Merge pull request #53 from gridap/moving_petsc_nonlinear_solver_stat…

…e_to_cache

Moving petsc nonlinear solver state to cache

src/PETScArrays.jl

@@ -106,53 +106,36 @@ function Base.convert(::Type{PETScVector},a::AbstractVector)
   PETScVector(array)
 end
 
-function Base.copy!(a::AbstractVector,petsc_vec::Vec)
-  aux=PETScVector()
-  aux.vec[] = petsc_vec.ptr
-  Base.copy!(a,aux)
-end
-
-function Base.copy!(petsc_vec::Vec,a::AbstractVector)
-  aux=PETScVector()
-  aux.vec[] = petsc_vec.ptr
-  Base.copy!(aux,a)
-end
-
-function Base.copy!(vec::AbstractVector,petscvec::PETScVector)
-  lg=get_local_oh_vector(petscvec)
-  if isa(lg,PETScVector) # petscvec is a ghosted vector
-    lx=get_local_vector(lg)
-    @assert length(lx)==length(vec)
-    vec .= lx
-    restore_local_vector!(lx,lg)
-    GridapPETSc.Finalize(lg)
-  else                   # petscvec is NOT a ghosted vector
-    @assert length(lg)==length(vec)
-    vec .= lg
-    restore_local_vector!(lg,petscvec)
+function Base.copy!(a::AbstractVector,b::PETScVector)
+  @check length(a) == length(b)
+  _copy!(a,b.vec[])
+end
+
+function _copy!(a::Vector,b::Vec)
+  ni = length(a)
+  ix = collect(PetscInt,0:(ni-1))
+  v = convert(Vector{PetscScalar},a)
+  @check_error_code PETSC.VecGetValues(b.ptr,ni,ix,v)
+  if !(v === a)
+    a .= v
   end
 end
 
-function Base.copy!(petscvec::PETScVector,vec::AbstractVector)
-  lg=get_local_oh_vector(petscvec)
-  if isa(lg,PETScVector) # petscvec is a ghosted vector
-    lx=get_local_vector(lg)
-    @assert length(lx)==length(vec)
-    lx .= vec
-    restore_local_vector!(lx,lg)
-    GridapPETSc.Finalize(lg)
-  else                   # petscvec is NOT a ghosted vector
-    @assert length(lg)==length(vec)
-    lg .= vec
-    restore_local_vector!(lg,petscvec)
-  end
+function Base.copy!(a::PETScVector,b::AbstractVector)
+  @check length(a) == length(b)
+  _copy!(a.vec[],b)
 end
 
+function _copy!(a::Vec,b::AbstractVector)
+  ni = length(b)
+  ix = collect(PetscInt,0:(ni-1))
+  v = convert(Vector{PetscScalar},b)
+  @check_error_code PETSC.VecSetValues(a.ptr,ni,ix,v,PETSC.INSERT_VALUES)
+end
 
-
-function get_local_oh_vector(a::PETScVector)
+function get_local_oh_vector(a::Vec)
   v=PETScVector()
-  @check_error_code PETSC.VecGhostGetLocalForm(a.vec[],v.vec)
+  @check_error_code PETSC.VecGhostGetLocalForm(a.ptr,v.vec)
   if v.vec[] != C_NULL  # a is a ghosted vector
     v.ownership=a
     Init(v)
@@ -303,31 +286,28 @@ function Base.copy(a::PETScMatrix)
   Init(v)
 end
 
-function Base.copy!(petscmat::Mat,a::AbstractMatrix)
-  aux=PETScMatrix()
-  aux.mat[] = petscmat.ptr
-  Base.copy!(aux,a)
+function Base.copy!(a::PETScMatrix,b::AbstractMatrix)
+  _copy!(a.mat[],b)
 end
 
-
-function Base.copy!(petscmat::PETScMatrix,mat::AbstractMatrix)
+function _copy!(petscmat::Mat,mat::Matrix)
    n    = size(mat)[2]
    cols = [PetscInt(j-1) for j=1:n]
    row  = Vector{PetscInt}(undef,1)
    vals = Vector{eltype(mat)}(undef,n)
    for i=1:size(mat)[1]
      row[1]=PetscInt(i-1)
      vals .= view(mat,i,:)
-     PETSC.MatSetValues(petscmat.mat[],
+     PETSC.MatSetValues(petscmat.ptr,
                         PetscInt(1),
                         row,
                         n,
                         cols,
                         vals,
                         PETSC.INSERT_VALUES)
    end
-   @check_error_code PETSC.MatAssemblyBegin(petscmat.mat[], PETSC.MAT_FINAL_ASSEMBLY)
-   @check_error_code PETSC.MatAssemblyEnd(petscmat.mat[]  , PETSC.MAT_FINAL_ASSEMBLY)
+   @check_error_code PETSC.MatAssemblyBegin(petscmat.ptr, PETSC.MAT_FINAL_ASSEMBLY)
+   @check_error_code PETSC.MatAssemblyEnd(petscmat.ptr, PETSC.MAT_FINAL_ASSEMBLY)
 end
 
 
@@ -348,7 +328,7 @@ function Base.convert(::Type{PETScMatrix}, a::AbstractMatrix{PetscScalar})
   j = [PetscInt(j-1) for i=1:m for j=1:n]
   v = [ a[i,j] for i=1:m for j=1:n]
   A = PETScMatrix()
-  A.ownership = a
+  A.ownership = (i,j,v)
   @check_error_code PETSC.MatCreateSeqAIJWithArrays(MPI.COMM_SELF,m,n,i,j,v,A.mat)
   @check_error_code PETSC.MatAssemblyBegin(A.mat[],PETSC.MAT_FINAL_ASSEMBLY)
   @check_error_code PETSC.MatAssemblyEnd(A.mat[],PETSC.MAT_FINAL_ASSEMBLY)

src/PETScAssembly.jl

@@ -173,7 +173,9 @@ function Algebra.nz_allocation(a::MatCounter)
   m = a.nrows
   n = a.ncols
   nz = PETSC.PETSC_DEFAULT
-  nnz = a.rownnzmax
+  # nnz cannot be larger than the number of columns
+  # Otherwise PETSc complains when compiled in DEBUG mode
+  nnz = broadcast(min,a.rownnzmax,PetscInt(n))
   b = PETScMatrix()
   @check_error_code PETSC.MatCreateSeqAIJ(comm,m,n,nz,nnz,b.mat)
   Init(b)

src/PETScLinearSolvers.jl

@@ -87,7 +87,7 @@ function Algebra.solve!(x::PVector,ns::PETScLinearSolverNS,b::PVector)
   copy!(B,b)
   Y = convert(PETScVector,X)
   solve!(Y,ns,B)
-  _copy_and_exchange!(x,Y)
+  copy!(x,Y)
 end
 
 function Algebra.numerical_setup!(ns::PETScLinearSolverNS,A::AbstractMatrix)

src/PETScNonlinearSolvers.jl

@@ -1,33 +1,42 @@
 
-mutable struct PETScNonlinearSolver <: NonlinearSolver
+mutable struct PETScNonlinearSolver{F} <: NonlinearSolver
+  setup::F
   comm::MPI.Comm
-  snes::Ref{SNES}
-  initialized::Bool
 end
 
-mutable struct PETScNonlinearSolverCache{A,B,C,D}
+mutable struct PETScNonlinearSolverCache{A,B,C,D,E}
   initialized::Bool
+  snes::Ref{SNES}
   op::NonlinearOperator
 
+  # The input vector to solve!
+  x_fe_space_layout::A
+
   # Julia LA data structures
-  x_julia_vec::A
-  res_julia_vec::A
-  jac_julia_mat_A::B
-  jac_julia_mat_P::B
+  x_sys_layout::B
+  res_sys_layout::B
+  jac_mat_A::C
+  jac_mat_P::C
 
   # Counterpart PETSc data structures
-  x_petsc_vec::C
-  res_petsc_vec::C
-  jac_petsc_mat_A::D
-  jac_petsc_mat_P::D
-
-  function PETScNonlinearSolverCache(op::NonlinearOperator,x_julia_vec::A,res_julia_vec::A,
-                                     jac_julia_mat_A::B,jac_julia_mat_P::B,
-                                     x_petsc_vec::C,res_petsc_vec::C,
-                                     jac_petsc_mat_A::D,jac_petsc_mat_P::D) where {A,B,C,D}
-
-      cache=new{A,B,C,D}(true,op,x_julia_vec,res_julia_vec,jac_julia_mat_A,jac_julia_mat_P,
-                     x_petsc_vec,res_petsc_vec,jac_petsc_mat_A,jac_petsc_mat_P)
+  x_petsc::D
+  res_petsc::D
+  jac_petsc_mat_A::E
+  jac_petsc_mat_P::E
+
+  function PETScNonlinearSolverCache(snes::Ref{SNES}, op::NonlinearOperator,
+                                     x_fe_space_layout::A,
+                                     x_sys_layout::B, res_sys_layout::B,
+                                     jac_mat_A::C, jac_mat_P::C,
+                                     x_petsc::D, res_petsc::D,
+                                     jac_petsc_mat_A::E, jac_petsc_mat_P::E) where {A,B,C,D,E}
+      cache=new{A,B,C,D,E}(true,
+                         snes, op,
+                         x_fe_space_layout,
+                         x_sys_layout, res_sys_layout,
+                         jac_mat_A, jac_mat_P,
+                         x_petsc, res_petsc,
+                         jac_petsc_mat_A, jac_petsc_mat_P)
       finalizer(Finalize,cache)
   end
 end
@@ -39,13 +48,14 @@ function snes_residual(csnes::Ptr{Cvoid},
   cache  = unsafe_pointer_to_objref(ctx)
 
   # 1. Transfer cx to Julia data structures
-  copy!(cache.x_julia_vec, Vec(cx))
+  _copy!(cache.x_sys_layout, Vec(cx))
+  copy!(cache.x_fe_space_layout,cache.x_sys_layout)
 
   # 2. Evaluate residual into Julia data structures
-  residual!(cache.res_julia_vec, cache.op, cache.x_julia_vec)
+  residual!(cache.res_sys_layout, cache.op, cache.x_fe_space_layout)
 
   # 3. Transfer Julia residual to PETSc residual (cfx)
-  copy!(Vec(cfx), cache.res_julia_vec)
+  _copy!(Vec(cfx), cache.res_sys_layout)
 
   return PetscInt(0)
 end
@@ -60,46 +70,27 @@ function snes_jacobian(csnes:: Ptr{Cvoid},
 
   # 1. Transfer cx to Julia data structures
   #    Extract pointer to array of values out of cx and put it in a PVector
-  copy!(cache.x_julia_vec, Vec(cx))
+  _copy!(cache.x_sys_layout, Vec(cx))
+  copy!(cache.x_fe_space_layout,cache.x_sys_layout)
 
-  # 2.
-  jacobian!(cache.jac_julia_mat_A,cache.op,cache.x_julia_vec)
+  # 2. Evaluate Jacobian into Julia data structures
+  jacobian!(cache.jac_mat_A,cache.op,cache.x_fe_space_layout)
 
-  # 3. Transfer nls.jac_julia_mat_A/P to PETSc (cA/cP)
-  copy!(Mat(cA), cache.jac_julia_mat_A)
+  # 3. Transfer nls.jac_mat_A/P to PETSc (cA/cP)
+  _copy!(Mat(cA), cache.jac_mat_A)
 
   return PetscInt(0)
 end
 
-function PETScNonlinearSolver(setup,comm)
-  @assert Threads.threadid() == 1
-  _NREFS[] += 1
-  snes_ref=Ref{SNES}()
-  @check_error_code PETSC.SNESCreate(comm,snes_ref)
-  setup(snes_ref)
-  snes=PETScNonlinearSolver(comm,snes_ref,true)
-  finalizer(Finalize, snes)
-  snes
-end
-
-function Finalize(nls::PETScNonlinearSolver)
-  if GridapPETSc.Initialized() && nls.initialized
-    @check_error_code PETSC.SNESDestroy(nls.snes)
-    @assert Threads.threadid() == 1
-    nls.initialized=false
-    _NREFS[] -= 1
-  end
-  nothing
-end
-
 function Finalize(cache::PETScNonlinearSolverCache)
   if GridapPETSc.Initialized() && cache.initialized
-     GridapPETSc.Finalize(cache.x_petsc_vec)
-     GridapPETSc.Finalize(cache.res_petsc_vec)
+     GridapPETSc.Finalize(cache.x_petsc)
+     GridapPETSc.Finalize(cache.res_petsc)
      GridapPETSc.Finalize(cache.jac_petsc_mat_A)
      if !(cache.jac_petsc_mat_P === cache.jac_petsc_mat_A)
        GridapPETSc.Finalize(cache.jac_petsc_mat_P)
      end
+     @check_error_code PETSC.SNESDestroy(cache.snes)
      cache.initialized=false
   end
 end
@@ -116,71 +107,69 @@ PETScNonlinearSolver() = PETScNonlinearSolver(MPI.COMM_WORLD)
 function _set_petsc_residual_function!(nls::PETScNonlinearSolver, cache)
   ctx = pointer_from_objref(cache)
   fptr = @cfunction(snes_residual, PetscInt, (Ptr{Cvoid}, Ptr{Cvoid}, Ptr{Cvoid}, Ptr{Cvoid}))
-  PETSC.SNESSetFunction(nls.snes[],cache.res_petsc_vec.vec[],fptr,ctx)
+  PETSC.SNESSetFunction(cache.snes[],cache.res_petsc.vec[],fptr,ctx)
 end
 
 function _set_petsc_jacobian_function!(nls::PETScNonlinearSolver, cache)
   ctx = pointer_from_objref(cache)
   fptr = @cfunction(snes_jacobian, PetscInt, (Ptr{Cvoid}, Ptr{Cvoid}, Ptr{Cvoid}, Ptr{Cvoid},Ptr{Cvoid}))
-  PETSC.SNESSetJacobian(nls.snes[],cache.jac_petsc_mat_A.mat[],cache.jac_petsc_mat_A.mat[],fptr,ctx)
+  PETSC.SNESSetJacobian(cache.snes[],cache.jac_petsc_mat_A.mat[],cache.jac_petsc_mat_A.mat[],fptr,ctx)
 end
 
 function _setup_cache(x::AbstractVector,nls::PETScNonlinearSolver,op::NonlinearOperator)
-  res_julia_vec, jac_julia_mat_A = residual_and_jacobian(op,x)
-  res_petsc_vec   = convert(PETScVector,res_julia_vec)
-  jac_petsc_mat_A = convert(PETScMatrix,jac_julia_mat_A)
+
+  res_sys_layout, jac_mat_A = residual_and_jacobian(op,x)
+  res_petsc   = convert(PETScVector,res_sys_layout)
+  jac_petsc_mat_A = convert(PETScMatrix,jac_mat_A)
 
   # In a parallel MPI context, x is a vector with a data layout typically different from
-  # the one of res_julia_vec. On the one hand, x holds the free dof values of a FE
+  # the one of res_sys_layout. On the one hand, x holds the free dof values of a FE
   # Function, and thus has the data layout of the FE space (i.e., local DOFs
   # include all DOFs touched by local cells, i.e., owned and ghost cells).
-  # On the other hand, res_petsc_vec has the data layout of the rows of the
+  # On the other hand, res_petsc has the data layout of the rows of the
   # distributed linear system (e.g., local DoFs only include those touched from owned
   # cells/facets during assembly, assuming the SubAssembledRows strategy).
-  # The following lines of code generate a version of x, namely, x_julia_vec, with the
-  # same data layout as the columns of jac_julia_mat_A, but the contents of x
+  # The following lines of code generate a version of x, namely, x_sys_layout, with the
+  # same data layout as the columns of jac_mat_A, but the contents of x
   # (for the owned dof values).
-  x_julia_vec = similar(res_julia_vec,eltype(res_julia_vec),(axes(jac_julia_mat_A)[2],))
-  copy!(x_julia_vec,x)
-  x_petsc_vec = convert(PETScVector,x_julia_vec)
-  PETScNonlinearSolverCache(op, x_julia_vec,res_julia_vec,
-                           jac_julia_mat_A,jac_julia_mat_A,
-                           x_petsc_vec,res_petsc_vec,
-                           jac_petsc_mat_A, jac_petsc_mat_A)
-end
+  x_sys_layout = similar(res_sys_layout,eltype(res_sys_layout),(axes(jac_mat_A)[2],))
+  copy!(x_sys_layout,x)
+  x_petsc = convert(PETScVector,x_sys_layout)
 
-# Helper private functions to implement the solve! methods below.
-# It allows to execute the solve! methods below in a serial context, i.e.,
-# whenever
-function _myexchange!(x::AbstractVector)
-  x
-end
-function _myexchange!(x::PVector)
-  exchange!(x)
-end
+  snes_ref=Ref{SNES}()
+  @check_error_code PETSC.SNESCreate(nls.comm,snes_ref)
+  nls.setup(snes_ref)
 
-function _copy_and_exchange!(a::AbstractVector,b::PETScVector)
-  copy!(a,b.vec[])
-  _myexchange!(a)
+  PETScNonlinearSolverCache(snes_ref, op, x, x_sys_layout, res_sys_layout,
+                           jac_mat_A, jac_mat_A,
+                           x_petsc, res_petsc,
+                           jac_petsc_mat_A, jac_petsc_mat_A)
 end
 
-
 function Algebra.solve!(x::T,
                         nls::PETScNonlinearSolver,
                         op::NonlinearOperator,
                         cache::PETScNonlinearSolverCache{<:T}) where T <: AbstractVector
 
   @assert cache.op === op
-  @check_error_code PETSC.SNESSolve(nls.snes[],C_NULL,cache.x_petsc_vec.vec[])
-  _copy_and_exchange!(x,cache.x_petsc_vec)
+  @check_error_code PETSC.SNESSolve(cache.snes[],C_NULL,cache.x_petsc.vec[])
+  copy!(x,cache.x_petsc)
   cache
 end
 
-function Algebra.solve!(x::AbstractVector,nls::PETScNonlinearSolver,op::NonlinearOperator)
+function Algebra.solve!(x::AbstractVector,nls::PETScNonlinearSolver,op::NonlinearOperator,::Nothing)
   cache=_setup_cache(x,nls,op)
-  _set_petsc_residual_function!(nls,cache)
-  _set_petsc_jacobian_function!(nls,cache)
-  @check_error_code PETSC.SNESSolve(nls.snes[],C_NULL,cache.x_petsc_vec.vec[])
-  _copy_and_exchange!(x,cache.x_petsc_vec)
+
+  # set petsc residual function
+  ctx  = pointer_from_objref(cache)
+  fptr = @cfunction(snes_residual, PetscInt, (Ptr{Cvoid}, Ptr{Cvoid}, Ptr{Cvoid}, Ptr{Cvoid}))
+  PETSC.SNESSetFunction(cache.snes[],cache.res_petsc.vec[],fptr,ctx)
+
+  # set petsc jacobian function
+  fptr = @cfunction(snes_jacobian, PetscInt, (Ptr{Cvoid}, Ptr{Cvoid}, Ptr{Cvoid}, Ptr{Cvoid},Ptr{Cvoid}))
+  PETSC.SNESSetJacobian(cache.snes[],cache.jac_petsc_mat_A.mat[],cache.jac_petsc_mat_A.mat[],fptr,ctx)
+
+  @check_error_code PETSC.SNESSolve(cache.snes[],C_NULL,cache.x_petsc.vec[])
+  copy!(x,cache.x_petsc)
   cache
 end