Interactive desktop native options not being updated

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1

Hello,

I am trying to configure an interactive desktop submission script. We run PBS Pro, and we use the '-W group_list=' variable for tying accounting information to research groups. I am trying to pass the form value bc_account to this variable using native options. Here is what my submit.yml.erb file looks like:

---
script:
  native:
    - "-l"
    - "select=1:ncpus=<%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>:mem=<%= bc_num_slots.blank? ? 2 : bc_num_slots.to_i * 2 %>GB"
    - "-W"
    - "group_list=<%= bc_account %>"

The problem is, OOD is continuing to use a prior version of submit.yml.erb, and is not passing the updated select statement (addition of mem= directive) or the group_list variable. This is evident by the contents of job_script_options.json in the staged root directory for the job:

{
  "job_name": "sys/dashboard/sys/bc_desktop/thunder",
  "workdir": "/home/ndusek/ondemand/data/sys/dashboard/batch_connect/sys/bc_desktop/thunder/output/a7580e86-0683-4e53-92a4-663945b9cf13",
  "output_path": "/home/ndusek/ondemand/data/sys/dashboard/batch_connect/sys/bc_desktop/thunder/output/a7580e86-0683-4e53-92a4-663945b9cf13/output.log",
  "shell_path": "/bin/bash",
  "accounting_id": "x-ccast-prj-ndusek",
  "wall_time": 3600,
  "native": [
    "-l",
    "select=1:ncpus=2"
  ],
  "queue_name": "sys-devel",
  "email_on_started": false
}

I have restarted my web server multiple times, but still, OOD will not use the updated submit.yml.erb. Is there something I’m missing?

Thanks,
Nick

2

Hey, so I think you fell into a trap similar to this below. I think the solution is to not use bc_num_slots and instead create something like pbs_cores. The problem is is that bc_num_slots is overriding what you’re adding there in native.

3

Hi Jeff,

Thanks for the quick reply. I can try creating a new form value for pbs_cores (and probably pbs_mem too), but that still doesn’t explain why OOD isn’t picking up the mem= portion of my select statement, or why it’s ignoring my group_list= variable. Unless you’re saying it’s short circuiting after the first evaluation of bc_num_slots in the select statement?

By way of illustration, when I select 2 cores in the web form, the ncpus reflects that selection, as I would expect it to:

"native": [
    "-l",
    "select=1:ncpus=2"
  ],

For reference, my previous version of submit.yml.erb looked like this:

---
script:
  native:
    - "-l"
    - "select=1:ncpus=<%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>"

Which maps to the behavior I’m seeing currently.

Nick

4

Hi Again,

Nevermind, this was my fault. I had the path to the submit script referenced incorrectly, so it wasn’t actually using the correct script. Very sorry for the confusion.

Nick

5

Are you saying you didn’t hit that bug? That you can use bc_num_slots with other script.native attributes?

6

Yes. Here is my functioning submit.yml.erb:

---
script:
  native:
    - "-l"
    - "select=1:ncpus=<%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>:mem=<%= bc_num_slots.blank? ? 2 : bc_num_slots.to_i * 2 %>GB"
    - "-W"
    - "group_list=<%= bc_account %>"

And here is what ends up in the native section in job_script_options.json:

"native": [
    "-l",
    "select=1:ncpus=2:mem=4GB",
    "-W",
    "group_list=x-ccast-prj"
  ],

I can also confirm that the job was submitted with those arguments.

Happy to provide more information if needed.

Nick

7

Thanks! It was just the wrong file then? Alright, all’s well that ends well I guess.

8

Yes, mea culpa.

Nick

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