Comparison with other approaches

Introduction

The goal of this article is to compare the parabar package with other packages available on CRAN that provide progress tracking functionality for parallelized R code. While parabar provides more features, the comparisons and benchmarks presented in this article are specifically aimed at its progress-tracking functionality. The remainder of this article is organized as follows. I start with a section on how parabar tackles progress tracking. Then, I iterate over other packages that provide progress tracking for parallel tasks and briefly discuss the approaches these packages employ. Next, I provide rough benchmarks comparing the added overhead of these progress-tracking approaches to the baseline scenario of using the built-in package parallel (i.e., without progress tracking).

Progress tracking with `parabar`

The parabar package is aimed at two audiences: (1) end-users who intend to use our package in scripts executed in an interactive R session (i.e., see this resource), and (2) R package developers (i.e., see this resource). The two key concepts behind parabar are backends and contexts. Below I describe these concepts in more detail and demonstrate how they can be used to add new functionality to parabar. This example that follows is focused on progress tracking, and it represents but one example of what is possible. You may check out the UML diagram for a more detailed overview of the package design.

Backends

A backend is an R6 class wrapper around a cluster object obtained from the ?parallel::makeCluster function. The role of a backend is to abide by a standardized way of interacting with parallel clusters by implementing the ?BackendService interface. In a nutshell, the ?BackendService interface defines the set of operations that a backend can perform on a cluster object (e.g., exporting variables, evaluating expressions, running parallel tasks etc.). Backends can be of different types. Currently, parabar supports synchronous and asynchronous backends. A synchronous backend manages a cluster created in the same process as the backend instance itself. An asynchronous backend, on the other hand, manages a cluster created in a background R session (i.e., created via the callr package). In principle, it is possible to extend parabar with other types of backends (e.g., backends that are created on a remote server and managed over SSH).

Contexts

The parabar package is designed with extensibility in mind, which brings us to the second key concept, namely, contexts. New functionality can be implemented as custom contexts that extend the base context class. In simple terms, a context is an R6 wrapper class for a backend instance, with the role of determining how the backend operations defined by the ?BackendService interface should be executed. The base ?Context (i.e., that all other custom contexts extend) implements the same ?BackendService as the backend instance and simply forwards its method calls to the backend instance, which in turn interacts with the cluster. For example, calling the sapply method on a base ?Context instance will forward the call to the corresponding sapply method on the wrapped ?Backend instance, which contains the actual implementation details for interacting with the cluster object (e.g., via ?parallel::parSapply).

Progress tracking functionality

New functionality can be added by creating custom contexts that extends the base context. Custom contexts can then override and decorate the methods of the base context to provide the desired functionality. The ?ProgressTrackingContext is an example of such a custom context that decorates the sapply method to add progress tracking. This specific context works by overriding the sapply method of the base ?Context class to add the necessary functionality for progress tracking. More specifically, if we take a look at the [source code] (https://github.com/mihaiconstantin/parabar/blob/1164f76e4b8c21a983d15b5c23ecad25bd667eaf/R/Context.R#L201-L217) for the sapply method of the base ?Context (i.e., at commit 1164f76) we see the following:

# ...

sapply = function(x, fun, ...) {
    # Consume the backend API.
    private$.backend$sapply(x = x, fun = fun, ...)
}

# ...

This method simply passes its arguments to the sapply method of the wrapped backend instance (i.e., stored in the private field .backend). Note that the ?Backend and the ?Context classes share a sapply method since both implement the ?BackendService interface that requires them to provide an implementation for such a method. The custom ?ProgressTrackingContext can override the sapply method above to provide progress-tracking capabilities as follows:

# ...

sapply = function(x, fun, ...) {
    # Prepare the backend operation with early evaluated `...`.
    operation <- bquote(
        do.call(
            super$sapply, c(list(x = .(x), fun = fun), .(list(...)))
        )
    )

    # Execute the task using the desired backend operation.
    private$.execute(operation = operation, fun = fun, total = length(x))
}

# ...

We can see that the sapply operation is prepared as a quoted expression that is passed to and handled by the private method .execute. The .execute method is responsible for ensuring that the task function is decorated to log the progress after each task execution, and that the progress bar is displayed and updated based on the progress reported in the log file:

# ...

.execute = function(operation, fun, total) {
    # Create file for logging progress.
    log <- private$.make_log()

    # Clear the temporary file on function exit.
    on.exit({
        # Remove.
        unlink(log)
    })

    # Decorate the task function.
    fun <- private$.decorate(task = fun, log = log)

    # Evaluate the operation now referencing the decorated task.
    eval(operation)

    # Show the progress bar and block the main process.
    private$.show_progress(total = total, log = log)
}

# ...

Breaking down the implementation above, the following lines of code

# Create file for logging progress.
log <- private$.make_log()

# Clear the temporary file on function exit.
on.exit({
    # Remove.
    unlink(log)
})

create a temporary file where the task function will record the progress after each task execution, and remove this file when the parallel task has completed. The next line of code

# Decorate task function.
task <- private$.decorate(task = fun, log = log)

decorates the task function by injecting code that enables it to record the progress in the log file after each execution. Next, we evaluate the operation expression that contains the call to the sapply method of the base ?Context class (i.e., via the super access modifier). Evaluating this operation will implicitly use of the decorated task function available in the current environment:

# Evaluate the operation now referencing the decorated task.
eval(operation)

As mentioned earlier, this call is simply forwarded to the sapply method of the .backend instance. However, unlike before, the task function is now decorated to log the progress to a file. Finally, the following line of code

# Show the progress bar and block the main process.
private$.show_progress(total = length(x), log = log)

simply creates a ?Bar instance to display and update a progress bar based on the progress reported in the log file (i.e., see source code here).

In summary, parabar enables progress-tracking for parallel tasks by adjusting the task function to log to a file each time a task has finished executing. The log file is then monitored periodically and used to update the progress bar displayed in the console (i.e., see also the progress_timeout field of ?Options for how to adjust the timeout between subsequent checks of the log file). The benefits of this approach are two fold. First, the progress bar will accurately reflect the execution progress of the task. Second, this scales well to any kind of tasks (i.e., both simple and complex). On the other hand, one potential disadvantage of this approach is the overhead associated with the I/O for writing and reading the execution progress.

Progress tracking with `pbapply`

pbapply is a versatile package that provides progress tracking for various backends and vectorized R functions in the *apply family. To understand how pbapply approaches progress tracking, we can take a look at the implementation details of the ?pbapply::pblapply function, which seems to be the workhorse function used by the other *apply variants. At the time of writing this article, the most recent version of the function ?pbapply::pblapply is at the commit 0195d77 on May 23, 2023, in the file pblapply.R. Looking at the source code lines 51 to 66 in the file pblapply.R we see the following code:

# ...
if (inherits(cl, "cluster")) {                                  # 51
    ## switch on load balancing if needed                       # 52
    PAR_FUN <- if (isTRUE(getOption("pboptions")$use_lb))       # 53
        parallel::parLapplyLB else parallel::parLapply          # 54
    if (!dopb())                                                # 55
        return(PAR_FUN(cl, X, FUN, ...))                        # 56
    ## define split here and use that for counter               # 57
    Split <- splitpb(length(X), length(cl), nout = nout)        # 58
    B <- length(Split)                                          # 59
    pb <- startpb(0, B)                                         # 60
    on.exit(closepb(pb), add = TRUE)                            # 61
    rval <- vector("list", B)                                   # 62
    for (i in seq_len(B)) {                                     # 63
        rval[i] <- list(PAR_FUN(cl, X[Split[[i]]], FUN, ...))   # 64
        setpb(pb, i)                                            # 65
    }                                                           # 66
# ...
} # ...

Line 51 in the code snippet above is used to determine whether the parallel backend is a cluster object created via the parallel package. When that is the case, pbapply proceeds in lines 53 and 54 with choosing the appropriate ?parallel::parLapply function for the parallelization (i.e., with or without load balancing). Then, lines 55 and 56 determine whether a progress bar should be displayed based on the dopb function.

The more interesting part, is represented by lines 57 to 66, which are used to define how the progress bar will be created and updated. More specifically, line 58 splits the task repetitions into smaller chunks based on how many tasks we want to run (i.e., nx), how many nodes are in the cluster (i.e., ncl), and the maximum number of splits we want (i.e., nout). For example, suppose we want want to run $20$ tasks in parallel on a cluster with three nodes, with the default value of nout = NULL. In this case, pbapply creates the following splits:

# Create task splits.
splits <- pbapply::splitpb(nx = 20, ncl = 3, nout = NULL)

# Print the splits.
print(splits)
#> [[1]]
#> [1] 1 2 3
#>
#> [[2]]
#> [1] 4 5 6
#>
#> [[3]]
#> [1] 7 8 9
#>
#> [[4]]
#> [1] 10 11 12
#>
#> [[5]]
#> [1] 13 14 15
#>
#> [[6]]
#> [1] 16 17 18
#>
#> [[7]]
#> [1] 19 20

We see that ?pbapply::splitpb produced seven splits, each consisting of two or three task repetitions. In lines 59 and 60 pbapply counts how many splits were created and starts a progress bar with a minimum of zero and a maximum value set to the total number of splits (i.e., seven in this case). Even more interesting are lines 63 to 66. Here, pbapply loops over each split and calls the selected parallel function (e.g., ?parallel::parLapply) with the task repetitions corresponding to the current split processed. As soon as this parallel function returns, the progress bar is updated with the processed split index. Therefore, in the example above, pbapply will call the parallel function seven times, and hence update the progress bar seven times.

The code snippet above already provides us with two important insights into how pbapply works. First, by default, pbapply does not update the progress bar after each task repetition. Second, the overhead pbapply adds is likely given by the repeated calls to the parallel function (e.g., ?parallel::parLapply) that involves transferring the tasks to the different processes that make up the cluster nodes.

We can compare this with the source code of the built-in function ?parallel::parLapply displayed below, where we let X represent our $20$ task repetitions and fun the task function to be applied to each repetition:

function(cl = NULL, X, fun, ..., chunk.size = NULL) {   # 1
    cl <- defaultCluster(cl)                            # 2
    nchunks <- parallel:::staticNChunks(                # 3
        length(X),                                      # 4
        length(cl),                                     # 5
        chunk.size                                      # 6
    )                                                   # 7
    do.call(                                            # 8
        c,                                              # 9
        clusterApply(                                   # 10
            cl = cl,                                    # 11
            x = parallel:::splitList(X, nchunks),       # 12
            fun = lapply,                               # 13
            FUN = fun,                                  # 14
            ...                                         # 15
        ),                                              # 16
        quote = TRUE                                    # 17
    )                                                   # 18
}                                                       # 19

We can see on lines 3 and 12 calls to two internal functions of the parallel package, namely, parallel:::staticNChunks and parallel:::splitList. Applying these functions to our example results in the following splits:

# Task repetitions.
X <- 1:20

# Number of nodes in the cluster.
ncl <- 3

# Compute chunk size based on that repetitions and cluster size.
nchunks <- parallel:::staticNChunks(length(X), ncl, NULL)

# Print the chunk size.
print(nchunks)
#> [1] 3

# Create the task splits.
parallel:::splitList(X, nchunks)
#> [[1]]
#> [1] 1 2 3 4 5 6 7
#>
#> [[2]]
#> [1]  8  9 10 11 12 13
#>
#> [[3]]
#> [1] 14 15 16 17 18 19 20

We see that pbapply uses a similar approach for creating the task splits, however, unlike pbapply, the built-in parallel package creates by default as many tasks splits as nodes in the cluster. This means that the ?parallel::clusterApply function used within ?parallel::parLapply will only be called three times, i.e., as stated in the documentation:

clusterApply calls fun on the first node with arguments x[[1]] and …, on the second node with x[[2]] and …, and so on, recycling nodes as needed.

This approach is strikingly different from pbapply which, for this example, results in calling the parallel function (e.g., ?parallel::parLapply) seven times, which, in turn, results in calling the ?parallel::clusterApply for each individual task repetition. Put simply, for the example above, the parallel package calls the ?parallel::clusterApply for each chunk, whereas pbapply calls the ?parallel::clusterApply for each task repetition. Therefore, the pbapply progress tracking functionality can be regarded as a tradeoff between the granularity of the progress bar and the overhead associated with chunking the task repetitions and communicating with the cluster nodes. While this overhead is likely negligible when the number of tasks is low, such repeated calls to the ?parallel::clusterApply are definitely something one should consider when scaling things up.

In the next section, I provide rough estimates of the overhead associated with the progress-tracking approaches discussed above.

Overhead

To make things as comparable as possible, I start by defining a dummy task function that we can reliably measure how long it takes to execute. We then run $1000$ repetitions of this task in parallel via the built-in function ?parallel::parSapply to establish the baseline execution time. This baseline execution time serves as our benchmark for comparing the execution times of the progress-tracking approaches discussed above (e.g., pbapply and parabar). To obtain more stable results, we determine the execution times based on $100$ replications of the parallelized task replications, and provide a summary in the form of a figure. To achieve this, we use the microbenchmark package for benchmarking the execution times, and the ggplot2 package for plotting the results.

The task function

We start by loading the libraries needed for the benchmarks below.

# Load libraries.
library(parallel)
library(parabar)
library(pbapply)
library(microbenchmark)
library(ggplot2)

For our task, we can use the ?base::Sys.sleep function to simulate a task that takes a certain amount of time to execute. For the purposes of this article, we will use a task that takes roughly $0.05$ milliseconds to execute and simply adds one to the input argument.

# Define task function.
task <- function(x) {
    # Pretend to perform an expensive computation.
    Sys.sleep(0.00005)

    # Return the computation.
    return(x + 1)
}

Baseline execution time

Suppose that we want $1000$ repetitions of the task function to be executed in parallel on a cluster consisting of five nodes. We determine the execution time based on the ?parallel::parSapply function, which will serve as our benchmark. We can establish this benchmark using the following code:

# Define the task repetitions.
n_tasks <- 1:1000

# Define the benchmark repetitions.
n_benchmarks <- 100

# Create a cluster of five nodes.
cluster <- makeCluster(spec = 5, type = "PSOCK")

# Measure the execution time of the task function.
duration_parallel <- microbenchmark(
    # The task to benchmark.
    parallel = parSapply(cluster, X = n_tasks, FUN = task),

    # Benchmark repetitions.
    times = n_benchmarks
)

# Stop the cluster.
stopCluster(cluster)

# Print the duration.
print(duration_parallel, unit = "ms")
#> Unit: milliseconds
#>      expr      min       lq     mean   median       uq      max neval
#>  parallel 14.57251 14.81818 15.17978 15.01752 15.23622 22.07887   100

Running our task in parallel via the ?parallel::parSapply function takes on average $M = 15.18$ milliseconds, with a standard deviation of $SD = 0.88$ .

`parabar` execution time

We repeat the same setup as above, but this time using the parabar package. Since the end-user API prevents us from displaying progress bars in non-interactive sessions (e.g., knitting R vignettes), we can, more conveniently, use the R6 developer API to force progress-tracking, nevertheless. In this case, we use the ?parabar::ProgressTrackingContext that adds progress tracking functionality to tasks executed in parallel. To avoid issues with the progress bar not displaying correctly in a non-interactive R session, we will temporarily redirect the progress bar output to /dev/null using the ?base::sink function. Note that the progress tracking functionality is still employed (i.e., logging the execution progress to a file and reading the file to update the progress bar), only the progress bar is not displayed.

# Create a specification object.
specification <- Specification$new()

# Set the number of cores.
specification$set_cores(cores = 5)

# Set the cluster type.
specification$set_type(type = "psock")

# Get a backend instance that does support progress tracking.
backend <- AsyncBackend$new()

# Create a progress-tracking context object.
context <- ProgressTrackingContext$new()

# Register the backend with the context.
context$set_backend(backend)

# Start the backend.
context$start(specification)

# Get a modern bar instance.
bar <- BasicBar$new()

# Register the bar with the context.
context$set_bar(bar)

# Measure the execution time of the task function.
duration_parabar <- microbenchmark(
    # The task to benchmark.
    parabar = {
        # Redirect the output.
        sink("/dev/null")

        # Run a task in parallel.
        context$sapply(x = n_tasks, fun = task)

        # Get the task output.
        backend$get_output(wait = TRUE)

        # Disable the output redirection.
        sink()
    },

    # Benchmark repetitions.
    times = n_benchmarks
)

# Close the backend.
context$stop()

# Print the duration.
print(duration_parabar, unit = "ms")
#> Unit: milliseconds
#>     expr     min       lq     mean   median       uq      max neval
#>  parabar 85.3611 92.52532 99.01425 96.36281 100.6855 172.9809   100

Based on the results above, we observe that running our task function in parallel via parabar, with progress tracking, yields an execution time of $M = 99.01$ milliseconds, with a $SD = 12.85$ . Therefore, the overhead of parabar relative to parallel is roughly $83.83$ milliseconds.

`pbapply` execution time

We repeat, again, the setup above, but this time using the pbapply package via the ?pbapply::pbsapply function. Just like parabar, pbapply disables progress tracking for non-interactive R sessions. Therefore, we first need to force progress tracking, and, then, to avoid printing issues, redirect the progress bar output to /dev/null.

Adjust pbapply options

# Get original `pbapply` options.
pbapply_options <- getOption("pboptions")

# Get `knitr` progress option.
knitr_option <- getOption("knitr.in.progress")

# Create a copy of the `pbapply` options.
pbapply_options_copy <- pbapply_options

# Create a copy of the `knitr` progress option.
knitr_option_copy <- knitr_option

# Adjust the `pbapply` options to set a progress bar type.
pbapply_options_copy$type <- "timer"

# Adjust the `knitr` option to indicate no knitting.
knitr_option_copy <- NULL

# Set the adjusted options.
options(pboptions = pbapply_options_copy)
options(knitr.in.progress = knitr_option_copy)

# Check whether `pbapply` will use a progress bar.
dopb()
#> [1] TRUE

# Create a cluster of five nodes.
cluster <- makeCluster(spec = 5, type = "PSOCK")

# Measure the execution time of the task function.
duration_pbapply <- microbenchmark(
    # The task to benchmark.
    pbapply = {
        # Redirect the output.
        sink("/dev/null")

        # Run the task in parallel.
        pbsapply(X = n_tasks, FUN = task, cl = cluster)

        # Disable the output redirection.
        sink()
    },

    # Benchmark repetitions.
    times = n_benchmarks
)

# Stop the cluster.
stopCluster(cluster)

# Print the duration.
print(duration_pbapply, unit = "ms")
#> Unit: milliseconds
#>     expr      min       lq     mean   median       uq      max neval
#>  pbapply 142.1083 147.3204 154.3072 151.1385 156.6055 216.7699   100

Restore pbapply options

# Restore the original `pbapply` options.
options(pboptions = pbapply_options)

# Restore the original `knitr` option.
options(knitr.in.progress = knitr_option)

The results above indicate that running the task function in parallel via pbapply, with progress tracking, has an average execution time of $M = 154.31$ milliseconds, with a $SD = 12.4$ . Based on these results, the overhead of pbapply relative to parallel is roughly $139.13$ milliseconds.

Summary

In this section, I provide a brief summary of the differences in the execution times between the parallelization approaches discussed above. First, we can test whether there are significant differences in the average execution time of parabar and pbapply.

# Extract duration in milliseconds for `parabar`.
parabar_time_ms <- duration_parabar$time / 1e6

# Extract duration in milliseconds for `pbapply`.
pbapply_time_ms <- duration_pbapply$time / 1e6

# Test for mean differences.
test_result <- t.test(
    x = parabar_time_ms,
    y = pbapply_time_ms,
)

# Print the test result.
print(test_result)
#>
#>  Welch Two Sample t-test
#>
#> data:  parabar_time_ms and pbapply_time_ms
#> t = -30.96, df = 197.75, p-value < 2.2e-16
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>  -58.81492 -51.77103
#> sample estimates:
#> mean of x mean of y
#>  99.01425 154.30722

The test statistic indicates that there are statistically significant mean differences between the execution times of the parabar (i.e., $M = 99.01$ , $SD = 12.85$ ) and pbapply (i.e., $M = 154.31$ , $SD = 12.4$ ) packages, with $t(197.75) = -30.96$ , $p < 0.001$ .

Now, we can proceed to display the execution time of the different parallelization approaches we discussed. We start with a pre-processing step that combines all results into a data frame and computes additional variables (e.g., the execution time in milliseconds).

# Create data frame from duration objects.
results <- rbind(
    duration_parallel,
    duration_parabar,
    duration_pbapply
)

# Create execution time column in milliseconds.
results$time_ms <- results$time / 1e6

# Create column indicating progress tracking.
results$progress <- factor(
    ifelse(with(results, expr %in% c("parabar", "pbapply")), "yes", "no")
)

# Print the data frame.
print(results)
#> Unit: milliseconds
#>      expr       min        lq      mean    median        uq       max neval
#>  parallel  14.57251  14.81818  15.17978  15.01752  15.23622  22.07887   100
#>   parabar  85.36110  92.52532  99.01425  96.36281 100.68546 172.98093   100
#>   pbapply 142.10834 147.32038 154.30722 151.13853 156.60555 216.76987   100

Finally, we can plot the box plots of the execution times corresponding to the different parallelization approaches we discussed.

Code for plotting the results

# Plot the results.
ggplot(data = results, aes(x = expr, y = time_ms)) +
    geom_boxplot(
        aes(fill = progress),
        width = 0.6
    ) +
    scale_y_continuous(
        breaks = round(seq(min(results$time_ms), max(results$time_ms), length.out = 10)),
    ) +
    labs(
        title = "Execution time of different parallelization approaches",
        x = "Parallelization approach",
        y = "Execution time in milliseconds"
    ) +
    scale_fill_manual(
        name = "Progress tracking",
        values = c("#f9bcec", "#9aa9e3")
    ) +
    theme_bw() +
    theme(
        plot.title = element_text(
            face = "bold",
            vjust = 0.5,
            size = 13
        ),
        axis.title.x = element_text(
            margin = margin(t = 10, r = 0, b = 0, l = 0),
            size = 12
        ),
        axis.title.y = element_text(
            margin = margin(t = 0, r = 10, b = 0, l = 0),
            size = 12
        ),
        axis.text.x = element_text(
            margin = margin(t = 5, r = 0, b = 0, l = 0),
            size = 11,
            vjust = 0.5,
        ),
        axis.text.y = element_text(
            margin = margin(t = 0, r = 5, b = 0, l = 0),
            size = 11
        ),
        legend.title = element_text(
            size = 12
        ),
        legend.text = element_text(
            size = 11
        ),
        panel.grid.minor = element_line(
            linewidth = 0.1
        ),
        panel.grid.major = element_line(
            linewidth = 0.1
        )
    )

plot of chunk benchmarks

Conclusion

In this article, I discussed different approaches for adding progress-tracking functionality to parallelized R code, and showed that the parabar package is a good alternative to pbapply for achieving this. The parabar package demonstrated better performance over the pbapply in terms of execution time (i.e., when the number of tasks to run is large enough relative to the number of nodes in the cluster). Execution time aside, parabar also provides more granular progress bars that reflect the actual progress of the task, rather than the progress of the parallelization process. Despite the name, parabar is more than just a package that adds progress bars for parallelized R code. Through its design, it provides a standardized way of interacting with the built-in parallel package. On top of that, it proposes an extensible mechanism to augment the parallel package functions with new functionality. This is a key benefit that allows one to customize the parallelization process in many different ways, such as sending an email when the parallelized task is finished executing. Therefore, the progress tracking functionality discussed in this article is just one example of what is possible with parabar.

Mihai Constantin

17 November, 2024

Introduction

Progress tracking with `parabar`

Backends

Contexts

Progress tracking functionality

Progress tracking with `pbapply`

Overhead

The task function

Baseline execution time

`parabar` execution time

`pbapply` execution time

Summary

Conclusion

Comparison with other approaches

Mihai Constantin

17 November, 2024

Introduction

Progress tracking with parabar

Backends

Contexts

Progress tracking functionality

Progress tracking with pbapply

Overhead

The task function

Baseline execution time

parabar execution time

pbapply execution time

Summary

Conclusion

Progress tracking with `parabar`

Progress tracking with `pbapply`

`parabar` execution time

`pbapply` execution time