drake_config: Ending of _drake.R for r_make() and friends *[Stable]*

In wlandau-lilly/drake: A Pipeline Toolkit for Reproducible Computation at Scale

Ending of _drake.R for r_make() and friends

Description

Call this function inside the ⁠_drake.R⁠ script for r_make() and friends. All non-deprecated function arguments are the same between make() and drake_config().

Usage

drake_config(
  plan,
  targets = NULL,
  envir = parent.frame(),
  verbose = 1L,
  hook = NULL,
  cache = drake::drake_cache(),
  fetch_cache = NULL,
  parallelism = "loop",
  jobs = 1L,
  jobs_preprocess = 1L,
  packages = rev(.packages()),
  lib_loc = NULL,
  prework = character(0),
  prepend = NULL,
  command = NULL,
  args = NULL,
  recipe_command = NULL,
  timeout = NULL,
  cpu = Inf,
  elapsed = Inf,
  retries = 0,
  force = FALSE,
  log_progress = TRUE,
  graph = NULL,
  trigger = drake::trigger(),
  skip_targets = FALSE,
  skip_imports = FALSE,
  skip_safety_checks = FALSE,
  lazy_load = "eager",
  session_info = NULL,
  cache_log_file = NULL,
  seed = NULL,
  caching = c("main", "master", "worker"),
  keep_going = FALSE,
  session = NULL,
  pruning_strategy = NULL,
  makefile_path = NULL,
  console_log_file = NULL,
  ensure_workers = NULL,
  garbage_collection = FALSE,
  template = list(),
  sleep = function(i) 0.01,
  hasty_build = NULL,
  memory_strategy = "speed",
  spec = NULL,
  layout = NULL,
  lock_envir = NULL,
  history = TRUE,
  recover = FALSE,
  recoverable = TRUE,
  curl_handles = list(),
  max_expand = NULL,
  log_build_times = TRUE,
  format = NULL,
  lock_cache = TRUE,
  log_make = NULL,
  log_worker = FALSE
)

Arguments

plan	Workflow plan data frame. A workflow plan data frame is a data frame with a target column and a command column. (See the details in the drake_plan() help file for descriptions of the optional columns.) Targets are the objects that drake generates, and commands are the pieces of R code that produce them. You can create and track custom files along the way (see file_in(), file_out(), and knitr_in()). Use the function drake_plan() to generate workflow plan data frames.
targets	Character vector, names of targets to build. Dependencies are built too. You may supply static and/or whole dynamic targets, but no sub-targets.
envir	Environment to use. Defaults to the current workspace, so you should not need to worry about this most of the time. A deep copy of envir is made, so you don't need to worry about your workspace being modified by make. The deep copy inherits from the global environment. Wherever necessary, objects and functions are imported from envir and the global environment and then reproducibly tracked as dependencies.
verbose	Integer, control printing to the console/terminal. 0: print nothing. 1: print target-by-target messages as make() progresses. 2: show a progress bar to track how many targets are done so far.
hook	Deprecated.
cache	drake cache as created by new_cache(). See also drake_cache().
fetch_cache	Deprecated.
parallelism	Character scalar, type of parallelism to use. For detailed explanations, see ⁠https://books.ropensci.org/drake/hpc.html⁠. You could also supply your own scheduler function if you want to experiment or aggressively optimize. The function should take a single config argument (produced by drake_config()). Existing examples from drake's internals are the ⁠backend_*()⁠ functions: backend_loop() backend_clustermq() backend_future() However, this functionality is really a back door and should not be used for production purposes unless you really know what you are doing and you are willing to suffer setbacks whenever drake's unexported core functions are updated.
jobs	Maximum number of parallel workers for processing the targets. You can experiment with predict_runtime() to help decide on an appropriate number of jobs. For details, visit ⁠https://books.ropensci.org/drake/time.html⁠.
jobs_preprocess	Number of parallel jobs for processing the imports and doing other preprocessing tasks.
packages	Character vector packages to load, in the order they should be loaded. Defaults to rev(.packages()), so you should not usually need to set this manually. Just call library() to load your packages before make(). However, sometimes packages need to be strictly forced to load in a certain order, especially if parallelism is "Makefile". To do this, do not use library() or require() or loadNamespace() or attachNamespace() to load any libraries beforehand. Just list your packages in the packages argument in the order you want them to be loaded.
lib_loc	Character vector, optional. Same as in library() or require(). Applies to the packages argument (see above).
prework	Expression (language object), list of expressions, or character vector. Code to run right before targets build. Called only once if parallelism is "loop" and once per target otherwise. This code can be used to set global options, etc.
prepend	Deprecated.
command	Deprecated.
args	Deprecated.
recipe_command	Deprecated.
timeout	deprecated. Use elapsed and cpu instead.
cpu	Same as the cpu argument of setTimeLimit(). Seconds of cpu time before a target times out. Assign target-level cpu timeout times with an optional cpu column in plan.
elapsed	Same as the elapsed argument of setTimeLimit(). Seconds of elapsed time before a target times out. Assign target-level elapsed timeout times with an optional elapsed column in plan.
retries	Number of retries to execute if the target fails. Assign target-level retries with an optional retries column in plan.
force	Logical. If FALSE (default) then drake imposes checks if the cache was created with an old and incompatible version of drake. If there is an incompatibility, make() stops to give you an opportunity to downgrade drake to a compatible version rather than rerun all your targets from scratch.
log_progress	Logical, whether to log the progress of individual targets as they are being built. Progress logging creates extra files in the cache (usually the ⁠.drake/⁠ folder) and slows down make() a little. If you need to reduce or limit the number of files in the cache, call make(log_progress = FALSE, recover = FALSE).
graph	Deprecated.
trigger	Name of the trigger to apply to all targets. Ignored if plan has a trigger column. See trigger() for details.
skip_targets	Logical, whether to skip building the targets in plan and just import objects and files.
skip_imports	Logical, whether to totally neglect to process the imports and jump straight to the targets. This can be useful if your imports are massive and you just want to test your project, but it is bad practice for reproducible data analysis. This argument is overridden if you supply your own graph argument.
skip_safety_checks	Logical, whether to skip the safety checks on your workflow. Use at your own peril.
lazy_load	An old feature, currently being questioned. For the current recommendations on memory management, see ⁠https://books.ropensci.org/drake/memory.html#memory-strategies⁠. The lazy_load argument is either a character vector or a logical. For dynamic targets, the behavior is always "eager" (see below). So the lazy_load argument is for static targets only. Choices for lazy_load: "eager": no lazy loading. The target is loaded right away with assign(). "promise": lazy loading with delayedAssign() "bind": lazy loading with active bindings: bindr::populate_env(). TRUE: same as "promise". FALSE: same as "eager". If lazy_load is "eager", drake prunes the execution environment before each target/stage, removing all superfluous targets and then loading any dependencies it will need for building. In other words, drake prepares the environment in advance and tries to be memory efficient. If lazy_load is "bind" or "promise", drake assigns promises to load any dependencies at the last minute. Lazy loading may be more memory efficient in some use cases, but it may duplicate the loading of dependencies, costing time.
session_info	Logical, whether to save the sessionInfo() to the cache. Defaults to TRUE. This behavior is recommended for serious make()s for the sake of reproducibility. This argument only exists to speed up tests. Apparently, sessionInfo() is a bottleneck for small make()s.
cache_log_file	Name of the CSV cache log file to write. If TRUE, the default file name is used (drake_cache.CSV). If NULL, no file is written. If activated, this option writes a flat text file to represent the state of the cache (fingerprints of all the targets and imports). If you put the log file under version control, your commit history will give you an easy representation of how your results change over time as the rest of your project changes. Hopefully, this is a step in the right direction for data reproducibility.
seed	Integer, the root pseudo-random number generator seed to use for your project. In make(), drake generates a unique local seed for each target using the global seed and the target name. That way, different pseudo-random numbers are generated for different targets, and this pseudo-randomness is reproducible. To ensure reproducibility across different R sessions, set.seed() and .Random.seed are ignored and have no affect on drake workflows. Conversely, make() does not usually change .Random.seed, even when pseudo-random numbers are generated. The exception to this last point is make(parallelism = "clustermq") because the clustermq package needs to generate random numbers to set up ports and sockets for ZeroMQ. On the first call to make() or drake_config(), drake uses the random number generator seed from the seed argument. Here, if the seed is NULL (default), drake uses a seed of 0. On subsequent make()s for existing projects, the project's cached seed will be used in order to ensure reproducibility. Thus, the seed argument must either be NULL or the same seed from the project's cache (usually the ⁠.drake/⁠ folder). To reset the random number generator seed for a project, use clean(destroy = TRUE).
caching	Character string, either "main" or "worker". "main": Targets are built by remote workers and sent back to the main process. Then, the main process saves them to the cache (config$cache, usually a file system storr). Appropriate if remote workers do not have access to the file system of the calling R session. Targets are cached one at a time, which may be slow in some situations. "worker": Remote workers not only build the targets, but also save them to the cache. Here, caching happens in parallel. However, remote workers need to have access to the file system of the calling R session. Transferring target data across a network can be slow.
keep_going	Logical, whether to still keep running make() if targets fail.
session	Deprecated. Has no effect now.
pruning_strategy	Deprecated. See memory_strategy.
makefile_path	Deprecated.
console_log_file	Deprecated in favor of log_make.
ensure_workers	Deprecated.
garbage_collection	Logical, whether to call gc() each time a target is built during make().
template	A named list of values to fill in the {{ ... }} placeholders in template files (e.g. from drake_hpc_template_file()). Same as the template argument of clustermq::Q() and clustermq::workers. Enabled for clustermq only (make(parallelism = "clustermq")), not future or batchtools so far. For more information, see the clustermq package: ⁠https://github.com/mschubert/clustermq⁠. Some template placeholders such as {{ job_name }} and {{ n_jobs }} cannot be set this way.
sleep	Optional function on a single numeric argument i. Default: function(i) 0.01. To conserve memory, drake assigns a brand new closure to sleep, so your custom function should not depend on in-memory data except from loaded packages. For parallel processing, drake uses a central main process to check what the parallel workers are doing, and for the affected high-performance computing workflows, wait for data to arrive over a network. In between loop iterations, the main process sleeps to avoid throttling. The sleep argument to make() and drake_config() allows you to customize how much time the main process spends sleeping. The sleep argument is a function that takes an argument i and returns a numeric scalar, the number of seconds to supply to Sys.sleep() after iteration i of checking. (Here, i starts at 1.) If the checking loop does something other than sleeping on iteration i, then i is reset back to 1. To sleep for the same amount of time between checks, you might supply something like function(i) 0.01. But to avoid consuming too many resources during heavier and longer workflows, you might use an exponential back-off: say, function(i) { 0.1 + 120 * pexp(i - 1, rate = 0.01) }.
hasty_build	Deprecated
memory_strategy	Character scalar, name of the strategy drake uses to load/unload a target's dependencies in memory. You can give each target its own memory strategy, (e.g. drake_plan(x = 1, y = target(f(x), memory_strategy = "lookahead"))) to override the global memory strategy. Choices: "speed": Once a target is newly built or loaded in memory, just keep it there. This choice maximizes speed and hogs memory. "autoclean": Just before building each new target, unload everything from memory except the target's direct dependencies. After a target is built, discard it from memory. (Set garbage_collection = TRUE to make sure it is really gone.) This option conserves memory, but it sacrifices speed because each new target needs to reload any previously unloaded targets from storage. "preclean": Just before building each new target, unload everything from memory except the target's direct dependencies. After a target is built, keep it in memory until drake determines they can be unloaded. This option conserves memory, but it sacrifices speed because each new target needs to reload any previously unloaded targets from storage. "lookahead": Just before building each new target, search the dependency graph to find targets that will not be needed for the rest of the current make() session. After a target is built, keep it in memory until the next memory management stage. In this mode, targets are only in memory if they need to be loaded, and we avoid superfluous reads from the cache. However, searching the graph takes time, and it could even double the computational overhead for large projects. "unload": Just before building each new target, unload all targets from memory. After a target is built, do not keep it in memory. This mode aggressively optimizes for both memory and speed, but in commands and triggers, you have to manually load any dependencies you need using readd(). "none": Do not manage memory at all. Do not load or unload anything before building targets. After a target is built, do not keep it in memory. This mode aggressively optimizes for both memory and speed, but in commands and triggers, you have to manually load any dependencies you need using readd(). For even more direct control over which targets drake keeps in memory, see the help file examples of drake_envir(). Also see the garbage_collection argument of make() and drake_config().
spec	Deprecated.
layout	Deprecated.
lock_envir	Deprecated in ⁠drake >= 7.13.10⁠. Environments are no longer locked.
history	Logical, whether to record the build history of your targets. You can also supply a txtq, which is how drake records history. Must be TRUE for drake_history() to work later.
recover	Logical, whether to activate automated data recovery. The default is FALSE because Automated data recovery is still stable. It has reproducibility issues. Targets recovered from the distant past may have been generated with earlier versions of R and earlier package environments that no longer exist. It is not always possible, especially when dynamic files are combined with dynamic branching (e.g. dynamic = map(stuff) and format = "file" etc.) since behavior is harder to predict in advance. How it works: if recover is TRUE, drake tries to salvage old target values from the cache instead of running commands from the plan. A target is recoverable if There is an old value somewhere in the cache that shares the command, dependencies, etc. of the target about to be built. The old value was generated with make(recoverable = TRUE). If both conditions are met, drake will Assign the most recently-generated admissible data to the target, and skip the target's command. Functions recoverable() and r_recoverable() show the most upstream outdated targets that will be recovered in this way in the next make() or r_make().
recoverable	Logical, whether to make target values recoverable with make(recover = TRUE). This requires writing extra files to the cache, and it prevents old metadata from being removed with garbage collection (clean(garbage_collection = TRUE), gc() in storrs). If you need to limit the cache size or the number of files in the cache, consider make(recoverable = FALSE, progress = FALSE). Recovery is not always possible, especially when dynamic files are combined with dynamic branching (e.g. dynamic = map(stuff) and format = "file" etc.) since behavior is harder to predict in advance.
curl_handles	A named list of curl handles. Each value is an object from curl::new_handle(), and each name is a URL (and should start with "http", "https", or "ftp"). Example: list( ⁠http://httpbin.org/basic-auth⁠ = curl::new_handle( username = "user", password = "passwd" ) ) Then, if your plan has file_in("http://httpbin.org/basic-auth/user/passwd") drake will authenticate using the username and password of the handle for ⁠http://httpbin.org/basic-auth/⁠. drake uses partial matching on text to find the right handle of the file_in() URL, so the name of the handle could be the complete URL ("http://httpbin.org/basic-auth/user/passwd") or a part of the URL (e.g. "http://httpbin.org/" or "http://httpbin.org/basic-auth/"). If you have multiple handles whose names match your URL, drake will choose the closest match.
max_expand	Positive integer, optional. max_expand is the maximum number of targets to generate in each map(), cross(), or group() dynamic transform. Useful if you have a massive number of dynamic sub-targets and you want to work with only the first few sub-targets before scaling up. Note: the max_expand argument of make() and drake_config() is for dynamic branching only. The static branching max_expand is an argument of drake_plan() and transform_plan().
log_build_times	Logical, whether to record build_times for targets. Mac users may notice a 20% speedup in make() with build_times = FALSE.
format	Character, an optional custom storage format for targets without an explicit target(format = ...) in the plan. Details about formats: ⁠https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets⁠ # nolint
lock_cache	Logical, whether to lock the cache before running make() etc. It is usually recommended to keep cache locking on. However, if you interrupt make() before it can clean itself up, then the cache will stay locked, and you will need to manually unlock it with drake::drake_cache("xyz")$unlock(). Repeatedly unlocking the cache by hand is annoying, and lock_cache = FALSE prevents the cache from locking in the first place.
log_make	Optional character scalar of a file name or connection object (such as stdout()) to dump maximally verbose log information for make() and other functions (all functions that accept a config argument, plus drake_config()). If you choose to use a text file as the console log, it will persist over multiple function calls until you delete it manually. Fields in each row the log file, from left to right: - The node name (short host name) of the computer (from Sys.info()["nodename"]). - The process ID (from Sys.getpid()). - A timestamp with the date and time (in microseconds). - A brief description of what drake was doing.⁠ The fields are separated by pipe symbols (⁠"|"').
log_worker	Logical, same as the log_worker argument of clustermq::workers() and clustermq::Q(). Only relevant if parallelism is "clustermq".

Details

In drake, make() has two stages:

1. Configure a workflow to your environment and plan.

2. Build targets. The drake_config() function just does step (1), which is a common requirement for not only make(), but also utility functions like vis_drake_graph() and outdated(). That is why drake_config() is a requirement for the ⁠_drake.R⁠ script, which powers r_make(), r_outdated(), r_vis_drake_graph(), etc.

Value

A configured drake workflow.

Recovery

make(recover = TRUE, recoverable = TRUE) powers automated data recovery. The default of recover is FALSE because targets recovered from the distant past may have been generated with earlier versions of R and earlier package environments that no longer exist.

How it works: if recover is TRUE, drake tries to salvage old target values from the cache instead of running commands from the plan. A target is recoverable if

1. There is an old value somewhere in the cache that shares the command, dependencies, etc. of the target about to be built.

2. The old value was generated with make(recoverable = TRUE).

If both conditions are met, drake will

1. Assign the most recently-generated admissible data to the target, and

2. skip the target's command.

See Also

make(), drake_plan(), vis_drake_graph()

Examples

## Not run: 
isolate_example("quarantine side effects", {
if (requireNamespace("knitr", quietly = TRUE)) {
writeLines(
  c(
    "library(drake)",
    "load_mtcars_example()",
    "drake_config(my_plan, targets = c(\"small\", \"large\"))"
  ),
  "_drake.R" # default value of the `source` argument
)
cat(readLines("_drake.R"), sep = "\n")
r_outdated()
r_make()
r_outdated()
}
})

## End(Not run)

wlandau-lilly/drake documentation built on Dec. 3, 2024, 11:09 p.m.