High-Performance Open-Source Archive
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
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