[SciPy-dev] Python/Fortran multi-dimensional array issues
Pearu Peterson
pearu at cens.ioc.ee
Mon Jan 14 11:10:28 EST 2002
Hi!
In this long posting I will describe a new idea how to overcome with the
difficulties caused by different storage-orders in C and Fortran
multi-dimensional arrays.
I have send this message also to scipy developers list because I think the
issue here is also very relevant in SciPy project. It should
improve the quality of the lapack and blas wrappers and reduce lots of
code there.
I'll greately appreciate if you could review what follows. Comments and
criticism are most welcome. Of cource, real code contributions are most
welcome ;)
Regards,
Pearu
--------------------------------------------------------------
_____________________________________________________________
/ Proposed internal structure for f2py generated extension \
< modules regarding the issues with different storage-orders >
\ of multi-dimensional matrices in Fortran and C. /
=============================================================
Author: Pearu Peterson
Date: 14 January, 2001
Definitions:
============
In the following I will use the following definitions:
1) A matrix is a mathematical object that represents a collection of
objects (elements), usually visualized in a table form, and one can
define a set of various (algebraic,etc) operations for matrices.
One can think of a matrix as a defintion of a certain mapping:
(i) |--> A(i)
where i belongs to the set of indices (an index itself can be a
sequence of objects, for example, a sequence of integers) and A(i)
is an element from a specified set, for example, a set of fruits.
Symbol A then denotes a matrix of fruits.
2) An array is a storage object that represents a collection of
objects stored in a certain systematic way, for example, as an
ordered sequence of array elements in computer memory.
In order to manipulate matrices using computers, one must store matrix
elements in computer memory. In the following, I will assume that the
elements of a matrix are stored as an array. There is no unique way in
which order one should save matrix elements in the array. However, in
C and Fortran programming languages, two, unfortunately different,
conventions are used.
Aim:
====
The purpose of this writing is to work out an interface for Python
language so that C and Fortran routines can be called without
bothering about how multi-dimensional matrices are stored in memory.
For example, accessing a matrix element A[i,j] in Python will be
equivalent to accessing the same matrix in C, using A[i][j], or in
Fortran, using A(i,j).
External conditions:
====================
In C programming language, it is custom to think that matrices are
stored in the so-called row-major order, that is, a matrix is stored
row by row, each row is as a contiguous array in computer memory.
In Fortran programming language, matrices are stored in the
column-major order: each column is a contiguous array in computer
memory.
In Python programming language, matrices can be stored using Python
Numeric array() function that uses internally C approach, that is,
elements of matrices are stored in row-major order. For example,
A = array([[1,2,3],[4,5,6]]) represents a 2-by-3 matrix
/ 1 2 3 \
| |
\ 4 5 6 /
and its elements are stored in computer memory as the following array:
1 2 3 4 5 6
The same matrix, if used in Fortran, would be stored in computer
memory as the following array:
1 4 2 5 3 6
Problem and solution:
=====================
A problem arises if one wants to use the same matrix both in C and in
Fortran functions. Then the difference in storage order of a matrix
elements must be taken into account. This technical detail can be very
confusing even for an experienced programmer. This is because when
passing a matrix to a Fortran subroutine, you must (mentally or
programmically) transpose the matrix and when the subroutine returns,
you must transpose it back.
As will be discussed below, there is a way to overcome these
difficulties in Python by creating an interface between Python and
Fortran code layers that takes care of this transition internally. So
that if you will read the manual pages of the Fortran codes, you
need not to think about how matrices are actually stored, the storage
order will be the same, seemingly.
Python / C / Fortran interface:
===============================
The interface between Python and Fortran codes will use the following
Python Numeric feature: transposing a Numeric array does not involve
copying of its data but just permuting the dimensions and strides of
the array (the so-called lazy transpose).
However, when passing a Numeric array data pointer to Fortran or C
function, the data must be contiguous in memory. If it is not, then
data is rearranged inplace. I don't think that it can be avoided.
This is certainly a penalty hit to performance. However, one can
easily avoid it by creating a Numeric array with the right storage
order, so that after transposing, the array data will be contiguous in
memory and the data pointer can safely passed on to the Fortran
subroutine. This lazy-transpose operation will be done within the
interface and users need not to bother about this detail anymore (that
is, after they initialize Numeric array with matrix elements using the
proper order. Of course, the proper order depends on the target
function: C or Fortran). The interface should be smart enough to
minimize the need of real-transpose operations and the need to
additional memory storage as well.
Statement of the problem:
=========================
Consider a M-by-N matrix A of integers, where M and N are the number A
rows and columns, respectively.
In Fortran language, the storing array of this matrix can be defined
as follows:
integer A(M,N)
in C:
int A[M][N];
and in Python:
A = Numeric.zeros((M,N),'i')
Consider also the corresponding Fortran and C functions that
use matrix arguments:
Fortran:
subroutine FUN(A,M,N)
integer A(M,N)
...
end
C:
void cun(int *a,int m,int n) {
...
}
and the corresponding Python interface signatures:
def py_fun(a):
...
def py_cun(a):
...
Main goal:
==========
Our goal is to generate Python C/API functions py_fun and py_cun such
that their usage in Python would be identical. The cruical part of
their implementation is in functions that take a PyObject and
return a PyArrayObject such that it is contiguous and its data pointer
is suitable for passing on to the arguments of C or Fortran functions.
The prototypes of these functions are:
PyArrayObject* fortran_array_from_pyobj(
int typecode,
int *dims,
int rank,
int intent,
PyObject *obj);
and
PyArrayObject* c_array_from_pyobj(
int typecode,
int *dims,
int rank,
int intent,
PyObject *obj);
when wrapping Fortran and C functions, respectively.
Pseudo-code for fortran_array_from_pyobj:
=========================================
if type(obj) is ArrayType:
#raise not check(len(ravel(obj)) >= dims[0]*dims[1]*...*dims[rank-1])
if obj.typecode is typecode:
if is_contiguous(obj):
transpose_data_inplace(obj) # real-transpose
set_transpose_strides(obj) # lazy-transpose
Py_INCREF(obj);
return obj
set_transpose_strides(obj)
if is_contiguous(obj):
set_transpose_strides(obj)
Py_INCREF(obj);
return obj
else:
tmp_obj = PyArray_ContiguousFromObject(obj,typecode,0,0)
swap_datapointer_and_typeinfo(obj,tmp_obj)
Py_DECREF(tmp_obj);
set_transpose_strides(obj)
Py_INCREF(obj);
return obj
else:
tmp_obj = PyArray_FromDims(rank,dims,typecode)
set_transpose_strides(tmp_obj)
if intent in [in,inout]:
copy_ND_array(obj,tmp_obj)
swap_datapointer_and_typeinfo(obj,tmp_obj)
Py_DECREF(tmp_obj);
Py_INCREF(obj);
return obj
elif obj is None: # happens when only intent is 'hide'
tmp_obj = PyArray_FromDims(rank,dims,typecode)
if intent is out:
set_transpose_strides(tmp_obj)
# otherwise tmp_obj->data is used as a work array
Py_INCREF(tmp_obj)
return tmp_obj
else:
tmp_obj = PyArray_ContiguousFromObject(obj,typecode,0,0)
#raise not check(len(ravel(obj)) >= dims[0]*dims[1]*...*dims[rank-1])
set_transpose_strides(tmp_obj)
transpose_data_inplace(tmp_obj)
Py_INCREF(tmp_obj)
return tmp_obj
Notes:
1) CPU expensive tasks are in transpose_data_inplace and
copy_ND_array, PyArray_ContiguousFromObject.
2) Memory expensive tasks are in PyArray_FromDims,
PyArray_ContiguousFromObject
3) Side-effects are expected when set_transpose_strides and
transpose_data_inplace are used. For example:
>>> a = Numeric([[1,2,3],[4,5,6]],'d')
>>> a.is_contiguous()
1
>>> py_fun(a)
>>> a.typecode()
'i'
>>> a.is_contiguous()
0
>>> transpose(a).is_contiguous()
1
Pseudo-code for c_array_from_pyobj:
===================================
if type(obj) is ArrayType:
#raise not check(len(ravel(obj)) >= dims[0]*dims[1]*...*dims[rank-1])
if obj.typecode is typecode:
if is_contiguous(obj):
Py_INCREF(obj);
return obj
else:
tmp_obj = PyArray_ContiguousFromObject(obj,typecode,0,0)
swap_datapointer_and_typeinfo(obj,tmp_obj)
Py_DECREF(tmp_obj);
Py_INCREF(obj);
return obj
else:
tmp_obj = PyArray_FromDims(rank,dims,typecode)
if intent in [in,inout]:
copy_ND_array(obj,tmp_obj)
swap_datapointer_and_typeinfo(obj,tmp_obj)
Py_DECREF(tmp_obj);
Py_INCREF(obj);
return obj
elif obj is None: # happens when only intent is 'hide'
tmp_obj = PyArray_FromDims(rank,dims,typecode)
Py_INCREF(tmp_obj)
return tmp_obj
else:
tmp_obj = PyArray_ContiguousFromObject(obj,typecode,0,0)
#raise not check(len(ravel(obj)) >= dims[0]*dims[1]*...*dims[rank-1])
Py_INCREF(tmp_obj)
return tmp_obj
14 January, 2002
Pearu Peterson <pearu at cens.ioc.ee>
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