Cannot find mppncombine after compiling ACCESS-OM2-wombatlite

Technical spack
, , , ,
1

Description of request:

Environment:

NCI-Gadi 1) singularity 2) payu/1.1.7(default)

Spack Environment as follows:
pack:

add package specs to the specs list

specs:

  • access-om2@git.2024.03.0=latest
    packages:
    cice5:
    require:
    • ‘@git.2025.03.001=access-om2’
      mom5:
      require:
    • ‘@git.2025.08.000=access-om2’
      libaccessom2:
      require:
    • ‘@git.2025.05.001=access-om2’
      oasis3-mct:
      require:
    • ‘@git.2025.03.001’
      netcdf-c:
      require:
    • ‘@4.7.4’
      netcdf-fortran:
      require:
    • ‘@4.5.2’
      parallelio:
      require:
    • ‘@2.5.2’
      openmpi:
      require:
    • ‘@4.0.2’
      access-fms:
      require:
    • ‘@git.mom5-2025.05.000=mom5’
    • cppflags=“-DMAXFIELDMETHODS_=600”
      access-generic-tracers:
      require:
    • ‘@2025.08.000’
      access-mocsy:
      require:
    • ‘@2025.07.002’
      all:
      require:
    • ‘%intel@19.0.5.281’
    • target=x86_64
      view: true
      concretizer:
      unify: true
      develop:
      access-generic-tracers:
      spec: access-generic-tracers@=2025.08.000
      path: ./GFDL-generic-tracers/

What executed:

I installed spack and activated it and typed "spack install". The install completed but did not install any "mppncombine" executable anywhere, and I need this in order to collate my output following running the model.

Actual results:

Compile is succesful for everything else, but doesn't compile an mppncombine executable.

Expected results:

Additional info:

2

Are you using an ACCESS-NRI supported configuration?

There are versions of access-om2 compiled and installed on gadi that are used in those configurations:

$ module use /g/data/vk83/modules
$ module avail access-om2
--------------------------- /g/data/vk83/modules ---------------------------
access-om2-bgc/2024.03.0  access-om2/2023.11.23  access-om2/2025.09.000  
access-om2-bgc/2024.07.0  access-om2/2024.03.0

Do you need to compile your own version of access-om2?

If you need mppnccombine it is available in the fre-nctools module:

$ module load fre-nctools
$ which mppnccombine
/g/data/vk83/apps/spack/0.22/release/linux-rocky8-x86_64_v4/intel-2021.10.0/fre-nctools-2024.05-1-b7s7yifeqhlj3ydibuwfp3ee6zgag2vl/bin/mppnccombine

or mppnccombine-fast

$ module avail mppnccombine-fast
------------------------------- /g/data/vk83/modules --------------------------------
mppnccombine-fast/2025.07.000
3

Hi Aidan,

Answer is yes we need to be compiling our own version of ACCESS-OM2. Rama is doing development work as part of her PhD and Dougie (before he went on leave) set her up with her own spack environment configuration where she can do that development, recompile and run the model.

I’m unfortunately not well placed to help with trouble shooting for her set up because her spack environment/set-up (whatever you call it) is different to mine, which is because i was set up many moons ago. My “spack install” command does compile an mppncombine executable, whereas hers appears not to. So, I’m not sure how to help.

RE mppncombine: Is it possible for her to use the “off-the-shelf” mppncombine that you point to or does she need to use the mppncombine that is compiled in her specific build?

Thanks

pearse

4

Off the shelf is fine. The ACCESS-OM3 configs give an example of how this might be done:

But replace model-tools/mppnccombine-fast with fre-nctools/2024.05-1, e.g.

modules:
    use:
        - /g/data/vk83/modules
    load:
        - fre-nctools/2024.05-1

And that should work out of the box. Please let us know if that didn’t fix your issue @raslekar.

3 Likes
5

Thanks Aidan :slight_smile:

6

Hi Rama

I am at IMAS most days - happy to come and trouble-shoot this with you if its unresolved!

1 Like
7

Thanks Aidan

8

Thanks Anton

9

Happy to help. I have marked my post as the solution. If you disagree please let me know or deselect it.

12

When @raslekar ran this, there was an error saying -z was not found in the input files. In the end, we needed to set the collate flags through the payu config as well.

In config.yaml, under the collate: section, we needed to set:

    flags: -n4 -m -r​

which removes the -z flag which payu includes by default

1 Like