diff --git a/404.html b/404.html index e8dcebb..23ba984 100644 --- a/404.html +++ b/404.html @@ -6,7 +6,7 @@ Page not found (404) • slurmjobs - + @@ -33,7 +33,7 @@ slurmjobs - 1.2.2 + 1.2.3 @@ -92,7 +92,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 63c6731..676afe6 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -1,5 +1,5 @@ -NA • slurmjobsNA • slurmjobs @@ -17,7 +17,7 @@ slurmjobs - 1.2.2 + 1.2.3 @@ -79,7 +79,7 @@

NA

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 47157a5..4a0fa8c 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -1,5 +1,5 @@ -Contributing to slurmjobs • slurmjobsContributing to slurmjobs • slurmjobs @@ -17,7 +17,7 @@ slurmjobs - 1.2.2 + 1.2.3 @@ -95,7 +95,7 @@

Code of Conduct
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/SUPPORT.html b/SUPPORT.html index 62b2bd6..ed9bc0a 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -1,5 +1,5 @@ -Getting help with slurmjobs • slurmjobsGetting help with slurmjobs • slurmjobs @@ -17,7 +17,7 @@ slurmjobs - 1.2.2 + 1.2.3 @@ -79,7 +79,7 @@

Issues or Feature Requests
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/articles/index.html b/articles/index.html index f51f1e9..dba9aa6 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,5 +1,5 @@ -Articles • slurmjobsArticles • slurmjobs @@ -17,7 +17,7 @@ slurmjobs - 1.2.2 + 1.2.3 @@ -65,7 +65,7 @@

All vignettes

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/articles/slurmjobs.html b/articles/slurmjobs.html index 597103a..c2545ae 100644 --- a/articles/slurmjobs.html +++ b/articles/slurmjobs.html @@ -6,7 +6,7 @@ Introduction to slurmjobs • slurmjobs - + @@ -34,7 +34,7 @@ slurmjobs - 1.2.2 + 1.2.3 @@ -85,7 +85,7 @@

Leonardo University
lcolladotor@gmail.com -

2 April 2024

+

31 July 2024

Source: vignettes/slurmjobs.Rmd @@ -161,7 +161,7 @@

Citing slurmjobs#> doi:10.18129/B9.bioc.slurmjobs #> <https://doi.org/10.18129/B9.bioc.slurmjobs>, #> https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package -#> version 1.2.2, <http://www.bioconductor.org/packages/slurmjobs>. +#> version 1.2.3, <http://www.bioconductor.org/packages/slurmjobs>. #> #> LieberInstitute (2024). "slurmjobs: Helper Functions for SLURM Jobs." #> _bioRxiv_. doi:10.1101/TODO <https://doi.org/10.1101/TODO>, @@ -207,7 +207,7 @@

Creating Shell Scripts to sbatch job_single( name = "my_shell_script", memory = "10G", cores = 2, create_shell = FALSE ) -#> 2024-04-02 20:30:32.853889 creating the logs directory at: logs +#> 2024-07-31 16:49:21.65054 creating the logs directory at: logs #> #!/bin/bash #> #SBATCH -p shared #> #SBATCH --mem=10G @@ -231,7 +231,7 @@

Creating Shell Scripts to sbatch #> echo "Task id: ${SLURM_ARRAY_TASK_ID}" #> #> ## Load the R module -#> module load conda_R/4.3 +#> module load conda_R/4.4 #> #> ## List current modules for reproducibility #> module list @@ -242,7 +242,7 @@

Creating Shell Scripts to sbatch #> echo "**** Job ends ****" #> date #> -#> ## This script was made using slurmjobs version 1.2.2 +#> ## This script was made using slurmjobs version 1.2.3 #> ## available from http://research.libd.org/slurmjobs/

Similarly, we can specify task_num to create an array job– in this case, one with 10 tasks.

@@ -251,7 +251,7 @@

Creating Shell Scripts to sbatch name = "my_array_job", memory = "5G", cores = 1, create_shell = FALSE, task_num = 10 ) -#> 2024-04-02 20:30:32.925053 creating the logs directory at: logs +#> 2024-07-31 16:49:21.720842 creating the logs directory at: logs #> #!/bin/bash #> #SBATCH -p shared #> #SBATCH --mem=5G @@ -276,7 +276,7 @@

Creating Shell Scripts to sbatch #> echo "Task id: ${SLURM_ARRAY_TASK_ID}" #> #> ## Load the R module -#> module load conda_R/4.3 +#> module load conda_R/4.4 #> #> ## List current modules for reproducibility #> module list @@ -287,7 +287,7 @@

Creating Shell Scripts to sbatch #> echo "**** Job ends ****" #> date #> -#> ## This script was made using slurmjobs version 1.2.2 +#> ## This script was made using slurmjobs version 1.2.3 #> ## available from http://research.libd.org/slurmjobs/

Another function, job_loop(), can be used to create more complex array jobs as compared with job_single(). It’s @@ -346,7 +346,7 @@

Creating Shell Scripts to sbatch #> echo "Task id: ${SLURM_ARRAY_TASK_ID}" #> #> ## Load the R module -#> module load conda_R/4.3 +#> module load conda_R/4.4 #> #> ## List current modules for reproducibility #> module list @@ -359,7 +359,7 @@

Creating Shell Scripts to sbatch #> #> } > $log_path 2>&1 #> -#> ## This script was made using slurmjobs version 1.2.2 +#> ## This script was made using slurmjobs version 1.2.3 #> ## available from http://research.libd.org/slurmjobs/

First, note the line Rscript bsp2_test.R --region ${region} --feature ${feature}. @@ -395,7 +395,7 @@

Creating Shell Scripts to sbatch #> #> session_info() #> -#> ## This script was made using slurmjobs version 1.2.2 +#> ## This script was made using slurmjobs version 1.2.3 #> ## available from http://research.libd.org/slurmjobs/

The code related to getopt at the top of the script reads in the unique combination of variable values into a list called @@ -424,8 +424,8 @@

Submitting and Resubmitting Jobs name = "my_array_job", memory = "5G", cores = 1, create_shell = TRUE, task_num = 10 ) -#> 2024-04-02 20:30:33.131896 creating the logs directory at: logs -#> 2024-04-02 20:30:33.133023 creating the shell file my_array_job.sh +#> 2024-07-31 16:49:21.924151 creating the logs directory at: logs +#> 2024-07-31 16:49:21.925211 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 @@ -618,7 +618,7 @@

ReproducibilityThe slurmjobs package (LieberInstitute, 2024) was made possible thanks to:

    -
  • R (R Core Team, 2023)
  • +
  • R (R Core Team, 2024)
  • BiocStyle (Oleś, 2023)
  • @@ -627,7 +627,7 @@

    Reproducibility
  • knitr (Xie, -2023)
  • +2024)
  • RefManageR (McLean, 2017)
  • @@ -653,30 +653,30 @@

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

    Date the vignette was generated.

    -
    #> [1] "2024-04-02 20:30:34 UTC"
    +
    #> [1] "2024-07-31 16:49:22 UTC"

    Wallclock time spent generating the vignette.

    -
    #> Time difference of 2.007 secs
    +
    #> Time difference of 1.979 secs

    R session information.

    #> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
     #>  setting  value
    -#>  version  R version 4.3.2 (2023-10-31)
    -#>  os       Ubuntu 22.04.3 LTS
    +#>  version  R version 4.3.3 (2024-02-29)
    +#>  os       Ubuntu 22.04.4 LTS
     #>  system   x86_64, linux-gnu
     #>  ui       X11
     #>  language en
     #>  collate  en_US.UTF-8
     #>  ctype    en_US.UTF-8
     #>  tz       UTC
    -#>  date     2024-04-02
    +#>  date     2024-07-31
     #>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
     #> 
     #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
     #>  package       * version date (UTC) lib source
     #>  backports       1.4.1   2021-12-13 [1] RSPM (R 4.3.0)
     #>  bibtex          0.5.1   2023-01-26 [1] RSPM (R 4.3.0)
    -#>  BiocManager     1.30.22 2023-08-08 [2] CRAN (R 4.3.2)
    +#>  BiocManager     1.30.22 2023-08-08 [1] RSPM (R 4.3.0)
     #>  BiocStyle     * 2.30.0  2023-10-24 [1] Bioconductor
    -#>  bookdown        0.38    2024-03-04 [1] RSPM (R 4.3.0)
    +#>  bookdown        0.39    2024-04-15 [1] RSPM (R 4.3.0)
     #>  bslib           0.7.0   2024-03-29 [2] RSPM (R 4.3.0)
     #>  cachem          1.0.8   2023-05-01 [2] RSPM (R 4.3.0)
     #>  cli             3.6.2   2023-12-11 [2] RSPM (R 4.3.0)
    @@ -690,19 +690,20 @@ 

    Reproducibility#> fs 1.6.3 2023-07-20 [2] RSPM (R 4.3.0) #> generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0) #> glue 1.7.0 2024-01-09 [2] RSPM (R 4.3.0) -#> htmltools 0.5.8 2024-03-25 [2] RSPM (R 4.3.0) +#> htmltools 0.5.8.1 2024-04-04 [2] RSPM (R 4.3.0) +#> htmlwidgets 1.6.4 2023-12-06 [2] RSPM (R 4.3.0) #> httr 1.4.7 2023-08-15 [2] RSPM (R 4.3.0) #> jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.3.0) #> jsonlite 1.8.8 2023-12-04 [2] RSPM (R 4.3.0) #> knitcitations * 1.0.12 2021-01-10 [1] RSPM (R 4.3.0) -#> knitr 1.45 2023-10-30 [2] RSPM (R 4.3.0) +#> knitr 1.46 2024-04-06 [2] RSPM (R 4.3.0) #> lifecycle 1.0.4 2023-11-07 [2] RSPM (R 4.3.0) #> lubridate 1.9.3 2023-09-27 [1] RSPM (R 4.3.0) #> magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.3.0) #> memoise 2.0.1 2021-11-26 [2] RSPM (R 4.3.0) #> pillar 1.9.0 2023-03-22 [2] RSPM (R 4.3.0) #> pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.3.0) -#> pkgdown 2.0.7 2022-12-14 [2] RSPM (R 4.3.0) +#> pkgdown 2.0.9 2024-04-18 [2] RSPM (R 4.3.0) #> plyr 1.8.9 2023-10-02 [1] RSPM (R 4.3.0) #> purrr 1.0.2 2023-08-10 [2] RSPM (R 4.3.0) #> R6 2.5.1 2021-08-19 [2] RSPM (R 4.3.0) @@ -713,7 +714,7 @@

    Reproducibility#> rmarkdown 2.26 2024-03-05 [2] RSPM (R 4.3.0) #> sass 0.4.9 2024-03-15 [2] RSPM (R 4.3.0) #> sessioninfo * 1.2.2 2021-12-06 [2] RSPM (R 4.3.0) -#> slurmjobs * 1.2.2 2024-04-02 [1] local +#> slurmjobs * 1.2.3 2024-07-31 [1] local #> stringi 1.8.3 2023-12-11 [2] RSPM (R 4.3.0) #> stringr 1.5.1 2023-11-14 [2] RSPM (R 4.3.0) #> systemfonts 1.0.6 2024-03-07 [2] RSPM (R 4.3.0) @@ -739,7 +740,7 @@

    BibliographyBiocStyle (Oleś, 2023) with knitr (Xie, -2023) and rmarkdown +2024) and rmarkdown (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.

    Citations made with RefManageR (McLean, 2017).

    @@ -752,7 +753,7 @@

    Bibliography[2] LieberInstitute. slurmjobs: Helper Functions for SLURM Jobs. https://github.com/LieberInstitute/slurmjobs/slurmjobs - -R package version 1.2.2. 2024. DOI: +R package version 1.2.3. 2024. DOI: 10.18129/B9.bioc.slurmjobs. URL: http://www.bioconductor.org/packages/slurmjobs. @@ -773,10 +774,10 @@

    Bibliographyhttps://bioconductor.org/packages/BiocStyle.

    -[5] +[5] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, -2023. URL: +2024. URL: https://www.R-project.org/.

    @@ -798,9 +799,9 @@

    Bibliographyhttps://dplyr.tidyverse.org.

    -[9] +[9] Y. Xie. knitr: A General-Purpose Package for Dynamic Report -Generation in R. R package version 1.45. 2023. URL: +Generation in R. R package version 1.46. 2024. URL: https://yihui.org/knitr/.

    @@ -823,7 +824,7 @@

    Bibliography

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/authors.html b/authors.html index 347fdc1..d7d54bc 100644 --- a/authors.html +++ b/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • slurmjobsAuthors and Citation • slurmjobs @@ -17,7 +17,7 @@ slurmjobs - 1.2.2 + 1.2.3 @@ -47,7 +47,7 @@
    @@ -66,14 +66,14 @@

    Citation

    LieberInstitute (2024). slurmjobs: Helper Functions for SLURM Jobs. -doi:10.18129/B9.bioc.slurmjobs, https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package version 1.2.2, http://www.bioconductor.org/packages/slurmjobs. +doi:10.18129/B9.bioc.slurmjobs, https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package version 1.2.3, http://www.bioconductor.org/packages/slurmjobs.

    @Manual{,
       title = {slurmjobs: Helper Functions for SLURM Jobs},
       author = {{LieberInstitute}},
       year = {2024},
       url = {http://www.bioconductor.org/packages/slurmjobs},
    -  note = {https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package version 1.2.2},
    +  note = {https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package version 1.2.3},
       doi = {10.18129/B9.bioc.slurmjobs},
     }

    LieberInstitute (2024). @@ -101,7 +101,7 @@

    Citation

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/index.html b/index.html index 986b7fa..4b185c9 100644 --- a/index.html +++ b/index.html @@ -6,17 +6,14 @@ Helper Functions for SLURM jobs • slurmjobs - + - + Changelog • slurmjobsChangelog • slurmjobs @@ -17,7 +17,7 @@ slurmjobs - 1.2.2 + 1.2.3 @@ -50,6 +50,11 @@

    Changelog

    Source: NEWS.md +
    + +

    BUG FIXES

    +
    • Fix submission of jobs, modification of the appropriate shell script, and finding of log files when using array_submit() with an absolute path to the name parameter
    • +
    • Use the HOSTNAME instead of SLURMD_NODENAME environment variable to determine host running a SLURM job
    • @@ -108,7 +113,7 @@
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/pkgdown.yml b/pkgdown.yml index fb4efd6..b4f5165 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,7 +1,7 @@ pandoc: 3.1.1 -pkgdown: 2.0.7 +pkgdown: 2.0.9 pkgdown_sha: ~ articles: slurmjobs: slurmjobs.html -last_built: 2024-04-02T20:30Z +last_built: 2024-07-31T16:49Z diff --git a/reference/array_submit.html b/reference/array_submit.html index 9788a66..500f269 100644 --- a/reference/array_submit.html +++ b/reference/array_submit.html @@ -1,5 +1,5 @@ -Submit an array job with a specified set of task IDs — array_submit • slurmjobsSubmit an array job with a specified set of task IDs — array_submit • slurmjobs slurmjobs - 1.2.2 + 1.2.3 @@ -136,9 +136,9 @@

    Examples

    create_shell = TRUE, task_num = 100 ) -#> 2024-04-02 20:30:29.270351 creating the logs directory at: logs -#> 2024-04-02 20:30:29.271871 creating the shell file array_submit_example_2024-04-02.sh -#> To submit the job use: sbatch array_submit_example_2024-04-02.sh +#> 2024-07-31 16:49:17.785699 creating the logs directory at: logs +#> 2024-07-31 16:49:17.78693 creating the shell file array_submit_example_2024-07-31.sh +#> To submit the job use: sbatch array_submit_example_2024-07-31.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) @@ -162,7 +162,7 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/reference/array_submit_example_2024-07-31.sh b/reference/array_submit_example_2024-07-31.sh new file mode 100644 index 0000000..9add54f --- /dev/null +++ b/reference/array_submit_example_2024-07-31.sh @@ -0,0 +1,37 @@ +#!/bin/bash +#SBATCH -p shared +#SBATCH --mem=10G +#SBATCH --job-name=array_submit_example_2024-07-31 +#SBATCH -c 1 +#SBATCH -t 1-00:00:00 +#SBATCH -o logs/array_submit_example_2024-07-31.%a.txt +#SBATCH -e logs/array_submit_example_2024-07-31.%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: ${HOSTNAME}" +echo "Task id: ${SLURM_ARRAY_TASK_ID}" + +## Load the R module +module load conda_R/4.4 + +## 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 1.2.3 +## available from http://research.libd.org/slurmjobs/ diff --git a/reference/get_list_indexing.html b/reference/get_list_indexing.html index 9b997b2..1b523f9 100644 --- a/reference/get_list_indexing.html +++ b/reference/get_list_indexing.html @@ -1,5 +1,5 @@ -Subset a specific list index given a particular array task index — get_list_indexing • slurmjobs slurmjobs - 1.2.2 + 1.2.3 @@ -125,7 +125,7 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/reference/get_short_flags.html b/reference/get_short_flags.html index 98b067d..ce395e7 100644 --- a/reference/get_short_flags.html +++ b/reference/get_short_flags.html @@ -1,5 +1,5 @@ -Find initials for a character vector — get_short_flags • slurmjobsFind initials for a character vector — get_short_flags • slurmjobsFunction reference • slurmjobsFunction reference • slurmjobs @@ -17,7 +17,7 @@ slurmjobs - 1.2.2 + 1.2.3 @@ -80,9 +80,7 @@

    All functions

    job_report()

    -

    Given the ID for a completed or currently running SLURM job, return a tibble -containing outputs from 'sacct'. In particular, returns information about -job name, ID, user, status, and allocated and used memory and CPUs.

    +

    Given the ID for a completed or currently running SLURM job, return a tibble containing outputs from 'sacct'. In particular, returns information about job name, ID, user, status, and allocated and used memory and CPUs.

    job_single()

    @@ -120,7 +118,7 @@

    All functions
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/reference/job_info.html b/reference/job_info.html index 7134b96..57c6882 100644 --- a/reference/job_info.html +++ b/reference/job_info.html @@ -1,5 +1,5 @@ -Return a tibble containing information about currently running jobs. — job_info • slurmjobsReturn a tibble containing information about currently running jobs. — job_info • slurmjobsExample output from job_info(user = NULL, partition = "shared") — job_info_df • slurmjobsExample output from job_info(user = NULL, partition = "shared") — job_info_df • slurmjobsBuild a bash script that loops over variables and submits SLURM jobs — job_loop • slurmjobsBuild a bash script that loops over variables and submits SLURM jobs — job_loop • slurmjobsGiven the ID for a completed or currently running SLURM job, return a tibble -containing outputs from 'sacct'. In particular, returns information about -job name, ID, user, status, and allocated and used memory and CPUs. — job_report • slurmjobsGiven the ID for a completed or currently running SLURM job, return a tibble containing outputs from 'sacct'. In particular, returns information about job name, ID, user, status, and allocated and used memory and CPUs. — job_report • slurmjobsBuild a SLURM job bash script — job_single • slurmjobsBuild a SLURM job bash script — job_single • slurmjobsParse script name or path into shell script path — parse_file_or_name • slurmjobsParse script name or path into shell script path — parse_file_or_name • slurmjobsParse time intervals reported by SLURM commands into difftimes — parse_slurm_time • slurmjobsParse time intervals reported by SLURM commands into difftimes — parse_slurm_time • slurmjobsExample output from partition_info(partition = NULL, all_nodes = FALSE) — partition_df • slurmjobsExample output from partition_info(partition = NULL, all_nodes = FALSE) — partition_df • slurmjobsReturn a tibble containing information about partitions. — partition_info • slurmjobsReturn a tibble containing information about partitions. — partition_info • slurmjobsGet the segment of code used to construct a given character vector — vector_as_code • slurmjobsGet the segment of code used to construct a given character vector — vector_as_code • slurmjobs