R help - Feb 2013 - parallel execution in R

Dear all,
I have a piece of code that  I want to run in parallel (I am working in system
of 16 cores)


foreach (i=(seq(-93,-73,length.out=21))) %dopar% 
 {
          threshold<-i
 
         print(i)
         do_analysis1(i,path)
         do_analysis2(i,path)
           do_something_else_analysis1(i,path)
           something_else_now(i,path)
 }


as you can see I have already tried to make this run in parallel, meaning for
every  i   value each of the 16 processor shoule take a block of the body such
as:

    threshold<-i
 
         print(i)
         do_analysis1(i,path)
         do_analysis2(i,path)
           do_something_else_analysis1(i,path)
           something_else_now(i,,path)
 



and execute it . Unfortunately this does not work and oonly one processor looks
utilized.

Alternatively, mclapply have worked well in the past, but in this case I am not
sure how to convert the serial execution of the body of the loop to a list that
would be compatible with the mclapply.

I would like to thank you in advance for your help

Regards
Alex

	[[alternative HTML version deleted]]

On 26.02.2013 14:00, Alaios wrote:
> Dear all,
> I have a piece of code that  I want to run in parallel (I am working in
system of 16 cores)
>
>
> foreach (i=(seq(-93,-73,length.out=21))) %dopar%
>   {
>            threshold<-i
>
>           print(i)
>           do_analysis1(i,path)
>           do_analysis2(i,path)
>             do_something_else_analysis1(i,path)
>             something_else_now(i,path)
>   }

We do not know how your cluster was set up, hence cannot respond.


I'd just use the parallel (an R base package) and do:

library("parallel")
cl <- makeCluster(.....)
result <- parSapply(cl, seq(-93,-73,length.out=21), function(i){
            threshold<-i
            print(i)
            do_analysis1(i,path)
            do_analysis2(i,path)
            do_something_else_analysis1(i,path)
            something_else_now(i,path)
})
stopCluster(cl)

(untested, of course)

Uwe Ligges



>
> as you can see I have already tried to make this run in parallel, meaning
for every  i   value each of the 16 processor shoule take a block of the body
such as:
>
>      threshold<-i
>
>           print(i)
>           do_analysis1(i,path)
>           do_analysis2(i,path)
>             do_something_else_analysis1(i,path)
>             something_else_now(i,,path)
>
>
>
>
> and execute it . Unfortunately this does not work and oonly one processor
looks utilized.
>
> Alternatively, mclapply have worked well in the past, but in this case I am
not sure how to convert the serial execution of the body of the loop to a list
that would be compatible with the mclapply.
>
> I would like to thank you in advance for your help
>
> Regards
> Alex
>
> 	[[alternative HTML version deleted]]
>
>
>
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