3. Customize Attributes

Now we will customize the app to work on a given cluster. Be sure that you walk through Software Requirements for the given cluster ahead of time.

The main responsibility of the form.yml file (User Form) located in the root of the app is for defining the attributes (their values or HTML form elements) used when generating the batch script.

1. We will begin by adding a cluster for the Jupyter app to use. You do this by editing the form.yml in your favorite editor as such:

   # ~/ondemand/dev/jupyter/form.yml
   ---
   cluster: "my_cluster"
   attributes:
     modules: "python"
     extra_jupyter_args: ""
   form:
     - modules
     - extra_jupyter_args
     - bc_account
     - bc_queue
     - bc_num_hours
     - bc_num_slots
     - bc_email_on_started
   

   where we replace my_cluster with a valid cluster that corresponds to a cluster configuration file located under /etc/ood/config/clusters.d/my_cluster.yml.

2. We will also edit the module(s) that is(are) required to be loaded within our batch job to get a Jupyter Notebook Server running:

   # ~/ondemand/dev/jupyter/form.yml
   ---
   cluster: "my_cluster"
   attributes:
     modules: "python"
     extra_jupyter_args: ""
   form:
     - modules
     - extra_jupyter_args
     - bc_account
     - bc_queue
     - bc_num_hours
     - bc_num_slots
     - bc_email_on_started
   

   where we replace python with a list of required modules for our given cluster.

   This will be called within the batch script as:

   module load <modules>
   

3. We test our changes by again clicking the Launch Jupyter Notebook button back in our details view of our sandbox app.

4. You should see a web form for the Jupyter app. Fill in the form now and try to Launch a Jupyter batch job.

   Note

   While you are waiting for the job to start it is recommended that you click the link under the “Session ID:”. This will open the File Explorer in the working directory of the currently launched Jupyter batch job.

   Useful debugging files (before job runs):

   user_defined_context.json

   attributes submitted by the user in the web form

   job_script_content.sh

   the batch script content

   job_script_options.json

   the job submission parameters (this will be used in the next section if you have trouble submitting the job)

   /var/log/nginx/<user>/error.log

   the per-user NGINX (PUN) log file (this will contain the command line called when submitting the batch job, look for execve=...)

   Useful debugging files (after job runs):

   output.log

   this is the log file of the batch job (useful if batch job runs but then dies abruptly)

Continue to the next section to learn about job submission parameters.

Note

It is recommended you commit any changes you made to form.yml to git:

# Stage the modified file and commit your changes
git commit form.yml -m 'updated form with cluster attributes'