[R-sig-hpc] serialize() slow

[Paul Johnson]

On Sat, Aug 21, 2010 at 2:16 PM, Fernando Saldanha <fsaldan1 at gmail.com> wrote:
> In this post:
>
> http://www.mail-archive.com/r-devel@r-project.org/msg13248.html
>
> Henrik Bengtsson observes that the R function serialize() can run very
> slowly when the argument connection is null and provides a function
> serialize2() that runs much faster. The post is dated 7/24/2008.
>
> Some code I wrote using package Rmpi was running slowly and I found
> out the bottleneck was exactly the function serialize(), which is
> called by some functions in Rmpi.
>
> So I inserted the command
>
> serialize <- serialize2
>
> in my code and there was a dramatic acceleration of the relevant
> portions of the program.
>

If serialize2 fixes it for you, doesn't that answer your own question?

You ask why the different computers may perform differently. Can I ask
if there is any chance you have been fiddling around with alternative
BLAS?

I see a huge horrible Rmpi slowdown when GOTOBLAS2 is installed with
threads allowed > 1.

I had not heard of the serialize/serialize2 thing you mention, but I'm
interested to try it to see what effect it has. I will let you know if
I see any difference.

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas