The {targets} R package user manual (2024)

This chapter explains simple options and settings to improve the efficiency of your targets pipelines. It also explains how to monitor the progress of a pipeline currently running.1

Basic efficiency:

  • Storage: choose efficient data storage formats for targets with large data output.
  • Memory: consider memory = "transient" and garbage_collection = TRUE for high-memory tasks.
  • Overhead: if each task runs quickly, batch the workload into smaller numbers of targets to reduce overhead.

Parallel processing:

  • Distributed computing: consider distributed computing with crew.
  • Worker storage: parallelize the data processing with storage = "worker" and retrieval = "worker".
  • Local targets: consider deployment = "main" for quick targets that do not need parallel workers.

Esoteric optimizations:

  • Metadata: set seconds_meta_append, seconds_meta_upload, and seconds_reporter to be kind to the local file system and R console.
  • Timestamps: Set trust_object_timestamps = TRUE and format = "file_fast and the leave data alone during tar_make().
  • targets has functions like tar_progress() and tar_watch() to monitor the progress of the pipeline.
  • Profiling with the proffer package can help discover bottlenecks.

14.1 Basic efficiency

These basic tips help most pipelines run efficiently.

14.1.1 Storage

The default data storage format is RDS, which can be slow and bulky for large data. For large data pipelines, consider alternative formats to more efficiently store and manage your data. Set the storage format using tar_option_set() or tar_target():

tar_option_set(format = "qs")

Some formats such as "qs" work on all kinds of data, whereas others like "feather" works only on data frames. Most non-default formats store the data faster and in smaller files than the default "rds" format, but they require extra packages to be installed. For example, format = "qs" requires the qs package, and format = "feather" requires the arrow package.

For extremely large datasets that cannot fit into memory, consider format = "file" to treat the data as a file on disk. Downstream targets are free to load only the subsets of the data they need.

14.1.2 Memory

By default, tar_make() keeps all target data in memory while it is running. To free superfluous data and consume less memory, activate transient memory and garbage collection:

tar_option_set(memory = "transient", garbage_collection = TRUE)tar_make(garbage_collection = TRUE)

memory = "transient" tells targets to remove data from the R environment as soon as it is no longer needed. However, the computer memory itself is not freed until garbage collection is run, and even then, R may not decrease the size of its heap. You can run garbage collection yourself with the gc() function in R.

Transient memory and garbage collection have tradeoffs: the pipeline reads data from storage far more often, and these data reads take additional time. In addition, garbage collection is usually a slow operation, and repeated garbage collections could slow down a pipeline with thousands of targets.

tar_target() storage formats "file" and "file_fast" are less convenient, but they let you take more control of how R uses memory.

14.2 Overhead

Each target incurs overhead, and it is not good practice to create thousands of targets which each run quickly. Instead, consider grouping the same amount of work into a smaller number of targets. See the sections on what a target should do and how much a target should do.

Simulation studies and other iterative stochastic pipelines may need to run thousands of independent random replications. For these pipelines, consider batching to reduce the number of targets while preserving the number of replications. In batching, each batch is a dynamic branch target that performs a subset of the replications. For 1000 replications, you might want 40 batches of 25 replications each, 10 batches with 100 replications each, or a different balance depending on the use case. Functions tarchetypes::tar_rep(), tarchetypes::tar_map_rep(), and stantargets::tar_stan_mcmc_rep_summary() are examples of target factories that set up the batching structure without needing to understand dynamic branching.

14.3 Parallel processing

These tips add parallel processing to your pipeline and help you use it effectively.

14.3.1 Distributed computing

Consider distributed computing with crew, as explained at https://books.ropensci.org/targets/crew.html. The targets package knows how to run independent tasks in parallel and wait for tasks that depend on upstream dependencies. crew supports backends such as crew.cluster for traditional clusters and crew.aws.batch for AWS Batch.

14.3.2 Worker storage

If you run tar_make() with a crew controller, then parallel processes will run your targets, but the main R process still manages all the data by default. To delegate data management to the parallel crew workers, set the storage and retrieval settings in tar_target() or tar_option_set():

tar_option_set(storage = "worker", retrieval = "worker")

But be sure those workers have access to the data. They must either find the local data, or the targets must use cloud storage.

14.3.3 Local targets

In distributed computing with targets, not every target needs to run on a remote worker. For targets that run quickly and cheaply, consider setting deployment = "main" in tar_target() to run them on the main local process:

tar_target(dataset, get_dataset(), deployment = "main")tar_target(summary, compute_summary_statistics(), deployment = "main")

14.4 Esoteric optimizations

These next tips are advanced and obscure, but they may still help.

14.4.1 Metadata

By default, tar_make() writes to the R console and local metadata files up to hundreds of times per second. And if you opt into cloud, it uploads local metadata files to the cloud every few seconds. All this can slow down the pipeline and negatively impact the performance of shared file systems.

Please help targets be kind to your file system, R console, and cloud API rate limit. The following arguments are available in tar_make() and tar_config_set():

  • seconds_meta_append: how often to write to the local metadata files. The default is 0 seconds, but we recommend about 15.
  • seconds_meta_upload: how often to upload the local metadata files to the cloud. The default of 15 seconds should be okay.
  • seconds_reporter: how often to print progress messages to the R console. The default is 0, but we recommend 0.5.

If seconds_meta_append is 15, then tar_make() waits at least 15 seconds before updating the local metadata files. It spends at least 15 seconds collecting a backlog new metadata, and then it writes all that metadata in bulk. seconds_reporter does the same thing with R console progress messages. Be warned: a long-running local target may block the R session and make the actual delay much longer. So when a target completes, tar_make() may not notify you immediately, and the target may not be up to date in the metadata until long after it actually finishes. So please be patient and allow the pipeline to continue until the end.

14.4.2 Timestamps

Another esoteric tip: targets uses hashes to check each target. Because these hashes are slow, by default targets uses time stamps to speed up checks on local data files in _targets/objects/. The default setting of tar_option_set(trust_object_timestamps = TRUE) opts into fast time stamps, and you can set tar_option_set(trust_object_timestamps = FALSE) to opt out. For similarly fast processing of external file targets, set format = "file_fast" instead of format = "file".

Dangers of timestamps

If you use trust_object_timestamps = TRUE or format = "file_fast", do not manually edit those files while the pipeline is running. _targets/objects/ in particular should never be modified by hand. And if you have on file system with low-precision time stamps (EXT3, FAT, XFS) wait at least 2 seconds after the pipeline finishes.

A hash is a fixed-length fingerprint of an object or file. Except in rare cases, different files have different hashes, and two files with the same hash have the same contents. targets uses hashes to check if files have changed, which helps decide whether to rerun or skip each target. Unfortunately, hashes are expensive to compute, so a large number of targets or a large data file could slow down your pipeline.

File modification timestamps offer a workaround. Operating systems keep track of when each file was last modified, and R functions file.mtime() and file.info() can look up these timestamps much faster than hashes can be computed. When you tell targets to use timestamps, the package compares the current timestamp to the old timestamp from when the pipeline last ran. If the timestamps agree, then targets assumes the file is up to date and does not bother to recompute the hash. Otherwise, if the timestamps disagree, then targets recomputes the hash to find out if the contents of the file have really changed. When used safely, this behavior speeds up tar_make(), tar_outdated(), tar_visnetwork(), etc. by avoiding superfluous hash computations when targets are up to date.

14.5 Monitoring the pipeline

Even the most efficient targets pipelines can take time to complete because the user-defined tasks themselves are slow. There are convenient ways to monitor the progress of a running pipeline:

  1. tar_poll() continuously refreshes a text summary of runtime progress in the R console. Run it in a new R session at the project root directory. (Only supported in targets version 0.3.1.9000 and higher.)
  2. tar_visnetwork(), tar_progress_summary(), tar_progress_branches(), and tar_progress() show runtime information at a single moment in time.
  3. tar_watch() launches an Shiny app that automatically refreshes the graph every few seconds.
# Define an example target script file with a slow pipeline.library(targets)tar_script({ sleep_run <- function(...) { Sys.sleep(10) } list( tar_target(settings, sleep_run()), tar_target(data1, sleep_run(settings)), tar_target(data2, sleep_run(settings)), tar_target(data3, sleep_run(settings)), tar_target(model1, sleep_run(data1)), tar_target(model2, sleep_run(data2)), tar_target(model3, sleep_run(data3)), tar_target(figure1, sleep_run(model1)), tar_target(figure2, sleep_run(model2)), tar_target(figure3, sleep_run(model3)), tar_target(conclusions, sleep_run(c(figure1, figure2, figure3))) )})# Launch the app in a background process.# You may need to refresh the browser if the app is slow to start.# The graph automatically refreshes every 10 secondstar_watch(seconds = 10, outdated = FALSE, targets_only = TRUE)# Now run the pipeline and watch the graph change.px <- tar_make()

The {targets} R package user manual (1) tar_watch_ui() and tar_watch_server() make this functionality available to other apps through a Shiny module.

14.6 Profiling

Profiling tools like proffer figure out specific places where code runs slowly. It is important to identify these bottlenecks before you try to optimize. Steps:

  1. Install the proffer R package and its dependencies.
  2. Run proffer::pprof(tar_make(callr_function = NULL)) on your project.
  3. Examine the flame graph to figure out which R functions are taking the most time.
  1. cue = tar_cue(file = FALSE) is no longer recommended for cloud storage. This unwise shortcut is no longer necessary, as of https://github.com/ropensci/targets/pull/1181 (targets version >= 1.3.2.9003).↩︎

The {targets} R package user manual (2024)
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