Python ctypes将结构字段中的指针传递给Fortran派生类型

Question

我想做一个可变大小的数组传递给Fortran DLL并获取结果（通过引用），这样我就可以直接获取值了。

在 Fortran 代码中，我使用可分配变量，我认为这就像指向已分配地址的指针。

我可以做到以下，但我不知道如何在结构上做到这一点：

test = POINTER(c_double)()

sim.structtest(input, byref(test))

test在Fortran中的定义是

real(kind=8), allocatable, dimension (:) :: test

allocate(test(1))

原代码：

Python 代码（structtest.py）：

from ctypes import *
import sys
import os


sim = cdll.LoadLibrary("struct.so")

class Input( Structure ):
    _fields_ = [( "a", c_double * 1 ),
                ( "b", c_double )]

class Output( Structure ):
    _fields_ = [( "a", c_double ),
                ( "b", POINTER(c_double) )] #-> don't know how to do

def main(): 
    input = Input()
    output = Output()
    input.a[0] = 1   
    input.b = 2

    sim.structtest(input, byref(output))

Fortran 代码（struct.f90）：

subroutine structtest(input, output) bind(c, name='structtest')

    USE ISO_C_BINDING
    IMPLICIT NONE

    !define input structure
    TYPE T_INPUT
        !real*8, allocatable :: a(:)
        real(kind=8) :: a(1)
        real(kind=8) :: b
    END TYPE T_INPUT

    !define output structure
    TYPE T_OUTPUT
        real(kind=8) :: a
        real(kind=8), allocatable, dimension (:) :: b
    END TYPE T_OUTPUT


    !define a variable "input" with structure "INPUT"
    TYPE (T_INPUT), value :: input

    TYPE (T_OUTPUT) :: output


    allocate(output%d(1))


    output%b(1) = 5
    PRINT *, output%d(1)

我将 Fortran 编译为 DLL，例如：

ifort -shared -fPIC -static-intel -o struct.so struct.f90

我将 Python 执行为：

python structtest.py

我得到了结果：

*** Error in `python': free(): corrupted unsorted chunks: 0x0000000001f7af00 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fc9027f57e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7fc9027fe37a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fc90280253c]
/lib/x86_64-linux-gnu/libc.so.6(__open_catalog+0xe8)[0x7fc9027b2008]
/lib/x86_64-linux-gnu/libc.so.6(catopen+0x4c)[0x7fc9027b1c2c]
/home/mingster/simGeo.docker/simgeo/lib/struct.so(for__issue_diagnostic+0x11e)[0x7fc90147a77e]
/home/mingster/simGeo.docker/simgeo/lib/struct.so(for_allocate+0x303)[0x7fc90146b9a3]
/home/mingster/simGeo.docker/simgeo/lib/struct.so(structtest+0xae)[0x7fc90146b16e]
/usr/lib/x86_64-linux-gnu/libffi.so.6(ffi_call_unix64+0x4c)[0x7fc901757e40]
/usr/lib/x86_64-linux-gnu/libffi.so.6(ffi_call+0x2eb)[0x7fc9017578ab]
/usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so(_ctypes_callproc+0x48f)[0x7fc9019673df]
/usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so(+0x11d82)[0x7fc90196bd82]
python(PyObject_Call+0x43)[0x4b0c93]
python(PyEval_EvalFrameEx+0x602f)[0x4c9f9f]
python(PyEval_EvalFrameEx+0x5e0f)[0x4c9d7f]
python(PyEval_EvalCodeEx+0x255)[0x4c2705]
python(PyEval_EvalCode+0x19)[0x4c24a9]
python[0x4f19ef]
python(PyRun_FileExFlags+0x82)[0x4ec372]
python(PyRun_SimpleFileExFlags+0x191)[0x4eaaf1]
python(Py_Main+0x6c8)[0x49e208]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fc90279e830]
python(_start+0x29)[0x49da59]
======= Memory map: ========
00400000-006e9000 r-xp 00000000 08:01 525090                             /usr/bin/python2.7
008e8000-008ea000 r--p 002e8000 08:01 525090                             /usr/bin/python2.7
008ea000-00961000 rw-p 002ea000 08:01 525090                             /usr/bin/python2.7
00961000-00984000 rw-p 00000000 00:00 0
01f10000-01ff6000 rw-p 00000000 00:00 0                                  [heap]
7fc8fc000000-7fc8fc021000 rw-p 00000000 00:00 0
7fc8fc021000-7fc900000000 ---p 00000000 00:00 0
7fc901246000-7fc90125c000 r-xp 00000000 08:01 38797837                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fc90125c000-7fc90145b000 ---p 00016000 08:01 38797837                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fc90145b000-7fc90145c000 rw-p 00015000 08:01 38797837                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fc90145c000-7fc901504000 r-xp 00000000 08:01 51643749                   /home/mingster/simGeo.docker/simgeo/lib/struct.so
7fc901504000-7fc901704000 ---p 000a8000 08:01 51643749                   /home/mingster/simGeo.docker/simgeo/lib/struct.so
7fc901704000-7fc90170a000 rw-p 000a8000 08:01 51643749                   /home/mingster/simGeo.docker/simgeo/lib/struct.so
7fc90170a000-7fc901752000 rw-p 00000000 00:00 0
7fc901752000-7fc901759000 r-xp 00000000 08:01 526635                     /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fc901759000-7fc901958000 ---p 00007000 08:01 526635                     /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fc901958000-7fc901959000 r--p 00006000 08:01 526635                     /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fc901959000-7fc90195a000 rw-p 00007000 08:01 526635                     /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fc90195a000-7fc901978000 r-xp 00000000 08:01 30543353                   /usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so
7fc901978000-7fc901b77000 ---p 0001e000 08:01 30543353                   /usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so
7fc901b77000-7fc901b78000 r--p 0001d000 08:01 30543353                   /usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so
7fc901b78000-7fc901b7c000 rw-p 0001e000 08:01 30543353                   /usr/lib/python2.7/lib-dynload/_ctypes.x86_64-linux-gnu.so
7fc901b7c000-7fc901e54000 r--p 00000000 08:01 529135                     /usr/lib/locale/locale-archive
7fc901e54000-7fc901f5c000 r-xp 00000000 08:01 38797852                   /lib/x86_64-linux-gnu/libm-2.23.so
7fc901f5c000-7fc90215b000 ---p 00108000 08:01 38797852                   /lib/x86_64-linux-gnu/libm-2.23.so
7fc90215b000-7fc90215c000 r--p 00107000 08:01 38797852                   /lib/x86_64-linux-gnu/libm-2.23.so
7fc90215c000-7fc90215d000 rw-p 00108000 08:01 38797852                   /lib/x86_64-linux-gnu/libm-2.23.so
7fc90215d000-7fc902176000 r-xp 00000000 08:01 38797934                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7fc902176000-7fc902375000 ---p 00019000 08:01 38797934                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7fc902375000-7fc902376000 r--p 00018000 08:01 38797934                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7fc902376000-7fc902377000 rw-p 00019000 08:01 38797934                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7fc902377000-7fc902379000 r-xp 00000000 08:01 38797927                   /lib/x86_64-linux-gnu/libutil-2.23.so
7fc902379000-7fc902578000 ---p 00002000 08:01 38797927                   /lib/x86_64-linux-gnu/libutil-2.23.so
7fc902578000-7fc902579000 r--p 00001000 08:01 38797927                   /lib/x86_64-linux-gnu/libutil-2.23.so
7fc902579000-7fc90257a000 rw-p 00002000 08:01 38797927                   /lib/x86_64-linux-gnu/libutil-2.23.so
7fc90257a000-7fc90257d000 r-xp 00000000 08:01 38797825                   /lib/x86_64-linux-gnu/libdl-2.23.so
7fc90257d000-7fc90277c000 ---p 00003000 08:01 38797825                   /lib/x86_64-linux-gnu/libdl-2.23.so
7fc90277c000-7fc90277d000 r--p 00002000 08:01 38797825                   /lib/x86_64-linux-gnu/libdl-2.23.so
7fc90277d000-7fc90277e000 rw-p 00003000 08:01 38797825                   /lib/x86_64-linux-gnu/libdl-2.23.so
7fc90277e000-7fc90293e000 r-xp 00000000 08:01 38797811                   /lib/x86_64-linux-gnu/libc-2.23.so
7fc90293e000-7fc902b3e000 ---p 001c0000 08:01 38797811                   /lib/x86_64-linux-gnu/libc-2.23.so
7fc902b3e000-7fc902b42000 r--p 001c0000 08:01 38797811                   /lib/x86_64-linux-gnu/libc-2.23.so
7fc902b42000-7fc902b44000 rw-p 001c4000 08:01 38797811                   /lib/x86_64-linux-gnu/libc-2.23.so
7fc902b44000-7fc902b48000 rw-p 00000000 00:00 0
7fc902b48000-7fc902b60000 r-xp 00000000 08:01 38797898                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fc902b60000-7fc902d5f000 ---p 00018000 08:01 38797898                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fc902d5f000-7fc902d60000 r--p 00017000 08:01 38797898                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fc902d60000-7fc902d61000 rw-p 00018000 08:01 38797898                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fc902d61000-7fc902d65000 rw-p 00000000 00:00 0
7fc902d65000-7fc902d8b000 r-xp 00000000 08:01 38797787                   /lib/x86_64-linux-gnu/ld-2.23.so
7fc902dc5000-7fc902f7b000 rw-p 00000000 00:00 0
7fc902f86000-7fc902f87000 rw-p 00000000 00:00 0
7fc902f87000-7fc902f88000 rwxp 00000000 00:00 0
7fc902f88000-7fc902f8a000 rw-p 00000000 00:00 0
7fc902f8a000-7fc902f8b000 r--p 00025000 08:01 38797787                   /lib/x86_64-linux-gnu/ld-2.23.so
7fc902f8b000-7fc902f8c000 rw-p 00026000 08:01 38797787                   /lib/x86_64-linux-gnu/ld-2.23.so
7fc902f8c000-7fc902f8d000 rw-p 00000000 00:00 0
7ffc38bde000-7ffc38bff000 rw-p 00000000 00:00 0                          [stack]
7ffc38cd8000-7ffc38cda000 r--p 00000000 00:00 0                          [vvar]
7ffc38cda000-7ffc38cdc000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

Answer 1

所谓的可分配组件描述符在内存中的布局是特定于 Fortran 处理器的。对于可分配的数组组件，它总是不仅仅是一个内存地址。有关描述符的详细信息，您需要查阅 Fortran 处理器的文档。依赖于描述符布局的代码本质上是特定于处理器的。

当前版本的英特尔编译器的相关文档可以在标题为Handling Fortran Array Descriptors 的部分中找到。

Fortran 2018 的当前草案为与可分配的虚拟参数进行互操作提供了额外的工具，但仍有特定于平台的特性。

（在显示的代码中，您使用了内部模块 ISO_C_BINDING，但代码似乎没有从中引用任何内容...）

Answer 2

谢谢大家，

以下是 Python 将多维数组传递给 Fortran 的工作示例

python 代码：

from ctypes import *
import ctypes
import sys
import os
import numpy as np

sim = cdll.LoadLibrary(os.path.dirname(os.path.abspath(__file__)) + "/lib/struct.so")


class Param( Structure ):
    pass

class Result( Structure ):
    pass

def main():

    x = 2
    y = 3
    z = 4
    Param._fields_ = [( "len_x", c_int ),
                ( "len_y", c_int ),
                ( "len_z", c_int ),
                ( "c", POINTER(c_double)),
                ( "d", POINTER(c_double * x)),
                ( "e", POINTER(c_double * x * y))]

    Result._fields_ = [( "len_x", c_int ),
                ( "len_y", c_int ),
                ( "len_z", c_int ),
                ( "f", POINTER(c_double)),
                ( "g", POINTER(c_double * x)),
                ( "h", POINTER(c_double * x * y))]

    param = Param() 
    result = Result()

    cc = (c_double * x)()
    dd = ( (c_double * x) * y )()
    ee = ( ( ( (c_double * x) * y ) * z ) )()

    #[x]    
    cc[0] = 10.0
    cc[1] = 20.0

    #[y][x]
    dd[0][0] = 10.0
    dd[1][0] = 20.0
    dd[2][0] = 30.0
    dd[0][1] = 40.0
    dd[1][1] = 50.0
    dd[2][1] = 60.0

    #[z][y][x]
    ee[0][0][0] = 1.0
    ee[1][0][0] = 2.0
    ee[2][0][0] = 3.0
    ee[0][1][0] = 4.0
    ee[1][1][0] = 5.0
    ee[2][1][0] = 6.0


    param.len_x = x
    param.len_y = y
    param.len_z = z

    param.c = cc
    param.d = dd
    param.e = ee

    sim.structtest(byref(param), byref(result))

    #[x]
    print "1D"
    print result.f[0]
    print result.f[1]

    #[y][x]
    print "2D"
    print result.g[0][0] 
    print result.g[1][0]
    print result.g[2][0] 
    print result.g[0][1] 
    print result.g[1][1] 
    print result.g[2][1] 

    #[z][y][x]
    print "3D"
    print result.h[0][0][0]
    print result.h[1][0][0]
    print result.h[2][0][0]
    print result.h[0][1][0]
    print result.h[1][1][0]
    print result.h[2][1][0]



if __name__ == "__main__":
    result = main() 

fortran 代码：

subroutine structtest(param, result) bind(c, name="structtest")

    use, intrinsic :: ISO_C_BINDING
    implicit none

    type, BIND(C) :: args
        integer (C_INT) :: len_x
        integer (C_INT) :: len_y
        integer (C_INT) :: len_z
        type (C_PTR) :: c
        type (C_PTR) :: d
        type (C_PTR) :: e
    end type args

    type, BIND(C) :: output
        integer (C_INT) :: len_x
        integer (C_INT) :: len_y
        integer (C_INT) :: len_z
        type (C_PTR) :: f
        type (C_PTR) :: g
        type (C_PTR) :: h
    end type output    

    type (args), intent(in):: param   
    type (output), intent(out):: result   

    real (C_DOUBLE), pointer :: arg_array_c(:)
    real (C_DOUBLE), pointer :: arg_array_d(:,:)
    real (C_DOUBLE), pointer :: arg_array_e(:,:,:)
    real (C_DOUBLE), ALLOCATABLE, target, save :: result_array_f(:)
    real (C_DOUBLE), ALLOCATABLE, target, save :: result_array_g(:,:)
    real (C_DOUBLE), ALLOCATABLE, target, save :: result_array_h(:,:,:)

    ! Associate c_array with an array allocated in C
    call C_F_POINTER (param%c, arg_array_c, [param%len_x] )
    call C_F_POINTER (param%d, arg_array_d, [param%len_x,param%len_y] )
    call C_F_POINTER (param%e, arg_array_e, [param%len_x,param%len_y,param%len_z] )

    ![x]
    print *,"1D"
    print *,arg_array_c(1)
    print *,arg_array_c(2)

    ![x][y]
    print *,"2D"
    print *,arg_array_d(1,1)
    print *,arg_array_d(1,2)
    print *,arg_array_d(1,3)
    print *,arg_array_d(2,1)
    print *,arg_array_d(2,2)
    print *,arg_array_d(2,3)

    ![x][y][z]
    print *,"3D"
    print *,arg_array_e(1,1,1)
    print *,arg_array_e(1,1,2)
    print *,arg_array_e(1,1,3)
    print *,arg_array_e(1,2,1)
    print *,arg_array_e(1,2,2)
    print *,arg_array_e(1,2,3)

    ! Allocate an array and make it available in C

    result%len_x = param%len_x
    result%len_y = param%len_y
    result%len_z = param%len_z

    ALLOCATE (result_array_f(result%len_x))
    ALLOCATE (result_array_g(result%len_x, result%len_y))
    ALLOCATE (result_array_h(result%len_x, result%len_y, result%len_z))


    result%f = c_loc(result_array_f)
    result%g = c_loc(result_array_g)
    result%h = c_loc(result_array_h)

    ![x]
    result_array_f(1) = arg_array_c(1)
    result_array_f(2) = arg_array_c(2)

    ![x][y]
    result_array_g(1,1) = arg_array_d(1,1)
    result_array_g(1,2) = arg_array_d(1,2)
    result_array_g(1,3) = arg_array_d(1,3)
    result_array_g(2,1) = arg_array_d(2,1)
    result_array_g(2,2) = arg_array_d(2,2)
    result_array_g(2,3) = arg_array_d(2,3)        

    ![x][y][z]
    result_array_h(1,1,1) = arg_array_e(1,1,1)
    result_array_h(1,1,2) = arg_array_e(1,1,2)
    result_array_h(1,1,3) = arg_array_e(1,1,3)
    result_array_h(1,2,1) = arg_array_e(1,2,1)
    result_array_h(1,2,2) = arg_array_e(1,2,2)
    result_array_h(1,2,3) = arg_array_e(1,2,3)

end

输出：

 1D
   10.0000000000000
   20.0000000000000
 2D
   10.0000000000000
   20.0000000000000
   30.0000000000000
   40.0000000000000
   50.0000000000000
   60.0000000000000
 3D
   1.00000000000000
   2.00000000000000
   3.00000000000000
   4.00000000000000
   5.00000000000000
   6.00000000000000
1D
10.0
20.0
2D
10.0
20.0
30.0
40.0
50.0
60.0
3D
1.0
2.0
3.0
4.0
5.0
6.0