Payu collate not working from "out-of-the-box" access-om2 config

Technical
, ,
1

Hi all,

I’ve been running an ACCESS-OM2-WOMBATlite simulation, which i cloned from GitHub - ACCESS-NRI/access-om2-configs at dev-1deg_jra55_ryf+wombatlite

The model runs fine, but the collation step does not. When I attempt to run

payu collate -d /path/to/my/directory/with/ocean/output/

I get the following error:

Loading access-om2/2025.09.000
Loading requirement: openmpi/4.1.5-7hthlkf oasis3-mct/2025.03.001-uiy5hq5
libaccessom2/2025.05.001-4twfnoz cice5/2025.03.001-vhnfg6z
mom5/2025.08.000-2ix4rqz
payu: error: Thread 0 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 1 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 2 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 3 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 4 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 5 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 6 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 7 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 8 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 9 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 10 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 11 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 12 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 13 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 14 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

payu: error: Thread 15 crashed with error code 9.
Error message:
ERROR: missing at least -m from the input file set.  Exiting.

Any idea why the mppnccombine executable is consistently failing?

Thanks,
pearse

2

This sounds like mppnccombine default flags don't always exist · Issue #646 · payu-org/payu · GitHub

Which version of payu are you using ?

Can you re-try with payu-dev (module use /g/data/vk83/prerelease/modules; module load payu/dev) ?

3

Hi Anton,

The new payu version does the job.

Just FYI, it still throws an error though, although this doesn’t appear to inhibit the collation.

Loading access-om2/2025.09.000

Loading requirement: openmpi/4.1.5-7hthlkf oasis3-mct/2025.03.001-uiy5hq5

libaccessom2/2025.05.001-4twfnoz cice5/2025.03.001-vhnfg6z

mom5/2025.08.000-2ix4rqz

payu: error: Thread 16 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 17 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 18 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 19 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 20 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 21 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 22 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 23 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 24 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 25 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 26 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 27 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 28 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 29 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 30 crashed with error code 1.

Error message:

Error: output file seems to exist already!

payu: error: Thread 31 crashed with error code 1.

Error message:

Error: output file seems to exist already!
4

Looks like your previous attempts at collation left unsuccessfully collated files lying around. It doesn’t look like you can tell mppnccombine to force overwrite these, so you may have to manually clean up any .nc files that also have all their .nc.???? tiles available. Then you can try running payu collate again.

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