Job Submission

The configuration file submit.yml.erb controls the content of the batch script as well as the submission arguments used when submitting the batch job. It is located in the root of the application directory.

Assuming we already have a sandbox Interactive App deployed under:

${HOME}/ondemand/dev/my_app

The submit.yml.erb configuration file can be found at:

${HOME}/ondemand/dev/my_app/submit.yml.erb

The .erb file extension will cause the YAML configuration file to be processed using the eRuby (Embedded Ruby) templating system. This allows you to embed Ruby code into the YAML configuration file for flow control, variable substitution, and more.

Configuration

The three possible configuration options that can be used in the submit.yml.erb file are given as:

batch_connect (Hash)

the configuration describing the batch script content (see OodCore::BatchConnect::Template for valid configuration options)

Example

Use the default basic web server template

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
batch_connect:
  template: "basic"

script (Hash)

the configuration describing the job submission parameters for the batch script (see OodCore::Job::Script for valid configuration options)

Example

Set the job’s charged account and queue

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
script:
  accounting_id: "PZS0001"
  queue_name: "parallel"

cluster (String) (Optional)

the cluster to submit to

Tip

Use this field when you need to choose the cluster in a more dynamic way than what’s provided in the form. Or when you want to choose the cluster for the user given some choices like the example below.

Example

Submit the job to the the large cluster if requesting more than 29 cores, else submit to the small cluster.

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
<%-
  cluster = if num_cores >= 29
              "large_cluster"
            else
               "small_cluster"
            end
->
---
cluster: "<%= cluster %>"

Each of these configuration options take a set of their own configuration options described below.

Configure Batch Connect

All batch scripts are generated from either the basic template or the vnc template specified with the following configuration option:

template (String)

the template used for rendering the batch script ("basic" or "vnc")

Default

"basic"

Example

Render a batch script for a VNC Interactive Application

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
batch_connect:
  template: "vnc"

Aside from the above configuration option, a list of all possible configuration options for batch_connect can be found under the code documentation for OodCore::BatchConnect::Template.

Note

The configuration template: "vnc" comes with more batch_connect configuration options which can be found under the code documentation for OodCore::BatchConnect::Templates::VNC.

Configure Script

The script configuration option defines the batch job submission parameters (e.g., number of nodes, wall time, queue, …). The list of all possible options can be found under the code documentation for OodCore::Job::Script.

It is recommended to refrain from using the native option to best keep your Interactive App as portable as possible. Although we understand this may not be possible for all job submission parameters (e.g., number of nodes, memory, GPU) it would be best to use the respective option corresponding to the submission parameter if it is available.

For example, if I want to specify the charged account for the job, it is recommended I use:

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
script:
  accounting_id: "PZS0001"

as this is resource manager agnostic. But this can also be added for a Slurm resource manager as:

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
script:
  native: ["-A", "PZS0001"]

but now this app may not work at a center with a different resource manager.

Warning

Care must be taken when using the native option as this is resource manager specific. For all supported resource managers (e.g., Slurm, LSF, PBSPro, …) other than Torque, the native option is specified as an array of command line arguments that are fed to the resource manager’s batch submission tool (e.g., sbatch, qsub, bsub, …)

So for Slurm, the following configuration will submit a job to 5 nodes with feature c12:

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
script:
  native: ["-N", "5", "-C", "c12"]

Examples

The simplest example consists of submitting a batch script built from the basic web server template using all the default options for the cluster’s batch job submission tool (e.g., sbatch, qsub, bsub, …).

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
batch_connect:
  template: "basic"

VNC Server

To submit a batch script built from the VNC server template:

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
batch_connect:
  template: "vnc"

Change Executable for Main Script

When the batch script is rendered from the template, one of the possible configuration options is specifying the executable command called for the main script it forks off into the background. This can be configured with:

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
batch_connect:
  template: "basic"
  script_file: "./my_custom_script.sh"

Specify Job Submission Parameters

Cherry-picking some possible options from OodCore::Job::Script gives a batch job built from the basic web server template submitted with the following parameters:

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
batch_connect:
  template: "basic"
script:
  wall_time: 3600
  queue_name: "debug"
  email_on_started: true
  job_environment:
    LICENSE_FILE: "1234@license.center.edu"

Dynamically Set Submission Parameters

Feel free to take advantage of the eRuby (Embedded Ruby) templating system in the submit.yml.erb file. You have access to all the User Form attributes.

For example, if you had a form attribute called number_of_hours that you had the user fill out. You can add this to the submission parameters as such:

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
batch_connect:
  template: "basic"
script:
  wall_time: <%= (number_of_hours.blank? ? 1 : number_of_hours.to_i) * 3600 %>

We have to be careful here, because all form attributes are returned as Ruby Strings. So we need to:

1. First determine if the user filled in the attribute (check if it is #blank?).
2. If they did, then we need to convert the string to an integer (#to_i) before performing arithmetic operations on it.
3. Finally we convert hours to seconds.

Another scenario would be if the user specified the queue directly with a custom form attribute called my_queue. We can then add this user-supplied queue conditionally to the submission parameters as such:

# ${HOME}/ondemand/dev/my_app/submit.yml.erb
---
batch_connect:
  template: "basic"
script:
  wall_time: 3600
  <%- unless my_queue.blank? -%>
  queue_name: <%= my_queue %>
  <%- end -%>
  email_on_started: true

In this case, queue_name will only be added to the submission parameters if the user supplied a non-blank value to the form attribute my_queue.

Note

Most of the common form attributes that manipulate the job submission parameters are provided for you as Predefined Attributes. These special attributes fill-in the script configuration options internally, so you do not have to.

For example, if you used the predefined form attribute bc_queue, you do not need to specify queue_name: in the submit.yml.erb.