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In continuation of this question (https://stackoverflow.com/questions/17222942/allow-foreach-workers-to-register-and-distribute-sub-tasks-to-other-workers), what is a best practice to connect doSNOW and SOCK cluster to Torque/MOAB scheduler in order to avoid processor affinity in an inner parallel loop that handles some part of the code of an outer parallel loop?

From the Steve's answer to that question, the baseline code without intraction with the scheduler could be:

library(doSNOW)
hosts <- c('host-1', 'host-2')
cl <- makeSOCKcluster(hosts)
registerDoSNOW(cl)
r <- foreach(i=1:4, .packages='doMC') %dopar% {
  registerDoMC(2)
  foreach(j=1:8, .combine='c') %dopar% {
    i * j
  }
}
stopCluster(cl)
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1 Answers1

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Torque always creates a file containing the node names that have been allocated to your job by Moab, and it passes the path of that file to your job via the PBS_NODEFILE environment variable. Node names may be listed multiple times to indicate that it allocated multiple cores to your job on that node. In this case, we want to start a cluster worker for each unique node name in PBS_NODEFILE, but keep track of the number of allocated cores on each of those nodes so we can specify the correct number of cores when registering doMC.

Here is a function that reads PBS_NODEFILE and returns a data frame with the allocated node information:

getnodes <- function() {
  f <- Sys.getenv('PBS_NODEFILE')
  x <- if (nzchar(f)) readLines(f) else rep('localhost', 3)
  as.data.frame(table(x), stringsAsFactors=FALSE)
}

The returned data frame contains a column named "x" of node names and a column named "Freq" of corresponding core counts.

This makes it simple to create and register a SOCK cluster with one worker per unique node:

nodes <- getnodes()
cl <- makeSOCKcluster(nodes$x)
registerDoSNOW(cl)

We can now easily execute a foreach loop with one task per worker, but it's not so easy to pass the correct number of allocated cores to each of those workers without depending on some implementation details of both snow and doSNOW, specifically relating to the implementation of the clusterApplyLB function used by doSNOW. Of course, it's easy if you happen to know that the number of allocated cores is the same on each node, but it's harder if you want a general solution to the problem.

One (not so elegant) general solution is to assign the number of allocated cores to a global variable on each of the workers via the snow clusterApply function:

setcores <- function(cl, nodes) {
  f <- function(cores) assign('allocated.cores', cores, pos=.GlobalEnv)
  clusterApply(cl, nodes$Freq, f)
}
setcores(cl, nodes)

This guarantees that the value of the "allocated.cores" variable on each of the workers is equal to the number of times that that node appeared in PBS_NODEFILE.

Now we can use that global variable when registering doMC:

r <- foreach(i=seq_along(nodes$x), .packages='doMC') %dopar% {
  registerDoMC(allocated.cores)
  foreach(j=1:allocated.cores, .combine='c') %dopar% {
    i * j
  }
}

Here is an example job script that could be used to execute this R script:

#!/bin/sh
#PBS -l nodes=4:ppn=8
cd "$PBS_O_WORKDIR"
R --slave -f hybridSOCK.R

When this is submitted via the qsub command, the R script will create a SOCK cluster with four workers, and each of those workers will execute the inner foreach loop using 8 cores. But since the R code is general, it should do the right thing regardless of the resources requested via qsub.

Steve Weston
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  • has this changed? my system doesn't have registerDoMC() or registerDoSNOW(), only registerDoParallel(). – Dominik Jan 14 '15 at 23:32
  • @Dominik No, it's hasn't changed. The registerDoMC function is defined in the doMC package, which depends on the parallel package. – Steve Weston Jan 14 '15 at 23:42
  • Sorry, I see that now. Where do you set `cores` in your `setcores` function? or am I supposed to change it to a number? – Dominik Jan 15 '15 at 01:31
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    @Dominik The setcores function uses clusterApply to set the "allocated.cores" variable on each of the workers using the counts in `nodes$Freq`. I added a bit more explanation in the answer to make this more clear (I hope). – Steve Weston Jan 15 '15 at 13:53
  • Interesting. However when i log on interactively to one node , there is only one node in `node` despite them being dual proc quad core nodes....you re suggesting it should be 8 or at least 4 (cant remember if there is node sharing) – Dominik Jan 16 '15 at 02:17
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    @Dominik When you log on interactively with `qsub` and request 4 cores on one node with an option such as `-l nodes=1:ppn=4`, you should see the local host listed in `$PBS_NODEFILE` four times. If you don't, you should talk to your system administrator. – Steve Weston Jan 16 '15 at 15:12
  • you are correct. I didn't realize that ppn (i.e. processors per node) refers to cores as opposed to strictly processors. So I expected to have 4 cores available with ppn=1. This makes more sense now. Thanks for the clarifications. – Dominik Jan 16 '15 at 15:59
  • any chance you could take a look at my followup question? http://stackoverflow.com/questions/28073142/setup-torque-moab-cluster-to-use-multiple-cores-per-node?noredirect=1#comment44682316_28073142 – Dominik Jan 31 '15 at 20:35