[Fwd: Re: [R] Multithreading]
rossini at blindglobe.net
Tue Apr 16 23:21:09 CEST 2002
>>>>> "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
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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