From simon.urbanek at r-project.org  Sun Sep  6 04:49:25 2009
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Sat, 5 Sep 2009 22:49:25 -0400
Subject: [Rd] Running two R instances at the same time
In-Reply-To: <b2050ab90909051131i15b413bci18300426406cbcea@mail.gmail.com>
References: <b2050ab90909051131i15b413bci18300426406cbcea@mail.gmail.com>
Message-ID: <45D572B5-E71D-4398-989D-BAD3071295B2@r-project.org>


On Sep 5, 2009, at 2:31 PM, Peter Juhasz wrote:

> Reposting from R-help:
>
> Dear R experts,
>
> please excuse me for writing to the mailing list without subscribing.
> I have a somewhat urgent problem that relates to R.
>
> I have to process large amounts of data with R - I'm in an
> international collaboration and the data processing protocol is fixed,
> that is a specific set of R commands has to be used.
>
> I wrote a perl program that manages creation of data subsets from my
> database and feeds these subsets to an R process via pipes.
>
> This worked all right, however, I wanted to speed things up by
> exploiting the fact that I have a dual-core machine. So I rewrote my
> perl driver program to use two threads, each starting its own R
> instance, getting data off a queue and feeding it to its R process.
>
> This also worked, except that I noticed something very peculiar: the
> processing time was almost exactly the same for both cases. I did some
> tests to look at this, and it seems that R needs twice the time to do
> the exact same thing if there are two instances of it running.
>
> I don't understand how is this possible. Maybe there is an issue of
> thread-safety with the R backend, meaning that the two R *interpreter*
> instances are talking to the same backend that's capable of processing
> only one thing at a time?
>

No, are least not in R itself. Clearly there are many explanations  
(you are accessing the data in some way that is not parallelizable, R  
is already using both cores, perl does something funny that you are  
not anticipating ...), but I see too little evidence. The perl code to  
too much of a mess to really tell - why don't you just start two of  
your jobs manually in the background and clock them? For starters use  
simply
time .. &

In perl I wouldn't use threads, it should be as simple as

#!/usr/bin/perl

sub run {
     $children++;
     if (fork() == 0) {
	print "job $children started\n";
	system $_[0];
	print "job $children done\n";
	exit 0;
     }
}

run "sleep 1";
run "sleep 2";
#etc.

while ($children) { wait; $children--; }
print "Jobs done.\n";

Fino:sandbox$ ./tt
job 1 started
job 2 started
job 1 done
job 2 done
Jobs done.

(replace sleep by your R invocation ... use your imagination to  
improve it since it's admittedly very crude but helps to track it  
down ...)

Cheers,
Simon


> Technical details: OS was Ubuntu 9.04 running on a Core2Dou E7300, and
> the R version used was the default one from the Ubuntu repository.
>
> Please see http://www.perlmonks.org/?node_id=792460 for an extended
> discussion of the problem, and especially
> http://www.perlmonks.org/?node_id=793506 for excerpts of output and
> actual code.
>
> I have received several suggestions about R packages that would enable
> parallel processing in some way or other, and I'm thankful for those.
>
> However, at this point I'm interested in having two completely
> unrelated R processes that run simultaneously, not in parallel
> processing from within R.
> I have to admit that I'm an absolute beginner when it comes to R and
> this project will be finished before I could learn everything I'd need
> for a pure R solution. I'm familiar with perl, however, so I'd like to
> stick to that.
>
> Thanks for your answers in advance and please excuse me if this causes
> too much noise:
>
> P?ter Juh?sz
> physicist
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



[Rd] Running two R instances at the same time
Simon Urbanek