[Numpy-discussion] How to speed up this function?

Brent Pedersen bpederse at gmail.com
Tue Dec 5 12:30:41 CST 2006


it looks like you could use weave.blitz() without much change to your code.
or weave.inline() if needed. see this page:
http://scipy.org/PerformancePython

On 12/3/06, fsenkel at verizon.net <fsenkel at verizon.net> wrote:
>
> Hello,
>
> I'm taking a CFD class, one of the codes I wrote runs very slow. When I
> look at hotshot is says the function below is the problem. Since this is an
> explicit step, the for loops are only traversed once, so I think it's caused
> by memory usage, but I'm not sure if it's the local variables or the loop? I
> can vectorize the inner loop,  would declaring the data structures in the
> calling routine and passing them in be a better idea than using local
> storage?
>
> I'm new at python and numpy, I need to look at how to get profiling
> information for the lines within a function.
>
>
> Thank you,
>
> Frank
>
>
> PS
> I tried to post this via google groups, but it didn't seem to go through,
> sorry if it ends up as multiple postings
>
>
> def findw(wnext,wprior,phiprior,uprior,vprior):
>    #format here is x[i,j] where i's are rows, j's columns, use flipud() to
> get the
>    #print out consistent with the spacial up-down directions
>
>    #assign local names that are more
>    #inline with the class notation
>    w = wprior
>    phi = phiprior
>    u = uprior
>    v = vprior
>
>
>    #three of the BC are known so just set them
>    #symetry plane
>    wnext[0,0:gcols] = 0.0
>
>    #upper wall
>    wnext[gN,0:gcols] = 2.0/gdy**2 * (phi[gN,0:gcols] - phi[gN-1,0:gcols])
>
>    #inlet, off the walls
>    wnext[1:grows-1,0] = 0.0
>
>
>    upos = where(u>0)
>    vpos = where(v>0)
>
>    Sx = ones_like(u)
>    Sx[upos] = 0.0
>
>    Sy = ones_like(v)
>    Sy[vpos] = 0.0
>
>    uw = u*w
>    vw = v*w
>
>    #interior nodes
>    for j in range(1,gasizej-1):
>        for i in range(1,gasizei-1):
>
>            wnext[i,j] =( w[i,j] + gnu*gdt/gdx**2 * (w[i,j-1] - 2.0*w[i,j]
> + w[i,j+1]) +
>                          gnu*gdt/gdy**2 * (w[i-1,j] - 2.0*w[i,j] +
> w[i+1,j]) -
>                          (1.0 - Sx[i,j]) * gdt/gdx * (uw[i,j] - uw[i,j-1])
> -
>                          Sx[i,j] * gdt/gdx * (uw[i,j+1] - uw[i,j]) -
>                          (1.0 - Sy[i,j]) * gdt/gdy * (vw[i,j] - vw[i-1,j])
> -
>                          Sy[i,j] * gdt/gdy * (vw[i+1,j] - vw[i,j]) )
>
> ##        print "***wnext****"
> ##        print "i: ", i, "j: ", j, "wnext[i,j]: ", wnext[i,j]
>
>    #final BC at outlet, off walls
>    wnext[1:grows-1,gM] = wnext[1:grows-1,gM-1]
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