This is a patch release to initiate automatic generation of DOIs by Zenodo with each future release.
Argument job_array_task_limit included in slurm_*() functions to
allow the user to set JobArrayTaskLimit
(#70).
get_job_status() now checks whether slurm_*.out files exist
before attempting to open them, avoiding an error
(#72).
New function slurm_map() with similar syntax to lapply()
(#48).
Better handling of additional arguments to f in slurm_apply(), and
of how R objects are made available to the Slurm jobs
(#48).
Slurm jobID added to slurm_job objects
(#55).
processes_per_node argument added to support hyperthreading
(#57).
get_slurm_out()) is now compatible with partitions that cannot
accept interactive jobs and with newer releases of Slurm,
though there is a potential incompatibility with versions of Slurm older than 16.05.0,
which was released on May 2016
(#65).
Improved status with get_job_status, deprecating print_job_status
(#37).
Use mclapply within get_slurm_out to gather results
(#30).
Allow user to provide custom .R and .sh templates (#47).
Allow user to specify path to Rscript (#45)
and number of CPUS per task (#36).
Allow user to disable core prescheduling if tasks have high variance in completion time (816b40e).
Pass (serialized) functions to Slurm nodes without stringifying.
Save add_objects objects from correct environment.
Package tests evaluate on a cluster when available.
Include reverse dependency check in release process.
README now separate from package documentation.
Vignette can be built on CRAN tests again (no slurm submissions).
Returned to parallel::mcmapply, without SIMPLIFY, to prevent
mc.cores error when checking on Windows.
wait argument adds option to slurm_apply and slurm_call to
block the calling script until the submitted job completes. This
option can be used to allow immediate processing of a submitted
job's output (#2).
Use ".RDS" file extension, rather than ".RData", for serialized objects (#4).
Minor bug fixes (#4).
First version on CRAN
Added a submit argument to slurm_apply and slurm_call. If submit = FALSE,
the submission scripts are created but not run. This is useful if the files need
to be transferred from a local machine to the cluster and run at a later time.
Added new optional arguments to slurm_apply and slurm_call, allowing users to give
informative names to SLURM jobs (jobname) and set any options understood by
sbatch (slurm_options).
The data_file argument to slurm_apply and slurm_call is replaced with
add_objects, which accepts a vector of R object names from the active workspace
and automatically saves them in a .RData file to be loaded on each node.
slurm_apply and slurm_call now generate R and Bash scripts through
whisker templates. Advanced users may want
to edit those templates in the templates folder of the installed R package
(e.g. to set default SBATCH options in submit.sh).
Files generated by the package (scripts, data files and output) are now saved
in a subfolder named _rslurm_[jobname] in the current working directory.
Minor updates, including reformatting the output of print_job_status and
removing this package's dependency on stringr.
2015-11-23
Changed the slurm_apply function to use parallel::mcMap instead of mcmapply,
which fixes a bug where list outputs (i.e. each function call returns a list)
would be collapsed in a single list (rather than returned as a list of lists).
Changed the interface so that the output type (table or raw) is now an argument
of get_slurm_out rather than of slurm_apply, and defaults to raw.
Added cpus_per_node argument to slurm_apply, indicating the number of
parallel processes to be run on each node.
2015-07-13
Added the slurm_call function, which submits a single function evaluation
on the cluster, with syntax similar to the base function do.call.
get_slurm_out can now process the output even if some files are missing,
in which case it issues a warning.
2015-06-29
pkgs to slurm_apply, indicating which packages
should be loaded on each node (by default, all packages currently attached to
the user's R session).2015-06-24
Added the optional argument output to slurm_apply, which can take the
value table (each function evaluation returns a row, output is a data frame) or
raw (each function evaluation returns an arbitrary R object, output is a list).
Fixed a bug in the chunk size calculation for slurm_apply.
2015-06-16