vignettes/slurmjobs.Rmd
slurmjobs.Rmdslurmjobs#> doi:10.18129/B9.bioc.slurmjobs
#> <https://doi.org/10.18129/B9.bioc.slurmjobs>,
#> https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package
-#> version 1.2.3, <http://www.bioconductor.org/packages/slurmjobs>.
+#> version 1.2.4, <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
)
-#> 2024-07-31 16:49:21.65054 creating the logs directory at: logs
+#> 2024-08-13 13:06:43.930463 creating the logs directory at: logs
#> #!/bin/bash
#> #SBATCH -p shared
#> #SBATCH --mem=10G
@@ -242,7 +242,7 @@ Creating Shell Scripts to sbatch
#> echo "**** Job ends ****"
#> date
#>
-#> ## This script was made using slurmjobs version 1.2.3
+#> ## This script was made using slurmjobs version 1.2.4
#> ## 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
)
-#> 2024-07-31 16:49:21.720842 creating the logs directory at: logs
+#> 2024-08-13 13:06:43.999427 creating the logs directory at: logs
#> #!/bin/bash
#> #SBATCH -p shared
#> #SBATCH --mem=5G
@@ -287,7 +287,7 @@ Creating Shell Scripts to sbatch
#> echo "**** Job ends ****"
#> date
#>
-#> ## This script was made using slurmjobs version 1.2.3
+#> ## This script was made using slurmjobs version 1.2.4
#> ## 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
@@ -359,7 +359,7 @@
Creating Shell Scripts to sbatch
#>
#> } > $log_path 2>&1
#>
-#> ## This script was made using slurmjobs version 1.2.3
+#> ## This script was made using slurmjobs version 1.2.4
#> ## 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 1.2.3
+#> ## This script was made using slurmjobs version 1.2.4
#> ## 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
)
-#> 2024-07-31 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
+#> 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
#> 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] "2024-07-31 16:49:22 UTC"
+#> [1] "2024-08-13 13:06:45 UTC"
Wallclock time spent generating the vignette.
-#> Time difference of 1.979 secs
+#> Time difference of 1.903 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 2024-07-31
+#> date 2024-08-13
#> 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 * 1.2.3 2024-07-31 [1] local
+#> slurmjobs * 1.2.4 2024-08-13 [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)
@@ -753,7 +753,7 @@ Bibliography[2]
LieberInstitute. slurmjobs: Helper Functions for SLURM Jobs. https://github.com/LieberInstitute/slurmjobs/slurmjobs -
-R package version 1.2.3. 2024. DOI:
+R package version 1.2.4. 2024. DOI:
10.18129/B9.bioc.slurmjobs.
URL:
http://www.bioconductor.org/packages/slurmjobs.
diff --git a/authors.html b/authors.html
index d7d54bc..ac76eec 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
@@ -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 1.2.3, http://www.bioconductor.org/packages/slurmjobs.
+doi:10.18129/B9.bioc.slurmjobs, https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package version 1.2.4, 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 1.2.3},
+ note = {https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package version 1.2.4},
doi = {10.18129/B9.bioc.slurmjobs},
}
LieberInstitute (2024).
diff --git a/index.html b/index.html
index 4b185c9..4580919 100644
--- a/index.html
+++ b/index.html
@@ -34,7 +34,7 @@
diff --git a/news/index.html b/news/index.html
index c35b9b0..ffdd6a2 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
@@ -50,6 +50,12 @@
Changelog
Source: NEWS.md
+
+slurmjobs 1.2.4
+BUG FIXES
+- Recognize/ handle
OUT_OF_MEMORY job status, fixing a fatal error in job_report()
+
+
slurmjobs 1.2.3
BUG FIXES
diff --git a/pkgdown.yml b/pkgdown.yml
index b4f5165..d3b1b83 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.9
pkgdown_sha: ~
articles:
slurmjobs: slurmjobs.html
-last_built: 2024-07-31T16:49Z
+last_built: 2024-08-13T13:06Z
diff --git a/reference/array_submit.html b/reference/array_submit.html
index 500f269..028923b 100644
--- a/reference/array_submit.html
+++ b/reference/array_submit.html
@@ -23,7 +23,7 @@
@@ -136,9 +136,9 @@ Examples
create_shell = TRUE,
task_num = 100
)
-#> 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
+#> 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
## 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_2024-08-13.sh b/reference/array_submit_example_2024-08-13.sh
new file mode 100644
index 0000000..45810dc
--- /dev/null
+++ b/reference/array_submit_example_2024-08-13.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+#SBATCH -p shared
+#SBATCH --mem=10G
+#SBATCH --job-name=array_submit_example_2024-08-13
+#SBATCH -c 1
+#SBATCH -t 1-00:00:00
+#SBATCH -o logs/array_submit_example_2024-08-13.%a.txt
+#SBATCH -e logs/array_submit_example_2024-08-13.%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/get_list_indexing.html b/reference/get_list_indexing.html
index 1b523f9..c28ca37 100644
--- a/reference/get_list_indexing.html
+++ b/reference/get_list_indexing.html
@@ -22,7 +22,7 @@
diff --git a/reference/get_short_flags.html b/reference/get_short_flags.html
index ce395e7..4d7719e 100644
--- a/reference/get_short_flags.html
+++ b/reference/get_short_flags.html
@@ -20,7 +20,7 @@
diff --git a/reference/index.html b/reference/index.html
index 06be7a2..caef935 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
diff --git a/reference/job_info.html b/reference/job_info.html
index 57c6882..615043e 100644
--- a/reference/job_info.html
+++ b/reference/job_info.html
@@ -19,7 +19,7 @@
diff --git a/reference/job_info_df.html b/reference/job_info_df.html
index 503df01..499763c 100644
--- a/reference/job_info_df.html
+++ b/reference/job_info_df.html
@@ -18,7 +18,7 @@
diff --git a/reference/job_loop.html b/reference/job_loop.html
index 117c0d1..287e238 100644
--- a/reference/job_loop.html
+++ b/reference/job_loop.html
@@ -18,7 +18,7 @@
diff --git a/reference/job_report.html b/reference/job_report.html
index ea6f7e8..6592cb4 100644
--- a/reference/job_report.html
+++ b/reference/job_report.html
@@ -19,7 +19,7 @@
diff --git a/reference/job_single.html b/reference/job_single.html
index 28f1f2e..44046eb 100644
--- a/reference/job_single.html
+++ b/reference/job_single.html
@@ -20,7 +20,7 @@
@@ -205,7 +205,7 @@ Examples
#> echo "**** Job ends ****"
#> date
#>
-#> ## This script was made using slurmjobs version 1.2.3
+#> ## This script was made using slurmjobs version 1.2.4
#> ## available from http://research.libd.org/slurmjobs/
#>
job_single("~/jhpce_job.sh", create_logdir = FALSE)
@@ -243,7 +243,7 @@ Examples
#> echo "**** Job ends ****"
#> date
#>
-#> ## This script was made using slurmjobs version 1.2.3
+#> ## This script was made using slurmjobs version 1.2.4
#> ## available from http://research.libd.org/slurmjobs/
#>
@@ -286,7 +286,7 @@ Examples
#> echo "**** Job ends ****"
#> date
#>
-#> ## This script was made using slurmjobs version 1.2.3
+#> ## This script was made using slurmjobs version 1.2.4
#> ## available from http://research.libd.org/slurmjobs/
#>
@@ -327,7 +327,7 @@ Examples
#> echo "**** Job ends ****"
#> date
#>
-#> ## This script was made using slurmjobs version 1.2.3
+#> ## This script was made using slurmjobs version 1.2.4
#> ## available from http://research.libd.org/slurmjobs/
#>
diff --git a/reference/parse_file_or_name.html b/reference/parse_file_or_name.html
index d9c31c2..967507a 100644
--- a/reference/parse_file_or_name.html
+++ b/reference/parse_file_or_name.html
@@ -20,7 +20,7 @@
diff --git a/reference/parse_slurm_time.html b/reference/parse_slurm_time.html
index 7b1fe8f..524cf8a 100644
--- a/reference/parse_slurm_time.html
+++ b/reference/parse_slurm_time.html
@@ -18,7 +18,7 @@
diff --git a/reference/partition_df.html b/reference/partition_df.html
index 2146fdb..5df9a16 100644
--- a/reference/partition_df.html
+++ b/reference/partition_df.html
@@ -18,7 +18,7 @@
diff --git a/reference/partition_info.html b/reference/partition_info.html
index ad22e34..7860583 100644
--- a/reference/partition_info.html
+++ b/reference/partition_info.html
@@ -19,7 +19,7 @@
diff --git a/reference/vector_as_code.html b/reference/vector_as_code.html
index 378aacb..7d878af 100644
--- a/reference/vector_as_code.html
+++ b/reference/vector_as_code.html
@@ -18,7 +18,7 @@