[R] Working with R in a multi-processor machine.

[Sean Davis]

On 1/10/06 11:41 AM, "Seth Falcon" <sfalcon at fhcrc.org> wrote:

> On 10 Jan 2006, aitor_doctorado at yahoo.es wrote:
> 
>> Hi everyone!!
>> 
>> This is my first message to the list, so I hope not to disturb
>> anyone if the subject of my message has been already treated.
>> 
>> The question is that I have a tool, a GUI made with Java, connected
>> to R using Rserve, and I'd like to get R and Rserve in a
>> multi-processor machine.  Now, when I'm going to start the migration
>> I wonder whether R is prepared, 'itself' to optimize the use of
>> multiple processors or if I should change the code so that it could
>> be a real multi-processor tool.
>> 
>> In other words... Will the R code adapt itself to the new machine
>> (Unix with al least 4 processors)? Or shall I change the code to
>> have multiple real threads and transform the algorithms into
>> parallel computing strategies?
> 
> R is not multi-threaded and will not be able to automagically make use
> of a SMP machine.  I'm pretty sure what you want to do is configure
> your app to launch 4 R instances and manage of queue of some sort.

An alternative is to do all of the parallelization within R using nice tools
like the snow package combined with Rmpi.  If your task is computationally
intensive on the R side, but not on the client, then parallelizing R code
may be the better way to go.  All depends on your application, I think.

Sean