A Universal Foreach Parallel Adaptor using the Future API of the 'future' Package

Provides a '%dopar%' adaptor such that any type of futures can be used as backends for the 'foreach' framework.


News

Package: doFuture

Version: 0.6.0 [2017-10-17]

NEW FEATURES:

o doFuture now respects option 'future.globals.resolve' instead of being hardcoded to always resolve globals (future.globals.resolve = TRUE). This makes doFuture consistent with other future frontends.

o Added option 'doFuture.foreach.export' making it possible ignore a faulty '.export' argument to foreach() and instead rely on the future framework to identify globals. For instance, all examples of caret 6.0-77 works with doFuture() and any backend when setting this option to "automatic" (or ".export-and-automatic") whereas they will only work on forked backends if using ".export" or the default "automatic-unless-.export". If using ".export-and-automatic-with-warning", a warning that lists globals potentially missing from the '.export' argument is produced - this is helpful for developers writing foreach() code.

DOCUMENTATION:

o Added help("doFuture.options").

SOFTWARE QUALITY:

o TESTS: The doFuture package gained more opt-in tests for third-party packages across all known future backends. These tests are not performed on the CRAN servers; instead they are performed on Travis CI. Third-party packages that are currently tested are: caret, foreach, glmnet, NMF, plyr, and TSP.

o TESTS: Testing global functions that call themselves recursively.

Version: 0.5.1 [2017-09-11]

RANDOM NUMBER GENERATION:

o Package now suggests doRNG (>= 1.6.6), which fixes several bugs in doRNG (>= 1.6) previously suggested.

SOFTWARE QUALITY:

o TESTS: Adding tests for globals part of other packages for future.BatchJobs and future.batchtools futures because in previous versions of those, such globals would not be found because the corresponding package was never attached in the worker.

Version: 0.5.0 [2017-03-31]

NEW FEATURES:

o Added foreach() option to control whether scheduling ("chunking") should take place or not, and if so, how granular it should be. This is specified as foreach(..., .options.future = list(scheduling = )). With scheduling = 1.0 (or equivalently scheduling = TRUE), the the elements (iterations) will be split up in equally sized chunks such that each backend worker will process exactly one chunk. With scheduling = Inf (or equivalently scheduling = FALSE), chunking is disabled, i.e. each worker process exactly one element at the time. If schedule = 0.0, then a single workers processes all elements (and the other workers will not be used). If 2.0, then each worker will process two chunks, and so on. If above option is not set, then .options.multicore = list(preschedule = )) which is defined by doParallel, is used to mean scheduling = preschedule. If that is not set, then scheduling = 1.0 is used by default.

SOFTWARE QUALITY:

o TESTS: Now the doFuture package tests can be configured to also run the the help examples of the foreach and plyr packages with the doFuture adaptor. To further increase the coverage of these tests, the plyr example code is tweaked on-the-fly to set .parallel = TRUE. The default is to test against all of the future strategies that comes with the future package, but it is possible to also test against future.BatchJobs, future.batchtools, and so on. These tests are performed on all possible future backends before each release (as well as via continuous integration).

BUG FIXES:

o Using a nested foreach() call would incorrectly produce an error on not being able to locate the iterator variable of the inner-most foreach() as a global variable.

o If a foreach() call would result in an error, the error thrown would report on "object 'expr' not found" and not the actually error message.

Version: 0.4.0 [2017-03-13]

SIGNIFICANT CHANGES:

o SPEED / LOAD BALANCING: The doFuture %dopar% backend now processes all elements in chunks such that each backend worker will process a subset of data at once (and only once). This significantly speeds up processing time when iterating over a large number of elements that each has short a processing time.

GLOBALS:

o For consistency, globals and packages are now identified the same way as they are when using regular futures.

SOFTWARE QUALITY:

o Now the package tests future.batchtools with foreach by itself, in combination with plyr (parallel = TRUE) as well as with BiocParallel::bplapply() and friends. Similar tests are already done using future.BatchJobs.

o Added test for foreach::times() %dopar% { ... }. Especially, it is now tested that global variables are properly identified. Note that times() does not allow you to specify neither '.export' nor '.packages' so it is not really designed for processing in external R process. Having said this, times() does indeed work also in those cases when used with doFuture because it internally handles this automatically.

o ROBUSTNESS: The package redundancy tests (not run by 'R CMD check'; needed to be run manually for now) that run 89 plyr examples with the doFuture foreach adaptor, now forces testing of '.parallel = TRUE' for all plyr functions that support that argument. Each example is run across various future strategies, including sequential, multicore, multisession, and cluster, as well as batchjobs_local and batchtools_local, if installed. See doFuture 0.2.0 notes below for how to run these tests.

Version: 0.3.0 [2016-10-27]

NEW FEATURES:

o Now argument '.export' of foreach() is acknowledged such that if a character vector of variables names to be exported is specified, then those variables and nothing else are exported to future. If NULL, then automatic lookup of global variables is used.

BUG FIXES:

o Nested future strategies were not respected by nested %dopar% calls, because doFuture forgot to remind foreach that doFuture should be used also deeper down. Thank you Alex Vorobiev for reporting on this.

Version: 0.2.1 [2016-09-07]

BUG FIXES:

o Internal R expression created to attach packages was not fully correct (but it still worked).

Version: 0.2.0 [2016-06-25]

SOFTWARE QUALITY:

o ROBUSTNESS: Added package redundancy tests that runs all examples of the 'foreach' and the 'plyr' packages using doFuture and all known types of futures. These tests are not package tests and need to be run manually. The test scripts are available in package directory path <- system.file("tests2", package="doFuture") and can be run as source(file.path(path, "plyr", "examples.R")).

o ROBUSTNESS: Added package tests validating foreach() on regular as well as future.BatchJobs futures. Same for plyr and BiocParallel apply functions.

Version: 0.1.3 [2016-05-07]

DOCUMENTATION:

o Added package help page, i.e. help("doFuture").

RANDOM NUMBER GENERATION:

o Added package tests asserting random number generator (RNG) reproducibility when using the doRNG package.

Version: 0.1.2 [2016-05-05]

NEW FEATURES:

o Now foreach::getDoParWorkers() gives useful information with registerDoFuture() in most cases. In cases where the number of workers cannot be inferred easily from future::plan() it will default to returning a large number (=99).

Version: 0.1.1 [2016-05-05]

NEW FEATURES:

o Now foreach::getDoParName() and foreach::getDoParVersion() gives useful information with registerDoFuture().

Version: 0.1.0 [2016-05-04]

o Created.

Reference manual

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install.packages("doFuture")

0.6.0 by Henrik Bengtsson, 8 months ago


https://github.com/HenrikBengtsson/doFuture


Report a bug at https://github.com/HenrikBengtsson/doFuture/issues


Browse source code at https://github.com/cran/doFuture


Authors: Henrik Bengtsson [aut, cre, cph]


Documentation:   PDF Manual  


Task views: High-Performance and Parallel Computing with R


LGPL (>= 2.1) license


Depends on future, foreach, iterators, parallel, utils

Suggests doRNG, markdown, R.rsp


Imported by drtmle, sperrorest.


See at CRAN