From 98df12519d19c48f64ce0a1d07c896035b8afc86 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Mon, 19 Aug 2024 18:38:26 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/slurmjobs@09404779d9eba0ffd48bf44e2c98a17a1ec593b5=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/slurmjobs.html | 18 +++++----- pkgdown.yml | 2 +- reference/array_submit.html | 6 ++-- reference/array_submit_example_2024-08-19.sh | 37 ++++++++++++++++++++ reference/job_single.html | 2 +- 5 files changed, 51 insertions(+), 14 deletions(-) create mode 100644 reference/array_submit_example_2024-08-19.sh diff --git a/articles/slurmjobs.html b/articles/slurmjobs.html index ea2a939..81ba00d 100644 --- a/articles/slurmjobs.html +++ b/articles/slurmjobs.html @@ -85,7 +85,7 @@

Leonardo University
-

13 August 2024

+

19 August 2024

Source: vignettes/slurmjobs.Rmd @@ -207,7 +207,7 @@

Creating Shell Scripts to sbatch 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/).

+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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