[Fwd: Re: [R] Multithreading]

[A.J. Rossini]

>>>>> "timothy" == Timothy H Keitt <tklistaddr at keittlab.bio.sunysb.edu> writes:

    timothy> On Tue, 2002-04-16 at 11:22, ripley at stats.ox.ac.uk wrote:
    >> Careful!  They are running (arbitrary) R code, and Luke's caveats apply.
    >> Internally lapply does an eval(), and we can't have more than one of
    >> those running at once without all the perils of user R-level threads,
    >> as I understand it.

    timothy> Ah, yes, I see the problem there. Sounds like the rpvm version might be
    timothy> interesting though. In practice, most of the problems I work on are of
    timothy> the 'embarrassingly parallel' variety -- running the same code with
    timothy> different parameters -- and wouldn't really benefit much from low-level
    timothy> parallelism. For those, I've found that having a process query a
    timothy> database for parameter sets, compute a result and then write the result
    timothy> back to the database before proceeding to the next parameter set works
    timothy> well. You get automatic load balancing and can query the database for
    timothy> intermediate results. Maybe I'll package that up for general consumption
    timothy> at some point.

While RPVM is annoying to setup, I should mention that features that
we are working for "Release Soon"(tm), are
1. use of the SPRNG library, as a separate package (this is a parallel
   RNG, which gives reasonable results and is designed for parallel
   situations).  This might be useful in other contexts as well
2. simple examples for bootstrap.

I should note that someone (to remain nameless) has offered to provide
a means to serialize R objects sensibly.  We'll see when that happens;
it's simple provided that you program carefully.  However, I'd like a
variant which is simple even when you are a programming klutz.

I'd also like to construct simple examples for simple global
optimization as well as MCMC, but I don't see doing these personally
in the near-ish future.

In addition, note that PVM jobs migrate on MOSIX/OpenMOSIX.  I've
preliminary evidence that this is true for RPVM jobs, as well (since
Python is problematic under MOSIX, I'm not going to claim more than
preliminary evidence). 

best,
-tony

-- 
A.J. Rossini				Rsrch. Asst. Prof. of Biostatistics
U. of Washington Biostatistics		rossini at u.washington.edu	
FHCRC/SCHARP/HIV Vaccine Trials Net	rossini at scharp.org
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