The script section of the :ref:`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 overidden.
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: nilNote the use of ERB templates throughout these examples.
.. describe:: content (String, nil)
The content of the script being submitted.
Default
Not set initially, but specified by OnDemand system automatically.
.. code-block:: yaml
content: ""
Example
**None given because users cannot specify this in batch connect applications.**
.. describe:: args (Array<String>, nil)
Extra arguments to pass to the schedulers' submit command.
Default
Empty, no extra arguments.
.. code-block:: yaml
args: nil
Example
Pass arguments ``--foo`` and ``--bar`` into the submit command.
.. code-block:: yaml
args:
- "--foo"
- "--bar"
.. describe:: submit_as_hold (Boolean, nil)
Hold the job after submitting.
Default
Empty, do not hold the job.
.. code-block:: yaml
submit_as_hold: nil
Example
Always hold the job.
.. code-block:: yaml
submit_as_hold: true
.. describe:: rerunnable (Boolean, nil)
Indicate whether the job is rerunnable.
Default
Empty, it is not rerunnable.
.. code-block:: yaml
rerunnable: nil
Example
The job is rerunnable.
.. code-block:: yaml
rerunnable: true
.. describe:: job_environment (Hash<String, String>, nil)
Extra environment variables to pass into the schedulers' submit command.
Default
Empty, no extra environment variables.
.. code-block:: yaml
job_environment: nil
Example
Set the ``SINGULARTITY_BIND_PATH`` environment variable to ``/etc,/tmp,/home`` and
``MY_APP_IMAGE`` to ``/opt/app.img``.
.. code-block:: yaml
job_environment:
SINGULARTITY_BIND_PATH: "/etc,/tmp/home"
MY_APP_IMG: "/opt/app.img"
.. describe:: workdir (String, nil)
The working directory of the job.
Default
Not set initially, but specified by OnDemand system automatically.
.. code-block:: yaml
workdir: nil
Example
**None given because users cannot specify this in batch connect applications.**
.. describe:: email (Array<String>, nil)
Addresses to send emails to when the job starts or stops.
Default
Empty, uses the schedulers' default.
.. code-block:: yaml
email: nil
Example
Use a specific email address.
.. code-block:: yaml
email:
- "<%= ENV['USER'] %>@the-real-domain-I-want.edu"
.. describe:: email_on_started (Boolean, nil)
Have the scheduler send an email when the job has started.
Default
Not set, uses the schedulers' default.
.. code-block:: yaml
email_on_started: nil
Example
**None given because users should use :ref:`bc_email_on_started` instead
of supplying it here**.
.. describe:: email_on_terminated (Boolean, nil)
Have the scheduler send an email when the job has finished.
Default
Not set, uses the schedulers' default.
.. code-block:: yaml
email_on_terminated: nil
Example
Given the form checkbox option ``email_on_terminated``, set this attribute.
.. code-block:: yaml
email_on_terminated: "<%= email_on_terminated %>"
.. describe:: job_name (String, nil)
The name of the job.
Default
Not set initially, but specified by OnDemand system automatically.
.. code-block:: yaml
job_name: nil
Example
**None given because users cannot specify this in batch connect applications.**
.. describe:: shell_path (String, nil)
The login shell path of the script.
Default
Not set initially, but specified by OnDemand system automatically.
.. code-block:: yaml
shell_path: nil
Example
**None given because users cannot specify this in batch connect applications.**
.. describe:: error_path (String, nil)
The path for the standard error of the job.
Default
Not set initially, but specified by OnDemand system automatically.
.. code-block:: yaml
error_path: nil
Example
**None given because users cannot specify this in batch connect applications.**
.. describe:: 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.
.. code-block:: yaml
input_path: nil
Example
**None given because this is likely to break batch connect applications.**
.. describe:: output_path (String, nil)
The path for the standard output of the job.
Default
Not set initially, but specified by OnDemand system automatically.
.. code-block:: yaml
output_path: nil
Example
**None given because users cannot specify this in batch connect applications.**
.. describe:: reservation_id (String, nil)
The reservation id the job will submit to.
Default
Not specified.
.. code-block:: yaml
reservation_id: nil
Example
Submit jobs to the ``next.may.2020`` reservation.
.. code-block:: yaml
reservation_id: "next.may.2020"
.. describe:: queue_name (String, nil)
The queue the job will submit to.
.. tip::
Users can use :ref:`bc_queue <bc_queue>` for a text field and
:ref:`auto_queues <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.
.. code-block:: yaml
queue_name: nil
Example
Submit jobs to the ``debug`` queue.
.. code-block:: yaml
queue_name: "debug"
.. describe:: priority (String, nil)
The priority the job has.
Default
Not specified.
.. code-block:: yaml
priority: nil
Example
Submit jobs with ``TOP`` priority.
.. code-block:: yaml
priority: "TOP"
.. describe:: start_time (String, nil)
The start time of the job.
Default
Not set, which schedulers generally interpret as now or as soon as possible.
.. code-block:: yaml
start_time: nil
Example
Start at midnight.
.. code-block:: yaml
start_time: "00:00:00"
.. describe:: wall_time (Integer, nil)
The wall time of the job in seconds.
.. tip::
Users can use :ref:`bc_num_hours <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.
.. code-block:: yaml
wall_time: nil
Example
Always limit this job to one hour.
.. code-block:: yaml
wall_time: 3600
.. describe:: accounting_id (String, nil)
The accounting id the job should be charged to.
.. tip::
Users can use :ref:`bc_account <bc_account>` for a text field and
:ref:`auto_accounts <auto_accounts>` or :ref:`auto_accounts <auto_groups>`
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.
.. code-block:: yaml
priority: nil
Example
All jobs to use the ``rstudio-class-account`` accounting id.
.. code-block:: yaml
accounting_id: 'rstudio-class-account'
.. describe:: 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
.. code-block:: yaml
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.
.. code-block:: yaml
native:
- "-N"
- "1"
- "-n"
- "<%= num_cores %>"
- "--mem"
- "<%= memory %>"
.. describe:: 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
.. code-block:: yaml
native: nil
Example
Copy the environment
.. code-block:: yaml
copy_environment: true