Hello,
I have a 2D system which is assembled by each elemental matrix. Ae is my
elemental matrix, auxRHSe(:) and RHSe(:) and corresponding right hand side, idx
is the global index. My code is as follow, however ,the assembling rate is
super slow(Marked red in the code). I am not sure whether the assembling type
is right or not. Since for each element, idx are not continuous numbers. Do you
have any idea what is the better way to assemble the matrix?
Thanks
block
PetscErrorCode ierr
PetscMPIInt rank,nproc, mystart
PetscInt nelem
integer,allocatable ::info(:)
real(wp), allocatable :: Ae(:,:), auxRHSe(:),RHSe(:)
integer, allocatable :: idx(:)
PetscScalar, pointer :: xx_v(:)
PC prec
PetscScalar :: val
Vec xvec,bvec,uvec
Mat Amat
KSP ksp
PetscViewer viewer
PetscInt geq,j,k,ne,M,Istart,Iend
PetscBool flg
KSPConvergedReason reason
Vec dummyVec, dummyVecs(1)
MatNullSpace nullspace
call PetscInitialize( PETSC_NULL_CHARACTER, ierr )
if (ierr .ne. 0) then
print*,'Unable to initialize PETSc'
stop
endif
call MPI_Comm_size(PETSC_COMM_WORLD,nproc,ierr)
call MPI_Comm_rank(PETSC_COMM_WORLD,rank,ierr)
mystart=rank+1
! Parameter set
info=ptsystem%getInitInfo()
nelem = info(Info_EleMatNum)+info(Info_FixedDOFNum)+info(Info_NumConstrain)
print*,'nelem',nelem
!-------------------------------------
! Create Matrix
call MatCreate(PETSC_COMM_WORLD,Amat,ierr)
call MatSetSizes( Amat,PETSC_DECIDE, PETSC_DECIDE, info(1), info(1), ierr )
call MatSetType( Amat, MATMPIBAIJ, ierr )
! call
MatMPIAIJSetPreallocation(Amat,f9,PETSC_NULL_INTEGER,f6,PETSC_NULL_INTEGER,
ierr)
call MatSetFromOptions( Amat, ierr )
call MatSetUp( Amat, ierr )
call MatGetOwnershipRange( Amat, Istart, Iend, ierr )
xvec = tVec(0)
call MatCreateVecs( Amat, PETSC_NULL_VEC, xvec, ierr )
call VecSetFromOptions( xvec, ierr )
call VecDuplicate( xvec, bvec, ierr )
call VecDuplicate( xvec, uvec, ierr )
t1 = MPI_WTime();
do i=mystart,nelem,nproc
call ptSystem%getElementalMAT(i, Ae, auxRHSe, idx)
ne=size(idx)
if (allocated(auxRHSe)) call
VecSetValues(bvec,ne,idx-1,auxRHSe,ADD_VALUES,ierr)
call MatSetValues(Amat,ne,idx-1,ne,idx-1,Ae,ADD_VALUES,ierr)
end do
nelem = info(Info_EleRHSNum)
mystart = rank+1
do i = mystart, nelem, nproc
call ptSystem%getElementalRHS(i, RHSe, idx)
print*,'idx',idx
ne=size(idx)
if (allocated(RHSe)) call
VecSetValues(bvec,ne,idx-1,RHSe,ADD_VALUES,ierr)
end do
call MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY,ierr)
call MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY,ierr)
! this part is slow, the for loop above is done but here it may get stuck
call VecAssemblyBegin(bvec,ierr)
! For a 2500 DOF system, assembling only takes over 2
seconds
call VecAssemblyEnd(bvec,ierr)
! But for a 10000 DOF system , it gets stuck
t2 = MPI_WTime();
print*,'assembeling time',t2-t1
! Solve
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,Amat,Amat,ierr)
call KSPSetFromOptions(ksp,ierr)
! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
! Solve the linear system
! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
call KSPSetType(ksp,KSPCG,ierr)
call KSPGetPC(ksp,prec,ierr)
! call KSPSetPCSide(ksp,PC_SYMMETRIC,ierr)
call PCSetType(prec,PCJACOBI,ierr)
call KSPSolve(ksp,bvec,xvec,ierr)
call PetscFinalize(ierr)
end block
Yaxiong Chen,
Ph.D. Student
School of Mechanical Engineering, 3171
585 Purdue Mall
West Lafayette, IN 47907
