NEWS.md

In rslurm: Submit R Calculations to a 'Slurm' Cluster

rslurm 0.6.2

• rslurm was adopted by the University of Colorado Boulder's Earth Lab
• All future maintenance will be done by Earth Lab

rslurm 0.6.1

This is a patch release to initiate automatic generation of DOIs by Zenodo with each future release.

New features and fixes

• 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).

rslurm 0.6.0

New features and fixes

• 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).

• Miscellaneous minor bug fixes (#49, #51, #53).

rslurm 0.5.0

New features and fixes

• 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).

rslurm 0.4.0

New features and fixes

• 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.

Reversions

• 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.

rslurm 0.3.3

New features and fixes

• Create README from R/slurm.R.

rslurm 0.3.2

New features and fixes

• 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).

rslurm 0.3.1

New features and fixes

• Minor bug fix: specify full path of 'Rscript' when running batch scripts.

rslurm 0.3.0

First version on CRAN

New features and fixes

• 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.

rslurm 0.2.0

2015-11-23

New features and fixes

• 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.

rslurm 0.1.3

2015-07-13

New features and fixes

• 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.

rslurm 0.1.2

2015-06-29

New features and fixes

• Added the optional argument 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).

rslurm 0.1.1

2015-06-24

New features and fixes

• 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.

rslurm 0.1.0

2015-06-16

Initial release

• First version of the package released on GitHub.

rslurm documentation built on March 7, 2023, 5:37 p.m.