,
Sepideh
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x4C29E39: malloc (vg_replace_malloc.c:309)
==236074== by 0x1B79E59B: MPID_Init (mpid_init.c:1649)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B805: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B810: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x218323C8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Use of uninitialised value of size 8
==236074== at 0x218323CF: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Use of uninitialised value of size 8
==236074== at 0x218323E5: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B805: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B810: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x218323C8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Use of uninitialised value of size 8
==236074== at 0x218323CF: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Use of uninitialised value of size 8
==236074== at 0x218323E5: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B69A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21836F9A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21834872: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217F7F5D: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B7B8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21836F9A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21834872: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217F7F5D: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B69A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217F88C8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B7B8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217F88C8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B69A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217F916B: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x2183B7B8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217F916B: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x1B1DA260: __I_MPI___intel_sse2_strncmp (in /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpifort.so.12.0)
==236074== by 0x1B8CFBA1: ??? (simple_pmi.c:2376)
==236074== by 0x1B8CBDAD: PMIi_InitIfSingleton (simple_pmi.c:2883)
==236074== by 0x1B8CBDAD: iPMI_KVS_Get (simple_pmi.c:751)
==236074== by 0x1B7CCC1E: ??? (mpidi_pg.c:949)
==236074== by 0x1B817EAA: MPID_nem_ofi_post_init (ofi_init.c:1736)
==236074== by 0x1B7B3575: MPID_nem_init_post (mpid_nem_init.c:1421)
==236074== by 0x1B5806E3: MPIDI_CH3_Init (ch3_init.c:146)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x1B1DA383: __I_MPI___intel_sse2_strncmp (in /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpifort.so.12.0)
==236074== by 0x1B8CFBA1: ??? (simple_pmi.c:2376)
==236074== by 0x1B8CBDAD: PMIi_InitIfSingleton (simple_pmi.c:2883)
==236074== by 0x1B8CBDAD: iPMI_KVS_Get (simple_pmi.c:751)
==236074== by 0x1B7CCC1E: ??? (mpidi_pg.c:949)
==236074== by 0x1B817EAA: MPID_nem_ofi_post_init (ofi_init.c:1736)
==236074== by 0x1B7B3575: MPID_nem_init_post (mpid_nem_init.c:1421)
==236074== by 0x1B5806E3: MPIDI_CH3_Init (ch3_init.c:146)
==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074== by 0x5264A94: PetscInitialize (pinit.c:907)
==236074== by 0x40219D: main (one.c:335)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x1E48032E: __intel_sse4_strcpy (in /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libirc.so)
==236074== by 0x51FD8BE: PetscStrcpy (str.c:354)
==236074== by 0x51FD7A3: PetscStrallocpy (str.c:188)
==236074== by 0x52A39CE: PetscEventRegLogRegister (eventlog.c:313)
==236074== by 0x527D89A: PetscLogEventRegister (plog.c:693)
==236074== by 0x6A56A20: PCBDDCInitializePackage (bddc.c:3115)
==236074== by 0x6E1A515: PCInitializePackage (dlregisksp.c:59)
==236074== by 0x6DB1A86: PCCreate (precon.c:382)
==236074== by 0x6E05167: KSPGetPC (itfunc.c:1837)
==236074== by 0x6E0FC5C: KSPSetDM (iterativ.c:1150)
==236074== by 0x6FDD27B: SNESSetDM (snes.c:5402)
==236074== by 0x70B85F7: TSGetSNES (ts.c:2914)
==236074== by 0x70BE430: TSSetDM (ts.c:4949)
==236074== by 0x402496: main (one.c:378)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x1E4782BA: __intel_ssse3_strncpy (in /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libirc.so)
==236074== by 0x51FFD24: PetscStrncpy (str.c:392)
==236074== by 0x51FEB03: PetscStrreplace (str.c:1142)
==236074== by 0x52C9958: PetscViewerFileSetName (filev.c:659)
==236074== by 0x52B743B: PetscViewerVTKOpen (vtkv.c:279)
==236074== by 0x70C76E6: TSMonitorSolutionVTK (ts.c:5580)
==236074== by 0x40313C: FormFunction (one.c:120)
==236074== by 0x7066531: TSComputeIFunction_DMDA (dmdats.c:82)
==236074== by 0x70BA5EF: TSComputeIFunction (ts.c:857)
==236074== by 0x711E2DC: SNESTSFormFunction_BDF (bdf.c:368)
==236074== by 0x70C6E46: SNESTSFormFunction (ts.c:5014)
==236074== by 0x6FDC8A6: SNESComputeFunction (snes.c:2383)
==236074== by 0x7023556: SNESSolve_NEWTONTR (tr.c:297)
==236074== by 0x6FD160F: SNESSolve (snes.c:4569)
==236074== by 0x711917E: PetscMemcpy (bdf.c:223)
==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074== by 0x70C363A: TSStep (ts.c:3757)
==236074== by 0x70C1999: TSSolve (ts.c:4154)
==236074== by 0x402594: main (one.c:391)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x1E4782BA: __intel_ssse3_strncpy (in /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libirc.so)
==236074== by 0x51FFD24: PetscStrncpy (str.c:392)
==236074== by 0x51FEB03: PetscStrreplace (str.c:1142)
==236074== by 0x5224E4B: PetscFOpen (mpiuopen.c:52)
==236074== by 0x63A074B: DMDAVTKWriteAll_VTS.A (grvtk.c:72)
==236074== by 0x639A589: DMDAVTKWriteAll (grvtk.c:545)
==236074== by 0x52B66F3: PetscViewerFlush_VTK (vtkv.c:100)
==236074== by 0x52CFAAE: PetscViewerFlush (flush.c:26)
==236074== by 0x52CEA95: PetscViewerDestroy (view.c:113)
==236074== by 0x70C7717: TSMonitorSolutionVTK (ts.c:5582)
==236074== by 0x40313C: FormFunction (one.c:120)
==236074== by 0x7066531: TSComputeIFunction_DMDA (dmdats.c:82)
==236074== by 0x70BA5EF: TSComputeIFunction (ts.c:857)
==236074== by 0x711E2DC: SNESTSFormFunction_BDF (bdf.c:368)
==236074== by 0x70C6E46: SNESTSFormFunction (ts.c:5014)
==236074== by 0x6FDC8A6: SNESComputeFunction (snes.c:2383)
==236074== by 0x7023556: SNESSolve_NEWTONTR (tr.c:297)
==236074== by 0x6FD160F: SNESSolve (snes.c:4569)
==236074== by 0x711917E: PetscMemcpy (bdf.c:223)
==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074== by 0x70C363A: TSStep (ts.c:3757)
==236074==
==236074== Conditional jump or move depends on uninitialised value(s)
==236074== at 0x5F10977: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:146)
==236074== by 0x5F10977: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074== by 0x6FD160F: SNESSolve (snes.c:4569)
==236074== by 0x711917E: PetscMemcpy (bdf.c:223)
==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074== by 0x70C363A: TSStep (ts.c:3757)
==236074== by 0x70C1999: TSSolve (ts.c:4154)
==236074== by 0x402594: main (one.c:391)
==236074==
==236074== Invalid write of size 4
==236074== at 0x5F10983: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:150)
==236074== by 0x5F10983: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074== by 0x6FD160F: SNESSolve (snes.c:4569)
==236074== by 0x711917E: PetscMemcpy (bdf.c:223)
==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074== by 0x70C363A: TSStep (ts.c:3757)
==236074== by 0x70C1999: TSSolve (ts.c:4154)
==236074== by 0x402594: main (one.c:391)
==236074== Address 0x3a94fa80 is 0 bytes after a block of size 73,960,000 alloc'd
==236074== at 0x4C2C480: memalign (vg_replace_malloc.c:909)
==236074== by 0x522FFE2: PetscMallocAlign (mal.c:52)
==236074== by 0x52305F9: PetscMallocA (mal.c:418)
==236074== by 0x5F10778: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:125)
==236074== by 0x5F10778: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074== by 0x6FD160F: SNESSolve (snes.c:4569)
==236074== by 0x711917E: PetscMemcpy (bdf.c:223)
==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074== by 0x70C363A: TSStep (ts.c:3757)
==236074== by 0x70C1999: TSSolve (ts.c:4154)
==236074== by 0x402594: main (one.c:391)
==236074==
==236074== Invalid write of size 8
==236074== at 0x5F10991: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:151)
==236074== by 0x5F10991: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074== by 0x6FD160F: SNESSolve (snes.c:4569)
==236074== by 0x711917E: PetscMemcpy (bdf.c:223)
==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074== by 0x70C363A: TSStep (ts.c:3757)
==236074== by 0x70C1999: TSSolve (ts.c:4154)
==236074== by 0x402594: main (one.c:391)
==236074== Address 0x3a94fa88 is 8 bytes after a block of size 73,960,000 alloc'd
==236074== at 0x4C2C480: memalign (vg_replace_malloc.c:909)
==236074== by 0x522FFE2: PetscMallocAlign (mal.c:52)
==236074== by 0x52305F9: PetscMallocA (mal.c:418)
==236074== by 0x5F10778: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:125)
==236074== by 0x5F10778: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074== by 0x6FD160F: SNESSolve (snes.c:4569)
==236074== by 0x711917E: PetscMemcpy (bdf.c:223)
==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074== by 0x70C363A: TSStep (ts.c:3757)
==236074== by 0x70C1999: TSSolve (ts.c:4154)
==236074== by 0x402594: main (one.c:391)
==236074==
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