Merge pull request #205 from lostella/julia-0.7-update

Julia 0.7 update

Author: haampie

.travis.yml

@@ -1,14 +1,14 @@
 language: julia
 os:
-    - linux
+  - linux
 julia:
-    - 0.6
-    - nightly
+  - 0.7
+  - nightly
 matrix:
   allow_failures:
     - julia: nightly
 notifications:
-    email: false
+  email: false
 after_success:
-    - julia -e 'Pkg.add("Coverage"); cd(Pkg.dir("IterativeSolvers")); using Coverage; Coveralls.submit(process_folder());'
-    - julia -e 'Pkg.add("Documenter"); cd(Pkg.dir("IterativeSolvers")); include(joinpath("docs", "make.jl"))'
+  - julia -e 'Pkg.add("Coverage"); cd(Pkg.dir("IterativeSolvers")); using Coverage; Coveralls.submit(process_folder());'
+  - julia -e 'Pkg.add("Documenter"); cd(Pkg.dir("IterativeSolvers")); include(joinpath("docs", "make.jl"))'

REQUIRE

@@ -1,3 +1,3 @@
-julia 0.6
+julia 0.7
 
-RecipesBase
+RecipesBase 0.3.1

benchmark/advection_diffusion.jl

@@ -19,7 +19,7 @@ function advection_dominated(;N = 50, β = 1000.0)
     Δ = laplace_matrix(Float64, N, 3) ./ -h^2
 
     # And the dx bit.
-    ∂x_1d = spdiagm((fill(-β / 2h, N - 1), fill(β / 2h, N - 1)), (-1, 1))
+    ∂x_1d = spdiagm(-1 => fill(-β / 2h, N - 1), 1 => fill(β / 2h, N - 1))
     ∂x = kron(speye(N^2), ∂x_1d)
 
     # Final matrix and rhs.
@@ -41,6 +41,6 @@ function laplace_matrix(::Type{T}, n, dims) where T
 end
 
 second_order_central_diff(::Type{T}, dim) where {T} = convert(
-    SparseMatrixCSC{T, Int}, 
+    SparseMatrixCSC{T, Int},
     SymTridiagonal(fill(2 * one(T), dim), fill(-one(T), dim - 1))
-)
+)

benchmark/benchmark-hessenberg.jl

@@ -16,24 +16,24 @@ function backslash_versus_givens(; n = 1_000, ms = 10 : 10 : 100)
         println(m)
 
         H = zeros(m + 1, m)
-        
+
         # Create an orthonormal basis for the Krylov subspace
         V = rand(n, m + 1)
         V[:, 1] /= norm(V[:, 1])
-        
+
         for i = 1 : m
             # Expand
             V[:, i + 1] = A * V[:, i]
-            
+
             # Orthogonalize
             H[1 : i, i] = view(V, :, 1 : i)' * V[:, i + 1]
             V[:, i + 1] -= view(V, :, 1 : i) * H[1 : i, i]
-            
+
             # Re-orthogonalize
             update = view(V, :, 1 : i)' * V[:, i + 1]
             H[1 : i, i] += update
             V[:, i + 1] -= view(V, :, 1 : i) * update
-            
+
             # Normalize
             H[i + 1, i] = norm(V[:, i + 1])
             V[:, i + 1] /= H[i + 1, i]
@@ -43,11 +43,11 @@ function backslash_versus_givens(; n = 1_000, ms = 10 : 10 : 100)
         rhs = [i == 1 ? 1.0 : 0.0 for i = 1 : size(H, 1)]
 
         # Run the benchmark
-        results["givens_qr"][m] = @benchmark A_ldiv_B!(IterativeSolvers.Hessenberg(myH), myRhs) setup = (myH = copy($H); myRhs = copy($rhs))
+        results["givens_qr"][m] = @benchmark ldiv!(IterativeSolvers.Hessenberg(myH), myRhs) setup = (myH = copy($H); myRhs = copy($rhs))
         results["backslash"][m] = @benchmark $H \ $rhs
     end
 
     return results
 end
 
-end
+end

benchmark/benchmark-linear-systems.jl

@@ -1,6 +1,6 @@
 module LinearSystemsBench
 
-import Base.A_ldiv_B!, Base.\
+import Base.ldiv!, Base.\
 
 using BenchmarkTools
 using IterativeSolvers
@@ -12,7 +12,7 @@ struct DiagonalPreconditioner{T}
     diag::Vector{T}
 end
 
-function A_ldiv_B!(y::AbstractVector{T}, A::DiagonalPreconditioner{T}, b::AbstractVector{T}) where T
+function ldiv!(y::AbstractVector{T}, A::DiagonalPreconditioner{T}, b::AbstractVector{T}) where T
     for i = 1 : length(b)
         @inbounds y[i] = A.diag[i] \ b[i]
     end
@@ -34,7 +34,7 @@ function cg(; n = 1_000_000, tol = 1e-6, maxiter::Int = 200)
     println("Symmetric positive definite matrix of size ", n)
     println("Eigenvalues in interval [0.01, 4.01]")
     println("Tolerance = ", tol, "; max #iterations = ", maxiter)
-    
+
     # Dry run
     initial = rand(n)
     IterativeSolvers.cg!(copy(initial), A, b, Pl = P, maxiter = maxiter, tol = tol, log = false)

benchmark/benchmark-svd-florida.jl

@@ -78,10 +78,10 @@ function runbenchmark(filename, benchmarkfilename)
     #Choose the same normalized unit vector to start with
     q = randn(n)
     eltype(A) <: Complex && (q += im*randn(n))
-    scale!(q, inv(norm(q)))
+    rmul!(q, inv(norm(q)))
     qm = randn(m)
     eltype(A) <: Complex && (q += im*randn(m))
-    scale!(qm, inv(norm(qm)))
+    rmul!(qm, inv(norm(qm)))
 
     #Number of singular values to request
     nv = min(m, n, 10)

docs/src/getting_started.md

@@ -25,7 +25,7 @@ Rather than constructing an explicit matrix `A` of the type `Matrix` or `SparseM
 For matrix-free types of `A` the following interface is expected to be defined:
 
 - `A*v` computes the matrix-vector product on a `v::AbstractVector`;
-- `A_mul_B!(y, A, v)` computes the matrix-vector product on a `v::AbstractVector` in-place;
+- `mul!(y, A, v)` computes the matrix-vector product on a `v::AbstractVector` in-place;
 - `eltype(A)` returns the element type implicit in the equivalent matrix representation of `A`;
 - `size(A, d)` returns the nominal dimensions along the `d`th axis in the equivalent matrix representation of `A`.
 

docs/src/iterators.md

@@ -43,7 +43,7 @@ end
 @show norm(b1 - A * x) / norm(b1)
 
 # Copy the next right-hand side into the iterable
-copy!(my_iterable.b, b2)
+copyto!(my_iterable.b, b2)
 
 for item in my_iterable
     println("Iteration for rhs 2")

docs/src/preconditioning.md

@@ -2,13 +2,13 @@
 
 Many iterative solvers have the option to provide left and right preconditioners (`Pl` and `Pr` resp.) in order to speed up convergence or prevent stagnation. They transform a problem $Ax = b$ into a better conditioned system $(P_l^{-1}AP_r^{-1})y = P_l^{-1}b$, where $x = P_r^{-1}y$.
 
-These preconditioners should support the operations 
+These preconditioners should support the operations
 
-- `A_ldiv_B!(y, P, x)` computes `P \ x` in-place of `y`;
-- `A_ldiv_B!(P, x)` computes `P \ x` in-place of `x`;
+- `ldiv!(y, P, x)` computes `P \ x` in-place of `y`;
+- `ldiv!(P, x)` computes `P \ x` in-place of `x`;
 - and `P \ x`.
 
-If no preconditioners are passed to the solver, the method will default to 
+If no preconditioners are passed to the solver, the method will default to
 
 ```julia
 Pl = Pr = IterativeSolvers.Identity()
@@ -18,4 +18,4 @@ Pl = Pr = IterativeSolvers.Identity()
 IterativeSolvers.jl itself does not provide any other preconditioners besides `Identity()`, but recommends the following external packages:
 
 - [ILU.jl](https://github.com/haampie/ILU.jl) for incomplete LU decompositions (using drop tolerance);
-- [IncompleteSelectedInversion.jl](https://github.com/ettersi/IncompleteSelectedInversion.jl) for incomplete LDLt decompositions.
+- [IncompleteSelectedInversion.jl](https://github.com/ettersi/IncompleteSelectedInversion.jl) for incomplete LDLt decompositions.

src/bicgstabl.jl

@@ -1,6 +1,6 @@
 export bicgstabl, bicgstabl!, bicgstabl_iterator, bicgstabl_iterator!, BiCGStabIterable
-
-import Base: start, next, done
+using Printf
+import Base: iterate
 
 mutable struct BiCGStabIterable{precT, matT, solT, vecT <: AbstractVector, smallMatT <: AbstractMatrix, realT <: Real, scalarT <: Number}
     A::matT
@@ -36,23 +36,23 @@ function bicgstabl_iterator!(x, A, b, l::Int = 2;
 
     # Large vectors.
     r_shadow = rand(T, n)
-    rs = Matrix{T}(n, l + 1)
+    rs = Matrix{T}(undef, n, l + 1)
     us = zeros(T, n, l + 1)
 
     residual = view(rs, :, 1)
-    
+
     # Compute the initial residual rs[:, 1] = b - A * x
     # Avoid computing A * 0.
     if initial_zero
-        copy!(residual, b)
+        copyto!(residual, b)
     else
-        A_mul_B!(residual, A, x)
+        mul!(residual, A, x)
         residual .= b .- residual
         mv_products += 1
     end
 
     # Apply the left preconditioner
-    A_ldiv_B!(Pl, residual)
+    ldiv!(Pl, residual)
 
     γ = zeros(T, l)
     ω = σ = one(T)
@@ -76,35 +76,37 @@ end
 @inline start(::BiCGStabIterable) = 0
 @inline done(it::BiCGStabIterable, iteration::Int) = it.mv_products ≥ it.max_mv_products || converged(it)
 
-function next(it::BiCGStabIterable, iteration::Int)
+function iterate(it::BiCGStabIterable, iteration::Int=start(it))
+    if done(it, iteration) return nothing end
+
     T = eltype(it.x)
     L = 2 : it.l + 1
 
     it.σ = -it.ω * it.σ
-    
+
     ## BiCG part
     for j = 1 : it.l
         ρ = dot(it.r_shadow, view(it.rs, :, j))
         β = ρ / it.σ
-        
+
         # us[:, 1 : j] .= rs[:, 1 : j] - β * us[:, 1 : j]
         it.us[:, 1 : j] .= it.rs[:, 1 : j] .- β .* it.us[:, 1 : j]
 
         # us[:, j + 1] = Pl \ (A * us[:, j])
         next_u = view(it.us, :, j + 1)
-        A_mul_B!(next_u, it.A, view(it.us, :, j))
-        A_ldiv_B!(it.Pl, next_u)
+        mul!(next_u, it.A, view(it.us, :, j))
+        ldiv!(it.Pl, next_u)
 
         it.σ = dot(it.r_shadow, next_u)
         α = ρ / it.σ
 
         it.rs[:, 1 : j] .-= α .* it.us[:, 2 : j + 1]
-        
+
         # rs[:, j + 1] = Pl \ (A * rs[:, j])
         next_r = view(it.rs, :, j + 1)
-        A_mul_B!(next_r, it.A , view(it.rs, :, j))
-        A_ldiv_B!(it.Pl, next_r)
-        
+        mul!(next_r, it.A , view(it.rs, :, j))
+        ldiv!(it.Pl, next_r)
+
         # x = x + α * us[:, 1]
         it.x .+= α .* view(it.us, :, 1)
     end
@@ -113,13 +115,13 @@ function next(it::BiCGStabIterable, iteration::Int)
     it.mv_products += 2 * it.l
 
     ## MR part
-    
+
     # M = rs' * rs
-    Ac_mul_B!(it.M, it.rs, it.rs)
+    mul!(it.M, adjoint(it.rs), it.rs)
 
-    # γ = M[L, L] \ M[L, 1] 
-    F = lufact!(view(it.M, L, L))
-    A_ldiv_B!(it.γ, F, view(it.M, L, 1))
+    # γ = M[L, L] \ M[L, 1]
+    F = lu!(view(it.M, L, L))
+    ldiv!(it.γ, F, view(it.M, L, 1))
 
     # This could even be BLAS 3 when combined.
     BLAS.gemv!('N', -one(T), view(it.us, :, L), it.γ, one(T), view(it.us, :, 1))
@@ -155,9 +157,9 @@ bicgstabl(A, b, l = 2; kwargs...) = bicgstabl!(zerox(A, b), A, b, l; initial_zer
 - `max_mv_products::Int = size(A, 2)`: maximum number of matrix vector products.
 For BiCGStab(l) this is a less dubious term than "number of iterations";
 - `Pl = Identity()`: left preconditioner of the method;
-- `tol::Real = sqrt(eps(real(eltype(b))))`: tolerance for stopping condition `|r_k| / |r_0| ≤ tol`. 
-   Note that (1) the true residual norm is never computed during the iterations, 
-   only an approximation; and (2) if a preconditioner is given, the stopping condition is based on the 
+- `tol::Real = sqrt(eps(real(eltype(b))))`: tolerance for stopping condition `|r_k| / |r_0| ≤ tol`.
+   Note that (1) the true residual norm is never computed during the iterations,
+   only an approximation; and (2) if a preconditioner is given, the stopping condition is based on the
    *preconditioned residual*.
 
 # Return values
@@ -184,10 +186,10 @@ function bicgstabl!(x, A, b, l = 2;
 
     # This doesn't yet make sense: the number of iters is smaller.
     log && reserve!(history, :resnorm, max_mv_products)
-    
+
     # Actually perform CG
     iterable = bicgstabl_iterator!(x, A, b, l; Pl = Pl, tol = tol, max_mv_products = max_mv_products, kwargs...)
-    
+
     if log
         history.mvps = iterable.mv_products
     end
@@ -200,10 +202,10 @@ function bicgstabl!(x, A, b, l = 2;
         end
         verbose && @printf("%3d\t%1.2e\n", iteration, iterable.residual)
     end
-    
+
     verbose && println()
     log && setconv(history, converged(iterable))
     log && shrink!(history)
-    
+
     log ? (iterable.x, history) : iterable.x
 end