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Aug 19, 2025
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docs: fix absolute urls in vigngette #320

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d7521fe
docs: fix absolute urls in vigngette
mllg Aug 18, 2025
b03e9e7
add some missing links
mllg Aug 18, 2025
b9074f7
fix some more links in README
mllg Aug 19, 2025
f1df4ba
fix links in description
mllg Aug 19, 2025
d1646b6
add section on porting to vignette again
mllg Aug 19, 2025
3aeb202
add articles to menu
mllg Aug 19, 2025
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49 changes: 26 additions & 23 deletions DESCRIPTION
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Expand Up @@ -2,31 +2,30 @@ Package: batchtools
Title: Tools for Computation on Batch Systems
Version: 0.9.18
Authors@R: c(
person("Michel", "Lang", NULL, "[email protected]",
role = c("cre", "aut"), comment = c(ORCID = "0000-0001-9754-0393")),
person("Bernd", "Bischl", NULL, "[email protected]", role = "aut"),
person("Dirk", "Surmann", NULL, "[email protected]",
role = "ctb", comment = c(ORCID = "0000-0003-0873-137X"))
)
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<https://www.ibm.com/products/hpc-workload-management>),
'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>),
'TORQUE/PBS'
person("Michel", "Lang", , "[email protected]", role = c("cre", "aut"),
comment = c(ORCID = "0000-0001-9754-0393")),
person("Bernd", "Bischl", , "[email protected]", role = "aut"),
person("Dirk", "Surmann", , "[email protected]", role = "ctb",
comment = c(ORCID = "0000-0003-0873-137X"))
)
Description: As a successor of the packages 'BatchJobs' and
'BatchExperiments', this package provides a parallel implementation of
the Map function for high performance computing systems managed by
schedulers 'IBM Spectrum LSF'
(<https://www.ibm.com/products/hpc-workload-management>), 'Univa Grid
Engine'/'Oracle Grid Engine'
(<https://altair.com/hpc-cloud-applications/>), 'Slurm'
(<https://slurm.schedmd.com/>), 'TORQUE/PBS'
(<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>),
or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>). A
multicore and socket mode allow the parallelization on a local
machines, and multiple machines can be hooked up via SSH to create a
makeshift cluster. Moreover, the package provides an abstraction
mechanism to define large-scale computer experiments in a
well-organized and reproducible way.
License: LGPL-3
URL: https://github.com/mlr-org/batchtools, https://batchtools.mlr-org.com
BugReports: https://github.com/mlr-org/batchtools/issues
NeedsCompilation: yes
ByteCompile: yes
Encoding: UTF-8
Depends:
R (>= 3.0.0)
Imports:
Expand All @@ -47,8 +46,8 @@ Imports:
withr (>= 2.0.0)
Suggests:
debugme,
doParallel,
doMPI,
doParallel,
e1071,
foreach,
future,
Expand All @@ -61,6 +60,10 @@ Suggests:
snow,
testthat,
tibble
VignetteBuilder: knitr
VignetteBuilder:
knitr
ByteCompile: yes
Encoding: UTF-8
NeedsCompilation: yes
Roxygen: list(r6 = FALSE)
RoxygenNote: 7.3.2
13 changes: 6 additions & 7 deletions README.Rmd
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Expand Up @@ -14,7 +14,7 @@ Package website: [release](https://batchtools.mlr-org.com/) | [dev](https://batc
[![Mattermost](https://img.shields.io/badge/chat-mattermost-orange.svg)](https://lmmisld-lmu-stats-slds.srv.mwn.de/mlr_invite/)
<!-- badges: end -->

As a successor of the packages [BatchJobs](https://github.com/tudo-r/BatchJobs) and [BatchExperiments](https://github.com/tudo-r/Batchexperiments), batchtools provides a parallel implementation of Map for high performance computing systems managed by schedulers like Slurm, Sun Grid Engine, OpenLava, TORQUE/OpenPBS, Load Sharing Facility (LSF) or Docker Swarm (see the setup section in the [vignette](https://batchtools.mlr-org.com/batchtools/articles/batchtools.html)).
As a successor of the packages [BatchJobs](https://github.com/tudo-r/BatchJobs) and [BatchExperiments](https://github.com/tudo-r/Batchexperiments), batchtools provides a parallel implementation of Map for high performance computing systems managed by schedulers like Slurm, Sun Grid Engine, OpenLava, TORQUE/OpenPBS, Load Sharing Facility (LSF) or Docker Swarm (see the setup section in the [vignette](https://batchtools.mlr-org.com/articles/batchtools.html)).

Main features:

Expand All @@ -37,7 +37,7 @@ devtools::install_github("mlr-org/batchtools")
```

Next, you need to setup `batchtools` for your HPC (it will run sequentially otherwise).
See the [vignette](https://mlr-org.github.io/batchtools/articles/batchtools.html#setup) for instructions.
See the [vignette](https://batchtools.mlr-org.com/articles/batchtools.html) for instructions.

## Why batchtools?
The development of [BatchJobs](https://github.com/tudo-r/BatchJobs/) and [BatchExperiments](https://github.com/tudo-r/Batchexperiments) is discontinued for the following reasons:
Expand All @@ -46,15 +46,14 @@ The development of [BatchJobs](https://github.com/tudo-r/BatchJobs/) and [BatchE
* Data base issues: Although we invested weeks to mitigate issues with locks of the SQLite data base or file system (staged queries, file system timeouts, ...), `BatchJobs` kept working unreliable on some systems with high latency under certain conditions. This made `BatchJobs` unusable for many users.

[BatchJobs](https://github.com/tudo-r/BatchJobs/) and [BatchExperiments](https://github.com/tudo-r/Batchexperiments) will remain on CRAN, but new features are unlikely to be ported back.
The [vignette](https://batchtools.mlr-org.com/batchtools/articles/batchtools.html#migration) contains a section comparing the packages.
The [vignette](https://batchtools.mlr-org.com/articles/batchtools.html) contains a section comparing the packages.


## Resources
* [NEWS](https://batchtools.mlr-org.com/batchtools/news/)
* [Function reference](https://batchtools.mlr-org.com/batchtools/reference/)
* [Vignette](https://batchtools.mlr-org.com/batchtools/articles/batchtools.html)
* [Function reference](https://batchtools.mlr-org.com/reference/)
* [Vignette](https://batchtools.mlr-org.com/articles/batchtools.html)
* [JOSS Paper](https://doi.org/10.21105/joss.00135): Short paper on batchtools. Please cite this if you use batchtools.
* [Paper on BatchJobs/BatchExperiments](https://www.jstatsoft.org/v64/i11): The described concept still holds for batchtools and most examples work analogously (see the [vignette](https://batchtools.mlr-org.com/batchtools/articles/batchtools.html#migration) for differences between the packages).
* [Paper on BatchJobs/BatchExperiments](https://www.jstatsoft.org/v64/i11): The described concept still holds for batchtools and most examples work analogously (see the [vignette](https://batchtools.mlr-org.com/articles/batchtools.html) for differences between the packages).

## Citation
Please cite the [JOSS paper](https://doi.org/10.21105/joss.00135) using the following BibTeX entry:
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2 changes: 1 addition & 1 deletion _pkgdown.yml
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Expand Up @@ -16,7 +16,7 @@ toc:

navbar:
structure:
left: [reference, news, book]
left: [reference, news, articles, book]
right: [search, github, mattermost, stackoverflow, rss, lightswitch]
components:
home: ~
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