v1.0.0 ARE run through

[fredjaya]

Goals

• To successfully spin up an RStudio instance on ARE following the if89 R libraries on NCI option
• Reproduce

Steps

Using if89 R libraries on NCI for installation, so not logging into Gadi for any installation steps.

ssh fj9712@gadi.nci.org.au
cd /scratch/vo75/fj9712
git clone https://github.com/Sydney-Informatics-Hub/scrna-analysis.git

• Went to https://are.nci.org.au/ and logged in
• Selected RStudio

parameter	value
walltime (hours)	8
queue	normalbw
compute size	medium
project	vo75
storage	gdata/vo75+scratch/vo75+gdata/if89
environment variables	R_LIBS_USER="/g/data/if89/R/scrna-analysis", XDG_DATA_HOME="/scratch/vo75/fj9712/.local/share"
jobfs size	32GB

• Selected save settings
• App settings name as scrna-analysis-v1.0.0
• Selected Save settings and close
• Reload and Launch

Successfully replicated error:

Failed to submit session with the following error:
usage: qsub [-a date_time] [-A account_string] [-c interval]
	[-C directive_prefix] [-e path] [-f ] [-h ] [-I [-X]] [-j oe|eo] [-J X-Y[:Z]]
	[-k keep] [-l resource_list] [-m mail_options] [-M user_list]
	[-N jobname] [-o path] [-p priority] [-P project] [-q queue] [-r y|n]
	[-R o|e|oe] [-S path] [-u user_list] [-W otherattributes=value...]
	[-v variable_list] [-V ] [-z] [script | -- command [arg1 ...]]
       qsub --version
If this job failed to submit because of an invalid job name please ask your administrator to configure OnDemand to set the environment variable OOD_JOB_NAME_ILLEGAL_CHARS.
The RStudio session data for this session can be accessed under the [staged root directory](https://are.nci.org.au/pun/sys/dashboard/files/fs/home/562/fj9712/ondemand/data/sys/dashboard/batch_connect/sys/rstudio/ncigadi/output/6e615b3c-45d2-49d8-ac40-e4af8e8e15b8).

Fix attempt 1: .local/share missing?

Checking whether /scratch/vo75/fj9712/.local/share exists.

ssh fj9712@gadi.nci.org.au
stat /scratch/vo75/fj9712/.local/share

Output:

stat: cannot statx '/scratch/vo75/fj9712/.local/share': No such file or directory

What happens if we create this beforehand?

mkdir /scratch/vo75/fj9712/.local/
mkdir /scratch/vo75/fj9712/.local/share

Still received the same error.

Fix attempt 2: environment variables when ARE

Kept the same values as above, but found an extra space in the environmental variables

parameter	value
walltime (hours)	8
queue	normalbw
compute size	medium
project	vo75
storage	gdata/vo75+scratch/vo75+gdata/if89
environment variables	R_LIBS_USER="/g/data/if89/R/scrna-analysis",XDG_DATA_HOME="/scratch/vo75/fj9712/.local/share"
jobfs size	32GB

🎉 Successfully queued and running!

However, received the following error:

WARNING: module directory 'R/4.4.2' is not a directory or does not exist
WARNING: module directory 'gcc/14.2.0' is not a directory or does not exist
Did you forget a storage option?
R: /apps/R/4.4.2/bin/R

Testing bad environmental variables

Noted that when I copied and pasted environmental variables from the README.md, it had an extra tab in the ARE field. Let's try reproduce the first error above.

As we are only testing the environmental variables, all resource settings are minimal.

parameter	value
walltime (hours)	1
queue	normalbw
compute size	tiny
project	vo75
storage	gdata/vo75+scratch/vo75+gdata/if89
environment variables	R_LIBS_USER="/g/data/if89/R/scrna-analysis",XDG_DATA_HOME="/scratch/vo75/fj9712/.local/share"
jobfs size	32GB

Carefully note: R_LIBS_USER="/g/data/if89/R/scrna-analysis",XDG_DATA_HOME="/scratch/vo75/fj9712/.local/share" contains a tab at the end of the string.

• Launch instance

Outcome: queued successfully!

Trying larger

parameter	value
walltime (hours)	8
queue	xxlarge
compute size	tiny
project	vo75
storage	gdata/vo75+scratch/vo75+gdata/if89
environment variables	R_LIBS_USER="/g/data/if89/R/scrna-analysis",XDG_DATA_HOME="/scratch/vo75/fj9712/.local/share"
jobfs size	64GB

🎉 Queued successfully!

Other notes

Things to be addressed in README.md:

• git clone should be in your user scratch
• no jobfs requirement?