Parallelize R code on a Slurm cluster

Many computing-intensive processes in R involve the repeated evaluation of a function over many items or parameter sets. These so-called embarrassingly parallel calculations can be run serially with the lapply or Map function, or in parallel on a single machine with mclapply or mcMap (from the parallel package).

The rslurm package simplifies the process of distributing this type of calculation across a computing cluster that uses the Slurm workload manager. Its main function, slurm_apply, automatically divides the computation over multiple nodes and writes the necessary submission scripts. It also includes functions to retrieve and combine the output from different nodes, as well as wrappers for common Slurm commands.

Table of contents

Basic example

To illustrate a typical rslurm workflow, we use a simple function that takes a mean and standard deviation as parameters, generates a million normal deviates and returns the sample mean and standard deviation.

test_func <- function(par_mu, par_sd) {
    samp <- rnorm(10^6, par_mu, par_sd)
    c(s_mu = mean(samp), s_sd = sd(samp))
}

We then create a parameter data frame where each row is a parameter set and each column matches an argument of the function.

pars <- data.frame(par_mu = 1:10,
                   par_sd = seq(0.1, 1, length.out = 10))
head(pars, 3)

We can now pass that function and the parameters data frame to slurm_apply, specifiying the number of cluster nodes to use and the number of CPUs per node. The latter (cpus_per_node) determines how many processes will be forked on each node, as the mc.cores argument of parallel::mcMap.

library(rslurm)
sjob <- slurm_apply(test_func, pars, jobname = 'test_apply',
                    nodes = 2, cpus_per_node = 2, submit = FALSE)

The output of slurm_apply is a slurm_job object that stores a few pieces of information (job name, job ID, and the number of nodes) needed to retrieve the job's output.

The default argument submit = TRUE would submit a generated script to the Slurm cluster and print a message confirming the job has been submitted to Slurm, assuming your are running R on a Slurm head node. When working from a R session without direct access to the cluster, you must set submit = FALSE. Either way, the function creates a folder called \_rslurm\_[jobname] in the working directory that contains scripts and data files. This folder may be moved to a Slurm head node, the shell command sbatch submit.sh run from within the folder, and the folder moved back to your working directory. The contents of the \_rslurm\_[jobname] folder after completion of the test_apply job, i.e. following either manual or automatic (i.e. with submit = TRUE) submission to the cluster, includes one results_*.RDS file for each node:

list.files('_rslurm_test_apply', 'results')

The results from all the nodes can be read back into R with the get_slurm_out() function.

res <- get_slurm_out(sjob, outtype = 'table')
head(res, 3)

The utility function print_job_status displays the status of a submitted job (i.e. in queue, running or completed), and cancel_slurm will remove a job from the queue, aborting its execution if necessary. These functions are R wrappers for the Slurm command line functions squeue and scancel, respectively.

When outtype = 'table', the outputs from each function evaluation are row-bound into a single data frame; this is an appropriate format when the function returns a simple vector. The default outtype = 'raw' combines the outputs into a list and can thus handle arbitrarily complex return objects.

res_raw <- get_slurm_out(sjob, outtype = 'raw')
res_raw[1:3]

The utility function cleanup_files deletes the temporary folder for the specified Slurm job.

cleanup_files(sjob)

Single function evaluation

In addition to slurm_apply, rslurm also defines a slurm_call function, which sends a single function call to the cluster. It is analogous in syntax to the base R function do.call, accepting a function and a named list of parameters as arguments.

sjob <- slurm_call(test_func, jobname = 'test_call',
                   list(par_mu = 5, par_sd = 1), submit = FALSE)

Because slurm_call involves a single process on a single node, it does not recognize the nodes and cpus_per_node arguments; otherwise, it accepts the same additional arguments (detailed in the sections below) as slurm_apply.

cleanup_files(sjob)

Adding auxiliary data and functions

The function passed to slurm_apply can only receive atomic parameters stored within a data frame. Suppose we want instead to apply a function func to a list of complex R objects, obj_list. To use slurm_apply in this case, we can wrap func in an inline function that takes an index as its sole parameter.

sjob <- slurm_apply(function(i) func(obj_list[[i]]), 
                    data.frame(i = seq_along(obj_list)),
                    add_objects = c("func", "obj_list"),
                    nodes = 2, cpus_per_node = 2)

The add_objects argument specifies the names of any R objects (besides the parameters data frame) that must be accessed by the function passed to slurm_apply. These objects are saved to a .RDS file that is loaded on each cluster node prior to evaluating the function in parallel.

By default, all R packages attached to the current R session will also be attached (with library) on each cluster node, though this can be modified with the optional pkgs argument.

Configuring Slurm options

Particular clusters may require the specification of additional Slurm options, such as time and memory limits for the job. The slurm_options argument allows you to set any of the command line options (view list) recognized by the Slurm sbatch command. It should be formatted as a named list, using the long names of each option (e.g. "time" rather than "t"). Flags, i.e. command line options that are toggled rather than set to a particular value, should be set to TRUE in slurm_options. For example, the following code sets the command line options --time=1:00:00 --share.

sopt <- list(time = '1:00:00', share = TRUE)
sjob <- slurm_apply(test_func, pars, slurm_options = sopt)

How it works / advanced customization

As mentioned above, the slurm_apply function creates a job-specific folder. This folder contains the parameters as a RDS file and (if applicable) the objects specified as add_objects saved together in a RData file. The function also generates a R script (slurm_run.R) to be run on each cluster node, as well as a Bash script (submit.sh) to submit the job to Slurm.

More specifically, the Bash script tells Slurm to create a job array and the R script takes advantage of the unique SLURM\_ARRAY\_TASK\_ID environment variable that Slurm will set on each cluster node. This variable is read by slurm_run.R, which allows each instance of the script to operate on a different parameter subset and write its output to a different results file. The R script calls parallel::mcMap to parallelize calculations on each node.

Both slurm_run.R and submit.sh are generated from templates, using the whisker package; these templates can be found in the rslurm/templates subfolder in your R package library. There are two templates for each script, one for slurm_apply and the other (with the word "single"" in its title) for slurm_call.

While you should avoid changing any existing lines in the template scripts, you may want to add #SBATCH lines to the submit.sh templates in order to permanently set certain Slurm command line options and thus customize the package to your particular cluster setup.



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rslurm documentation built on Nov. 17, 2017, 7:48 a.m.