>>>>> "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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