From 8b17e675663733c554d5cdba5a1d99b822ed7b7f Mon Sep 17 00:00:00 2001 From: Nick-Eagles <45461721+Nick-Eagles@users.noreply.github.com> Date: Tue, 17 Oct 2023 19:02:20 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/slurmjobs@deae1fea9ff5c1711bf024cd6ff0f2184367d5c3=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 | 26 +++++++------- pkgdown.yml | 2 +- reference/array_submit.html | 6 ++-- reference/array_submit_example_2023-10-17.sh | 36 ++++++++++++++++++++ reference/job_loop.html | 2 +- reference/job_single.html | 6 ++-- 6 files changed, 57 insertions(+), 21 deletions(-) create mode 100644 reference/array_submit_example_2023-10-17.sh diff --git a/articles/slurmjobs.html b/articles/slurmjobs.html index cec0461..86edcea 100644 --- a/articles/slurmjobs.html +++ b/articles/slurmjobs.html @@ -85,7 +85,7 @@

Leonardo University
lcolladotor@gmail.com -

16 October 2023

+

17 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 ) -#> 2023-10-16 17:58:29.905028 creating the logs directory at: logs +#> 2023-10-17 19:02:01.922508 creating the logs directory at: logs #> #!/bin/bash #> #SBATCH -p shared #> #SBATCH --mem-per-cpu=10G @@ -229,7 +229,7 @@

Creating Shell Scripts to sbatch #> echo "Task id: ${SLURM_ARRAY_TASK_ID}" #> #> ## Load the R module -#> module load conda_R +#> module load conda_R/4.3 #> #> ## List current modules for reproducibility #> module list @@ -249,7 +249,7 @@

Creating Shell Scripts to sbatch name = "my_array_job", memory = "5G", cores = 1, create_shell = FALSE, task_num = 10 ) -#> 2023-10-16 17:58:29.986669 creating the logs directory at: logs +#> 2023-10-17 19:02:02.020102 creating the logs directory at: logs #> #!/bin/bash #> #SBATCH -p shared #> #SBATCH --mem-per-cpu=5G @@ -273,7 +273,7 @@

Creating Shell Scripts to sbatch #> echo "Task id: ${SLURM_ARRAY_TASK_ID}" #> #> ## Load the R module -#> module load conda_R +#> module load conda_R/4.3 #> #> ## List current modules for reproducibility #> module list @@ -333,7 +333,7 @@

Creating Shell Scripts to sbatch #> [32] "echo \"Task id: ${SLURM_ARRAY_TASK_ID}\"" #> [33] "" #> [34] "## Load the R module" -#> [35] "module load conda_R" +#> [35] "module load conda_R/4.3" #> [36] "" #> [37] "## List current modules for reproducibility" #> [38] "module list" @@ -377,8 +377,8 @@

Submitting and Resubmitting Jobs name = "my_array_job", memory = "5G", cores = 1, create_shell = TRUE, task_num = 10 ) -#> 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 +#> 2023-10-17 19:02:02.221815 creating the logs directory at: logs +#> 2023-10-17 19:02:02.223787 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] "2023-10-16 17:58:31 UTC"
+
#> [1] "2023-10-17 19:02:03 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 2.263 secs
+
#> Time difference of 2.962 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     2023-10-16
+#>  date     2023-10-17
 #>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -627,7 +627,7 @@ 
Reproducibility#>  bibtex          0.5.1   2023-01-26 [1] RSPM (R 4.3.0)
 #>  BiocManager     1.30.22 2023-08-08 [2] CRAN (R 4.3.1)
 #>  BiocStyle     * 2.28.1  2023-09-14 [1] Bioconductor
-#>  bookdown        0.35    2023-08-09 [1] RSPM (R 4.3.0)
+#>  bookdown        0.36    2023-10-16 [1] RSPM (R 4.3.0)
 #>  bslib           0.5.1   2023-08-11 [2] RSPM (R 4.3.0)
 #>  cachem          1.0.8   2023-05-01 [2] RSPM (R 4.3.0)
 #>  cli             3.6.1   2023-03-23 [2] RSPM (R 4.3.0)
@@ -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  2023-10-16 [1] local
+#>  slurmjobs     * 0.99.0  2023-10-17 [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/pkgdown.yml b/pkgdown.yml
index e4d90ff..1a3ec0b 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   slurmjobs: slurmjobs.html
-last_built: 2023-10-16T17:58Z
+last_built: 2023-10-17T19:01Z
 
diff --git a/reference/array_submit.html b/reference/array_submit.html
index 39de8ef..95b6147 100644
--- a/reference/array_submit.html
+++ b/reference/array_submit.html
@@ -136,9 +136,9 @@ 
Examples

     create_shell = TRUE,
     task_num = 100
 )
-#> 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
+#> 2023-10-17 19:01:56.92567 creating the logs directory at:  logs
+#> 2023-10-17 19:01:56.927834 creating the shell file array_submit_example_2023-10-17.sh
+#> To submit the job use: sbatch array_submit_example_2023-10-17.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_2023-10-17.sh b/reference/array_submit_example_2023-10-17.sh
new file mode 100644
index 0000000..f72da72
--- /dev/null
+++ b/reference/array_submit_example_2023-10-17.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+#SBATCH -p shared
+#SBATCH --mem-per-cpu=10G
+#SBATCH --job-name=array_submit_example_2023-10-17
+#SBATCH -c 1
+#SBATCH -o logs/array_submit_example_2023-10-17.%a.txt
+#SBATCH -e logs/array_submit_example_2023-10-17.%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/4.3
+
+## 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_loop.html b/reference/job_loop.html
index 0bfb06c..d5f8cb5 100644
--- a/reference/job_loop.html
+++ b/reference/job_loop.html
@@ -182,7 +182,7 @@ 
Examples

 #> [32] "echo \"Task id: ${SLURM_ARRAY_TASK_ID}\""                                                                 
 #> [33] ""                                                                                                         
 #> [34] "## Load the R module"                                                                                     
-#> [35] "module load conda_R"                                                                                      
+#> [35] "module load conda_R/4.3"                                                                                  
 #> [36] ""                                                                                                         
 #> [37] "## List current modules for reproducibility"                                                              
 #> [38] "module list"                                                                                              
diff --git a/reference/job_single.html b/reference/job_single.html
index 2445b25..c5372e8 100644
--- a/reference/job_single.html
+++ b/reference/job_single.html
@@ -187,7 +187,7 @@ 
Examples

 #> echo "Task id: ${SLURM_ARRAY_TASK_ID}"
 #> 
 #> ## Load the R module
-#> module load conda_R
+#> module load conda_R/4.3
 #> 
 #> ## List current modules for reproducibility
 #> module list
@@ -229,7 +229,7 @@ 
Examples

 #> echo "Task id: ${SLURM_ARRAY_TASK_ID}"
 #> 
 #> ## Load the R module
-#> module load conda_R
+#> module load conda_R/4.3
 #> 
 #> ## List current modules for reproducibility
 #> module list
@@ -269,7 +269,7 @@ 
Examples

 #> echo "Task id: ${SLURM_ARRAY_TASK_ID}"
 #> 
 #> ## Load the R module
-#> module load conda_R
+#> module load conda_R/4.3
 #> 
 #> ## List current modules for reproducibility
 #> module list