Location of cylc-run not set in workflow?

Cylc Cylc Support
1

hi there,

i’m working on a workflow with a colleague who is not getting this error so i am assuming it’s something that is somehow hard-wired to their $HOME?

the task in question is trying to write to /cylc-run rather than $HOME/cylc-run and is hence failing.

how could i test for how this is being set incorrectly in this task?

strangely it is working for other tasks of mine in the same workflow!

thanks for any ideas!

jonny

2

It depends what you mean. Is the job producing output (i.e. is it managing to write to job.out / job.err)? If so the problem is happening within the job script. Try running the workflow with the --debug option - this will enable the bash xtrace option which should help you see what going on.

If the job isn’t producing any output then that probably implies a problem with the job submission. The job output files are specified as relative paths and assume the job is submitted from your $HOME directory. Make sure there is nothing in profile scripts which could change this (bash -l should put you in $HOME).

1 Like
3

@jonnyhtw - to expand a bit on what @dpmatthews said, do you mean:

  • the user-defined code in that task is trying to write there?
  • or Cylc is trying to write the job log files there?
  • or Cylc is trying to create the run directory there during “job init”?
1 Like
4

thanks @dpmatthews @hilary.j.oliver!

this is the workflow graph for what’s going on. the error is in set_unicicles

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image1392×751 37.5 KB

this is the error message that i am getting in the job.err…

[FAIL] [Errno 13] Permission denied: '/cylc-run'
InputError: Workflow ID not found: u-da879/run5
(Directory not found: /cylc-run/u-da879/run5)

this works for a colleague who i am working on this workflow with so i am assuming that there is an environment variable set somewhere in their environment.

@dpmatthews i’ll try cylc trigger with the --debug option as you suggest. thanks!

jonny

5

@jonnyhtw,

That’s coming from the running task job.

I’m guessing that somewhere in the task definition, or in a script that it runs, $HOME is being unset, or set to an undefined or empty variable.

I can’t imagine why, but the symptom kinda points in that direction!

1 Like
6

hi again,

just to update y’all, this is working now. this was the offending line in one of the ‘site’ optional config files, which is processed to make the flow-processed.cylc file…

init-script = "export HOME=$DATADIR"

i hadn’t come across init scripts before so i’ve learnt something!

cheers