diff --git a/404.html b/404.html index e8dcebb..23ba984 100644 --- a/404.html +++ b/404.html @@ -6,7 +6,7 @@
vignettes/slurmjobs.Rmd
slurmjobs.Rmd
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 @@ 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 • slurmjobs Authors and Citation • slurmjobs
@@ -17,7 +17,7 @@
@@ -47,7 +47,7 @@
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 • slurmjobs Changelog • slurmjobs
@@ -17,7 +17,7 @@
@@ -50,6 +50,11 @@ Changelog
Source: NEWS.md
+
+slurmjobs 1.2.3
+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
+
slurmjobs 1.2.2
- Use the
HOSTNAME
instead of SLURMD_NODENAME
environment variable to determine host running a SLURM job
@@ -108,7 +113,7 @@ slurmjobs 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 • slurmjobs Submit 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
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
@@ -125,7 +125,7 @@ Examples
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 • slurmjobs Find initials for a character vector — get_short_flags • slurmjobs Function reference • slurmjobs Function reference • slurmjobs
@@ -17,7 +17,7 @@
@@ -80,9 +80,7 @@ All functions
- 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.
@@ -120,7 +118,7 @@ All functions
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 • slurmjobs Return a tibble containing information about currently running jobs. — job_info • slurmjobs Example output from job_info(user = NULL, partition = "shared") — job_info_df • slurmjobs Example output from job_info(user = NULL, partition = "shared") — job_info_df • slurmjobs Build a bash script that loops over variables and submits SLURM jobs — job_loop • slurmjobs Build a bash script that loops over variables and submits SLURM jobs — job_loop • slurmjobs 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_report • slurmjobs 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_report • slurmjobs Build a SLURM job bash script — job_single • slurmjobs Build a SLURM job bash script — job_single • slurmjobs Parse script name or path into shell script path — parse_file_or_name • slurmjobs Parse script name or path into shell script path — parse_file_or_name • slurmjobs Parse time intervals reported by SLURM commands into difftimes — parse_slurm_time • slurmjobs Parse time intervals reported by SLURM commands into difftimes — parse_slurm_time • slurmjobs Example output from partition_info(partition = NULL, all_nodes = FALSE) — partition_df • slurmjobs Example output from partition_info(partition = NULL, all_nodes = FALSE) — partition_df • slurmjobs Return a tibble containing information about partitions. — partition_info • slurmjobs Return a tibble containing information about partitions. — partition_info • slurmjobs Get the segment of code used to construct a given character vector — vector_as_code • slurmjobs Get the segment of code used to construct a given character vector — vector_as_code • slurmjobs