Incorrect path to stdout and stderr files?

Cylc Cylc 8 Migration
1

I’ve (apparently) gotten past my issue with submitting jobs to the scheduler and have run into an issue with the stdout and stderr files not showing up. If I let cylc set the filenames by default I see the following in the job script:

# DIRECTIVES:
#PBS -N L96.1.debug_submit/run7
#PBS -o cylc-run/debug_submit/run7/log/job/1/L96/01/job.out
#PBS -e cylc-run/debug_submit/run7/log/job/1/L96/01/job.err

It looks like cylc is not picking up my home directory path. Is this a bug or is this configuration error on my part? If I specify the full path to a file in my flow.cyc using PBS directives it works without issue.

2

That job script looks correct to me, no Cylc configuration needed. Cylc uses relative paths here. PBS should evaluate these paths relative to $HOME on the platform for the account under which the job is run.

Not sure why you’re not seeing the out/err files, might be worth running echo $HOME in a job incase it gives a different result in the execution environment than expected.

3

@oliver.sanders - I don’t think that’s right. With Cylc 7 the full path gets used for any jobs submitted to localhost. Relative paths get used for any remote jobs. This doesn’t appear to be working correctly with Cylc 8.

4

I think PBS takes job log path relative to the current working directory when “qsub” is executed. That will be $HOME for remote jobs (where ssh gets you) but not for local jobs? Cylc 8 changes could have broken this, we’d better check…

5

Yes, unfortunately this is a Cylc8 bug, Cylc7 used to provide an absolute path for local job submissions.

I’ve opened an issue, it should be quick to fix:

If keen to push ahead with the Cylc8 beta in the meantime, then a small patch to the source code that adds $HOME to job file path should serve as a temporary workaround. Note this would fix local PBS submissions but break remote ones.

diff --git a/cylc/flow/job_runner_handlers/pbs.py b/cylc/flow/job_runner_handlers/pbs.py
index 8319aac71..5926fb129 100644
--- a/cylc/flow/job_runner_handlers/pbs.py
+++ b/cylc/flow/job_runner_handlers/pbs.py
@@ -94,6 +94,8 @@ class PBSHandler:
         if job_name_len_max:
             directives["-N"] = directives["-N"][0:job_name_len_max]
 
+        # hardcode the job file path, will NOT work for remote
+        # job submissions (where $HOME would vary) only local ones
+        from pathlib import Path
+        job_file_path = str(Path('~/', job_file_path).expanduser())
         directives["-o"] = job_file_path + ".out"
         directives["-e"] = job_file_path + ".err"
         if (job_conf["execution_time_limit"] and
6

Thanks everyone! I’m content to either wait for the fix or add in the absolute path myself. Since there was a call for 8 beta testers I’m happy to keep plugging along with it and reporting what I find here while I learn 8.

On that note, since I’m not really sure what is an error on my part and what is a bug is it most useful for me to report what I find here? Rather than opening an issue for each stumbling block I hit?

1 Like
7

That’s great, thanks!

And yes, it’s best to post questions to the forum at this stage, on usage or possible bugs.