NEWS.md
Improved performance of batchtools futures by avoiding re-checking the batchtools status if the batchtools job has already been observed to be resolved. Checking the batchtools status is fairly expense, especially since each status check queries a set of files on the file system.
Improved performance of batchtools futures by making the removal of the batchtools registry about 10-15 times faster.
run() for BatchtoolsFuture would update the RNG state, if the future would attach packages.R_FUTURE_BATCHTOOLS_* environment variables are now only read when the future.batchtools package is loaded, where they set the corresponding future.batchtools* option. This is in line with how all packages in the Futureverse works.
Add nbrOfFreeWorkers() for batchtools futures.
It is now possible to tweak arguments used by an underlying batchtools::makeClusterFunctionsNnn() function for some of the batchtools_nnn backends, e.g. plan(batchtools_slurm, scheduler.latency = 60).
plan(batchtools_multicore, workers = I(1)) overrides the fallback to batchtools_local and forces a single batchtools_multicore worker.
print() for BatchtoolsFuture now reports on the batchtools configuration file (an R script) and the the batchtools job template file (a shell script) with info on location, file size, and number of lines, if they exist.
run() for BatchtoolsFuture now produce an informative BatchtoolsFutureError in case batchtools::submitJobs() fails, for instance, due to invalid job-scheduler resource specifications.
Add BatchtoolsFuture subclasses; abstract BatchtoolsUniprocessFuture, abstract BatchtoolsMultiprocessFuture, BatchtoolsInteractiveFuture, BatchtoolsLocalFuture, BatchtoolsMulticoreFuture, BatchtoolsLsfFuture, BatchtoolsOpenLavaFuture, BatchtoolsSGEFuture, BatchtoolsSlurmFuture, BatchtoolsTorqueFuture, and BatchtoolsCustomFuture.
Add batchtools_bash and BatchtoolsBashFuture to illustrate how to create a basic batchtools_custom future based on a batchtools template file bash.tmpl part of the package.
Add batchtools_ssh and BatchtoolsSSHFuture for creating batchtools futures based on batchtools SSH workers created by batchtools::makeClusterFunctionsSSH().
Add example template files for SGE and Slurm.
result() for HPC batchtools backends would use a timeout of fs.latency seconds (as set for the cluster functions) when trying to collect the logged output. However, since it has already collected the results, the log file should be available already and there would be no need to have to wait for the log file to appear. Because of this, we temporarily set fs.latency = 1.0 (second) timeout for trying to find the log file. This makes a big difference in case the template used a --output=<path> location other than --output=<%= log.file %>. In such cases, the log file would not be found, requiring a full timeout to complete.Using plan(batchtools_nnn, finalize = FALSE) would give a warning on Detected 1 unknown future arguments: 'finalize'.
Template files in system.file(package = "future.batchtools", "templates") were not found.
run(), resolved(), and result() for BatchtoolsFuture would update the RNG state.
Lazy batchtools futures only creates the internal batchtools registry when the future is launched.
Removed S3 generic functions await(), finished(), and status(), which were functions that were used for internal purposes.
future.delete and clarify option future.cache.path in help("future.batchtools.options").run() was called twice for a BatchtoolsFuture, it would not produce a FutureError but only a regular non-classed error.It is now possible to configure the default number of workers on the job queue of an HPC scheduler via either R option future.batchtools.workers or environment variable R_FUTURE_BATCHTOOLS_WORKERS.
It is now possible to configure the batchtools registries that are used by batchtools futures via new argument registry to plan(). This argument should be a named list of parameters recognized by the batchtools package, e.g. plan(batchtools_sge, registry = list(...)). For notable example, see below news entries.
The default working directory for batchtools futures is the current working directory of R when the batchtools future is created. This corresponds to specifying plan(batchtools_nnn, registry = list(work.dir = NULL). Sometimes it is useful to use a explicit working directory that is guaranteed to be available on all workers on a shared file system, e.g. plan(batchtools_nnn, registry = list(work.dir = "~")).
It is possible to control if and how batchtools should use file compression for exported globals and results by specifying batchtools registry parameter compress. For example, to turn off file compression, use plan(batchtools_nnn, registry = list(compress = FALSE)).
The default location of the .future folder can be controlled by R option future.cache.path or environment variable R_FUTURE_CACHE_PATH.
batchtools_custom() and BatchtoolsFuture gained argument conf.file. Using plan(batchtools_custom) will now use any batchtools configuration file (an R script) found on the batchtools::findConfFile() search path.
help("future.batchtools.options") which descriptions R options and environment variables used specifically by the future.batchtools package.print() for BatchtoolsFuture would produce an error if the underlying batchtools Registry was incomplete.Setting option future.delete to FALSE will now prevent removal of the batchtools registry folders.
When a batchtools job expires, for instance when the scheduler terminates it because the job was running out of its allocated resources, then a BatchtoolsFutureError is produced which by default outputs the tail of the output logged by batchtools. The default number of lines displayed from the end is now increased from six to 48 - a number which now can be set via option future.batchtools.expiration.tail.
Now a more informative error message is produced if a batchtools *.tmpl template file was not found.
Debug messages are now prepended with a timestamp.
resolve() on a lazy batchtools future would stall and never return.batchtools_* backends support the handling of the standard output as implemented in future (>= 1.9.0).Error in readLog(id, reg = reg) : Log file for job with id 1 not available" when using one of the batchtools backends. It occurred when the value was queried. It was observed using batchtools_torque but not when using batchtools_local. This bug was missed because the 0.7.0 release was not tested on an TORQUE/PBS HPC scheduler as it should have.workers of future strategies may now also be a function, which is called without argument when the future strategy is set up and used as-is. For instance, plan(callr, workers = halfCores) where halfCores <- function() { max(1, round(availableCores() / 2)) } will use half of the number of available cores. This is useful when using nested future strategies with remote machines.If the built-in attempts of batchtools for finding a default template file fails, then system("templates", package = "future.batchtools") is searched for template files as well. Currently, there exists a torque.tmpl file.
A job’s name in the scheduler is now set as the future’s label (requires batchtools 0.9.4 or newer). If no label is specified, the default job name is controlled by batchtools.
The period between each poll of the scheduler to check whether a future (job) is finished or not now increases geometrically as a function of number of polls. This lowers the load on the scheduler for long running jobs.
The error message for expired batchtools futures now include the last few lines of the logged output, which sometimes includes clues on why the future expired. For instance, if a TORQUE/PBS job use more than the allocated amount of memory it might be terminated by the scheduler leaving the message PBS: job killed: vmem 1234000 exceeded limit 1048576 in the output.
print() for BatchtoolsFuture returns the object invisibly.
Calling future_lapply() with functions containing globals part of non-default packages would when using batchtools futures give an error complaining that the global is missing. This was due to updates in future (>= 1.4.0) that broke this package.
loggedOutput() for BatchtoolsFuture would always return NULL unless an error had occurred.
Added batchtools_custom() for specifying batchtools futures using any type of batchtools cluster functions.
batchtools_template(pathname = NULL, type = <type>) now relies on the batchtools package for locating the <type> template file.
nbrOfWorkers() for batchtools futures now defaults to +Inf unless the evaluator’s workers or cluster.functions specify something else.
Renamed argument pathname to template for batchtools_<tmpl>() functions.
plan(batchtools_*), when being created futures would produce an error on all(is.finite(workers)) is not TRUE due to an outdated sanity check.batchtools_* backends is reported as +Inf. However, as the number of workers is used by future_lapply() to decide how many futures should be used to best partition the elements, this means that future_lapply() will always use one future per element. Because of this, it is now possible to specify plan(batchtools_*, workers = n) where n is the target number of workers.