From c9ddb7ce9e218fab3402d5d4d9855109b20b71b0 Mon Sep 17 00:00:00 2001 From: Nick-Eagles <45461721+Nick-Eagles@users.noreply.github.com> Date: Mon, 16 Oct 2023 17:58:47 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/slurmjobs@4c550389de1df833cf6f1195b61935d209277393=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- SUPPORT.html | 16 +-------- articles/slurmjobs.html | 18 +++++----- index.html | 13 ++----- news/index.html | 6 ++-- pkgdown.yml | 2 +- reference/array_submit.html | 12 +++++-- reference/array_submit_example_2023-10-16.sh | 36 ++++++++++++++++++++ reference/job_info.html | 6 ++++ reference/job_loop.html | 6 ++++ reference/job_report.html | 6 ++++ reference/job_single.html | 6 ++++ reference/partition_info.html | 6 ++++ 12 files changed, 92 insertions(+), 41 deletions(-) create mode 100644 reference/array_submit_example_2023-10-16.sh diff --git a/SUPPORT.html b/SUPPORT.html index 1cb6ca5..8e9db23 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -58,24 +58,10 @@

Make a reprexStackOverflow link.

-

Where to post it?

-

The Bioconductor help web page gives an overview of places that may help answer your question.

-
-

Issues or Feature Requests

-

Before opening a new issue or feature request, be sure to search issues and pull requests to ensure that one does not already exist or has been implemented in the development version.

+

The best place to report issues or make feature requests is on the GitHub repository. Before opening a new issue or feature request, be sure to search issues and pull requests to ensure that one does not already exist or has been implemented in a more recent version.

Note. You can remove the is:open search term in the issues page to search through open and closed issues. See this link to learn more about modifying the search.

-
-

What happens next?

-

Our Bioconductor maintainers are limited in resources but they do strive to be as responsive as possible.

-

Please do not forget to tag the appropriate maintainer in the issue with their GitHub username (e.g., @username).

-

In order to make it easy as possible for Bioconductor core developers to remediate the issue. Provide an accurate, brief, and reproducible report as outlined in the issue templates.

-

Thank you for trusting Bioconductor.

-
diff --git a/articles/slurmjobs.html b/articles/slurmjobs.html index 14a2b90..cec0461 100644 --- a/articles/slurmjobs.html +++ b/articles/slurmjobs.html @@ -85,7 +85,7 @@

Leonardo University
lcolladotor@gmail.com -

13 October 2023

+

16 October 2023

Source: vignettes/slurmjobs.Rmd @@ -206,7 +206,7 @@

Creating Shell Scripts to sbatch job_single( name = "my_shell_script", memory = "10G", cores = 2, create_shell = FALSE ) -#> 2023-10-13 19:39:56.918628 creating the logs directory at: logs +#> 2023-10-16 17:58:29.905028 creating the logs directory at: logs #> #!/bin/bash #> #SBATCH -p shared #> #SBATCH --mem-per-cpu=10G @@ -249,7 +249,7 @@

Creating Shell Scripts to sbatch name = "my_array_job", memory = "5G", cores = 1, create_shell = FALSE, task_num = 10 ) -#> 2023-10-13 19:39:56.99789 creating the logs directory at: logs +#> 2023-10-16 17:58:29.986669 creating the logs directory at: logs #> #!/bin/bash #> #SBATCH -p shared #> #SBATCH --mem-per-cpu=5G @@ -377,8 +377,8 @@

Submitting and Resubmitting Jobs name = "my_array_job", memory = "5G", cores = 1, create_shell = TRUE, task_num = 10 ) -#> 2023-10-13 19:39:57.156427 creating the logs directory at: logs -#> 2023-10-13 19:39:57.157757 creating the shell file my_array_job.sh +#> 2023-10-16 17:58:30.14865 creating the logs directory at: logs +#> 2023-10-16 17:58:30.150015 creating the shell file my_array_job.sh #> To submit the job use: sbatch my_array_job.sh # Suppose that tasks 3, 6, 7, and 8 failed @@ -604,9 +604,9 @@

Reproducibilitylibrary("knitr") knit("slurmjobs.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2023-10-13 19:39:58 UTC"
+
#> [1] "2023-10-16 17:58:31 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 2.149 secs
+
#> Time difference of 2.263 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -618,7 +618,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2023-10-13
+#>  date     2023-10-16
 #>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -665,7 +665,7 @@ 
Reproducibility#>  rprojroot       2.0.3   2022-04-02 [2] RSPM (R 4.3.0)
 #>  sass            0.4.7   2023-07-15 [2] RSPM (R 4.3.0)
 #>  sessioninfo   * 1.2.2   2021-12-06 [2] RSPM (R 4.3.0)
-#>  slurmjobs     * 0.99.0  2023-10-13 [1] local
+#>  slurmjobs     * 0.99.0  2023-10-16 [1] local
 #>  stringi         1.7.12  2023-01-11 [2] RSPM (R 4.3.0)
 #>  stringr         1.5.0   2022-12-02 [2] RSPM (R 4.3.0)
 #>  systemfonts     1.0.5   2023-10-09 [2] RSPM (R 4.3.0)
diff --git a/index.html b/index.html
index c87be89..6c2a916 100644
--- a/index.html
+++ b/index.html
@@ -82,22 +82,15 @@
 

 
Installation instructions
 

-
Get the latest stable R release from CRAN. Then install slurmjobs from Bioconductor using the following code:

+
Get the latest stable R release from CRAN. Then install slurmjobs from GitHub with:

 
-if (!requireNamespace("BiocManager", quietly = TRUE)) {
-    install.packages("BiocManager")
-}
-
-BiocManager::install("slurmjobs")

-
And the development version from GitHub with:

-
-BiocManager::install("LieberInstitute/slurmjobs")

+remotes::install_github("LieberInstitute/slurmjobs")

Citation

Below is the citation output from using citation('slurmjobs') in R. Please run this yourself to check for any updates on how to cite slurmjobs.

-
+
 print(citation("slurmjobs"), bibtex = TRUE)
 #> To cite package 'slurmjobs' in publications use:
 #> 
diff --git a/news/index.html b/news/index.html
index ac1a0e1..52040a7 100644
--- a/news/index.html
+++ b/news/index.html
@@ -54,10 +54,10 @@ 
Changelog 

 
slurmjobs 0.99.0

 
NEW FEATURES

 
  • Added a NEWS.md file to track changes to the package.
    • 
+
  • Added core files (such as DESCRIPTION, NAMESPACE, etc) to make slurmjobs a Bioconductor-style package
    • 
 
SIGNIFICANT USER-VISIBLE CHANGES

-
  • Your main changes to a function foo() or parameter param.
    • 
-
BUG FIXES

-
diff --git a/pkgdown.yml b/pkgdown.yml index e638601..e4d90ff 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: slurmjobs: slurmjobs.html -last_built: 2023-10-13T19:39Z +last_built: 2023-10-16T17:58Z diff --git a/reference/array_submit.html b/reference/array_submit.html index e39817c..39de8ef 100644 --- a/reference/array_submit.html +++ b/reference/array_submit.html @@ -111,6 +111,12 @@

Value

The path to job_bash.

+
+
+

See also

+

Other shell-script creation and submission functions: +job_loop(), +job_single()

Author

@@ -130,9 +136,9 @@

Examples

create_shell = TRUE, task_num = 100 ) -#> 2023-10-13 19:39:53.603035 creating the logs directory at: logs -#> 2023-10-13 19:39:53.604424 creating the shell file array_submit_example_2023-10-13.sh -#> To submit the job use: sbatch array_submit_example_2023-10-13.sh +#> 2023-10-16 17:58:26.400503 creating the logs directory at: logs +#> 2023-10-16 17:58:26.401945 creating the shell file array_submit_example_2023-10-16.sh +#> To submit the job use: sbatch array_submit_example_2023-10-16.sh ## Now we can submit the job for a set of task IDs (or omit 'task_ids' ## to automatically grab those same failed task IDs) diff --git a/reference/array_submit_example_2023-10-16.sh b/reference/array_submit_example_2023-10-16.sh new file mode 100644 index 0000000..3bd567d --- /dev/null +++ b/reference/array_submit_example_2023-10-16.sh @@ -0,0 +1,36 @@ +#!/bin/bash +#SBATCH -p shared +#SBATCH --mem-per-cpu=10G +#SBATCH --job-name=array_submit_example_2023-10-16 +#SBATCH -c 1 +#SBATCH -o logs/array_submit_example_2023-10-16.%a.txt +#SBATCH -e logs/array_submit_example_2023-10-16.%a.txt +#SBATCH --mail-type=ALL +#SBATCH --array=1-100%20 + +set -e + +echo "**** Job starts ****" +date + +echo "**** JHPCE info ****" +echo "User: ${USER}" +echo "Job id: ${SLURM_JOB_ID}" +echo "Job name: ${SLURM_JOB_NAME}" +echo "Node name: ${SLURMD_NODENAME}" +echo "Task id: ${SLURM_ARRAY_TASK_ID}" + +## Load the R module +module load conda_R + +## List current modules for reproducibility +module list + +## Edit with your job command +Rscript -e "options(width = 120); sessioninfo::session_info()" + +echo "**** Job ends ****" +date + +## This script was made using slurmjobs version 0.99.0 +## available from http://research.libd.org/slurmjobs/ diff --git a/reference/job_info.html b/reference/job_info.html index 27acb86..eda6a04 100644 --- a/reference/job_info.html +++ b/reference/job_info.html @@ -80,6 +80,12 @@

Value

A tibble with job information about currently running jobs.

+
+
+

See also

+

Other monitoring and informational functions: +job_report(), +partition_info()

Author

diff --git a/reference/job_loop.html b/reference/job_loop.html index ce26868..0bfb06c 100644 --- a/reference/job_loop.html +++ b/reference/job_loop.html @@ -127,6 +127,12 @@

Value

A character vector with the script contents. If create_shell was specified then it also creates the actual script in the current working directory.

+
+
+

See also

+

Other shell-script creation and submission functions: +array_submit(), +job_single()

Author

diff --git a/reference/job_report.html b/reference/job_report.html index bd58d44..7879f20 100644 --- a/reference/job_report.html +++ b/reference/job_report.html @@ -81,6 +81,12 @@

Value

A tibble with information about the requested job.

+
+
+

See also

+

Other monitoring and informational functions: +job_info(), +partition_info()

Author

diff --git a/reference/job_single.html b/reference/job_single.html index 60a2158..2445b25 100644 --- a/reference/job_single.html +++ b/reference/job_single.html @@ -147,6 +147,12 @@

Value

Details

For a given SLURM job that is currently running you can alter the options using scontrol alter.

+
+
+

See also

+

Other shell-script creation and submission functions: +array_submit(), +job_loop()

Author

diff --git a/reference/partition_info.html b/reference/partition_info.html index aa270cd..791651c 100644 --- a/reference/partition_info.html +++ b/reference/partition_info.html @@ -81,6 +81,12 @@

Value

A tibble with memory and CPU information about partitions.

+
+
+

See also

+

Other monitoring and informational functions: +job_info(), +job_report()

Author