run a for loop in parallel in R

66,231

Thanks for your feedback. I did look up parallel after I posted this question.

Finally after a few tries, I got it running. I have added the code below in case it is useful to others

library(foreach)
library(doParallel)

#setup parallel backend to use many processors
cores=detectCores()
cl <- makeCluster(cores[1]-1) #not to overload your computer
registerDoParallel(cl)

finalMatrix <- foreach(i=1:150000, .combine=cbind) %dopar% {
   tempMatrix = functionThatDoesSomething() #calling a function
   #do other things if you want

   tempMatrix #Equivalent to finalMatrix = cbind(finalMatrix, tempMatrix)
}
#stop cluster
stopCluster(cl)

Note - I must add a note that if the user allocates too many processes, then user may get this error: Error in serialize(data, node$con) : error writing to connection

Note - If .combine in the foreach statement is rbind , then the final object returned would have been created by appending output of each loop row-wise.

Hope this is useful for folks trying out parallel processing in R for the first time like me.

References: http://www.r-bloggers.com/parallel-r-loops-for-windows-and-linux/ https://beckmw.wordpress.com/2014/01/21/a-brief-foray-into-parallel-processing-with-r/

Share:
66,231
kay
Author by

kay

R Noob

Updated on January 10, 2020

Comments

  • kay
    kay over 4 years

    I have a for loop that is something like this:

    for (i=1:150000) {
       tempMatrix = {}
       tempMatrix = functionThatDoesSomething() #calling a function
       finalMatrix =  cbind(finalMatrix, tempMatrix)
    
    }
    

    Could you tell me how to make this parallel ?

    I tried this based on an example online, but am not sure if the syntax is correct. It also didn't increase the speed much.

    finalMatrix = foreach(i=1:150000, .combine=cbind) %dopar%  {
       tempMatrix = {}
       tempMatrix = functionThatDoesSomething() #calling a function
    
       cbind(finalMatrix, tempMatrix)
    
    }