[R-sig-hpc] serialize() slow

Martin Morgan mtmorgan at fhcrc.org
Sat Aug 21 22:39:18 CEST 2010

On 08/21/2010 12:16 PM, Fernando Saldanha 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.

This has likely been fixed in R-devel



> 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.
> I have run the same code on two other computers and it did not run
> slowly. To be more specific:
> In all three computers I am running R 2.11.1.
> All three computers are made by HP.
> One dual core desktop PC (with no hyperthreading) running  Windows XP
> 32-bit and one Intel i5 notebook (dual core with hyperthreading)
> running Windows 7 64-bit are not slowed down by serialize().
> One dual core notebook (no hyperthreading) running Windows 7 64-bit
> executes serialize() very slowly.
> I used the function memory.limit() to increase memory allocation but
> that did not make any difference.
> Of course substituting serialize2 for serialize() is not an ideal
> situation, among other reasons because serialize2() needlessly writes
> to and reads from a connection (a temporary file).
> Does anyone have insights on what is going on and maybe better ways to
> deal with the issue?
> Thanks.
> Fernando Saldanha
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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