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Slack notifications with nmm

slack-alerts.Rmd
library(slurmtools)
#> 
#> 
#> ── Needed slurmtools options ───────────────────────────────────────────────────
#> ✖ options('slurmtools.slurm_job_template_path') is not set.
#> ✖ options('slurmtools.submission_root') is not set.
#> ✖ options('slurmtools.bbi_config_path') is not set.
#> ℹ Please set all options for job submission defaults to work.
library(bbr)
library(here)
#> here() starts at /home/runner/work/slurmtools/slurmtools

nonmem = file.path(here::here(), "vignettes", "model", "nonmem")
options('slurmtools.submission_root' = file.path(nonmem, "submission-log"))
mod_number <- "1001"

if (file.exists(file.path(nonmem, paste0(mod_number, ".yaml")))) {
  mod <- bbr::read_model(file.path(nonmem, mod_number))
} else {
  mod <- bbr::new_model(file.path(nonmem, mod_number))
}

Cut me some Slack

There is also functionality to pair nmm with slack_notifier and get messages sent directly to you via a slack bot. This requires you to download the slack_notifier binaries. You can download the latest release and extract the binary and again save it to ~/.local/bin.

Sys.which("snt")
                                               snt 
"/cluster-data/user-homes/matthews/.local/bin/snt"

snt requires the slack bot OAuth token which is found from https://api.slack.com/apps/<YOUR_APP_ID>/oauth?. This can be saved in a file and fed into the snt with the tokenFile flag.

token: "encrypted(Bot User OAuth Token)"

Again, we need to update the 1001.toml file to get slack notifications. If we look at the snt help message we see that it should be called via snt slack -c config_file -k decryption_key -a token -f tokenFile -e email -m message -t timestamp

the config_file can contain the key (if not using the default snt key), and token file so you don’t need to repeatedly use that information. I’ve saved the tokenFile location in a config file in ~/.local/bin/slack_notifier_settings.yaml and will use the -c flag to point to that.

With this our call to snt would look like:

snt slack -c ~/.local/bin/slack_notifier_settings.yaml -e matthews@a2-ai.com -m "Hello"

The timestamp flag is needed if we want to reply to a message, which to save on spamming alerts we want to do. However, since we can’t possible know the timestamp of a message we have yet to send we don’t have a way of specifying this argument now. This is what the use_stdout argument for nmm alerter is for. It will capture the standard out of the call to the alerter binary and parse it for additional flags to use on subsequent calls. With all this in mind, we can update our nmm config to achieve this slack messaging.

slurmtools::generate_nmm_config( 
  mod, 
  watched_dir = "/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem",
  output_dir = "/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/in_progress",
  alerter_opts = list(
    alerter = normalizePath('~/.local/bin/snt'), #binary location of nmm,
    command = "slack",
    message_flag = "m", #This is the default so we don't need to specify it
    use_stdout = TRUE, #captures output of snt -- which will include --timestamp aksfl;ajklajl;
    args = list(email = "matthews@a2-ai.com", config = "/cluster-data/user-homes/matthews/.local/bin/slack_notifier_settings.yaml")
  )
  )
#> Warning in normalizePath("~/.local/bin/snt"):
#> path[1]="/home/runner/.local/bin/snt": No such file or directory

This generates the following toml file:

model_number = '1001'
watched_dir = '/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem'
output_dir = '/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/in_progress'

[alerter]
alerter = '/cluster-data/user-homes/matthews/.local/bin/snt'
command = 'slack'
message_flag = 'm'
use_stdout = true

[alerter.args]
email = 'matthews@a2-ai.com'
config = '/cluster-data/user-homes/matthews/.local/bin/slack_notifier_settings.yaml'

With alert = 'Slack' and email set in the 1001.toml file nmm will send slack notifications directly to you when a NONMEM run starts and it will reply to that message with notifications if any gradients hit 0 and when the run finishes it checks if all -1E9 lines are present in the .ext file and gives another message about any parameters that hit 0 gradient.

submission_nmm <- slurmtools::submit_slurm_job( 
  mod, 
  overwrite = TRUE,
  slurm_job_template_path = file.path(nonmem, "slurm-job-nmm.tmpl"),
  slurm_template_opts = list(
    nmm_exe_path = normalizePath("~/.local/bin/nmm")
  )
)
#> Warning in normalizePath("~/.local/bin/nmm"):
#> path[1]="/home/runner/.local/bin/nmm": No such file or directory

submission_nmm
#> $status
#> [1] 0
#> 
#> $stdout
#> [1] "Submitted batch job 804\n"
#> 
#> $stderr
#> [1] ""
#> 
#> $timeout
#> [1] FALSE
slurmtools::get_slurm_jobs(user = 'matthews')
#> # A tibble: 1 × 13
#>   job_id partition  job_name     user_name job_state time    cpus standard_input
#>    <int> <chr>      <chr>        <chr>     <chr>     <time> <int> <chr>         
#> 1   1159 cpu2mem4gb 1001-nonmem… matthews  COMPLETED 00'13"     1 /dev/null     
#> # ℹ 5 more variables: standard_output <chr>, submit_time <dttm>,
#> #   start_time <dttm>, end_time <dttm>, current_working_directory <chr>
nmm slack alerts
nmm slack alerts