vignettes/slurmjobs.Rmd
slurmjobs.Rmdsbatch
job_single(
name = "my_shell_script", memory = "10G", cores = 2, create_shell = FALSE
)
-#> 2024-08-13 13:06:43.930463 creating the logs directory at: logs
+#> 2024-08-19 18:38:09.685331 creating the logs directory at: logs
#> #!/bin/bash
#> #SBATCH -p shared
#> #SBATCH --mem=10G
@@ -251,7 +251,7 @@ Creating Shell Scripts to sbatch
name = "my_array_job", memory = "5G", cores = 1, create_shell = FALSE,
task_num = 10
)
-#> 2024-08-13 13:06:43.999427 creating the logs directory at: logs
+#> 2024-08-19 18:38:09.756534 creating the logs directory at: logs
#> #!/bin/bash
#> #SBATCH -p shared
#> #SBATCH --mem=5G
@@ -424,8 +424,8 @@ Submitting and Resubmitting Jobs name = "my_array_job", memory = "5G", cores = 1, create_shell = TRUE,
task_num = 10
)
-#> 2024-08-13 13:06:44.199667 creating the logs directory at: logs
-#> 2024-08-13 13:06:44.200621 creating the shell file my_array_job.sh
+#> 2024-08-19 18:38:09.964419 creating the logs directory at: logs
+#> 2024-08-19 18:38:09.965473 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
@@ -653,9 +653,9 @@ Reproducibilitylibrary("knitr")
knit("slurmjobs.Rmd", tangle = TRUE)
Date the vignette was generated.
-#> [1] "2024-08-13 13:06:45 UTC"
+#> [1] "2024-08-19 18:38:10 UTC"
Wallclock time spent generating the vignette.
-#> Time difference of 1.903 secs
+#> Time difference of 2.011 secs
R session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
@@ -667,7 +667,7 @@ Reproducibility#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz UTC
-#> date 2024-08-13
+#> date 2024-08-19
#> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -714,7 +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 * 1.2.4 2024-08-13 [1] local
+#> slurmjobs * 1.2.4 2024-08-19 [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)
diff --git a/pkgdown.yml b/pkgdown.yml
index d3b1b83..655d410 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.9
pkgdown_sha: ~
articles:
slurmjobs: slurmjobs.html
-last_built: 2024-08-13T13:06Z
+last_built: 2024-08-19T18:38Z
diff --git a/reference/array_submit.html b/reference/array_submit.html
index 028923b..efdf347 100644
--- a/reference/array_submit.html
+++ b/reference/array_submit.html
@@ -136,9 +136,9 @@ Examples
create_shell = TRUE,
task_num = 100
)
-#> 2024-08-13 13:06:40.255308 creating the logs directory at: logs
-#> 2024-08-13 13:06:40.256411 creating the shell file array_submit_example_2024-08-13.sh
-#> To submit the job use: sbatch array_submit_example_2024-08-13.sh
+#> 2024-08-19 18:38:05.731713 creating the logs directory at: logs
+#> 2024-08-19 18:38:05.732956 creating the shell file array_submit_example_2024-08-19.sh
+#> To submit the job use: sbatch array_submit_example_2024-08-19.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_2024-08-19.sh b/reference/array_submit_example_2024-08-19.sh
new file mode 100644
index 0000000..bf58fee
--- /dev/null
+++ b/reference/array_submit_example_2024-08-19.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+#SBATCH -p shared
+#SBATCH --mem=10G
+#SBATCH --job-name=array_submit_example_2024-08-19
+#SBATCH -c 1
+#SBATCH -t 1-00:00:00
+#SBATCH -o logs/array_submit_example_2024-08-19.%a.txt
+#SBATCH -e logs/array_submit_example_2024-08-19.%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 1.2.4
+## available from http://research.libd.org/slurmjobs/
diff --git a/reference/job_single.html b/reference/job_single.html
index 44046eb..f3f55c4 100644
--- a/reference/job_single.html
+++ b/reference/job_single.html
@@ -109,7 +109,7 @@ Arguments
time_limit
character(1): time limit specified in a format accepted by
the --time parameter to sbatch (e.g. "4:00:00"). Defaults to 1
-day, following the JHPCE default (https://jhpce.jhu.edu/knowledge-base/setting-a-time-limit-for-your-slurm-job-on-jhpce/).
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