[petsc-users] SIGSEGV in Superlu_dist
Hong
hzhang at mcs.anl.gov
Wed Aug 12 10:58:50 CDT 2015
Anthony,
I just patched petsc-maint branch.
Your matrix Amat_binary.m has empty diagonal blocks. Most petsc solvers
require matrix diagonal entries to be allocated as 'non-zero', i.e., insert
zero values to these zero entries. I would suggest you add zeros to
Amat_binary.m during its buildup. This would enable petsc solvers, as well
as other packages.
Again, thanks for bug reporting.
Hong
On Tue, Aug 11, 2015 at 1:33 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> yes - the patch will be in petsc 3.6.2.
>
> However - you can grab the patch right now - and start using it
>
> If using a 3.6.1 tarball - you can do download the (raw) patch from
> the url below and apply with:
>
> cd petsc-3.6.1
> patch -Np1 < patchfile
>
> If using a git clone - you can do:
>
> git fetch
> git checkout ceeba3afeff0c18262ed13ef92e2508ca68b0ecf
>
> Satish
>
> On Tue, 11 Aug 2015, Anthony Haas wrote:
>
> > Hi Hong,
> >
> > Sorry for my late reply and thanks for the fix. Does that mean that I
> will be
> > able to run that matrix on 10 procs in the future (petsc 3.6.2?)?
> >
> > Thanks
> >
> > Anthony
> >
> >
> > On 08/11/2015 09:58 AM, Hong wrote:
> > > Anthony,
> > > I pushed a fix
> > >
> https://bitbucket.org/petsc/petsc/commits/ceeba3afeff0c18262ed13ef92e2508ca68b0ecf
> > >
> > > Once it passes our nightly tests, I'll merge it to petsc-maint, then
> > > petsc-dev.
> > > Thanks for reporting it!
> > >
> > > Hong
> > >
> > > On Mon, Aug 10, 2015 at 4:27 PM, Barry Smith <bsmith at mcs.anl.gov
> > > <mailto:bsmith at mcs.anl.gov>> wrote:
> > >
> > >
> > > Anthony,
> > >
> > > This crash is in PETSc code before it calls the SuperLU_DIST
> > > numeric factorization; likely we have a mistake such as assuming a
> > > process has at least one row of the matrix and need to fix it.
> > >
> > > Barry
> > >
> > > > 0x00007fe6ba609297 in MatLUFactorNumeric_SuperLU_DIST
> (F=0x1922b50,
> > > > A=0x14a6a70, info=0x19099f8)
> > > > at
> > >
> /home/anthony/LIB/petsc-3.6.1/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c:368
> > > > 368 colA_start = rstart + ajj[0]; /* the smallest
> > > global col index of A */
> > >
> > >
> > >
> > > > On Aug 10, 2015, at 3:50 PM, Anthony Haas <aph at email.arizona.edu
> > > <mailto:aph at email.arizona.edu>> wrote:
> > > >
> > > > Hi Sherry,
> > > >
> > > > I recently submitted a matrix for which I noticed that
> > > Superlu_dist was hanging when running on 4 processors with
> > > parallel symbolic factorization. I have been using the latest
> > > version of Superlu_dist and the code is not hanging anymore.
> > > However, I noticed that when running the same matrix (I have
> > > attached the matrix), the code crashes with the following SIGSEGV
> > > when running on 10 procs (with or without parallel symbolic
> > > factorization). It is probably overkill to run such a 'small'
> > > matrix on 10 procs but I thought that it might still be useful to
> > > report the problem?? See below for the error obtained when running
> > > with gdb and also a code snippet to reproduce the error.
> > > >
> > > > Thanks,
> > > >
> > > >
> > > > Anthony
> > > >
> > > >
> > > >
> > > > 1) ERROR in GDB
> > > >
> > > > Program received signal SIGSEGV, Segmentation fault.
> > > > 0x00007fe6ba609297 in MatLUFactorNumeric_SuperLU_DIST
> (F=0x1922b50,
> > > > A=0x14a6a70, info=0x19099f8)
> > > > at
> > >
> /home/anthony/LIB/petsc-3.6.1/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c:368
> > > > 368 colA_start = rstart + ajj[0]; /* the smallest
> > > global col index of A */
> > > > (gdb)
> > > >
> > > >
> > > >
> > > > 2) PORTION OF CODE TO REPRODUCE ERROR
> > > >
> > > > Subroutine HowBigLUCanBe(rank)
> > > >
> > > > IMPLICIT NONE
> > > >
> > > > integer(i4b),intent(in) :: rank
> > > > integer(i4b) :: i,ct
> > > > real(dp) :: begin,endd
> > > > complex(dpc) :: sigma
> > > >
> > > > PetscErrorCode ierr
> > > >
> > > >
> > > > if (rank==0) call cpu_time(begin)
> > > >
> > > > if (rank==0) then
> > > > write(*,*)
> > > > write(*,*)'Testing How Big LU Can Be...'
> > > > write(*,*)'============================'
> > > > write(*,*)
> > > > endif
> > > >
> > > > !sigma = (1.0d0,0.0d0)
> > > > !call MatAXPY(A,-sigma,B,DIFFERENT_NONZERO_PATTERN,ierr) !
> > > on exit A = A-sigma*B
> > > >
> > > > !call MatView(A,PETSC_VIEWER_STDOUT_WORLD,ierr)
> > > >
> > > > !.....Write Matrix to ASCII and Binary Format
> > > > !call
> > > PetscViewerASCIIOpen(PETSC_COMM_WORLD,"Amat.m",viewer,ierr)
> > > > !call MatView(DXX,viewer,ierr)
> > > > !call PetscViewerDestroy(viewer,ierr)
> > > >
> > > > !call
> > >
> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Amat_binary.m",FILE_MODE_WRITE,viewer,ierr)
> > > > !call MatView(A,viewer,ierr)
> > > > !call PetscViewerDestroy(viewer,ierr)
> > > >
> > > > !...Load a Matrix in Binary Format
> > > > call
> > >
> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Amat_binary.m",FILE_MODE_READ,viewer,ierr)
> > > > call MatCreate(PETSC_COMM_WORLD,DLOAD,ierr)
> > > > call MatSetType(DLOAD,MATAIJ,ierr)
> > > > call MatLoad(DLOAD,viewer,ierr)
> > > > call PetscViewerDestroy(viewer,ierr)
> > > >
> > > > !call MatView(DLOAD,PETSC_VIEWER_STDOUT_WORLD,ierr)
> > > >
> > > >
> > > > !.....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) !aha
> > > commented and replaced by next line
> > > >
> > > > !call KSPSetOperators(ksp,A,A,ierr) ! remember: here A =
> > > A-sigma*B
> > > > call KSPSetOperators(ksp,DLOAD,DLOAD,ierr) ! remember: here
> > > A = A-sigma*B
> > > >
> > > > !.....Set Relative and Absolute Tolerances and Uses Default for
> > > Divergence Tol
> > > > tol = 1.e-10
> > > > call
> > >
> KSPSetTolerances(ksp,tol,tol,PETSC_DEFAULT_REAL,PETSC_DEFAULT_INTEGER,ierr)
> > > >
> > > > !.....Set the Direct (LU) Solver
> > > > call KSPSetType(ksp,KSPPREONLY,ierr)
> > > > call KSPGetPC(ksp,pc,ierr)
> > > > call PCSetType(pc,PCLU,ierr)
> > > > call
> > > PCFactorSetMatSolverPackage(pc,MATSOLVERSUPERLU_DIST,ierr) !
> > > MATSOLVERSUPERLU_DIST MATSOLVERMUMPS
> > > >
> > > > !.....Create Right-Hand-Side Vector
> > > > !call MatCreateVecs(A,frhs,PETSC_NULL_OBJECT,ierr)
> > > > !call MatCreateVecs(A,sol,PETSC_NULL_OBJECT,ierr)
> > > >
> > > > call MatCreateVecs(DLOAD,frhs,PETSC_NULL_OBJECT,ierr)
> > > > call MatCreateVecs(DLOAD,sol,PETSC_NULL_OBJECT,ierr)
> > > >
> > > > call
> > > MatGetOwnershipRange(DLOAD,IstartA,IendA,ierr)!;CHKERRQ(ierr)
> > > >
> > > > allocate(xwork1(IendA-IstartA))
> > > > allocate(loc(IendA-IstartA))
> > > >
> > > > ct=0
> > > > do i=IstartA,IendA-1
> > > > ct=ct+1
> > > > loc(ct)=i
> > > > xwork1(ct)=(1.0d0,0.0d0)
> > > > enddo
> > > >
> > > > call
> > > VecSetValues(frhs,IendA-IstartA,loc,xwork1,INSERT_VALUES,ierr)
> > > > call VecZeroEntries(sol,ierr)
> > > >
> > > > deallocate(xwork1,loc)
> > > >
> > > > !.....Assemble Vectors
> > > > call VecAssemblyBegin(frhs,ierr)
> > > > call VecAssemblyEnd(frhs,ierr)
> > > >
> > > > !.....Solve the Linear System
> > > > call KSPSolve(ksp,frhs,sol,ierr)
> > > >
> > > > !call VecView(sol,PETSC_VIEWER_STDOUT_WORLD,ierr)
> > > >
> > > > if (rank==0) then
> > > > call cpu_time(endd)
> > > > write(*,*)
> > > > print '("Total time for HowBigLUCanBe = ",f21.3,"
> > > seconds.")',endd-begin
> > > > endif
> > > >
> > > > call SlepcFinalize(ierr)
> > > >
> > > > STOP
> > > >
> > > >
> > > > end Subroutine HowBigLUCanBe
> > > >
> > > > <Amat_binary.m.info <http://Amat_binary.m.info>>
> > >
> > >
> >
> >
>
>
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