arrays - Julia 回调中的 Fortran 数组

Question

我正在尝试为 twpbvpc(带重新网格化的 ODE BVP)Fortran-77 求解器编写一个包装器。求解器需要带签名的输入函数

subroutine fsub(ncomp, x, u, f, rpar, ipar)

在哪里

ncomp是一个整数(向量的长度)，

x (in) 是一个浮点数，

u (in) 是长度为 ncomp 的向量,

f (out) 是结果的位置，长度为 ncomp 的向量

rpar和 ipar是浮点数和整数外部参数的数组； Julia 的关闭将是更受欢迎的方式，但显然它存在困难(请参阅 the blog post here )。但暂时可以忽略它们。

在 Julia ，写 fsub我通常会使用签名

function fsub_julia(x :: Float64, y :: Vector{Float64}, dy :: Vector{Float64})
        dy[1] = ...
        dy[2] = ...
        ...
end

ncomp似乎没有必要，因为可以通过 length 获得长度或 size (但是，Julia 可以检测从 Fortran 传递的数组的大小吗？对于测试代码，我明确知道 ncomp，所以现在这不是问题)。

所以，为了符合 twpbvpc 格式，我写了一个包装器:

function fsub_par(n :: Int64, x :: Float64, y :: Vector{Float64}, dy :: Vector{Float64}, rpar :: Vector{Float64}, ipar :: Vector{Float64})
        fsub_julia(x, y, dy)
end

现在，要将这个函数传递给 Fortran 例程，需要使用 cfunction 进行转换。声明类型。问题是如何？

如果我把它写成:

cf_fsub = cfunction(fsub_par, Void, (Ref{Int64}, Ref{Float64}, Ref{Float64}, Ref{Float64}, Ref{Float64}, Ref{Int64}))

从 Fortran 调用时，出现错误:

ERROR: LoadError: MethodError: no method matching (::TWPBVP.#fsub_par#1{TWPBVP_Test.#f})(::Int64, ::Float64, ::Float64, ::Float64, ::Float64, ::Int64)
Closest candidates are:
  fsub_par(::Int64, ::Float64, !Matched::Array{Float64,1}, !Matched::Array{Float64,1}, !Matched::Array{Float64,1}, !Matched::Array{Float64,1})

所以，不知何故，签名与数组参数不匹配......

如果我更换 Ref{Float64}对于带有 Ref{Array{Float64,1}} 的数组参数(虽然看起来有点奇怪......):

cf_fsub = cfunction(fsub_par, Void, (Ref{Int64}, Ref{Float64}, Ref{Array{Float64,1}}, Ref{Array{Float64,1}}, Ref{Array{Float64,1}}, Ref{Array{Int64,1}}))

我在 fsub_par 时遇到段错误( cf_fsub ) 在 Fortran 代码中被调用(这大约位于，因为错误没有给出确切的位置)。

更换 Ref{Float54}与 Ptr{Float64} for 数组也不做任何事情。

我在 Fortran 代码中发现的一件有趣的事情是 fsub叫做:

call fsub (ncomp, xx(1), u(1,1), fval(1,1),rpar,ipar)

哪里 u和 fval声明为:

dimension xx(nmsh), u(nudim,nmsh), fval(ncomp,nmsh)

所以，我想，它使用了这样一个事实，即 Fortran 通过引用和引用来传递所有参数 u(1,1)应该是指向矩阵第一列的指针(据我所知，Fortran 和 Julia 以列优先顺序存储矩阵)。

有什么出路？我需要更改 fsub_julia的签名吗？接受指针并将它们手动转换为数组(这就是 ODEInterface.jl 在较低级别的工作方式)？

更新

遵循在 ODEInterface.jl 中如何完成并结合在 void* 中传递 Julia 函数的想法C中的-thunk参数我想出了这个:

immutable TWPBVPCProblem
    fsub :: Function            # RHS function
    dfsub :: Function           # Jacobian of RHS
    gsub :: Function            # BC function
    dgsub :: Function           # gradients of BC function
end

function unsafe_fsub(rn :: Ref{Int64}, rx :: Ref{Float64}, py :: Ptr{Float64}, pdy :: Ptr{Float64}, rpar :: Ptr{Float64}, ipar :: Ptr{Int64}) :: Void
    x = rx[]
    n = rn[]
    y = unsafe_wrap(Array, py, n)
    dy = unsafe_wrap(Array, pdy, n)
    problem = unsafe_pointer_to_objref(rpar) :: TWPBVPCProblem
    problem.fsub(x, y, dy)
    return nothing
end

const fsub_ptr = cfunction(unsafe_fsub, Void, (Ref{Int64}, Ref{Float64}, Ptr{Float64}, Ptr{Float64}, Ptr{Float64}, Ptr{Int64}))

当我调用求解器时(它很长):

function twpbvpc(nlbc :: Int64,
        aleft :: Float64, aright :: Float64,
        fixpnt :: Nullable{Vector{Float64}},
        ltol :: Vector{Int64}, tol :: Vector{Float64},
        linear :: Bool, givmsh :: Bool, giveu :: Bool, nmsh :: Ref{Int64},
        xx :: Vector{Float64}, u :: Array{Float64, 2}, nmax :: Ref{Int64},
        wrk :: Vector{Float64}, iwrk :: Vector{Int64},
        fsub :: Function, dfsub :: Function,
        gsub :: Function, dgsub :: Function,
        ckappa1 :: Ref{Float64}, gamma1 :: Ref{Float64},
        ckappa :: Ref{Float64},
        # rpar :: Vector{Float64},
        # ipar :: Vector{Int64},
        iflbvp :: Ref{Int64})

    # Keep problem functions in rpar
    # HACK!
    rpar = TWPBVPCProblem(fsub, dfsub, gsub, dgsub)

    # Fake external parameters
    # Can't have it 0-length as it would be Any[0] and not Float64[0]
    # local rpar :: Vector{Float64} = [0.0]
    local ipar :: Vector{Int64} = [0]

    # No need to pass these parameters
    # u is a matrix for the solution only!
    ncomp, nucol = size(u)
    # Get the maximum of xx
    nxxdim = length(xx)
    # max for mesh points must be the same as the number of column points of u
    assert(nucol == nxxdim)

    # Sizes of work arrays
    lwrkfl = length(wrk)
    lwrkin = length(iwrk)

    # Number of fixed mesh points
    if isnull(fixpnt)
        nfxpnt = 0
        fixpnt_v = [0.0]
    else
        fixpnt_v = get(fixpnt)
        nfxpnt = length(fixpnt_v)
    end

    # Size of tolerance vector ≤ ncomp
    ntol = length(ltol)

    ccall((:twpbvpc_, libtwpbvpc), Void,
        (Ref{Int64}, Ref{Int64},                    # ncomp, nlbc,
        Ref{Float64}, Ref{Float64},                 # aleft, aright
        Ref{Int64}, Ptr{Float64},                   # nfxpnt, fixpnt
        Ref{Int64}, Ptr{Int64}, Ptr{Float64},       # ntol, ltol, tol
        Ref{Int64}, Ref{Int64}, Ref{Int64},         # linear, givmsh, giveu
        Ref{Int64}, Ref{Int64},                     # nmsh, nxxdim
        Ptr{Float64}, Ref{Int64},                   # xx, nudim
        Ptr{Float64}, Ref{Int64},                   # u, nmax
        Ref{Int64}, Ptr{Float64},                   # lwrkfl, wrk
        Ref{Int64}, Ptr{Int64},                     # lwrkin, iwrk
        Ptr{Void}, Ptr{Void}, Ptr{Void}, Ptr{Void}, # fsub, dfsub, gsub, dgsub
        Ref{Float64}, Ref{Float64},                 # ckappa1, gamma1
        Ref{Float64}, Any, Ptr{Int64},              # ckappa, rpar, ipar
        Ref{Int64}),                                # iflbvp
        ncomp, nlbc, aleft, aright,
        nfxpnt, fixpnt_v, ntol, ltol, tol,
        linear, givmsh, giveu, nmsh,
        nxxdim, xx, nucol, u, nmax,                 # nudim = nucol
        lwrkfl, wrk, lwrkin, iwrk,
        fsub_ptr, dfsub_ptr, gsub_ptr, dgsub_ptr,
        ckappa1,gamma1,ckappa,pointer_from_objref(rpar),ipar,iflbvp)
end

Fortran 的 twpbvpc看起来像这样(显然是开头):

  subroutine twpbvpc(ncomp, nlbc, aleft, aright,
 *       nfxpnt, fixpnt, ntol, ltol, tol,
 *       linear, givmsh, giveu, nmsh,
 *       nxxdim, xx, nudim, u, nmax,
 *       lwrkfl, wrk, lwrkin, iwrk,
 *       fsub, dfsub, gsub, dgsub,
 *       ckappa1,gamma1,ckappa,rpar,ipar,iflbvp)

  implicit double precision (a-h,o-z)
  dimension rpar(*),ipar(*)
  dimension fixpnt(*), ltol(*), tol(*)
  dimension xx(*), u(nudim,*)
  dimension wrk(lwrkfl), iwrk(lwrkin)

  logical linear, givmsh, giveu
  external fsub, dfsub, gsub, dgsub

  logical pdebug, use_c, comp_c
  common/algprs/ nminit, pdebug, iprint, idum, uval0, use_c, comp_c
  ...

Fortran 代码使用 build.jl 编译:

cd(joinpath(Pkg.dir("TWPBVP"), "deps"))
pic = @windows ? "" : "-fPIC"
run(`gfortran -m$WORD_SIZE -fdefault-real-8 -fdefault-integer-8 -ffixed-form $pic -shared -O3 -o libtwpbvpc.so twpbvpc.f`)

所以，我路过 rpar如 Any (应该等同于 Ptr{Void} ):尽管 Fortran 需要一个浮点数数组，但这应该无关紧要。

现在，当我尝试运行一个简单的程序(在 Pkg.test("TWPBVP") 上)时出现段错误:

signal (11): Segmentation fault
while loading /home/alexey/.julia/v0.5/TWPBVP/test/runtests.jl, in expression starting on line 58
unknown function (ip: 0xffffffffffffffff)
Allocations: 1400208 (Pool: 1399373; Big: 835); GC: 0

由于代码越来越长，这里是github上完整代码的链接: https://github.com/mobius-eng/TWPBVP.jl

Answer 1

Do I need to change the signature of fsub_julia to accept the pointers and convert them to arrays manually (this is how ODEInterface.jl works at the lower level)?

是的，ODEInterface.jl 模型看起来很不错。

您需要找出的第一件事是您的 fortran 的大小 INTEGER类型( Int32 或 Int64 )。对于下面的代码，我将从 ODEInterface.jl 借用并使用 FInt (它可以是类型参数，也可以是 typealias )

由此产生的回退应该类似于:

# SUBROUTINE FSUB(NCOMP,X,Z,F,RPAR,IPAR)
# IMPLICIT NONE
# INTEGER NCOMP, IPAR
# DOUBLE PRECISION F, Z, RPAR, X
# DIMENSION Z(*),F(*)
# DIMENSION RPAR(*), IPAR(*)
function unsafe_fsub(ncomp::Ref{FInt}, x::Ref{Float64}, z::Ptr{Float64}, 
        f::Ptr{Float64}, rpar::Ptr{Float64}, ipar::Ptr{FInt})::Void
    xx = x[]
    zz = unsafe_wrap(Array, z, ncomp[])
    ff = unsafe_wrap(Array, f, ncomp[])
    fsub!(xx, zz, ff) # function which updates array ff
    return nothing
end

const fsub_ptr = cfunction(unsafe_fsub, Void,
    (Ref{FInt},Ref{Float64},Ptr{Float64},Ptr{Float64},Ptr{Float64},Ptr{FInt}))