[petsc-users] Problem with GAMG elasticity case:'createdefaultdata' not set(?) need to support NULL data!
Einar Sørheim
einar.sorheim at gmail.com
Thu Nov 21 07:41:52 CST 2013
I am on the windows platform so unfortunatley no valgrind, however have
been able to track down the problem in the debugger and it seems like a
matrixpointer gets corrupted when using the fortran-c interface in petsc.
At some point in the calculation the matrix pointer in MatSetSize gets
corrupted when called from fortran, propably in this cast:
void PETSC_STDCALL matsetsizes_(Mat A,PetscInt *m,PetscInt *n,PetscInt
*M,PetscInt *N, int *__ierr ){
*__ierr = MatSetSizes(
(Mat)PetscToPointer((A) ),*m,*n,*M,*N);
}
when entering the MatSetSize in the debugger the A-matrix pointer is
corrupt and I get an access violation on code line:
PetscValidHeaderSpecific(A,MAT_CLASSID,1);
Any ideas what may be the cause of this?
Regards
Einar
2013/10/24 Barry Smith <bsmith at mcs.anl.gov>
>
> So apparently no memory leak.
>
> If you are still getting crashes you will need to run the case that
> crashes 1) with valgrind if you haven’t or 2) using
> -on_error_attach_debugger or -start_in_debugger to track down the cause of
> the crash.
>
> Barry
>
>
>
> On Oct 24, 2013, at 2:09 AM, Einar Sørheim <einar.sorheim at gmail.com>
> wrote:
>
> > Well i I did a rerun without -malloc_log, this is what I got (I have
> also attached the log-sumary file):
> >
> > [0] PetscFinalize(): PetscFinalize() called
> > [0] PetscCommDuplicate(): Duplicating a communicator 1140850688
> -2080374784 max tags = 2147483647
> > Summary of Memory Usage in PETSc
> > [0]Current space PetscMalloc()ed 45936, max space PetscMalloced()
> 1.13728e+009
> > [0]OS cannot compute process memory
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> -2080374784
> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS CMP3.
> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS CMP3.
> > [0] PetscFOpen(): Opening file Log.0
> > [0] Petsc_DelViewer(): Removing viewer data attribute in an MPI_Comm
> -2080374784
> > [0] Petsc_DelComm_Inner(): Removing reference to PETSc communicator
> embedded in a user MPI_Comm -2080374784
> > [0] Petsc_DelComm_Outer(): User MPI_Comm 1140850688 is being freed after
> removing reference from inner PETSc comm to this outer comm
> > [0] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
> > [0] Petsc_DelViewer(): Removing viewer data attribute in an MPI_Comm
> -2080374784
> > [0] Petsc_DelThreadComm(): Deleting thread communicator data in an
> MPI_Comm -2080374784
> > [0] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374784
> >
> >
> >
> > 2013/10/23 Barry Smith <bsmith at mcs.anl.gov>
> >
> > Don’t run with the -malloc_log Mark did not suggest using that option.
> >
> >
> > On Oct 23, 2013, at 8:48 AM, Einar Sørheim <einar.sorheim at gmail.com>
> wrote:
> >
> > > I tried running with the following options :
> > > -info
> > > -malloc
> > > -malloc_log
> > > -malloc_dump
> > > -malloc_debug
> > > -memory_info
> > > -log_summary log_summary.txt
> > > -log
> > > but didn't get a lot wiser however in my case would it be more
> efficient to keep the ksp solver object, if so should I have one object eg.
> for the thermal problem and another one for the mechanical?
> > > The output from the end of the run:
> > > Total wall clock time actually solving: 856.231474
> > > [0] PetscFinalize(): PetscFinalize() called
> > > [0] PetscCommDuplicate(): Duplicating a communicator 1140850688
> -2080374784 max tags = 2147483647
> > > Summary of Memory Usage in PETSc
> > > [0]Current space PetscMalloc()ed 45936, max space PetscMalloced()
> 1.13728e+009
> > > [0]OS cannot compute process memory
> > > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> -2080374784
> > > [0] PetscGetHostName(): Rejecting domainname, likely is NIS CMP3.
> > > [0] PetscGetHostName(): Rejecting domainname, likely is NIS CMP3.
> > > [0] PetscFOpen(): Opening file Log.0
> > > [0] Petsc_DelViewer(): Removing viewer data attribute in an MPI_Comm
> -2080374784
> > > [0] Petsc_DelComm_Inner(): Removing reference to PETSc communicator
> embedded in a user MPI_Comm -2080374784
> > > [0] Petsc_DelComm_Outer(): User MPI_Comm 1140850688 is being freed
> after removing reference from inner PETSc comm to this outer comm
> > > [0] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
> > > [0] Petsc_DelViewer(): Removing viewer data attribute in an MPI_Comm
> -2080374784
> > > [0] Petsc_DelThreadComm(): Deleting thread communicator data in an
> MPI_Comm -2080374784
> > > [0] Petsc_DelCounter(): Deleting counter data in an MPI_Comm
> -2080374784
> > > [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > > [0]PETSC ERROR: Object is in wrong state!
> > > [0]PETSC ERROR: PetscMallocDumpLog() called without call to
> PetscMallocSetDumpLog() this is often due to
> > > setting the option -malloc_log AFTER
> PetscInitialize() with PetscOptionsInsert() or PetscOptionsInsertFile()!
> > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [0]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013
> > > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > > [0]PETSC ERROR: See docs/index.html for manual pages.
> > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [0]PETSC ERROR: D:\Programming\gits\Alsim\SharedModules -
> Copy\Source\Release\Alsim_nypetsc.exe on a arch-mswin-c-debug named CMP3 by
> admeinar Wed Oct 23 11:54:03 2013
> > > [0]PETSC ERROR: Libraries linked from
> /cygdrive/d/Programming/petsc-3.4.3/arch-mswin-c-debug/lib
> > > [0]PETSC ERROR: Configure run at Thu Oct 17 08:23:18 2013
> > > [0]PETSC ERROR: Configure options --with-debugging=1 --with-openmp=yes
> --with-pthread=no --with-cc="win32fe icl" --with-fc="win32fe ifort"
> --with-cxx="win32fe icl" --with-blas-lapack-dir="C:/Program Files
> (x86)/Intel/Composer XE 2013/mkl/lib/intel64" --download-superlu
> --with-sowing=0 --with-c2html=0 --with-mpi-dir="C:/Program Files
> (x86)/Intel/MPI/4.1.0.028/em64t" --useThreads=0 --useThreads=0
> > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [0]PETSC ERROR: PetscMallocDumpLog() line 652 in
> src/sys/memory/D:\PROGRA~1\PETSC-~1.3\src\sys\memory\mtr.c
> > > [0]PETSC ERROR: PetscFinalize() line 1185 in
> src/sys/objects/D:\PROGRA~1\PETSC-~1.3\src\sys\objects\pinit.c
> > >
> > >
> > > 2013/10/19 Mark F. Adams <mfadams at lbl.gov>
> > > You can try running a problem that finishes with
> > >
> > > -malloc
> > > -malloc_debug
> > > -malloc_dump
> > >
> > > to see if there are any memory issues. It looks like you are
> completely destroying the solver object each time and starting over.
> Valgrind would be very useful here because it looks like memory is getting
> corrupted if the same code runs many times.
> > >
> > >
> > > On Oct 19, 2013, at 3:39 PM, Einar Sørheim <einar.sorheim at gmail.com>
> wrote:
> > >
> > >> yes, I call the given code many times, what i have seen so far is
> that changing e.g. the order of destruction statements changes the time of
> failure,I will try to debug to get more details
> > >>
> > >>
> > >> 2013/10/18 Mark F. Adams <mfadams at lbl.gov>
> > >> I would guess there is some memory corruption or leak someplace. Try
> running with -on_error_attach_debugger, and try to get some more
> information. Do you just repeat a call to the code below many times? Is
> this deterministic, does it fail on the same solve each time?
> > >>
> > >>
> > >> On Oct 18, 2013, at 9:30 AM, Einar Sørheim <einar.sorheim at gmail.com>
> wrote:
> > >>
> > >>> Uncommenting KSPSetFromOptions solved my intial problem, however I
> got a new problem that occurs after many timesteps, in our code we use
> petsc gamg as a solver for several problems(e.g. thermal and mechanical) at
> each time step, I have a suspicion it might have something to do with
> cleanup after solving, the rror appears after many calls to the petsc gamg
> solver interface, the error message is the following:
> > >>>
> > >>> [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
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: 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] MatSetNearNullSpace line 7580
> src/mat/interface/D:\PROGRA~1\PETSC-~1.3\src\mat\INTERF~1\matrix.c
> > >>> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > >>> [0]PETSC ERROR: Signal received!
> > >>> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > >>> [0]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013
> > >>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > >>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > >>> [0]PETSC ERROR: See docs/index.html for manual pages.
> > >>> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > >>> [0]PETSC ERROR: D:\Programming\gits\Alsim\SharedModules -
> Copy\Source\Release\Alsim_nypetsc.exe on a arch-mswin-c-debug named CMP3 by
> admeinar Fri Oct 18 12:26:04 2013
> > >>> [0]PETSC ERROR: Libraries linked from
> /cygdrive/d/Programming/petsc-3.4.3/arch-mswin-c-debug/lib
> > >>> [0]PETSC ERROR: Configure run at Thu Oct 17 08:23:18 2013
> > >>> [0]PETSC ERROR: Configure options --with-debugging=1
> --with-openmp=yes --with-pthread=no --with-cc="win32fe icl"
> --with-fc="win32fe ifort" --with-cxx="win32fe icl"
> --with-blas-lapack-dir="C:/Program Files (x86)/Intel/Composer XE
> 2013/mkl/lib/intel64" --download-superlu --with-sowing=0 --with-c2html=0
> --with-mpi-dir="C:/Program Files (x86)/Intel/MPI/4.1.0.028/em64t"
> --useThreads=0 --useThreads=0
> > >>>
> > >>> The source code for the petsc interface:
> > >>>
> > >>> subroutine
> petscsolver(i_nodes,r_elements_,i_rowstart_,i_columnindex_,r_x_,r_b_,i_Nnz,i_Precond,
> i_Solver
> > >>> $ ,coords_,i_nodedof)
> > >>> #include <finclude/petscsys.h>
> > >>> #include <finclude/petscvec.h>
> > >>> #include <finclude/petscmat.h>
> > >>> #include <finclude/petscpc.h>
> > >>> #include <finclude/petscksp.h>
> > >>> #include <finclude/petscviewer.h>
> > >>>
> > >>> integer i_nodes, i_Nnz, i_Precond, i_solver, i_nodedof
> > >>> integer i_rowstart_(*),i_columnindex_(*)
> > >>> double precision r_elements_(*),r_x_(*), r_b_(*),coords_(*)
> > >>> integer, allocatable :: i_indices_(:)
> > >>> ! Variables:
> > >>> !
> > >>> ! A - matrix that defines linear system
> > >>> ! ksp - KSP context
> > >>> ! ksp - KSP context
> > >>> ! x, b, u - approx solution, RHS, exact solution vectors
> > >>> !
> > >>> ! implicit none
> > >>> Vec x,u,b,vec_coords
> > >>> PC pc
> > >>> Mat A,F,Matnull
> > >>> KSP ksp
> > >>> PetscInt i,j,II,JJ,m,n,i1,imaxiter
> > >>> PetscInt Istart,Iend
> > >>> PetscInt nsteps,one, neg_one
> > >>> PetscErrorCode ierr
> > >>> PetscBool flg
> > >>> PetscScalar v,x_array_(1), norm, tol, t0,t1
> > >>> PetscOffset i_x
> > >>> PetscViewer viewer
> > >>>
> > >>>
> > >>> call PetscTime(t0,ierr)
> > >>> write(*,*) "Enter petsc"
> > >>>
> > >>> n = 1
> > >>> nsteps = 1
> > >>> one = 1
> > >>> neg_one = 1
> > >>> i1 = 1
> > >>> imaxiter = 1200
> > >>>
> > >>>
> > >>> call MatCreate(PETSC_COMM_WORLD,A,ierr)
> > >>> call
> MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,i_nodes,i_nodes,ierr)
> > >>> call MatSetType(A, MATSEQAIJ,ierr)
> > >>> call MatSetUp(A,ierr)
> > >>> call MatSeqAIJSetPreallocation(A,100,PETSC_NULL_INTEGER,ierr)
> > >>> ! The matrix is partitioned by contiguous chunks of rows across the
> > >>> ! processors. Determine which rows of the matrix are locally owned.
> > >>>
> > >>> call MatGetOwnershipRange(A,Istart,Iend,ierr)
> > >>>
> > >>>
> > >>> write(*,*) "Start of matrix fill", i_nodes, Istart, Iend
> > >>> do i=1,i_nodes
> > >>> ! write(*,*) "Start of loop",i !!, i_indices_(i+1)
> > >>> ! i_indices_(i+1) = i
> > >>> ! write(*,*) "Start of loop2"
> > >>> do j=i_rowstart_(i),i_rowstart_(i+1)-1
> > >>> ! write(*,*) "Start of loop 3"
> > >>> v = r_elements_(j)
> > >>> ! write(*,*) i1,i,i1,j-1,v
> > >>> call
> MatSetValues(A,i1,i-1,i1,i_columnindex_(j)-1,v,INSERT_VALUES,ierr)
> > >>> if (ierr.gt.0) stop
> > >>> end do
> > >>> end do
> > >>> ! write(*,*) "End of matrix fill"
> > >>>
> > >>> ! Assemble matrix, using the 2-step process:
> > >>> ! MatAssemblyBegin(), MatAssemblyEnd()
> > >>> ! Computations can be done while messages are in transition
> > >>> ! by placing code between these two statements.
> > >>>
> > >>> call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr)
> > >>> call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr)
> > >>>
> > >>> ! Create parallel vectors.
> > >>> ! - When using VecCreate(), the parallel partitioning of the vector
> > >>> ! is determined by PETSc at runtime.
> > >>> ! - Note: We form 1 vector from scratch and then duplicate as
> needed.
> > >>> ! write(*,*) "Start of vector fill"
> > >>> call VecCreate(PETSC_COMM_WORLD,u,ierr)
> > >>> call VecSetType(u, VECSEQ,ierr)
> > >>> call VecSetSizes(u,PETSC_DECIDE,i_nodes,ierr)
> > >>> ! call VecSetFromOptions(u,ierr)
> > >>> call VecDuplicate(u,b,ierr)
> > >>> call VecDuplicate(b,x,ierr)
> > >>> do i=1,i_nodes
> > >>> call VecSetValues(x,i1,i-1,r_x_(i),INSERT_VALUES,ierr)
> > >>> call VecSetValues(b,i1,i-1,r_b_(i),INSERT_VALUES,ierr)
> > >>> enddo
> > >>> ! Assemble vector
> > >>>
> > >>> call VecAssemblyBegin(x,ierr)
> > >>> call VecAssemblyEnd(x,ierr)
> > >>> call VecAssemblyBegin(b,ierr)
> > >>> call VecAssemblyEnd(b,ierr)
> > >>> call PetscTime(t1,ierr)
> > >>> ! write(*,*) "End of vec fill time spent :", t1-t0
> > >>> ! Create linear solver context
> > >>>
> > >>> call KSPCreate(PETSC_COMM_WORLD,ksp,ierr)
> > >>>
> > >>>
> > >>> ! Set operators. Here the matrix that defines the linear system
> > >>> ! also serves as the preconditioning matrix.
> > >>>
> > >>> call KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN,ierr)
> > >>>
> > >>>
> > >>> call KSPGetPC(ksp,pc,ierr)
> > >>> tol = 1.e-20
> > >>> call
> KSPSetTolerances(ksp,tol,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_DOUBLE_PRECISION,imaxiter,ierr)
> > >>> select case (i_Precond)
> > >>> case ( 1 )
> > >>> call PCSetType(pc,PCJACOBI,ierr)
> > >>> case ( 2 )
> > >>> call PCSetType(pc,PCILU,ierr)
> > >>> call PCFactorSetMatSolverPackage(pc,MATSOLVERSUPERLU,ierr);
> > >>> call PCFactorSetUpMatSolverPackage(pc,ierr);
> > >>> call PCFactorGetMatrix(pc,F);
> > >>> call MatSuperluSetILUDropTol(F,1.e-4);
> > >>> case ( 3 )
> > >>> call PCSetType(pc,PCGAMG,ierr)
> > >>> ! call PCGAMGInitializePackage()
> > >>> ! call PCCreate_GAMG(pc,ierr)
> > >>> case DEFAULT
> > >>> call PCSetType(pc,PCJACOBI,ierr)
> > >>> end select
> > >>>
> > >>> ! call PCSetType(pc,PCJACOBI,ierr)
> > >>> select case (i_solver)
> > >>> case ( 0 )
> > >>> call KSPSetType(ksp,KSPCG,ierr)
> > >>> case DEFAULT
> > >>> call KSPSetType(ksp,KSPCG,ierr)
> > >>> end select
> > >>> call KSPCGSetType(ksp,KSP_CG_SYMMETRIC,ierr)
> > >>> if (i_nodedof==3) then
> > >>> write(*,*) "Set coord, number of nodes is:",
> i_nodes/i_nodedof
> > >>> call
> VecCreateSeqWithArray(MPI_COMM_SELF,3,i_nodes,coords_,vec_coords,ierr)
> > >>> call MatNullSpaceCreateRigidBody(vec_coords,Matnull,ierr)
> > >>> call MatSetNearNullSpace(A,Matnull,ierr)
> > >>> call MatNullSpaceDestroy(Matnull,ierr)
> > >>>
> > >>> write(*,*) "Finish setting null space ierr =", ierr
> > >>> ! call PCSetCoordinates( pc, 3,i_nodes/i_nodedof, coords_,
> ierr )
> > >>>
> > >>> end if
> > >>> ! call KSPMonitorSet(ksp, KSPMonitorDefault, PETSC_NULL,
> PETSC_NULL,ierr)
> > >>> ! Set runtime options, e.g.,
> > >>> ! -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
> > >>> ! These options will override those specified above as long as
> > >>> ! KSPSetFromOptions() is called _after_ any other customization
> > >>> ! routines.
> > >>>
> > >>> call KSPSetFromOptions(ksp,ierr)
> > >>> call KSPSetInitialGuessNonzero(ksp,PETSC_TRUE,ierr)
> > >>> call KSPSetUp(ksp,ierr)
> > >>> call PetscTime(t0,ierr)
> > >>> write(*,*) "Time setup", t0-t1
> > >>> ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> - -
> > >>> ! Solve the linear system
> > >>> ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> - -
> > >>>
> > >>> call KSPSolve(ksp,b,x,ierr)
> > >>> call PetscTime(t1,ierr)
> > >>> write(*,*) "end solve, time used:",t1-t0
> > >>> call KSPGetSolution(ksp,x,ierr)
> > >>> call VecGetArray(x,x_array_,i_x,ierr)
> > >>> do i=1,i_nodes
> > >>> r_x_(i) = x_array_(i_x + i)
> > >>> enddo
> > >>> call VecRestoreArray(x,x_array_,i_x,ierr)
> > >>>
> > >>>
> > >>> ! Free work space. All PETSc objects should be destroyed when they
> > >>> ! are no longer needed.
> > >>> ! call PCDestroy(pc,ierr)
> > >>>
> > >>> call VecDestroy(u,ierr)
> > >>> call VecDestroy(x,ierr)
> > >>> call VecDestroy(b,ierr)
> > >>> call MatDestroy(A,ierr)
> > >>> if (i_nodedof==3) then
> > >>> call VecDestroy(vec_coords,ierr)
> > >>> call MatDestroy(Matnull,ierr)
> > >>> endif
> > >>> call KSPDestroy(ksp,ierr)
> > >>> call PetscTime(t0,ierr)
> > >>> write(*,*) "time celan up :", t0-t1
> > >>>
> > >>> end
> > >>>
> > >>> --
> > >>> Einar Sørheim
> > >>> <Mail Attachment>
> > >>
> > >>
> > >>
> > >>
> > >> --
> > >> Einar Sørheim
> > >
> > >
> > >
> > >
> > > --
> > > Einar Sørheim
> >
> >
> >
> >
> > --
> > Einar Sørheim
> > <log_summary.txt>
>
>
--
Einar Sørheim
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