[SciPy-User] scipy+lapack array copy

Skipper Seabold jsseabold@gmail....
Mon Mar 8 12:10:32 CST 2010


On Mon, Mar 8, 2010 at 12:47 PM, Paul Anton Letnes
<paul.anton.letnes@gmail.com> wrote:
> Hi everyone.
>
> I have a numerical project where I link a fortran module to python using f2py. The fortran module basically sets up the left hand side coefficient matrix of a linear equation system. The right hand side is small, so I set that up in python. So far, everything works great.
>
> Now, when I call scipy-lapack, I am using:
> from scipy.linalg.lapack import flapack as lapack
> lu, piv, x, info = lapack.zgesv(A, b)
> A is created in the fortran part of the program. b is created from numpy.zeros(). Both report as F_CONTIGUOUS by printing A.flags and b.flags.
>
> The problem is that I'd like A to be large (>1GB), but the lapack wrapper (or lapack itself?) copies the array, doubling the memory use. Aside from being unnecessary, this also reduces the practical problem size I can solve by a factor 2, which of course is very annoying.
>
> How can I get around this problem?
>

It looks like zgesv allows you to set overwrite_a = 1.  If this isn't
what you want, there might be another way to proceed.

In [5]: from scipy.linalg.lapack import flapack as lapack

In [6]: lapack.zgesv?
Type:           fortran
String Form:    <fortran object at 0x7fccc4f6af08>
Namespace:      Interactive
Docstring:
    zgesv - Function signature:
      lu,piv,x,info = zgesv(a,b,[overwrite_a,overwrite_b])
    Required arguments:
      a : input rank-2 array('D') with bounds (n,n)
      b : input rank-2 array('D') with bounds (n,nrhs)
    Optional arguments:
      overwrite_a := 0 input int
      overwrite_b := 0 input int
    Return objects:
      lu : rank-2 array('D') with bounds (n,n) and a storage
      piv : rank-1 array('i') with bounds (n)
      x : rank-2 array('D') with bounds (n,nrhs) and b storage
      info : int


Skipper


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