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OBR submit

Usage

Usage: obr submit [OPTIONS]

Options:
  -f, --folder TEXT
  -p, --pretend          Set flag to only print submission script
  -o, --operations TEXT  Specify the operation(s) to run. Pass multiple
                         operations after -o, separated by commata (NO space),
                         e.g. obr run -o shell,apply. Run with --help to list
                         available operations.  [required]
  -l, --list-operations  Prints all available operations and returns.
  --filter TEXT          Pass a <key><predicate><value> value pair per
                         occurrence of --filter. Predicates include ==, !=,
                         <=, <, >=, >. For instance, obr submit --filter
                         "solver==pisoFoam"
  --bundling_key TEXT
  -p, --partition TEXT
  --account TEXT
  --pretend
  --scheduler_args TEXT  Currently required to be in --key1 value --key2
                         value2 form
  --help                 Show this message and exit.

Running custom commands before/after the solver

Arbitrary shell lines can be executed before and after the solver within the same submission by adding pre_cmds and post_cmds lists to the case or a variation values entry in the workflow yaml:

pre_cmds:
  - "of_watchdog.sh --loop &"
  - "watchdog_pid=${!}"
post_cmds:
  - "kill $watchdog_pid || true"

On obr submit -o execute ... the generated batch script body contains a single line obr run -o execute -j <jobid>. When that line executes on the compute node, the runParallelSolver operation composes one shell command with the pre and post lines inlined verbatim around the solver call:

of_watchdog.sh --loop &
watchdog_pid=${!}
mpirun -np N <solver> -parallel -case <path>/case > <path>/case/<solver>_<timestamp>.log 2>&1|| true && echo $? > <path>/case/solverExitCode.log
kill $watchdog_pid || true

All lines run in a single shell, so shell variables set by a pre command (such as watchdog_pid) remain visible to the post commands.

Caveats:

  1. The lines are inserted exactly as written — no log redirection and no || true are added. The exit status of the composite command is that of the last line, and a non-zero status marks the job as errored. Append || true to commands that may legitimately fail (e.g. kill).
  2. Commands run under /bin/sh (via subprocess with shell=True), not necessarily bash — avoid bashisms.
  3. With OBR_SKIP_COMPLETE set, pre_cmds/post_cmds are skipped together with the solver of a completed job.
  4. Do not combine -o runParallelPre,runParallelSolver — the execute group (i.e. runParallelSolver) already inlines the pre and post commands. The standalone runParallelPre/runParallelPost operations only exist to (re)run those commands independently.
  5. A literal ${{ ... }} inside a command is evaluated by the yaml preprocessor at obr init time; single-brace shell constructs like ${!} or $var pass through untouched.