Pre-golive my custom SLURM settings break OOD Rstudio

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1

Hi Folks, I have the basic RStudio form and submit script running without an issue. So I and others can run rstudio as designed but when I customise the form.yml & SLURM submit script the job submits and runs in slurm but when I go to launch RStudio is fails with the message. I will be presenting on this in 48 hrs to staff. Any help welcome, even Zoom. I’m in Melb AU so time zones may hurt.

RStudio Error:
Dialogue box in window.
"Error occured during transmission."

Requirements for SLURM / Rstudio
User should be able to set:

  • Wall time (–time=) with default 1 hour
  • Threads (–cpus-per-task=) with default 1 thread
  • Partition (–partition=) with default prod
  • Memory (–mem=) with default 4GB
    Invisibly set --ntasks=1

Here is my form.yml
[me@my_cluster1 RStudio]# less form.yml

cluster: “rozzy”
attributes:
num_mem:
widget: “number_field”
label: “Memory per core”
value: 4
help: |
Amount of memory per cores (4 GB per core).
min: 1
max: 6
step: 1
part_name:
widget: select
label: “Partition”
help: “If left blank default partition will be used”
options:
- [“debug”, “debug”]
- [“prod_short”, “prod_short”]
- [“prod_med”, “prod_med”]
- [“prod”, “prod”]
- [“Reserved”, “reserved”]
- [“m-dev”, “m-dev”]
num_tasks:
widget: “number_field”
label: “Number of Tasks”
value: 1
help: |
launch a maximum of number tasks and to provide for sufficient resources.
min: 1
max: 6
step: 1
num_threads:
widget: “number_field”
label: “Number of Threads”
value: 1
help: |
Ensuing job steps will require ncpus number of processors per task.
min: 1
max: 6
step: 1
form:

  • part_name
  • bc_num_hours
  • num_tasks
  • num_threads
  • num_mem
  • bc_num_slots
  • bc_email_on_started

Here is the submission script.

batch_connect:
template: “basic”
script:
native:
- “–mem”
- “<%= num_mem %>”
- “-n”
- “<%= num_tasks %>”
- “-c”
- “<%= num_threads %>”
- “-p”
- “<%= part_name %>”

Screen Shot 2020-04-06 at 7.14.43 pm
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Thx

2

Hi fellow Melburnian!

You are adding a --mem=<> field, but not giving it a unit. So if you select 1 as memory, you think it’s 1GB, but it’s showing up as 1MB in Slurm (by default the unit in Slurm is MB). So I think RStudio is being killed by your cgroup killer

So change your submission script to

  • “–mem”
  • “<%= num_mem %>G”

(note the G after the num_mem substitution)

Sean

3

Sean,

You are my new best friend! A second set of eyes makes all the difference. Many thanks!

Christopher