render_jinja files are not executable

[lcdumort]

The simple dynamic example does not seem to work.
The problem is that, when one renders the submit.sh file with jinja2, the resulting file is not executable and will therefore not be submitted due to a stepup check if the submit file is executable.

  testf = render_jinja(
      "dynamic_template_stepup_vasp.sh.j2",
      slurm_settings,
      f"{workdir}/slurmjob.sh"
  )
  print(testf.out[0])
  runsh(f"chmod +x {testf.out[0]}")

doesn't work either.

Current solution: downgrading to stepup 1.0.6

[tovrstra]

I think making dynamic_template_stepup_vasp.sh.j2 executable will fix this. This is typically something done outside the plan.py, just as part of the preparation of your static files.

I would not use the chmod command in the workflow as it goes against an assumption of StepUp that a file should not change during workflow execution after it has been created as output of a step or declared static.

[lcdumort]

Good to know, I will give it a try on Monday as I can't access the cluster right now.
I may have wrongly assumed that jinja2 "reads" in the text from a file, and then uses that string to make a new file.
In other words, I assumed all permissions of a file were lost after rendering with jinja2.

[tovrstra]

Allright. Please, let me know how it goes.

I guess it would be good to document the fact that permissions are transferred by render_jinja in StepUp core and also here as reminder.