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Problem with collating outputs with payu

Your simulation runs correctly but the collating of the outputs does not work and you have this error message in the log file:

Traceback (most recent call last):
  File "/jobfs/local/pbs/mom_priv/jobs/268316.r-man2.SC", line 9, in <module>
  File "/apps/payu/0.6/lib/payu/subcommands/", line 93, in runscript
  File "/apps/payu/0.6/lib/payu/", line 606, in collate
  File "/apps/payu/0.6/lib/payu/models/", line 78, in collate
    assert mppnc_path

This probably means you don't have a mppnccombine executable in you mom/bin directory. If you need such a file please contact to know where to find it. Include a copy of the error message with your email please.

Locating log files

Log files from a Payu run will be in:

  • $EXPERIMENT (Directory containing the 'config.yaml' file):
    • $RUNID.out, $RUNID.err: Stdout and stderr of model run
    • $RUNID.o123456, $RUNID.e123456: PBS logs
  • $WORK ('work' symlink in $EXPERIMENT, or found under the laboratory path if that's not accessible)
    • Any log files output by the component models
  • $ARCHIVE ('archive' symlink in $EXPERIMENT, or found under the laboratory path)
    • Log files from previous submissions

The laboratory path is configurable in config.yaml, normally it will be /scratch/$PROJECT/$USER/$MODEL