updated readme with job_name

A2-ai · Nov 26, 2024 · 60f1e3f · 60f1e3f
1 parent 11ad5ae
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Showing 2 changed files with 15 additions and 10 deletions.
diff --git a/README.Rmd b/README.Rmd
@@ -45,14 +45,14 @@ options('slurmtools.slurm_job_template_path' = file.path(nonmem, 'slurm-job-bbi.
 
 library(slurmtools)
 ```
-
+This block reads in a nonmem model with bbr and submits the job to slurm:
 ```{r submit}
 mod_number <- "1001"
 mod <- bbr::read_model(file.path(nonmem, mod_number))
 
 submit_slurm_job(mod, overwrite = TRUE)
 ```
-
+This block shows recently submitted and completed jobs:
 
 ```{r get}
 knitr::kable(get_slurm_jobs(user = 'matthews'))

diff --git a/README.md b/README.md
@@ -48,9 +48,11 @@ library(slurmtools)
 #> ✔ slurmtools.submission_root: /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log
 #> ✔ slurmtools.bbi_config_path: /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/bbi.yaml
 ```
-This block reads in a nonmem model with bbr and submits the job to slurm:
+
+This block reads in a nonmem model with bbr and submits the job to
+slurm:
+
 ``` r
-library(bbr)
 mod_number <- "1001"
 mod <- bbr::read_model(file.path(nonmem, mod_number))
 
@@ -59,21 +61,24 @@ submit_slurm_job(mod, overwrite = TRUE)
 #> [1] 0
 #> 
 #> $stdout
-#> [1] "Submitted batch job 608\n"
+#> [1] "Submitted batch job 612\n"
 #> 
 #> $stderr
 #> [1] ""
 #> 
 #> $timeout
 #> [1] FALSE
 ```
+
 This block shows recently submitted and completed jobs:
+
 ``` r
 knitr::kable(get_slurm_jobs(user = 'matthews'))
 ```
 
-| job_id | partition | user_name | job_state | time | cpus | standard_input | standard_output | submit_time | start_time | end_time | current_working_directory |
-|---:|:---|:---|:---|:---|---:|:---|:---|:---|:---|:---|:---|
-| 606 | cpu2mem4gb | matthews | FAILED | 00:00:01 | 1 | /dev/null | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-606.out | 2024-11-26 13:42:50 | 2024-11-26 13:42:50 | 2024-11-26 13:42:51 | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log |
-| 607 | cpu2mem4gb | matthews | COMPLETED | 00:00:16 | 1 | /dev/null | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-607.out | 2024-11-26 13:43:50 | 2024-11-26 13:43:50 | 2024-11-26 13:44:06 | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log |
-| 608 | cpu2mem4gb | matthews | PENDING | 00:00:00 | 1 | /dev/null | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-608.out | 2024-11-26 13:46:41 | 1970-01-01 00:00:00 | 1970-01-01 00:00:00 | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log |
+| job_id | partition | job_name | user_name | job_state | time | cpus | standard_input | standard_output | submit_time | start_time | end_time | current_working_directory |
+|---:|:---|:---|:---|:---|:---|---:|:---|:---|:---|:---|:---|:---|
+| 609 | cpu2mem4gb | 1001-nonmem-run | matthews | COMPLETED | 00:00:14 | 1 | /dev/null | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-609.out | 2024-11-26 13:51:15 | 2024-11-26 13:51:15 | 2024-11-26 13:51:29 | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log |
+| 610 | cpu2mem4gb | 1001-nonmem-run | matthews | COMPLETED | 00:00:14 | 1 | /dev/null | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-610.out | 2024-11-26 13:52:17 | 2024-11-26 13:52:17 | 2024-11-26 13:52:31 | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log |
+| 611 | cpu2mem4gb | 1001-nonmem-run | matthews | COMPLETED | 00:00:15 | 1 | /dev/null | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-611.out | 2024-11-26 13:52:40 | 2024-11-26 13:52:40 | 2024-11-26 13:52:55 | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log |
+| 612 | cpu2mem4gb | 1001-nonmem-run | matthews | PENDING | 00:00:00 | 1 | /dev/null | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-612.out | 2024-11-26 13:54:48 | 1970-01-01 00:00:00 | 1970-01-01 00:00:00 | /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log |