Parallelization considerations for dtwclust

In dtwclust: Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance

library("dtwclust")
library("RcppParallel")
library("parallel")

# knitr defaults
knitr::opts_chunk$set(eval = FALSE, comment = "#>")

Introduction

Up until dtwclust version 5.1.0, parallelization solely relied on the foreach package, which mostly leverages multi-processing parallelization. Thanks to the RcppParallel package, several included functions can now also take advantage of multi-threading. However, this means that there are some considerations to keep in mind when using the package in order to make the most of either parallelization strategy. The TL;DR version is:

# load dtwclust
library(dtwclust)
# load parallel
library(parallel)
# create multi-process workers
workers <- makeCluster(detectCores())
# load dtwclust in each one, and make them use 1 thread per worker
invisible(clusterEvalQ(workers, {
    library(dtwclust)
    RcppParallel::setThreadOptions(1L)
}))
# register your workers, e.g. with doParallel
require(doParallel)
registerDoParallel(workers)

For more details, continue reading.

Overview

Parallelization with RcppParallel uses multi-threading. All available threads are used by default, but this can be changed with RcppParallel::setThreadOptions. The maximum number of threads can be checked with RcppParallel::defaultNumThreads or parallel::detectCores. Parallelization with foreach requires a backend to be registered. Some packages that provide backends are:

• doParallel
• doMC
• doSNOW
• doFuture
• doMPI

See also this CRAN view.

The dtwclust functions that use RcppParallel are:

• dtw_lb for dtw.func = "dtw_basic".
• DBA.
• sdtw_cent
• The distance calculations in TADPole.
• All distances registered with proxy by dtwclust.

The dtwclust functions that use foreach are:

• tsclust for partitional and fuzzy clustering when either more than one k is specified in the call, or nrep > 1 in partitional_control.
• The distance calculations in tsclust for distances not included with dtwclust (more details below).
• TADPole (also when called through tsclust) for multiple dc values.
• compare_clusterings for each configuration.
• The "shape", "dba" and "sdtw_cent" centroids in partitional clustering with tsclust if only one k is specified and nrep = 1.
• dtw_lb for dtw.func = "dtw".

Calculation of cross-distance matrices

Distances included in dtwclust

As mentioned above, all included distance functions that are registered with proxy rely on RcppParallel, so it is not necessary to explicitly create parallel workers for the calculation of cross-distance matrices. Nevertheless, creating workers will not prevent the distances to use multi-threading when it is appropriate (more on this later). Using doParallel as an example:

data("uciCT")

# doing either of the following will calculate the distance matrix with parallelization
registerDoParallel(workers)
distmat <- proxy::dist(CharTraj, method = "dtw_basic")
registerDoSEQ()
distmat <- proxy::dist(CharTraj, method = "dtw_basic")

If you want to prevent the use of multi-threading, you can do the following, but it will not fall back on foreach, so it will be always sequential:

RcppParallel::setThreadOptions(1L)
distmat <- proxy::dist(CharTraj, method = "dtw_basic")

Distances not included with dtwclust

As mentioned in its documentation, the tsclustFamily class (used by tsclust) has a distance function that wraps proxy::dist and, with some restrictions, can use parallelization even with distances not included with dtwclust. This depends on foreach for non-dtwclust distances. For example:

# instantiate the family and use the dtw::dtw function
fam <- new("tsclustFamily", dist = "dtw")
# register the parallel workers
registerDoParallel(workers)
# calculate distance matrix
distmat <- fam@dist(CharTraj)
# go back to sequential calculations
registerDoSEQ()

Parallelization with foreach

Within dtwclust

Internally, any call to foreach first performs the following checks:

• Is there more than one parallel worker registered?
• If yes, see if the number of threads has been specified with RcppParallel::setThreadOptions.
  • If it has been specified, change nothing and evaluate the call.
  • If it has not been specified, configure each worker to use 1 thread, evaluate the call, and reset the number of threads in each worker afterwards.

This assumes that, when there are parallel workers, there are enough of them to use the CPU fully, so it would not make sense for each worker to try to spawn multiple threads. When the user has not changed any RcppParallel configuration, the dtwclust functions will configure each worker to use 1 thread, but it is best to be explicit (as shown in the introduction) because RcppParallel saves its configuration in an environment variable, and the following could happen:

RcppParallel::setThreadOptions()

# when this is *unset* (default), all threads are used
Sys.getenv("RCPP_PARALLEL_NUM_THREADS")

# parallel workers would seem the same,
# so dtwclust would try to configure 1 thread per worker
workers <- makeCluster(2L)
clusterEvalQ(workers, Sys.getenv("RCPP_PARALLEL_NUM_THREADS"))

# however, the environment variables get inherited by the workers upon creation
stopCluster(workers)
RcppParallel::setThreadOptions(2L)
Sys.getenv("RCPP_PARALLEL_NUM_THREADS") # for main process
workers <- makeCluster(2L)
clusterEvalQ(workers, Sys.getenv("RCPP_PARALLEL_NUM_THREADS")) # for each worker

stopCluster(workers)

In the last case above dtwclust would not change anything, so each worker would use 2 threads, resulting in 4 threads total. If the physical CPU only has 2 cores with 1 thread each, the previous would be suboptimal.

There are cases where a setup like above might make sense. For example if the CPU has 4 cores with 2 threads per core, the following would not be suboptimal:

workers <- makeCluster(4L)
clusterEvalQ(workers, RcppParallel::setThreadOptions(2L))

But, at least with dtwclust, it is unclear if this is advantageous when compared with makeCluster(8L). Using compare_clusterings with many different configurations, where some configurations might take much longer, might benefit if each worker is not limited to sequential calculations. As a very informal example, consider the last piece of code from the documentation of compare_clusterings:

comparison_partitional <- compare_clusterings(CharTraj, types = "p",
                                              configs = p_cfgs,
                                              seed = 32903L, trace = TRUE,
                                              score.clus = score_fun,
                                              pick.clus = pick_fun,
                                              shuffle.configs = TRUE,
                                              return.objects = TRUE)

A purely sequential calculation (main process with 1 thread) took more than 20 minutes, and the following parallelization scenarios were tested on a machine with 4 cores and 1 thread per core (each scenario tested only once with R v3.5.0):

• 4 workers required 7.36 minutes to finish.
• 2 workers and 2 threads per worker required 7.97 minutes to finish.
• 2 workers and 4 threads per worker required 7.46 minutes to finish.
• No workers and 4 threads required 10.35 minutes to finish.

The last scenario has the possible advantage that tracing is still possible.

Outside dtwclust

If you are using foreach for parallelization, there's a good chance you're already using all available threads/cores from your CPU. If you are calling dtwclust functions inside a foreach evaluation, you should specify the number of threads:

results <- foreach(...) %dopar% {
    RcppParallel::setThreadOptions(1L)
    # any code that uses dtwclust...
}

dtwclust documentation built on Sept. 11, 2024, 9:07 p.m.