Don’t run with the -malloc_log Mark did not suggest using that option.
On Oct 23, 2013, at 8:48 AM, Einar Sørheim <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 <[email protected]> >> 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 <[email protected]> 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]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] 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
