[Matrix-SIG] Proclamation: column-wise arrays (fwd)
Paul F. Dubois
Tue, 1 Feb 2000 08:24:29 -0800
I think there were two reasons for the sparse response. First, a lot of us
were at IPC8. Second, I don't think anyone has any real problems with this
idea except the worry that problems may arise when you try to implement it.
As various people have said, the existing source is extremely hard to work
with. Introducing such an extensive change will not be any fun. If you were
going to try it I would urge that we set you up as a developer on
SourceForge and that you do it on a branch. CVS is not real good at
branching but this is a case where it would be called for because it would
take a long time from when you started, and we wouldn't know if the
performance, etc. would be ok until the end. It would take a lot of testing
to be sure nothing was broken.
The situation wrt using Fortran is, however, not completely as bleak as you
picture it. For example, Pyfort produces an interface in which an array from
Python is transposed on input but the output is not actually transposed back
unless required by subsequent usage. In particular, if the result is passed
into more Fortran the transposes cancel themselves without data movement.
Also, data space for temporaries is not transposed. I don't know what f2py
does, but at least in principle this much is possible.
From: email@example.com [mailto:firstname.lastname@example.org]On
Behalf Of Pearu Peterson
Sent: Tuesday, February 01, 2000 12:34 AM
Subject: [Matrix-SIG] Proclamation: column-wise arrays (fwd)
OK, this is my second attempt for the subject as there was little response
from the numpy-discussion list.
I would like to hear from the experts why it 'is not possible to
implement' the column-wise arrays or why it 'should not be implemented' in
Python Numeric. If the reasons are other than 'it takes too much work'
then I will not bother you again and will not try to do that myself.
---------- Forwarded message ----------
Date: Wed, 26 Jan 2000 19:00:31 +0200 (EET)
From: Pearu Peterson <email@example.com>
Cc: Paul F. Dubois <firstname.lastname@example.org>,
Travis Oliphant <Oliphant.Travis@mayo.edu>
Subject: [Numpy-discussion] Proclamation: column-wise arrays
Using Fortran routines from Python C/API is "tricky" when
multi-dimensional arrays are passed in.
Arrays in Fortran are stored in column-wise order while arrays in
C are stored in row-wise order.
1) Create a new C array; copy the data from the old one in
column-wise order; pass the new array to fortran; copy changed array back
to old one in row-wise order; deallocate the array.
2) Change the storage order of an array in place: element-wise
swapping; pass the array to fortran; change the storage order back with
Why standard solutions are not good?
1) Additional memory allocation, that is problem for large arrays;
Element-wise copying is time consuming (2 times).
2) It is good as no extra memory is needed but element-wise
swapping (2 times) is approx. equivalent with the element-wise copying (4
Introduce a column-wise array to Numeric Python where data is
stored in column-wise order that can be used specifically for fortran
1) Introduce a new flag `row_order'to PyArrayObject structure:
row_order == 1 -> the data is stored in row-wise order (default, as it is
row_order == 0 -> the data is stored in column-wise order
Note that now the concept of contiguousness depends on this flag.
2) Introduce new array "constructors" such as PyArray_CW_FromDims,
PyArray_CW_CopyFromObject, PyArray_CW_FromObject, etc. that all return
arrays with row_order=0 and data stored in column-wise order (that is in
case of contiguous results, otherwise strides feature is employd).
3) In order to operations between arrays (possibly with different
storage order) would work correctly, many internal functions of NumPy
C/API need to be modifyied.
4) anything else?
What is the good of this?
1) The fact is that there is a large number of very good scietific
tools freely available written in Fortran (Netlib, for instance). And I
don't mean only Fortran 77 codes but also Fortran 90/95 codes.
2) Having Numeric Python arrays with data stored in column-wise
order, calling Fortran routines from Python becomes really efficient and
3) There should be little performance hit if, say, two
arrays with different storage order are multiplied (compared to the
operations between non-contiguous arrays in the current implementation).
4) I don't see any reason why older C/API modules would broke
because of this change if it is carried out carefully enough. So,
back-ward compability should be there.
5) anything else?
What are against of this?
1) Lots of work but with current experience it should not be a
2) The size of the code will grow.
3) I suppose that most people using Numerical Python will not care
of calling Fortran routines from Python. Possible reasons: too "tricky" or
no need. In the first case, the answer is that there are tools such as
PyFort, f2py that solve this problem. In the later case, there is no
4) anything else?
I understand that my proposal is quite radical but taking into account
that we want to use Python for many years to come, the use would be more
pleasing if one cause of (constant) confusion would be less during this
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