Configuring the R BatchJobs package for Torque batch queues

March 31, 2015

(This article was first published on What You're Doing Is Rather Desperate » R, and kindly contributed to R-bloggers)

I was asked recently to look at some R code which performs “embarrassingly parallel” computations (the same function, multiple times, different parameters) and see whether I could modify it to run on one of our high-performance computing clusters. The machine has 63 virtual compute nodes and uses the TORQUE batch queue system to allocate nodes to compute jobs.

First stop: the CRAN Task View High-Performance and Parallel Computing with R. Two promising packages there: BatchJobs and BatchExperiments. Their documentation is quite extensive with useful examples, but I found it a little disjointed and confusing. What I wanted was a simple, step-by-step guide to setting up for a first-time user. So here is my attempt. As always, it’s for “Linux-like” systems.

1. Installation
Quite easy from Github using devtools.

install_github("tudo-r/BatchExperiments") # if required

My system runs an older R version (3.0.2) and so gave a warning that testthat was not available, but that did not prevent installation of the other packages.

2. Edit the batch system template file
One aspect of the BatchJobs documentation that I found unclear was that the term “configuration file” is used, but it was not always obvious which file was being discussed.

BatchJobs requires two files. One of these is a template file which tells R how to submit jobs to the batch queue. The other, discussed in the next section, is a more general configuration file which defines more generally how BatchJobs runs (email notifications, database system and so on).

I started by creating a working directory named jobs and copying the example template file for the TORQUE batch queue system, simple.tmpl, from Github:

mkdir ~/jobs
cd ~/jobs
wget --no-check-certificate

I use that file pretty much as-is, except (a) there appears to be a stray “M” character at the end of line 6 which I removed and (b) my system uses modules, so requires the addition of module load R before R is called.

#PBS -N <%= %>
## merge standard error and output
#PBS -j oe
## direct streams to our logfile
#PBS -o <%= log.file %>
#PBS -l walltime=<%= resources$walltime %>,nodes=<%= resources$nodes %>,vmem=<%= resources$memory %>
## remove this line if your cluster does not support arrayjobs
#PBS -t 1-<%= arrayjobs %>
## Run R:
## we merge R output with stdout from PBS, which gets then logged via -o option
module load R
R CMD BATCH --no-save --no-restore "<%= rscript %>" /dev/stdout

Note the variables used in line 6: you need to recall their names later on.

3. Edit the main configuration file
When you load the BatchJobs library, you’ll see a message telling you that a global configuration file was sourced. I’m assuming here that you installed BatchJobs into ~/R/x86_64-pc-linux-gnu-library/3.0.2/lib; if not, change for the location of your R libraries.

Loading required package: BBmisc
Sourcing configuration file: '~/R/x86_64-pc-linux-gnu-library/3.0.2/lib/BatchJobs/etc/BatchJobs_global_config.R'
# more output...

This is not what you want, since the default configuration runs “interactive” jobs; that is they run sequentially on the head node of your cluster and don’t use the batch queue.

You override the defaults by creating a configuration file named .BatchJobs.R in the working directory. To use TORQUE, the only line that differs from the default file is the first one. It just says that we want to use a cluster with TORQUE and points to the template file from step (2).

cp ~/R/x86_64-pc-linux-gnu-library/3.0.2/lib/BatchJobs/etc/BatchJobs_global_config.R
# edit the first line to look like this
cluster.functions = makeClusterFunctionsTorque("simple.tmpl")

Now the next time that you run R code from ~/jobs and call library(BatchJobs), the local .BatchJobs.R file will override the global configuration. You can also load and override at any time in R using loadConfig().

Sourcing configuration file: '.BatchJobs.R'

4. Submitting jobs
We’re configured and ready to go. In this toy example (inspired by this mailing list discussion), we’ll create a list of 10 elements, each containing a numeric vector with 100 values. Then we’ll write a function to calculate the median value for each of the 10 vectors. This will be split into 10 jobs for submission to the batch queue. Each job will run on one node and return the median value for its set of 100 values.

# define the data and the function
starts <- replicate(10, rnorm(100), simplify = FALSE)
myFun  <- function(start) { median(start) }

# create a registry
reg <- makeRegistry(id = "batchtest")

# map function and data to jobs and submit
ids  <- batchMap(reg, myFun, starts)
done <- submitJobs(reg, resources = list(nodes = 1))

## if it all goes badly wrong run this to delete and start over

When you run makeRegistry() with the id argument, a directory named id-files is created in the working directory with the following contents:

|-- BatchJobs.db
|-- conf.RData
|-- exports/
|-- functions/
|-- jobs/
|-- pending/
|-- registry.RData
`-- resources/

batchMap() sets up the jobs which are then submitted using submitJobs(). The names in list resources map to line 6 in the .BatchJobs.R config file. You need to specify at a minimum the nodes parameter, one per job in this case.

If everything work as expected, you should see something like this:

Saving conf: /datastore/sau103/scratch/jobs/batchtest-files/conf.RData
Submitting 10 chunks / 10 jobs.
Cluster functions: Torque.
Auto-mailer settings: start=none, done=none, error=none.
Writing 10 R scripts...
SubmitJobs |+                                                       
           |   0% (00:00:00)SubmitJobs |+                                                       
           |   0% (00:00:00)SubmitJobs |++++++                                                  
           |  10% (00:00:00)SubmitJobs |+++++++++++                                             
           |  20% (00:00:00)SubmitJobs |+++++++++++++++++                                       
           |  30% (00:00:00)SubmitJobs |++++++++++++++++++++++                                  
           |  40% (00:00:00)SubmitJobs |++++++++++++++++++++++++++++                            
           |  50% (00:00:00)SubmitJobs |++++++++++++++++++++++++++++++++++                      
           |  60% (00:00:00)SubmitJobs |+++++++++++++++++++++++++++++++++++++++                 
           |  70% (00:00:00)SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++           
           |  80% (00:00:00)SubmitJobs |++++++++++++++++++++++++++++++++++++++++++++++++++      
           |  90% (00:00:00)SubmitJobs |++++++++++++++++++++++++++++++++++++++++++++++++++++++++
           | 100% (00:00:00)
Sending 10 submit messages...
Might take some time, do not interrupt this!

and qsub will show jobs in the queue.

The results of each job are saved in the sub-directories jobs/NN where NN is the job number (01, 02, 03…10 in this case). You’ll find the R script which was submitted to the node, a text output file that you can inspect and an RData file containing the result.

|-- 1-result.RData
|-- 1.R
`-- 1.out-1

BatchJobs provides a number of “reduce-like” functions to summarise output. The function reduceResultsVector() returns a vector of the 10 median values.

reduceResultsVector(reg, fun = function(job, res) res, progressbar = FALSE)
Reducing 10 results...
           1            2            3            4            5            6            7            8 
 0.032699812  0.035309734 -0.025205021  0.224939960 -0.024140551  0.119700979  0.022718529  0.003126253 
           9           10 
-0.129746085  0.056802318

# we can check the result by comparing with sapply
sapply(starts, median)
 [1]  0.032699812  0.035309734 -0.025205021  0.224939960 -0.024140551  0.119700979  0.022718529  0.003126253
 [9] -0.129746085  0.056802318

That’s the basics of BatchJobs + TORQUE. There’s a lot more to it and the associated BatchExperiments, which looks very useful.

Filed under: programming, R, research diary, statistics Tagged: batch queue, cluster, hpc, torque

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