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updated readme
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@mduncans
mduncans committed Nov 26, 2024
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29 changes: 24 additions & 5 deletions README.Rmd
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[![R-CMD-check](https://github.com/A2-ai/slurmtools/actions/workflows/RunChecks.yaml/badge.svg)](https://github.com/A2-ai/slurmtools/actions/workflows/RunChecks.yaml)
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`slurmtools` is a collection of utility functions suitable for interacting with slurm and submitting nonmem jobs.
`slurmtools` is a collection of utility functions suitable for interacting with slurm and submitting nonmem jobs. There are three main functions of `slurmtools`

1. `submit_slurm_jobs` - submits a job to slurm via `sbatch`. The job is defined by a template file that is filled in during the call of this function
2. `get_slurm_jobs` - gives a tibble of currently runing jobs via `squeue`.
3. `cancel_slurm_jobs` - cancels a running slurm job via `scancel`.

## Installation

Expand All @@ -30,11 +34,26 @@ You can install the development version of slurmtools from [GitHub](https://gith
pak::pkg_install("a2-ai/slurmtools")
```

## Example
## Examples
This block sets up options used by slurmtools:
```{r setup}
nonmem = file.path(here::here(), "vignettes", "model", "nonmem")
This is a basic example which shows you how to solve a common problem:
options('slurmtools.submission_root' = file.path(nonmem, "submission-log"))
options('slurmtools.bbi_config_path' = file.path(nonmem, "bbi.yaml"))
options('slurmtools.slurm_job_template_path' = file.path(nonmem, 'slurm-job-bbi.tmpl'))
```{r example}
library(slurmtools)
knitr::kable(get_slurm_jobs())
```

```{r submit}
mod_number <- "1001"
mod <- bbr::read_model(file.path(nonmem, mod_number))
submit_slurm_job(mod, overwrite = TRUE)
```


```{r get}
knitr::kable(get_slurm_jobs(user = 'matthews'))
```
67 changes: 48 additions & 19 deletions README.md
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`slurmtools` is a collection of utility functions suitable for
interacting with slurm and submitting nonmem jobs.
interacting with slurm and submitting nonmem jobs. There are three main
functions of `slurmtools`

1. `submit_slurm_jobs` - submits a job to slurm via `sbatch`. The job
is defined by a template file that is filled in during the call of
this function
2. `get_slurm_jobs` - gives a tibble of currently runing jobs via
`squeue`.
3. `cancel_slurm_jobs` - cancels a running slurm job via `scancel`.

## Installation

Expand All @@ -21,29 +29,50 @@ You can install the development version of slurmtools from
pak::pkg_install("a2-ai/slurmtools")
```

## Example
## Examples

This is a basic example which shows you how to solve a common problem:
This block sets up options used by slurmtools:

``` r
nonmem = file.path(here::here(), "vignettes", "model", "nonmem")

options('slurmtools.submission_root' = file.path(nonmem, "submission-log"))
options('slurmtools.bbi_config_path' = file.path(nonmem, "bbi.yaml"))
options('slurmtools.slurm_job_template_path' = file.path(nonmem, 'slurm-job-bbi.tmpl'))

library(slurmtools)
#> ── Needed slurmtools options ───────────────────────────────────────────────────
#> ✖ option('slurmtools.slurm_job_template_path') is not set.
#> ✖ option('slurmtools.submission_root') is not set.
#> ✖ option('slurmtools.bbi_config_path') is not set.
#> ℹ Please set all options for job submission defaults to work.
knitr::kable(get_slurm_jobs())
#>
#>
#> ── Set slurmtools options ──────────────────────────────────────────────────────
#> ✔ slurmtools.slurm_jon_template_path: /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/slurm-job-bbi.tmpl
#> ✔ 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
```

``` r
mod_number <- "1001"
mod <- bbr::read_model(file.path(nonmem, mod_number))

submit_slurm_job(mod, overwrite = TRUE)
#> $status
#> [1] 0
#>
#> $stdout
#> [1] "Submitted batch job 608\n"
#>
#> $stderr
#> [1] ""
#>
#> $timeout
#> [1] FALSE
```

``` 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 |
|---:|:---|:---|:---|:---|---:|:---|:---|:---|:---|:---|:---|
| 87 | cpu2mem4gb | matthews | FAILED | 2 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-87.out | 2024-11-01 15:20:24 | 2024-11-01 15:20:24 | 2024-11-01 15:20:26 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
| 88 | cpu2mem4gb | matthews | COMPLETED | 1 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-88.out | 2024-11-01 15:20:24 | 2024-11-01 15:20:25 | 2024-11-01 15:20:26 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
| 89 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-89.out | 2024-11-01 15:20:25 | 2024-11-01 15:20:26 | 2024-11-01 15:20:26 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
| 90 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-90.out | 2024-11-01 15:20:25 | 2024-11-01 15:24:06 | 2024-11-01 15:24:06 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
| 91 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log/slurm-91.out | 2024-11-01 15:20:26 | 2024-11-01 15:20:26 | 2024-11-01 15:20:26 | /tmp/Rtmpci7qIE/Rbuild1941e339490588/slurmtools/vignettes/model/nonmem/submission-log |
| 92 | cpu2mem4gb | matthews | FAILED | 1 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-92.out | 2024-11-01 15:20:49 | 2024-11-01 15:24:06 | 2024-11-01 15:24:07 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
| 93 | cpu2mem4gb | matthews | COMPLETED | 0 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-93.out | 2024-11-01 15:20:50 | 2024-11-01 15:20:52 | 2024-11-01 15:20:52 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
| 94 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-94.out | 2024-11-01 15:20:51 | 2024-11-01 15:20:52 | 2024-11-01 15:20:52 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
| 95 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-95.out | 2024-11-01 15:20:52 | 2024-11-01 15:20:52 | 2024-11-01 15:20:52 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
| 96 | cpu2mem4gb | matthews | FAILED | 0 secs | 1 | /dev/null | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log/slurm-96.out | 2024-11-01 15:20:54 | 2024-11-01 15:20:55 | 2024-11-01 15:20:55 | /tmp/Rtmp5NSlzS/file187f0067bd515b/slurmtools.Rcheck/vign_test/slurmtools/vignettes/model/nonmem/submission-log |
| 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 |

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