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

**URL:** <https://forum.access-hive.org.au/t/payu-collate-not-working-from-out-of-the-box-access-om2-config/5752>\
**Category:** Technical\
**Tags:** help, access-om2, payu\
**Created:** [7 January 2026 03:51 UTC](https://forum.access-hive.org.au/t/payu-collate-not-working-from-out-of-the-box-access-om2-config/5752 "2026-01-07T03:51:54Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![pearseb](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/pearseb/32/1033_2.png) [@pearseb](https://forum.access-hive.org.au/u/pearseb)\
**Post date:** [7 January 2026 03:51 UTC](https://forum.access-hive.org.au/t/payu-collate-not-working-from-out-of-the-box-access-om2-config/5752/1 "2026-01-07T03:51:54Z")

</div>

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](https://github.com/ACCESS-NRI/access-om2-configs/tree/dev-1deg_jra55_ryf%2Bwombatlite)

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:

```auto
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

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<div class="post-metadata">

**Author:** ![anton](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/anton/32/1836_2.png) [@anton](https://forum.access-hive.org.au/u/anton)\
**Post date:** [7 January 2026 21:59 UTC](https://forum.access-hive.org.au/t/payu-collate-not-working-from-out-of-the-box-access-om2-config/5752/2 "2026-01-07T21:59:29Z")

</div>

This sounds like [mppnccombine default flags don't always exist · Issue #646 · payu-org/payu · GitHub](https://github.com/payu-org/payu/issues/646)

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`) ?

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<div class="post-metadata">

**Author:** ![pearseb](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/pearseb/32/1033_2.png) [@pearseb](https://forum.access-hive.org.au/u/pearseb)\
**Post date:** [7 January 2026 22:47 UTC](https://forum.access-hive.org.au/t/payu-collate-not-working-from-out-of-the-box-access-om2-config/5752/3 "2026-01-07T22:47:17Z")

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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.

```auto
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!

```

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<div class="post-metadata">

**Author:** ![dougiesquire](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/dougiesquire/32/16_2.png) [@dougiesquire](https://forum.access-hive.org.au/u/dougiesquire)\
**Post date:** [7 January 2026 23:17 UTC](https://forum.access-hive.org.au/t/payu-collate-not-working-from-out-of-the-box-access-om2-config/5752/4 "2026-01-07T23:17:17Z")

</div>

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.