How can I use all of my Amazon EC2 cores to carry out a parallel simulation in R?

Question

I would like to run 1000 iterations of a simulation in R. Each iteration takes 20 seconds which would take ~6 hours in serial. And I have several dozen simulations to run, each with 1000 iterations. So I want to use parallel computing to accomplish this work in less time.

I am new at this. After reading material on the web, I am now using Amazon’s EC2 service, running an AMI with RStudio Server and OpenBLAS that was helpfully provided by Louis Aslett. Details of the software loaded to the AMI are here: http://www.louisaslett.com/RStudio_AMI.

I experimented with several EC2 instances and am currently using a c4.8xlarge ubuntu instance with 36 cores. Or virtual cores, I’m not entirely sure of the difference.

My problem is that I can’t seem to use anywhere near the available 36 cores. I have successfully used up to 10 cores, but I get errors when I attempt to use >10 cores.

Here is minimal code (using the cars dataset) to reproduce the error:

library(parallel)
detectCores() #36
ptm<-proc.time()
cl <- makeCluster(getOption("cl.cores", 20)) #specify number of cores
clusterSetRNGStream(cl, 123) 
sims <- clusterEvalQ(cl, { 
  cars[sample(1:nrow(cars), 10, replace=FALSE),]
}) 
stopCluster(cl)

That code usually works fine when I specify 10 cores in the makeCluster() statement. It produces a list with 10 elements, each of which was produced by one of the 10 cores. But specifying >10 cores (i.e., as above) usually results in errors such as what I have pasted below.

As I mentioned above, I’m new at this and my code is based on an example I found online that was meant to be run on a single, multi-core computer (not an EC2 machine). So I realize I may have misspecified the makeCluster() statement for the purposes of running on EC2.

I would appreciate any help or suggestions to get this working!

Many thanks,

Mark B.

Here is the error I get when attempting to use >10 cores:

OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
/usr/lib/R/bin/R: fork: retry: Resource temporarily unavailable
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
/usr/lib/R/bin/R: fork: retry: No child processes
/usr/lib/R/bin/R: fork: retry: Resource temporarily unavailable
/usr/lib/R/bin/R: fork: retry: No child processes
/usr/lib/R/bin/R: fork: retry: No child processes
/usr/lib/R/bin/R: fork: retry: Resource temporarily unavailable
/usr/lib/R/bin/R: fork: retry: No child processes
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 241473 current, 241473 max
/usr/lib/R/bin/R: fork: retry: No child processes
/usr/lib/R/bin/R: fork: retry: No child processes
/usr/lib/R/bin/R: fork: retry: No child processes
/usr/lib/R/bin/R: fork: retry: No child processes
/usr/lib/R/bin/R: fork: retry: No child processes
/usr/lib/R/bin/R: fork: retry: No child processes
/usr/lib/R/bin/R: fork: Resource temporarily unavailable
ERROR: option '-e' requires a non-empty argument

Maybe this helps... http://stackoverflow.com/q/27825280/2836621 — Mark Setchell, Jun 01 '16 at 21:45

score 1 · Answer 1 · answered Jul 22 '16 at 03:52

We also encountered the problem this week. What I did was to remove the openBLAS and exiting R from the EC2 and re-installed R without openBLAS. Then it worked. But if you really need openBLAS to accelerate your algorithm, you may need to build R with openBLAS from source codes (we haven't tried this approach yet).

How can I use all of my Amazon EC2 cores to carry out a parallel simulation in R?

1 Answers1