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Running Nonmem with slurmtools

Running-nonmem.Rmd

Slurmtools for submitting NONMEM runs

slurmtools is an R package for interacting with slurm (fka Simple Linux Utility for Resource Management) and submitting NONMEM jobs. You can submit a NONMEM job with submit_nonmem_model, you can view current jobs with get_slurm_jobs, and you can see the available partitions with get_slurm_partitions.

Installing slurmtools

To install slurmtools use the following commands:

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.

We are given a message when loading slurmtools that some options are not set and that default job submission will not work without them. These options are used for default arguments in the submit_nonmem_model function. Running ?submit_nonmem_model we can see the documentation

Default variables and values provided to the template

This function uses the inputs to populate a template Bash shell script that submits the NONMEM job to slurm. A default template file is supplied with the Project Starter and it can be modified to do additional tasks as long as they are possible within Bash.

By default these values are provided to the slurm template file:

  • partition is an argument to submit_nonmem_model by default this will be the first element of get_slurm_partitions()

  • parallel is TRUE if ncpu > 1, else FALSE

  • ncpu is an argument to submit_nonmem_model - your input of ncpu must be less than or equal to the number of cpus on the partition

  • job_name is created from the .mod argument supplied to submit_nonmem_model - default is <nonmem_model_name>-nonmem-run

  • project_path is determined from here::here() and should be the root of the Rproject

  • project_name is determined from here::here() %>% basename() - for this project it would be slurmtools

  • bbi_exe_path is determined via `Sys.which(“bbi”)

  • bbi_config_path is determined via getOption(“slurmtools.bbi_config_path”)

  • model_path is determined from the .mod argument supplied to submit_nonmem_model

  • config_toml_path is determined from the .mod argument supplied to submit_nonmem_model and is required to use nmm (NONMEM monitor)

  • nmm_exe_path is determined via Sys.which("nmm")

If you need to feed more arguments to the template you simply supply them in the slurm_template_opts argument as a list. More on that later.

default_template_list = list(
  partition = partition,
  parallel = parallel,
  ncpu = ncpu,
  job_name = sprintf("%s-nonmem-run", basename(.mod$absolute_model_path)),
  project_path = project_path,
  project_name = project_name,
  bbi_exe_path = Sys.which("bbi"),
  bbi_config_path = bbi_config_path,
  model_path = .mod$absolute_model_path,
  config_toml_path = config_toml_path,
  nmm_exe_path = Sys.which("nmm")
)

Submitting a NONMEM job with bbi

To submit a NONMEM job, we need to supply either the path to a mod file or create a model object from bbr, and supply a slurm-template.tmpl file. To use bbi we also need a bbi.yaml file, which I’ve also supplied in /model/nonmem/bbi.yaml (and is also supplied with the R project starter).

Here is an example of a template file that will call bbi:

#!/bin/bash
#SBATCH --job-name="{{job_name}}"
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task={{ncpu}}
#SBATCH --partition={{partition}}
#SBATCH --account={{project_name}}

#{{project_path}}
# submit_nonmem_model uses the whisker package to populate template files
# https://github.com/edwindj/whisker

{{#parallel}}
{{bbi_exe_path}} nonmem run local {{model_path}}.mod --parallel --threads={{ncpu}} --config {{bbi_config_path}}
{{/parallel}}


{{^parallel}}
{{bbi_exe_path}} nonmem run local {{model_path}}.mod --config {{bbi_config_path}}
{{/parallel}}

This file will call bbi to run our supplied model ({{model_path}}.mod) if ncpu > 1 then parallel will be true and the code between {{#parallel}} and {{/parallel}} will be populated. if ncpu = 1 then parallel will be false and the code between {{^parallel}} and {{/parallel}} will be populated. By default, submit_nonmem_model will inject Sys.which("bbi") into the template, so if bbi is not on your path we’ll have to supply the bbi_exe_path for it to start the NONMEM run.

Sys.which("bbi")
#> bbi 
#>  ""

We will use a few different template files with different functionality so we’ll inject those template file paths to submit_nonmem_model. However, we’ll use the submission-log directory for the output, so we’ll set that option as well as bbi_config_path so submit_nonmem_model defaults can be used. The slurm template files are saved in ~/model/nonmem/ Additionally, there is a simple NONMEM control stream in 1001.mod in the same directory that we can use for testing.

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"))
options('slurmtools.bbi_config_path' = file.path(nonmem, "bbi.yaml"))

To create the bbr model object, we need to have both 1001.mod and 1001.yaml which contains metadata about the model in the supplied directory (./model/nonmem/). We’ll check for mod_number.yaml and if it exists, read in the model otherwise create it and then read it.

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))
}

We can now submit the job and point to the template file in model/nonmem/slurm-job-bbi.tmpl.

submission <- slurmtools::submit_nonmem_model(
  mod,
  overwrite = TRUE,
  slurm_job_template_path = file.path(nonmem, "slurm-job-bbi.tmpl"),
)

submission
#> $status
#> [1] 0
#> 
#> $stdout
#> [1] "Submitted batch job 804\n"
#> 
#> $stderr
#> [1] ""
#> 
#> $timeout
#> [1] FALSE

We see a status with an exit code of 0 suggesting a successful command, and the stdout gives us the batch job number. We can use slurmtools::get_slurm_jobs() to monitor the status of the job. Here, we can supply the user = “matthews” argument to filter to just the jobs I’ve submitted.

slurmtools::get_slurm_jobs(user = "matthews")
#> # A tibble: 1 × 12
#>   job_id partition  user_name job_state time    cpus standard_input
#>    <int> <chr>      <chr>     <chr>     <time> <int> <chr>         
#> 1   1159 cpu2mem4gb 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>

If we look in the slurmtools.submisstion_root directory we can see the shell script that was generated with submit_nonmem_model. Here is the whisker replaced call to bbi:

#!/bin/bash
#SBATCH --job-name="1001-nonmem-run"
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --partition=cpu2mem4gb
#SBATCH --account=slurmtools

#/cluster-data/user-homes/matthews/Packages/slurmtools
# submit_nonmem_model uses the whisker package to populate template files
# https://github.com/edwindj/whisker

/usr/local/bin/bbi nonmem run local /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/1001.mod --config /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/bbi.yaml

Extending templates

Because the templates create a bash shell script there is an almost infinite number of things we can do with our template. Anything you can do in bash you can do by appropriately updating the template file and injecting the needed information!

Let’s add a notification feature that will send a notification when the job has started and finished. We can use ntfy.sh and add the necessary info to our template to achieve this.

Here is a modified template file that adds a JOBID=$SLURM_JOBID and some ntfy calls. To get a notification we can supply submit_nonmem_model with ntfy variable to send notifications. I’ll use ntfy = ntfy_demo for this.

#!/bin/bash
#SBATCH --job-name="{{job_name}}"
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task={{ncpu}}
#SBATCH --partition={{partition}}
#SBATCH --account={{project_name}}

JOBID=$SLURM_JOBID

# submit_nonmem_model uses the whisker package to populate template files
# https://github.com/edwindj/whisker

{{#ntfy}}
curl -d "Starting model run: {{job_name}} $JOBID" ntfy.sh/{{ntfy}}
{{/ntfy}}

{{#parallel}}
{{bbi_exe_path}} nonmem run local {{model_path}}.mod --parallel --threads={{ncpu}} --config {{bbi_config_path}}
{{/parallel}}

{{^parallel}}
{{bbi_exe_path}} nonmem run local {{model_path}}.mod --config {{bbi_config_path}}
{{/parallel}}

{{#ntfy}}
curl -d "Finished model run: {{job_name}} $JOBID" ntfy.sh/{{ntfy}}
{{/ntfy}}

Since we’ve already run this model we will provide the overwrite = TRUE argument to force a new nonmem run.

submission_ntfy <- slurmtools::submit_nonmem_model(
  mod, 
  slurm_job_template_path = file.path(nonmem, "slurm-job-bbi-ntfy.tmpl"),
  overwrite = TRUE,
  slurm_template_opts = list(
    ntfy = "ntfy_demo")
)

submission_ntfy
#> $status
#> [1] 0
#> 
#> $stdout
#> [1] "Submitted batch job 804\n"
#> 
#> $stderr
#> [1] ""
#> 
#> $timeout
#> [1] FALSE

We again get a 0 exit code status and now instead of using slurmtools::get_slurm_jobs() to monitor the job, we can rely on the new notifications we just set up. NONMEM job starting ntfy alert

and when the run finished we get another notification: NONMEM Job finished ntfy alert

Note that the run number will match the run specified in submission$stdout. We can see the new shell script this updated template file generated

#!/bin/bash
#SBATCH --job-name="1001-nonmem-run"
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --partition=cpu2mem4gb
#SBATCH --account=slurmtools

JOBID=$SLURM_JOBID

curl -d "Starting model run: 1001-nonmem-run $JOBID" ntfy.sh/ntfy_demo

/usr/local/bin/bbi nonmem run local /cluster-data/user-homes/matthews/Projects/slurmtools_vignette/model/nonmem/1001.mod --config /cluster-data/user-homes/matthews/Projects/slurmtools_vignette/model/nonmem/bbi.yaml

curl -d "Finished model run: 1001-nonmem-run $JOBID" ntfy.sh/ntfy_demo

To reiterate, this template file is run as a bash shell script so anything you can do in bash you can put into the template and pass the needed arguments and customize the behavior to your liking.