new_drake_settings: 'drake_settings' constructor

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

drake_settings constructor

Description

List of class drake_settings.

Usage

new_drake_settings(
  cache_log_file = NULL,
  curl_handles = NULL,
  garbage_collection = NULL,
  jobs = NULL,
  jobs_preprocess = NULL,
  keep_going = NULL,
  lazy_load = NULL,
  lib_loc = NULL,
  lock_envir = NULL,
  lock_cache = NULL,
  log_build_times = NULL,
  log_progress = NULL,
  memory_strategy = NULL,
  parallelism = NULL,
  recover = NULL,
  recoverable = NULL,
  seed = NULL,
  session_info = NULL,
  skip_imports = NULL,
  skip_safety_checks = NULL,
  skip_targets = NULL,
  sleep = NULL,
  template = NULL,
  log_worker = NULL
)

Arguments

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.
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.
garbage_collection	Logical, whether to call gc() each time a target is built during make().
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.
keep_going	Logical, whether to still keep running make() if targets fail.
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.
lib_loc	Character vector, optional. Same as in library() or require(). Applies to the packages argument (see above).
lock_envir	Logical, whether to lock config$envir during make(). If TRUE, make() quits in error whenever a command in your drake plan (or prework) tries to add, remove, or modify non-hidden variables in your environment/workspace/R session. This is extremely important for ensuring the purity of your functions and the reproducibility/credibility/trust you can place in your project. lock_envir will be set to a default of TRUE in drake version 7.0.0 and higher. Namespaces are never locked, e.g. if envir is getNamespace("packagename").
lock_cache	Logical, whether to lock the cache before running make() etc. It is usually recommended to keep cache locking on. However, if you interrupt make() before it can clean itself up, then the cache will stay locked, and you will need to manually unlock it with drake::drake_cache("xyz")$unlock(). Repeatedly unlocking the cache by hand is annoying, and lock_cache = FALSE prevents the cache from locking in the first place.
log_build_times	Logical, whether to record build_times for targets. Mac users may notice a 20% speedup in make() with build_times = FALSE.
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).
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().
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.
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.
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).
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.
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.
skip_targets	Logical, whether to skip building the targets in plan and just import objects and files.
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) }.
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.
log_worker	Logical, same as the log_worker argument of clustermq::workers() and clustermq::Q(). Only relevant if parallelism is "clustermq".

Value

A drake_settings object.

Examples

if (FALSE) { # stronger than roxygen dontrun
new_drake_settings()
}

wlandau-lilly/drake documentation built on March 6, 2024, 8:18 a.m.