Batch Connect Script Options

The script section of the submit.yml.erb file defines the arguments you're passing to the scheduler when you submit the script.

Warning

These options are documented here for completeness. Some may not be available to override in batch connect applications.

For example, workdir is set by the OnDemand system in batch connect applications, and cannot be overridden.

Tip

If you're using the ood_core gem (where all these are defined and used) you should refer to ood_core gem Ruby docs.

script:
  content: nil
  args: nil
  submit_as_hold: nil
  rerunnable: nil
  job_environment: nil
  workdir: nil
  email: nil
  email_on_started: nil
  email_on_terminated: nil
  job_name: nil
  shell_path: nil
  error_path: nil
  input_path: nil
  output_path: nil
  reservation_id: nil
  queue_name: nil
  priority: nil
  start_time: nil
  wall_time: nil
  accounting_id: nil
  native: nil
  copy_environment: nil

Note the use of ERB templates throughout these examples.

content (String, nil)

The content of the script being submitted.

Default

Not set initially, but specified by OnDemand system automatically.

content: ""

Example

None given because users cannot specify this in batch connect applications.

args (Array<String>, nil)

Extra arguments to pass to the schedulers' submit command.

Default

Empty, no extra arguments.

args: nil

Example

Pass arguments --foo and --bar into the submit command.

args:
  - "--foo"
  - "--bar"

submit_as_hold (Boolean, nil)

Hold the job after submitting.

Default

Empty, do not hold the job.

submit_as_hold: nil

Example

Always hold the job.

submit_as_hold: true

rerunnable (Boolean, nil)

Indicate whether the job is re-runnable.

Default

Empty, it is not re-runnable.

rerunnable: nil

Example

The job is re-runnable.

rerunnable: true

job_environment (Hash<String, String>, nil)

Extra environment variables to pass into the schedulers' submit command.

Default

Empty, no extra environment variables.

job_environment: nil

Example

Set the SINGULARTITY_BIND_PATH environment variable to /etc,/tmp,/home and MY_APP_IMAGE to /opt/app.img.

job_environment:
  SINGULARTITY_BIND_PATH: "/etc,/tmp/home"
  MY_APP_IMG: "/opt/app.img"

workdir (String, nil)

The working directory of the job.

Default

Not set initially, but specified by OnDemand system automatically.

workdir: nil

Example

None given because users cannot specify this in batch connect applications.

email (Array<String>, nil)

Addresses to send emails to when the job starts or stops.

Default

Empty, uses the schedulers' default.

email: nil

Example

Use a specific email address.

email:
- "<%= ENV['USER'] %>@the-real-domain-I-want.edu"

email_on_started (Boolean, nil)

Have the scheduler send an email when the job has started.

Default

Not set, uses the schedulers' default.

email_on_started: nil

Example

None given because users should use :ref:`bc_email_on_started` instead of supplying it here.

email_on_terminated (Boolean, nil)

Have the scheduler send an email when the job has finished.

Default

Not set, uses the schedulers' default.

email_on_terminated: nil

Example

Given the form checkbox option email_on_terminated, set this attribute.

email_on_terminated: "<%= email_on_terminated %>"

job_name (String, nil)

The name of the job.

Default

Not set initially, but specified by OnDemand system automatically.

job_name: nil

Example

None given because users cannot specify this in batch connect applications.

shell_path (String, nil)

The login shell path of the script.

Default

Not set initially, but specified by OnDemand system automatically.

shell_path: nil

Example

None given because users cannot specify this in batch connect applications.

error_path (String, nil)

The path for the standard error of the job.

Default

Not set initially, but specified by OnDemand system automatically.

error_path: nil

Example

None given because users cannot specify this in batch connect applications.

input_path (String, nil)

Use this file for standard input for the job's script. Batch connect applications do not expect to read anything from standard in.

Default

Not set.

input_path: nil

Example

None given because this is likely to break batch connect applications.

output_path (String, nil)

The path for the standard output of the job.

Default

Not set initially, but specified by OnDemand system automatically.

output_path: nil

Example

None given because users cannot specify this in batch connect applications.

reservation_id (String, nil)

The reservation id the job will submit to.

Default

Not specified.

reservation_id: nil

Example

Submit jobs to the next.may.2020 reservation.

reservation_id: "next.may.2020"

queue_name (String, nil)

The queue the job will submit to.

Tip

Users can use bc_queue for a text field and auto_queues for a select widget. Both of these form fields know how to submit to schedulers, removing the need to use this field in this file.

Default

Not specified.

queue_name: nil

Example

Submit jobs to the debug queue.

queue_name: "debug"

priority (String, nil)

The priority the job has.

Default

Not specified.

priority: nil

Example

Submit jobs with TOP priority.

priority: "TOP"

start_time (String, nil)

The start time of the job.

Default

Not set, which schedulers generally interpret as now or as soon as possible.

start_time: nil

Example

Start at midnight.

start_time: "00:00:00"

wall_time (Integer, nil)

The wall time of the job in seconds.

Tip

Users can use bc_num_hours for a number field that knows how to submit to schedulers, removing the need to use this field in this file.

Default

Not specified.

wall_time: nil

Example

Always limit this job to one hour.

wall_time: 3600

accounting_id (String, nil)

The accounting id the job should be charged to.

Tip

Users can use bc_account for a text field and auto_accounts or auto_accounts for a select widget.

All of these form fields know how to submit to schedulers, removing the need to use this field in this file.

Default

Not specified, uses the schedulers' default.

priority: nil

Example

All jobs to use the rstudio-class-account accounting id.

accounting_id: 'rstudio-class-account'

native (Object, nil)

Native arguments to pass to the schedulers' submit command.

Warning

All schedulers use Array<String> for native attributes except for Torque. Torque schedulers use Hash<String, String>.

Default

not specified

native: nil

Example

Submit the job with SLURM requests for one node, num_cores (a form variable) cores and memory (another form variable) amount of memory.

native:
  - "-N"
  - "1"
  - "-n"
  - "<%= num_cores %>"
  - "--mem"
  - "<%= memory %>"

copy_environment (Boolean, nil)

Have the scheduler to copy the environment. SLURM uses --export=ALL (OnDemand's default is NONE). PBS/Torque and LSF set the -V flag.

Default

not specified

native: nil

Example

Copy the environment

copy_environment: true