# How to build ACCESS-OM3 on Setonix

**URL:** <https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523>\
**Category:** spack\
**Tags:** spack, access-om3\
**Created:** [14 November 2025 01:07 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523 "2025-11-14T01:07:26Z")\
**Posts on this page:** 9\
**Page:** 1

<div class="post-metadata">

**Author:** ![harshula](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/harshula/32/256_2.png) [@harshula](https://forum.access-hive.org.au/u/harshula)\
**Post date:** [14 November 2025 01:07 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523/1 "2025-11-14T01:07:26Z")

</div>

### How to build ACCESS-OM3 on Setonix (v2)

[18/11/2025: Refer to [How to set up access-spack-packages on Setonix to build ACCESS models](https://forum.access-hive.org.au/t/how-to-set-up-access-spack-packages-on-setonix-to-build-access-models/5560)]

1. Ensure that the initial setup requirements have been completed: [How to set up access-spack-packages on Setonix to build ACCESS models](https://forum.access-hive.org.au/t/how-to-set-up-access-spack-packages-on-setonix-to-build-access-models/5560)

2. Login to Setonix

3. `module load spack/0.23.1`

4. `cd /software/projects/$PAWSEY_PROJECT/$USER`

5. Build ACCESS-OM3 (initialisation may take a long time without any output):

```auto
git clone https://github.com/ACCESS-NRI/ACCESS-OM3.git --branch api-v1-setonix
spack env activate -p ./ACCESS-OM3
spack concretize -f --fresh
spack install

```

---

<div class="post-metadata">

**Author:** ![cbull](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/cbull/32/2203_2.png) [@cbull](https://forum.access-hive.org.au/u/cbull)\
**Post date:** [14 November 2025 01:32 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523/2 "2025-11-14T01:32:44Z")

</div>

### Compiling OM3

So far…

```bash
cbull@setonix-01:~> cd /software/projects/$PAWSEY_PROJECT/$USER
cbull@setonix-01:/software/projects/pawsey0889/cbull> module load spack/0.23.1
Note: when this module is unloaded, the shell environment will NOT revert to its original state, and retain some Spack settings. If you need the original shell environment, start a new
shell session instead.
cbull@setonix-01:/software/projects/pawsey0889/cbull> git clone https://github.com/ACCESS-NRI/ACCESS-OM3.git --branch api-v1-setonix
Cloning into 'ACCESS-OM3'...
remote: Enumerating objects: 950, done.
remote: Counting objects: 100% (344/344), done.
remote: Compressing objects: 100% (128/128), done.
remote: Total 950 (delta 314), reused 220 (delta 216), pack-reused 606 (from 3)
Receiving objects: 100% (950/950), 274.73 KiB | 1.29 MiB/s, done.
Resolving deltas: 100% (587/587), done.
cbull@setonix-01:/software/projects/pawsey0889/cbull> git clone https://github.com/ACCESS-NRI/access-spack-packages.git --branch api-v1-setonix
Cloning into 'access-spack-packages'...
remote: Enumerating objects: 2586, done.
remote: Counting objects: 100% (239/239), done.
remote: Compressing objects: 100% (84/84), done.
remote: Total 2586 (delta 159), reused 199 (delta 133), pack-reused 2347 (from 2)
Receiving objects: 100% (2586/2586), 558.63 KiB | 2.16 MiB/s, done.
Resolving deltas: 100% (1371/1371), done.
cbull@setonix-01:/software/projects/pawsey0889/cbull> spack repo add access-spack-packages
==> Added repo with namespace 'access.nri'.
cbull@setonix-01:/software/projects/pawsey0889/cbull> spack env create om3 ACCESS-OM3/spack.yaml
==> Created environment om3 in: /software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3
==> Activate with: spack env activate om3

==> Warning: upstream not found: /software/projects/pawsey0889/setonix/2025.08/software/.spack-db/index.json
cbull@setonix-01:/software/projects/pawsey0889/cbull> spack env activate -p om3
==> Warning: upstream not found: /software/projects/pawsey0889/setonix/2025.08/software/.spack-db/index.json
[om3] cbull@setonix-01:/software/projects/pawsey0889/cbull> spack concretize -f --fresh
==> Warning: upstream not found: /software/projects/pawsey0889/setonix/2025.08/software/.spack-db/index.json
==> Warning: upstream not found: /software/projects/pawsey0889/setonix/2025.08/software/.spack-db/index.json
==> Fetching https://ghcr.io/v2/spack/bootstrap-buildcache-v1/blobs/sha256:29fda6eb0e8149d3fb662e9e3047fc49584c940c6450c56b36cadac0f59f0300
==> Fetching https://ghcr.io/v2/spack/bootstrap-buildcache-v1/blobs/sha256:a572ab6db954f4a850d1292bb1ef6d6055916784a894d149d657996fa98d0367
==> Installing "clingo-bootstrap@=spack%gcc@=10.2.1~docs+ipo+optimized+python+static_libstdcpp build_system=cmake build_type=Release generator=make patches=bebb819,ec99431 arch=linux-centos7-x86_64" from a buildcache
==> Warning: using "curl@8.6.0" which is a deprecated version
==> Concretized 1 spec:
 - nw2teqx access-om3@git.2025.08.001=2025.08.001%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=bundle arch=linux-sles15-zen3
 - iu4ibaa ^access3@2025.08.000%gcc@14.2.0 cflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' cppflags=-O3 cxxflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' fflags='-O3 -fallow-argument-mismatch -march=sapphirerapids -mtune=sapphirerapids -unroll' ~ipo build_system=cmake build_type=Release configurations=MOM6,MOM6-CICE6,MOM6-CICE6-WW3 generator=make arch=linux-sles15-zen3
 - 65x24fz ^access-cice@CICE6.6.1-0%gcc@14.2.0 cflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' cppflags=-O3 cxxflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' fflags='-O3 -fallow-argument-mismatch -march=sapphirerapids -mtune=sapphirerapids -unroll' +access3~ipo~openmp build_system=cmake build_type=Release driver=none generator=make io_type=PIO arch=linux-sles15-zen3
 - ihwnawx ^parallelio@2.6.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +fortran~ipo~logging+mpi~ncint~pnetcdf+shared~timing build_system=cmake build_type=Release generator=make arch=linux-sles15-zen3
 - dod3pr3 ^access-mom6@2025.07.000%gcc@14.2.0 cflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' cppflags=-O3 cxxflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' fflags='-O3 -fallow-argument-mismatch -march=sapphirerapids -mtune=sapphirerapids -unroll' +access3~asymmetric_mem~ipo~openmp build_system=cmake build_type=Release generator=make arch=linux-sles15-zen3
 - mrz4b6u ^access-generic-tracers@2025.08.000%gcc@14.2.0 cflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' cppflags=-O3 cxxflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' fflags='-O3 -fallow-argument-mismatch -march=sapphirerapids -mtune=sapphirerapids -unroll' ~ipo~shared~use_access_fms build_system=cmake build_type=Release generator=make arch=linux-sles15-zen3
 - hlhyz4u ^access-mocsy@2025.07.002%gcc@14.2.0 cflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' cppflags=-O3 cxxflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' fflags='-O3 -fallow-argument-mismatch -march=sapphirerapids -mtune=sapphirerapids -unroll' ~ipo~shared build_system=cmake build_type=RelWithDebInfo generator=make precision=2 arch=linux-sles15-zen3
 - vlcfotv ^fms@2025.03%gcc@14.2.0 cflags=-O3 cppflags='-O3 -DMAXFIELDMETHODS_=600' cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~gfs_phys+internal_file_nml~ipo+large_file~openmp~pic~quad_precision~yaml build_system=cmake build_type=Release constants=GFDL generator=make precision=32,64 arch=linux-sles15-zen3
 - 6qigqni ^netcdf-fortran@4.6.1%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~doc+pic+shared build_system=autotools arch=linux-sles15-zen3
 - jvysvf2 ^access-ww3@2025.08.000%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +access3~ipo~openmp build_system=cmake build_type=Release generator=make arch=linux-sles15-zen3
 - 7eiveac ^access3-share@2025.08.000%gcc@14.2.0 cflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' cppflags=-O3 cxxflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' fflags='-O3 -fallow-argument-mismatch -march=sapphirerapids -mtune=sapphirerapids -unroll' ~ipo~openmp build_system=cmake build_type=Release generator=make arch=linux-sles15-zen3
 - 6kwyyow ^fortranxml@4.1.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] jygykst ^cmake@3.30.5%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~doc+ncurses+ownlibs~qtgui build_system=generic build_type=Release patches=dbc3892 arch=linux-sles15-zen3
[e] sl4qb2d ^curl@8.6.0%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-sles15-zen3
[^] ukwxigu ^ncurses@6.5%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-sles15-zen3
[e] xli5wec ^pkg-config@0.29.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +internal_glib build_system=autotools arch=linux-sles15-zen3
[^] mqzqbcq ^zlib-ng@2.2.1%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-sles15-zen3
[e] a5jqbog ^cray-mpich@8.1.32%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +wrappers build_system=generic arch=linux-sles15-zen3
 - ppkeqdu ^esmf@8.7.0%gcc@14.2.0 cflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' cppflags=-O3 cxxflags='-O3 -march=sapphirerapids -mtune=sapphirerapids -unroll' fflags='-O3 -fallow-argument-mismatch -march=sapphirerapids -mtune=sapphirerapids -unroll' ~debug~external-lapack+external-parallelio+mpi+netcdf~pnetcdf~python+shared~xerces build_system=makefile esmf_comm=auto esmf_os=auto esmf_pio=auto patches=f63d405 snapshot=none arch=linux-sles15-zen3
 - di3viab ^netcdf-c@4.9.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +blosc~byterange~dap~fsync+hdf4~ipo~jna~logging+mpi~nczarr_zip+optimize~parallel-netcdf+pic+shared+szip+zstd build_system=cmake build_type=RelWithDebInfo generator=make patches=0161eb8,3b09181 arch=linux-sles15-zen3
[^] kfuf6os ^bzip2@1.0.8%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~debug~pic+shared build_system=generic arch=linux-sles15-zen3
[^] ci4uve7 ^diffutils@3.10%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] nktjd7s ^c-blosc@1.21.5%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +avx2~ipo build_system=cmake build_type=Release generator=make arch=linux-sles15-zen3
[^] qovlzcb ^lz4@1.10.0%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +pic build_system=makefile libs=shared,static arch=linux-sles15-zen3
[^] 2z3bpqa ^snappy@1.2.1%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~ipo+pic+shared build_system=cmake build_type=Release generator=make arch=linux-sles15-zen3
[^] ckxxi3s ^hdf@4.2.15%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +external-xdr~fortran~java~netcdf+pic+shared~szip build_system=autotools patches=49733dd,5434f29,ce75518,d54592d,f7d67e8 arch=linux-sles15-zen3
[^] 35hyzgc ^bison@3.8.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~color build_system=autotools arch=linux-sles15-zen3
[^] 3wlkb34 ^flex@2.6.3%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +lex~nls build_system=autotools arch=linux-sles15-zen3
[^] nahfbta ^findutils@4.9.0%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools patches=440b954 arch=linux-sles15-zen3
[^] dazlbri ^libjpeg-turbo@3.0.3%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~ipo~jpeg8~partial_decoder+pic build_system=cmake build_type=Release generator=make libs=shared,static arch=linux-sles15-zen3
[^] litr5ri ^nasm@2.16.03%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] 34smd2y ^libtirpc@1.3.3%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] qpxoj2t ^krb5@1.21.3%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +shared build_system=autotools arch=linux-sles15-zen3
[e] g2fhp7a ^openssl@3.1.4%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~docs+shared build_system=generic certs=mozilla arch=linux-sles15-zen3
[^] yf5a6v5 ^hdf5@1.14.5%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~cxx+fortran+hl~ipo~java~map+mpi+shared~subfiling+szip~threadsafe+tools api=v112 build_system=cmake build_type=Release generator=make arch=linux-sles15-zen3
[^] gtrucs4 ^libaec@1.0.6%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~ipo+shared build_system=cmake build_type=Release generator=make arch=linux-sles15-zen3
[^] 5fhjwl3 ^m4@1.4.19%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-sles15-zen3
[^] mt6plhr ^libsigsegv@2.14%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] 32cfurx ^zstd@1.5.6%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +programs build_system=makefile compression=none libs=shared,static arch=linux-sles15-zen3
 - df5eiqv ^py-pyyaml@6.0.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +libyaml build_system=python_pip arch=linux-sles15-zen3
[e] ma2mcxr ^libyaml@0.1.7%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] 35suhcg ^py-cython@3.0.11%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=python_pip arch=linux-sles15-zen3
[^] f36jkhv ^py-pip@23.1.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=generic arch=linux-sles15-zen3
[^] z2oi3cj ^py-setuptools@59.4.0%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=generic arch=linux-sles15-zen3
[^] vq74grw ^py-wheel@0.41.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=generic arch=linux-sles15-zen3
[^] m2n7szy ^python-venv@1.0%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=generic arch=linux-sles15-zen3
[^] qbfq4gi ^python@3.11.6%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis+optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3~ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-sles15-zen3
[^] jumrpbz ^expat@2.6.4%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +libbsd build_system=autotools arch=linux-sles15-zen3
[^] pxijb7l ^libbsd@0.12.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] 4zoe4mx ^libmd@1.0.4%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] 3h74ofb ^gdbm@1.23%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] 2whuzu2 ^gettext@0.22.5%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-sles15-zen3
[^] njnwstq ^libiconv@1.17%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools libs=shared,static arch=linux-sles15-zen3
[^] kn23dmb ^libxml2@2.13.4%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +pic~python+shared build_system=autotools arch=linux-sles15-zen3
[^] oo2eqqg ^tar@1.34%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools zip=pigz arch=linux-sles15-zen3
[^] sjzyf2a ^pigz@2.8%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=makefile arch=linux-sles15-zen3
[^] tffygrs ^libffi@3.4.6%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] d7up7xp ^libxcrypt@4.4.35%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~obsolete_api build_system=autotools patches=4885da3 arch=linux-sles15-zen3
[^] 7pxyvrk ^perl@5.40.0%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +cpanm+opcode+open+shared+threads build_system=generic arch=linux-sles15-zen3
[^] mkfwww6 ^berkeley-db@18.1.40%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-sles15-zen3
[^] dmmw2we ^readline@8.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools patches=bbf97f1 arch=linux-sles15-zen3
[^] ub6ftsc ^sqlite@3.46.0%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' +column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-sles15-zen3
[^] vloo6pu ^util-linux-uuid@2.40.2%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3
[^] rzuagzv ^xz@5.4.6%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~pic build_system=autotools libs=shared,static arch=linux-sles15-zen3
[^] n4mzbrz ^gmake@4.4.1%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' ~guile build_system=generic arch=linux-sles15-zen3
[^] lcqimel ^gcc-runtime@14.2.0%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=generic arch=linux-sles15-zen3
[e] kq4yvye ^glibc@2.38%gcc@14.2.0 cflags=-O3 cppflags=-O3 cxxflags=-O3 fflags='-O3 -fallow-argument-mismatch' build_system=autotools arch=linux-sles15-zen3

==> Updating view at /software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3/.spack-env/view

```

Then the install step

```bash
[om3] cbull@setonix-01:/software/projects/pawsey0889/cbull> spack install
==> Warning: upstream not found: /software/projects/pawsey0889/setonix/2025.08/software/.spack-db/index.json
[+] /usr (external curl-8.6.0-sl4qb2dyuzgnrr5qvnfcxvuyibejdare)
[+] / (external glibc-2.38-kq4yvyeeueb43pw2gpecw4zbq7v6dtvu)
==> cray-mpich@8.1.32 : has external module in ['cray-mpich/8.1.32', 'craype-network-ofi']
[+] /opt/cray/pe/mpich/8.1.32/ofi/gnu/12.3 (external cray-mpich-8.1.32-a5jqbog3kruhjbqtmjzs6gwmvwgbuwxj)
[+] /usr (external openssl-3.1.4-g2fhp7anq73hyomxcdndqi5g2swxnsif)
[+] /usr (external pkg-config-0.29.2-xli5wecpnhekyoboorrn5kcuj2i2jluq)
[+] /usr (external libyaml-0.1.7-ma2mcxrhybmypbc2a32w2fs7svwv426a)
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gcc-runtime-14.2.0-lcqimelwhbmkb62p2hq53j5wg25pxvdr
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/bzip2-1.0.8-kfuf6os5dk32gezabo775mjneroqgtmi
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/zstd-1.5.6-32cfurxs4cvlxh4327v4m5vbg3atr3yr
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libaec-1.0.6-gtrucs4ow5dylpkbrz5d4wy56yedmaiv
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libiconv-1.17-njnwstq3buh4oevyto5glzy3x7sqhj36
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/util-linux-uuid-2.40.2-vloo6pubnobsd5zjmock7brozrr3u3e7
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/zlib-ng-2.2.1-mqzqbcqdqvpnteot62mwtxcbduldaxp7
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libjpeg-turbo-3.0.3-dazlbri7rs46332wqaeomfskigp76cyv
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libxcrypt-4.4.35-d7up7xpk5vjef7ldyczbuc6ti6lmgokk
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/snappy-1.2.1-2z3bpqagig4o2b2raxs4f6rmcy2m5v6g
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/ncurses-6.5-ukwxiguvkceewckyyv4hw54o7l7v2n2o
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libsigsegv-2.14-mt6plhrbfpqqsqtpjp5rxhfzah6kezpk
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gmake-4.4.1-n4mzbrz4wgwbu3bsh5hysivvkjyc7orb
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/m4-1.4.19-5fhjwl3g5ijbrgeryvxcnl4acesh7f5v
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/pigz-2.8-sjzyf2aaumxyaptiyz4xl2vwgxehxcnq
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/cmake-3.30.5-jygyksts5elbfbkne45cr3quznf3cjxr
==> Installing fortranxml-4.1.2-6kwyyowujc3ajklcyv33n4ejyeb5dfch [23/60]
==> No binary for fortranxml-4.1.2-6kwyyowujc3ajklcyv33n4ejyeb5dfch found: installing from source
==> Fetching https://github.com/andreww/fox/tarball/4.1.2
==> No patches needed for fortranxml
==> fortranxml: Executing phase: 'autoreconf'
==> fortranxml: Executing phase: 'configure'
==> fortranxml: Executing phase: 'build'
==> fortranxml: Executing phase: 'install'
==> fortranxml: Successfully installed fortranxml-4.1.2-6kwyyowujc3ajklcyv33n4ejyeb5dfch
  Stage: 5.00s. Autoreconf: 0.00s. Configure: 14.49s. Build: 26.22s. Install: 3.44s. Post-install: 0.28s. Total: 50.81s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/fortranxml-4.1.2-6kwyyowujc3ajklcyv33n4ejyeb5dfch
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/readline-8.2-dmmw2wewlpfwzhfr27cxziouwyg36fja
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/lz4-1.10.0-qovlzcbgmyzfg5mrfpvq3daumktcphxa
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libmd-1.0.4-4zoe4mxrcgs6qqp33v3or2cov46rjmjh
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libffi-3.4.6-tffygrsy53vvf22tb2izuu6ozfgnquv7
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/xz-5.4.6-rzuagzvd4mrgzn4gmgwda72nuiqxjwgg
==> Installing access-mocsy-2025.07.002-hlhyz4uoqsqhap4c42hpzjpsy6hkqqfg [29/60]
==> No binary for access-mocsy-2025.07.002-hlhyz4uoqsqhap4c42hpzjpsy6hkqqfg found: installing from source
==> No patches needed for access-mocsy
==> access-mocsy: Executing phase: 'cmake'
==> access-mocsy: Executing phase: 'build'
==> access-mocsy: Executing phase: 'install'
==> access-mocsy: Successfully installed access-mocsy-2025.07.002-hlhyz4uoqsqhap4c42hpzjpsy6hkqqfg
  Stage: 5.41s. Cmake: 2.75s. Build: 10.85s. Install: 0.54s. Post-install: 0.20s. Total: 20.02s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/access-mocsy-2025.07.002-hlhyz4uoqsqhap4c42hpzjpsy6hkqqfg
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/hdf5-1.14.5-yf5a6v5ydtegwuxmzf775deq52235a63
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gdbm-1.23-3h74ofbjfhkhm6cdpoztizefixui4xue
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/sqlite-3.46.0-ub6ftscnmofndwymtjwhlt3tknjrdzzm
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/c-blosc-1.21.5-nktjd7sm24fmit6jep4yl3mwdkdwqogo
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libbsd-0.12.2-pxijb7l2q55qcnh6v6i7eqcmodpgy65y
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libxml2-2.13.4-kn23dmbzlj3kakprw3c45dftt4pg52il
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/tar-1.34-oo2eqqgmdtktvlofny5rdocqwoxlg565
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/expat-2.6.4-jumrpbzexd5mvupy7gtiovlb6h2yrdrr
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gettext-0.22.5-2whuzu2omsfzbbd5lk4v7hfnxdexi3ju
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/python-3.11.6-qbfq4gia36gtjz7mhw7moqn2xuxsgdkv
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/krb5-1.21.3-qpxoj2tn7vjc3s3ru5nz7hh2c5w4wpul
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/python-venv-1.0-m2n7szydtgb7bpi6wgox2eybyfnm653r
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libtirpc-1.3.3-34smd2ydzuojiq3lklsnp4ib6vzmynhq
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/py-setuptools-59.4.0-z2oi3cjomim5kh6luxt6nod7hicqoc2v
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/py-pip-23.1.2-f36jkhvqk3v24dayeabio3picqugcmvw
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/hdf-4.2.15-ckxxi3syyundk6oqliejy53hady43svd
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/py-wheel-0.41.2-vq74grwh6mneus5jubwbto4xf4mijv7u
==> Installing netcdf-c-4.9.2-di3viabtlfd5q4pimzfnjnq3v26sciju [47/60]
==> No binary for netcdf-c-4.9.2-di3viabtlfd5q4pimzfnjnq3v26sciju found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/bc/bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7.tar.gz
==> Fetching https://mirror.spack.io/_source-cache/archive/01/0161eb870fdfaf61be9d70132c9447a537320342366362e76b8460c823bf95ca
==> Applied patch /software/setonix/2025.08/spack/var/spack/repos/pawsey/packages/netcdf-c/netcdfc_correct_and_export_link_interface.patch
==> Applied patch https://github.com/Unidata/netcdf-c/commit/f8904d5a1d89420dde0f9d2c0e051ba08d08e086.patch?full_index=1
==> netcdf-c: Executing phase: 'cmake'
==> netcdf-c: Executing phase: 'build'
==> netcdf-c: Executing phase: 'install'
==> netcdf-c: Successfully installed netcdf-c-4.9.2-di3viabtlfd5q4pimzfnjnq3v26sciju
  Stage: 11.47s. Cmake: 1m 58.27s. Build: 42.46s. Install: 4.45s. Post-install: 0.44s. Total: 2m 58.28s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/netcdf-c-4.9.2-di3viabtlfd5q4pimzfnjnq3v26sciju
[+] /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/py-cython-3.0.11-35suhcge2l474lb65g2ydfgnq5k3fahd
==> Installing netcdf-fortran-4.6.1-6qigqniy4t5a5pvjnfhy5yrwimyhuhjy [49/60]
==> No binary for netcdf-fortran-4.6.1-6qigqniy4t5a5pvjnfhy5yrwimyhuhjy found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/b5/b50b0c72b8b16b140201a020936aa8aeda5c79cf265c55160986cd637807a37a.tar.gz
==> No patches needed for netcdf-fortran
==> netcdf-fortran: Executing phase: 'autoreconf'
==> netcdf-fortran: Executing phase: 'configure'
==> netcdf-fortran: Executing phase: 'build'
==> netcdf-fortran: Executing phase: 'install'
==> netcdf-fortran: Successfully installed netcdf-fortran-4.6.1-6qigqniy4t5a5pvjnfhy5yrwimyhuhjy
  Stage: 1.70s. Autoreconf: 0.00s. Configure: 56.52s. Build: 1m 14.19s. Install: 1.43s. Post-install: 0.39s. Total: 2m 15.27s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/netcdf-fortran-4.6.1-6qigqniy4t5a5pvjnfhy5yrwimyhuhjy
==> Installing py-pyyaml-6.0.2-df5eiqvebj5owzno7v26xt7v6q3efrm6 [50/60]
==> No binary for py-pyyaml-6.0.2-df5eiqvebj5owzno7v26xt7v6q3efrm6 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/d5/d584d9ec91ad65861cc08d42e834324ef890a082e591037abe114850ff7bbc3e.tar.gz
==> No patches needed for py-pyyaml
==> py-pyyaml: Executing phase: 'install'
==> py-pyyaml: Successfully installed py-pyyaml-6.0.2-df5eiqvebj5owzno7v26xt7v6q3efrm6
  Stage: 3.72s. Install: 19.27s. Post-install: 0.44s. Total: 24.02s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/py-pyyaml-6.0.2-df5eiqvebj5owzno7v26xt7v6q3efrm6
==> Installing parallelio-2.6.2-ihwnawxlyn2bzxk33dmaxxs2lug57vlv [51/60]
==> No binary for parallelio-2.6.2-ihwnawxlyn2bzxk33dmaxxs2lug57vlv found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/c3/c318894f0230197458917e932ec66301b4407a744df481e9c6a6d9d85f7e5ab1.tar.gz
==> Moving resource stage
        source: /scratch/pawsey0889/cbull/setonix/2025.08/software/cbull/build_stage/resource-genf90-ihwnawxlyn2bzxk33dmaxxs2lug57vlv/spack-src/
        destination: /scratch/pawsey0889/cbull/setonix/2025.08/software/cbull/build_stage/spack-stage-parallelio-2.6.2-ihwnawxlyn2bzxk33dmaxxs2lug57vlv/spack-src/genf90
==> Moving resource stage
        source: /scratch/pawsey0889/cbull/setonix/2025.08/software/cbull/build_stage/resource-CMake_Fortran_utils-ihwnawxlyn2bzxk33dmaxxs2lug57vlv/spack-src/
        destination: /scratch/pawsey0889/cbull/setonix/2025.08/software/cbull/build_stage/spack-stage-parallelio-2.6.2-ihwnawxlyn2bzxk33dmaxxs2lug57vlv/spack-src/CMake_Fortran_utils
==> No patches needed for parallelio
==> parallelio: Executing phase: 'cmake'
==> parallelio: Executing phase: 'build'
==> parallelio: Executing phase: 'install'
==> parallelio: Successfully installed parallelio-2.6.2-ihwnawxlyn2bzxk33dmaxxs2lug57vlv
  Stage: 8.49s. Cmake: 27.83s. Build: 7.71s. Install: 0.28s. Post-install: 0.40s. Total: 47.73s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/parallelio-2.6.2-ihwnawxlyn2bzxk33dmaxxs2lug57vlv
==> Installing fms-2025.03-vlcfotvluhrsdxite7gzm2gjka3syg5z [52/60]
==> No binary for fms-2025.03-vlcfotvluhrsdxite7gzm2gjka3syg5z found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/17/17bdbac86bd3b1e5c1c3a5496c1495e8badcd5f671c659b17921532c990f014c.tar.gz
==> No patches needed for fms
==> fms: Executing phase: 'cmake'
==> fms: Executing phase: 'build'
==> fms: Executing phase: 'install'
==> fms: Successfully installed fms-2025.03-vlcfotvluhrsdxite7gzm2gjka3syg5z
  Stage: 2.89s. Cmake: 13.18s. Build: 4m 24.61s. Install: 4.17s. Post-install: 0.69s. Total: 4m 47.04s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/fms-2025.03-vlcfotvluhrsdxite7gzm2gjka3syg5z
==> Installing esmf-8.7.0-ppkeqdu6fovqwydnyqwehiyxecx7po5s [53/60]
==> No binary for esmf-8.7.0-ppkeqdu6fovqwydnyqwehiyxecx7po5s found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/d7/d7ab266e2af8c8b230721d4df59e61aa03c612a95cc39c07a2d5695746f21f56.tar.gz
==> Applied patch /software/setonix/2025.08/spack/var/spack/repos/builtin/packages/esmf/esmf_cpp_info.patch
==> esmf: Executing phase: 'edit'
==> esmf: Executing phase: 'build'
==> esmf: Executing phase: 'install'
==> esmf: Successfully installed esmf-8.7.0-ppkeqdu6fovqwydnyqwehiyxecx7po5s
  Stage: 21.37s. Edit: 0.00s. Build: 29m 23.61s. Install: 45.50s. Post-install: 0.95s. Total: 30m 34.12s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/esmf-8.7.0-ppkeqdu6fovqwydnyqwehiyxecx7po5s
==> Installing access-generic-tracers-2025.08.000-mrz4b6ug5nzvksspz2afovryww7qpae5 [54/60]
==> No binary for access-generic-tracers-2025.08.000-mrz4b6ug5nzvksspz2afovryww7qpae5 found: installing from source
==> No patches needed for access-generic-tracers
==> access-generic-tracers: Executing phase: 'cmake'
==> access-generic-tracers: Executing phase: 'build'
==> access-generic-tracers: Executing phase: 'install'
==> access-generic-tracers: Successfully installed access-generic-tracers-2025.08.000-mrz4b6ug5nzvksspz2afovryww7qpae5
  Stage: 5.01s. Cmake: 7.90s. Build: 1m 4.66s. Install: 0.38s. Post-install: 0.41s. Total: 1m 19.22s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/access-generic-tracers-2025.08.000-mrz4b6ug5nzvksspz2afovryww7qpae5
==> Installing access3-share-2025.08.000-7eiveacn23d5oqob3uf4ihyqqhwlhony [55/60]
==> No binary for access3-share-2025.08.000-7eiveacn23d5oqob3uf4ihyqqhwlhony found: installing from source
==> No patches needed for access3-share
==> access3-share: Executing phase: 'cmake'
==> access3-share: Executing phase: 'build'
==> access3-share: Executing phase: 'install'
==> access3-share: Successfully installed access3-share-2025.08.000-7eiveacn23d5oqob3uf4ihyqqhwlhony
  Stage: 19.64s. Cmake: 4.26s. Build: 1m 23.87s. Install: 1.04s. Post-install: 0.66s. Total: 1m 51.37s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/access3-share-2025.08.000-7eiveacn23d5oqob3uf4ihyqqhwlhony
==> Installing access-cice-CICE6.6.1-0-65x24fzwognzrz4g2celi7in4jfeffnn [56/60]
==> No binary for access-cice-CICE6.6.1-0-65x24fzwognzrz4g2celi7in4jfeffnn found: installing from source
==> No patches needed for access-cice
==> access-cice: Executing phase: 'cmake'
==> access-cice: Executing phase: 'build'
==> access-cice: Executing phase: 'install'
==> access-cice: Successfully installed access-cice-CICE6.6.1-0-65x24fzwognzrz4g2celi7in4jfeffnn
  Stage: 17.49s. Cmake: 11.92s. Build: 7m 51.25s. Install: 1.00s. Post-install: 0.59s. Total: 8m 24.47s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/access-cice-CICE6.6.1-0-65x24fzwognzrz4g2celi7in4jfeffnn
==> Installing access-ww3-2025.08.000-jvysvf22rqptbhhcbtesl5jd7alusigm [57/60]
==> No binary for access-ww3-2025.08.000-jvysvf22rqptbhhcbtesl5jd7alusigm found: installing from source
==> No patches needed for access-ww3
==> access-ww3: Executing phase: 'cmake'
==> access-ww3: Executing phase: 'build'
==> access-ww3: Executing phase: 'install'
==> access-ww3: Successfully installed access-ww3-2025.08.000-jvysvf22rqptbhhcbtesl5jd7alusigm
  Stage: 1m 21.13s. Cmake: 6.40s. Build: 46.74s. Install: 0.50s. Post-install: 0.69s. Total: 2m 16.65s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/access-ww3-2025.08.000-jvysvf22rqptbhhcbtesl5jd7alusigm
==> Installing access-mom6-2025.07.000-dod3pr3ans4iy32kqnivpmbdtz2cn54h [58/60]
==> No binary for access-mom6-2025.07.000-dod3pr3ans4iy32kqnivpmbdtz2cn54h found: installing from source
==> No patches needed for access-mom6
==> access-mom6: Executing phase: 'cmake'
==> access-mom6: Executing phase: 'build'
==> access-mom6: Executing phase: 'install'
==> access-mom6: Successfully installed access-mom6-2025.07.000-dod3pr3ans4iy32kqnivpmbdtz2cn54h
  Stage: 21.20s. Cmake: 7.13s. Build: 2m 21.88s. Install: 1.79s. Post-install: 0.61s. Total: 2m 54.26s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/access-mom6-2025.07.000-dod3pr3ans4iy32kqnivpmbdtz2cn54h
==> Installing access3-2025.08.000-iu4ibaazibp3pt2mcvysw5oys2mwilqk [59/60]
==> No binary for access3-2025.08.000-iu4ibaazibp3pt2mcvysw5oys2mwilqk found: installing from source
==> Using cached archive: /scratch/pawsey0889/cbull/setonix/2025.08/software/cbull/source_cache/_source-cache/git//ACCESS-NRI/access3-share/f2f35ce5915e82a83899b69560d826deab53b668.tar.gz
==> Warning: Using download cache instead of version control
  The required sources are normally checked out from a version control system, but have been archived in download cache: file:///scratch/pawsey0889/cbull/setonix/2025.08/software/cbull/source_cache/_source-cache/git//ACCESS-NRI/access3-share/f2f35ce5915e82a83899b69560d826deab53b668.tar.gz. Spack lacks a tree hash to verify the integrity of this archive. Make sure your download cache is in a secure location.
==> No patches needed for access3
==> access3: Executing phase: 'cmake'
==> access3: Executing phase: 'build'
==> access3: Executing phase: 'install'
==> access3: Successfully installed access3-2025.08.000-iu4ibaazibp3pt2mcvysw5oys2mwilqk
  Stage: 6.26s. Cmake: 6.67s. Build: 11.05s. Install: 0.68s. Post-install: 0.69s. Total: 27.57s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/access3-2025.08.000-iu4ibaazibp3pt2mcvysw5oys2mwilqk
==> Installing access-om3-git.2025.08.001=2025.08.001-nw2teqxom7njw5emnxuhfvifkxbhrfpe [60/60]
==> No binary for access-om3-git.2025.08.001=2025.08.001-nw2teqxom7njw5emnxuhfvifkxbhrfpe found: installing from source
==> No patches needed for access-om3
==> access-om3: Executing phase: 'install'
==> access-om3: Successfully installed access-om3-git.2025.08.001=2025.08.001-nw2teqxom7njw5emnxuhfvifkxbhrfpe
  Stage: 0.38s. Install: 0.00s. Post-install: 0.56s. Total: 3.62s
[+] /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/access-om3-git.2025.08.001_2025.08.001-nw2teqxom7njw5emnxuhfvifkxbhrfpe
==> Updating view at /software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3/.spack-env/view

```

Success!

Note spack environment is [installed in](https://access-nri.zulipchat.com/#narrow/channel/470325-model-release/topic/ACCESS-OM3.20on.20Setonix/near/556745884):  
`cd /software/projects/$PAWSEY_PROJECT/$USER/setonix/2025.08/environments/`

---

<div class="post-metadata">

**Author:** ![cbull](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/cbull/32/2203_2.png) [@cbull](https://forum.access-hive.org.au/u/cbull)\
**Post date:** [14 November 2025 03:14 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523/3 "2025-11-14T03:14:56Z")

</div>

### Getting the forcing files

Next step is to try and run this:

> <https://github.com/ACCESS-NRI/access-om3-configs/blob/dev-MC_100km_jra_iaf/config.yaml>

Grabbing the input files

```bash
#/home/561/cyb561/repos/access-om3-configs/config.yaml
#from
# - /g/data/vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-ESMFmesh.nc
# - /g/data/vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-nomask-ESMFmesh.nc
# - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-datm-ESMFmesh.nc
# - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-drof-ESMFmesh.nc
# - /g/data/vk83/configurations/inputs/access-om3/share/grids/global.1deg/2020.10.22/topog.nc
# - /g/data/vk83/configurations/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc
# - /g/data/vk83/prerelease/configurations/inputs/access-om3/mom/grids/vertical/share/2025.03.12/ocean_vgrid.nc
# - /g/data/vk83/configurations/inputs/access-om3/mom/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc
# - /g/data/vk83/configurations/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc
# - /g/data/vk83/configurations/inputs/access-om3/cice/grids/global.1deg/2024.05.14/kmt.nc
# - /g/data/vk83/configurations/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/iced.1900-01-01-10800.nc
# - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0

set -x
#SYNCME=rsync -avz --progress cyb561@gadi.nci.org.au:

LCLDIR=/scratch/pawsey0889/cbull/om3forcing/

mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/
mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/
mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/
mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/
mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/share/grids/global.1deg/2020.10.22/
mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/
mkdir -p ${LCLDIR}vk83/prerelease/configurations/inputs/access-om3/mom/grids/vertical/share/2025.03.12/
mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/mom/initial_conditions/global.1deg/2020.10.22/
mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/
mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/cice/grids/global.1deg/2024.05.14/
mkdir -p ${LCLDIR}vk83/configurations/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/
mkdir -p ${LCLDIR}qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0

rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-ESMFmesh.nc ${LCLDIR}vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-nomask-ESMFmesh.nc ${LCLDIR}vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-datm-ESMFmesh.nc ${LCLDIR}vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-drof-ESMFmesh.nc ${LCLDIR}vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/share/grids/global.1deg/2020.10.22/topog.nc ${LCLDIR}vk83/configurations/inputs/access-om3/share/grids/global.1deg/2020.10.22/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc ${LCLDIR}vk83/configurations/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/prerelease/configurations/inputs/access-om3/mom/grids/vertical/share/2025.03.12/ocean_vgrid.nc ${LCLDIR}vk83/prerelease/configurations/inputs/access-om3/mom/grids/vertical/share/2025.03.12/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/mom/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc ${LCLDIR}vk83/configurations/inputs/access-om3/mom/initial_conditions/global.1deg/2020.10.22/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc ${LCLDIR}vk83/configurations/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/cice/grids/global.1deg/2024.05.14/kmt.nc ${LCLDIR}vk83/configurations/inputs/access-om3/cice/grids/global.1deg/2024.05.14/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/vk83/configurations/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/iced.1900-01-01-10800.nc ${LCLDIR}vk83/configurations/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/
rsync -avz --progress cyb561@gadi.nci.org.au:/g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0 ${LCLDIR}qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0

```

The above, whilst worked was very slow, so I tried this for the JRA forcing, now going _from_ Gadi to setonix, i.e.:

```bash
[cyb561@gadi-login-04 cyb561]$ cat push_jra.sh
#!/bin/bash -l

#to submit this
#qsub -P tm70 -q copyq -l walltime=10:00:00,ncpus=1,mem=8GB,jobfs=100GB,storage=gdata/tm70+scratch/tm70+gdata/qv56 /g/data/tm70/cyb561/push_jra.sh

#CBull
#17/11/2025

cd /g/data/tm70/cyb561/
rsync -avz --progress /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0 cbull@data-mover.pawsey.org.au:/scratch/pawsey0889/cbull/

echo "job finished: `date`"

[cyb561@gadi-login-04 cyb561]$ qsub -P tm70 -q copyq -l walltime=10:00:00,ncpus=1,mem=8GB,jobfs=100GB,storage=gdata/tm70+scratch/tm70+gdata/qv56 /g/data/tm70/cyb561/push_jra.sh
154527107.gadi-pbs
[cyb561@gadi-login-04 cyb561]$ pwd
/g/data/tm70/cyb561

```

( **not currently working** )

See [this link](https://pawsey.atlassian.net/wiki/spaces/US/pages/51925882/Transferring+Files+in+out+Pawsey+Filesystems).

… Something is weird with the way submitted jobs are different to log-in node jobs, @joshuatorrance and I decided to run on screen on Setonix.. (note the use of Gadi’s `dm`)

```bash
rsync -avz --progress cyb561@gadi-dm.nci.org.au:/g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0 /scratch/pawsey0889/cbull/joshtest

```

Update (fuller instructions from talking to @helen on 11/3 and now with follow ups)

```auto
ssh pawsey
screen
ssh data-mover
screen
rsync -avz --progress --no-times hm6113@gadi-dm.nci.org.au:/g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-6-0 .

#if you loose connection -- need to match host name number!
ssh pawsey
screen -list
screen -r
ssh data-mover
screen -list
screen -r

```

---

<div class="post-metadata">

**Author:** ![cbull](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/cbull/32/2203_2.png) [@cbull](https://forum.access-hive.org.au/u/cbull)\
**Post date:** [14 November 2025 03:51 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523/4 "2025-11-14T03:51:25Z")

</div>

### Attempting to run OM3

```bash
cd https://github.com/ACCESS-NRI/
git clone https://github.com/ACCESS-NRI/access-om3-configs.git
git checkout dev-MC_100km_jra_iaf

```

```bash
cbull@setonix-06:~> module unload access-om3/git.2025.08.001_2025.08.001-nw2teqx
cbull@setonix-06:~> ldd /software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3/.spack-env/view/bin/access-om3-MOM6-CICE6
        linux-vdso.so.1 (0x00007ffc7a082000)
        /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/esmf-8.7.0-ppkeqdu6fovqwydnyqwehiyxecx7po5s/lib/libesmf.so (0x000014c290b03000)
        libpiof.so => /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/parallelio-2.6.2-ihwnawxlyn2bzxk33dmaxxs2lug57vlv/lib/libpiof.so (0x000014c290a97000)
        libpioc.so => /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/parallelio-2.6.2-ihwnawxlyn2bzxk33dmaxxs2lug57vlv/lib/libpioc.so (0x000014c290a53000)
        libnetcdff.so.7 => /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/netcdf-fortran-4.6.1-6qigqniy4t5a5pvjnfhy5yrwimyhuhjy/lib64/libnetcdff.so.7 (0x000014c290957000)
        libnetcdf.so.19 => /software/projects/pawsey0889/cbull/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/netcdf-c-4.9.2-di3viabtlfd5q4pimzfnjnq3v26sciju/lib64/libnetcdf.so.19 (0x000014c290773000)
        libgfortran.so.5 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gcc-runtime-14.2.0-lcqimelwhbmkb62p2hq53j5wg25pxvdr/lib/libgfortran.so.5 (0x000014c29046d000)
        libm.so.6 => /lib64/libm.so.6 (0x000014c290369000)
        libmvec.so.1 => /lib64/libmvec.so.1 (0x000014c29026e000)
        libstdc++.so.6 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gcc-runtime-14.2.0-lcqimelwhbmkb62p2hq53j5wg25pxvdr/lib/libstdc++.so.6 (0x000014c290018000)
        libmpifort_gnu_123.so.12 => /opt/cray/pe/mpich/8.1.32/ofi/gnu/12.3/lib/libmpifort_gnu_123.so.12 (0x000014c28ff81000)
        libxpmem.so.0 => /opt/xpmem/lib64/libxpmem.so.0 (0x000014c28ff7e000)
        libmpi_gnu_123.so.12 => /opt/cray/pe/mpich/8.1.32/ofi/gnu/12.3/lib/libmpi_gnu_123.so.12 (0x000014c28d7a4000)
        libgomp.so.1 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gcc-runtime-14.2.0-lcqimelwhbmkb62p2hq53j5wg25pxvdr/lib/libgomp.so.1 (0x000014c28d74e000)
        libgcc_s.so.1 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gcc-runtime-14.2.0-lcqimelwhbmkb62p2hq53j5wg25pxvdr/lib/libgcc_s.so.1 (0x000014c28d71f000)
        libc.so.6 => /lib64/libc.so.6 (0x000014c28d400000)
        libhugetlbfs.so => /usr/lib64/libhugetlbfs.so (0x000014c28d6e9000)
        libmfhdf.so.0 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/hdf-4.2.15-ckxxi3syyundk6oqliejy53hady43svd/lib64/libmfhdf.so.0 (0x000014c28d6b8000)
        libdf.so.0 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/hdf-4.2.15-ckxxi3syyundk6oqliejy53hady43svd/lib64/libdf.so.0 (0x000014c28d343000)
        libhdf5_hl.so.310 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/hdf5-1.14.5-yf5a6v5ydtegwuxmzf775deq52235a63/lib/libhdf5_hl.so.310 (0x000014c28d693000)
        libhdf5.so.310 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/hdf5-1.14.5-yf5a6v5ydtegwuxmzf775deq52235a63/lib/libhdf5.so.310 (0x000014c28cea9000)
        libz.so.1 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/zlib-ng-2.2.1-mqzqbcqdqvpnteot62mwtxcbduldaxp7/lib/libz.so.1 (0x000014c28d662000)
        libzstd.so.1 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/zstd-1.5.6-32cfurxs4cvlxh4327v4m5vbg3atr3yr/lib/libzstd.so.1 (0x000014c28cdb7000)
        libbz2.so.1.0 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/bzip2-1.0.8-kfuf6os5dk32gezabo775mjneroqgtmi/lib/libbz2.so.1.0 (0x000014c28d648000)
        libcurl.so.4 => /usr/lib64/libcurl.so.4 (0x000014c28ccda000)
        libxml2.so.2 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libxml2-2.13.4-kn23dmbzlj3kakprw3c45dftt4pg52il/lib64/libxml2.so.2 (0x000014c28cb5c000)
        /lib64/ld-linux-x86-64.so.2 (0x000014c292804000)
        libfabric.so.1 => /opt/cray/libfabric/1.22.0/lib64/libfabric.so.1 (0x000014c28ca24000)
        libatomic.so.1 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gcc-runtime-14.2.0-lcqimelwhbmkb62p2hq53j5wg25pxvdr/lib/libatomic.so.1 (0x000014c28d63c000)
        libpmi.so.0 => /opt/cray/pe/lib64/libpmi.so.0 (0x000014c28d619000)
        libpmi2.so.0 => /opt/cray/pe/lib64/libpmi2.so.0 (0x000014c28ca01000)
        libquadmath.so.0 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gcc-runtime-14.2.0-lcqimelwhbmkb62p2hq53j5wg25pxvdr/lib/libquadmath.so.0 (0x000014c28c9ba000)
        libdl.so.2 => /lib64/libdl.so.2 (0x000014c28c9b7000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x000014c28c9b4000)
        libjpeg.so.62 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libjpeg-turbo-3.0.3-dazlbri7rs46332wqaeomfskigp76cyv/lib64/libjpeg.so.62 (0x000014c28c8c1000)
        libtirpc.so.3 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libtirpc-1.3.3-34smd2ydzuojiq3lklsnp4ib6vzmynhq/lib64/libtirpc.so.3 (0x000014c28c891000)
        libnghttp2.so.14 => /usr/lib64/libnghttp2.so.14 (0x000014c28c868000)
        libidn2.so.0 => /usr/lib64/libidn2.so.0 (0x000014c28c600000)
        libssh.so.4 => /usr/lib64/libssh.so.4 (0x000014c28c591000)
        libpsl.so.5 => /usr/lib64/libpsl.so.5 (0x000014c28c200000)
        libssl.so.3 => /usr/lib64/libssl.so.3 (0x000014c28c4db000)
        libcrypto.so.3 => /usr/lib64/libcrypto.so.3 (0x000014c28bc00000)
        libgssapi_krb5.so.2 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/krb5-1.21.3-qpxoj2tn7vjc3s3ru5nz7hh2c5w4wpul/lib64/libgssapi_krb5.so.2 (0x000014c28c485000)
        libldap_r-2.4.so.2 => /usr/lib64/libldap_r-2.4.so.2 (0x000014c28c430000)
        liblber-2.4.so.2 => /usr/lib64/liblber-2.4.so.2 (0x000014c28c856000)
        libbrotlidec.so.1 => /usr/lib64/libbrotlidec.so.1 (0x000014c28c847000)
        liblzma.so.5 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/xz-5.4.6-rzuagzvd4mrgzn4gmgwda72nuiqxjwgg/lib64/liblzma.so.5 (0x000014c28c1cb000)
        libiconv.so.2 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/libiconv-1.17-njnwstq3buh4oevyto5glzy3x7sqhj36/lib64/libiconv.so.2 (0x000014c28baef000)
        libcxi.so.1 => /usr/lib64/libcxi.so.1 (0x000014c28c826000)
        libpals.so.0 => /opt/cray/pals/1.6/lib/libpals.so.0 (0x000014c28c81e000)
        libkrb5.so.3 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/krb5-1.21.3-qpxoj2tn7vjc3s3ru5nz7hh2c5w4wpul/lib64/libkrb5.so.3 (0x000014c28ba17000)
        libk5crypto.so.3 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/krb5-1.21.3-qpxoj2tn7vjc3s3ru5nz7hh2c5w4wpul/lib64/libk5crypto.so.3 (0x000014c28c19a000)
        libcom_err.so.3 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/krb5-1.21.3-qpxoj2tn7vjc3s3ru5nz7hh2c5w4wpul/lib64/libcom_err.so.3 (0x000014c28c429000)
        libunistring.so.2 => /usr/lib64/libunistring.so.2 (0x000014c28b600000)
        libjitterentropy.so.3 => /usr/lib64/libjitterentropy.so.3 (0x000014c28c41f000)
        libkrb5support.so.0 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/krb5-1.21.3-qpxoj2tn7vjc3s3ru5nz7hh2c5w4wpul/lib64/libkrb5support.so.0 (0x000014c28c18c000)
        libresolv.so.2 => /lib64/libresolv.so.2 (0x000014c28c17a000)
        libintl.so.8 => /software/setonix/2025.08/software/linux-sles15-zen3/gcc-14.2.0/gettext-0.22.5-2whuzu2omsfzbbd5lk4v7hfnxdexi3ju/lib64/libintl.so.8 (0x000014c28ba00000)
        libsasl2.so.3 => /usr/lib64/libsasl2.so.3 (0x000014c28b9e2000)
        libbrotlicommon.so.1 => /usr/lib64/libbrotlicommon.so.1 (0x000014c28b9c0000)
        libnl-3.so.200 => /usr/lib64/libnl-3.so.200 (0x000014c28b99d000)

```

To find the executable (@helen the bit you asked about)

```bash
module load access-om3/git.2025.08.001_2025.08.001-nw2teqx
module load spack/0.23.1
spack env activate -p om3
which access-om3-MOM6-CICE6

```

then `/software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3/.spack-env/view/bin/access-om3-MOM6-CICE6`

#### running tips

- [https://pawsey.atlassian.net/wiki/spaces/US/pages/51927426/Example+Slurm+Batch+Scripts+for+Setonix+on+CPU+Compute+Nodes#ExampleSlurmBatchScriptsforSetonixonCPUComputeNodes-MPIjobs](https://pawsey.atlassian.net/wiki/spaces/US/pages/51927426/Example+Slurm+Batch+Scripts+for+Setonix+on+CPU+Compute+Nodes#ExampleSlurmBatchScriptsforSetonixonCPUComputeNodes-MPIjobs)
- [mpi - any use case for mpirun on slurm-managed cluster? - Stack Overflow](https://stackoverflow.com/questions/51300165/any-use-case-for-mpirun-on-slurm-managed-cluster)

In particular, from first link:

> examples of batch scripts designed to run parallel and distributed computations making use of MPI. In this scenario, the use of the `srun` command is critical for the creation of many tasks on multiple nodes.

#### submitting…

```bash
[356][cbull.setonix-02: cbull]$ pwd
/scratch/pawsey0889/cbull

[cbull.setonix-02: cbull]$ cat runom3.sh
#!/bin/bash --login

# SLURM directives
#
# Here we specify to SLURM we want 512 tasks
# distributed by 128 tasks per node (using all available cores on 4 nodes)
# a wall-clock time limit of 24 hours
#
# Replace [your-project] with the appropriate project name
# following --account (e.g., --account=pawsey00XX)

#SBATCH --account=pawsey0889
#SBATCH --partition=work
#SBATCH --ntasks=512
#SBATCH --ntasks-per-node=128
#SBATCH --exclusive
#SBATCH --time=00:01:00

# ---
# Load here the needed modules

# ---
# Set MPI related environment variables. (Not all need to be set)
# Main variables for multi-node jobs (activate for multinode jobs)
export MPICH_OFI_STARTUP_CONNECT=1
export MPICH_OFI_VERBOSE=1
#Ask MPI to provide useful runtime information (activate if debugging)
export MPICH_ENV_DISPLAY=1
export MPICH_MEMORY_REPORT=1

# https://pawsey.atlassian.net/wiki/spaces/US/pages/51927426/Example+Slurm+Batch+Scripts+for+Setonix+on+CPU+Compute+Nodes#ExampleSlurmBatchScriptsforSetonixonCPUComputeNodes-MPIjobs

# ---
# Run the desired code:
cd /scratch/pawsey0889/cbull/access-om3-configs
srun -N $SLURM_JOB_NUM_NODES -n $SLURM_NTASKS /software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3/.spack-env/view/bin/access-om3-MOM6-CICE6

```

It not working

```bash
[cbull.setonix-02: cbull]$ cat slurm-34894388.out
srun: error: nid001879: tasks 0-2,4-7,9,11-15,18-29,31-48,51-63,65-77,79,81-111,113-115,117,119,121-123,125-127: Illegal instruction
srun: Terminating StepId=34894388.0
srun: error: nid001879: tasks 3,8,10,16-17,30,49-50,64,78,80,112,116,118,120,124: Illegal instruction (core dumped)
srun: error: nid001923: tasks 128-130,144,149,167,188,191,204-205,226,232,238,240,248,255: Illegal instruction (core dumped)
srun: error: nid001923: tasks 131-143,145-148,150-166,168-187,189-190,192-203,206-225,227-231,233-237,239,241-247,249-254: Illegal instruction
srun: error: nid001925: tasks 384-390,392-394,396-404,406-409,411-413,415-427,429-436,438-441,444-456,458-491,495,497,499-503,505-511: Illegal instruction
srun: error: nid001925: tasks 391,395,405,410,414,428,437,442-443,457,492-494,496,498,504: Illegal instruction (core dumped)
srun: error: nid001924: tasks 256-383: Terminated
srun: Force Terminated StepId=34894388.0

```

Or interactively on 256 cores

```bash
[cbull.nid001681: cbull]$ srun -N 2 -n 256 /software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3/.spack-env/view/bin/access-om3-MOM6-CICE6
srun: error: nid001681: tasks 0-1,10,15,27,41-42,46,58-59,91,106-107,122-123,126: Illegal instruction (core dumped)
srun: Terminating StepId=34894765.0
srun: error: nid001681: tasks 2-9,11-14,16-26,28-40,43-45,47-57,60-90,92-105,108-121,124-125,127: Illegal instruction
srun: error: nid001738: tasks 128-129,131-164,166-175,178-181,183,186-188,190-197,199,201-212,215-222,224-228,230-231,233-237,239-255: Illegal instruction
srun: error: nid001738: tasks 130,165,176-177,182,184-185,189,198,200,213-214,223,229,232,238: Illegal instruction (core dumped)

```

---

<div class="post-metadata">

**Author:** ![cbull](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/cbull/32/2203_2.png) [@cbull](https://forum.access-hive.org.au/u/cbull)\
**Post date:** [17 November 2025 00:15 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523/5 "2025-11-17T00:15:43Z")

</div>

### quality of life

Interactive jobs  
`salloc -p work -n 1 -N 1 -c 128 --exclusive -A pawsey0889`

And now asking for 256 cores across two nodes:  
`salloc -p work -n 256 -N 2 --exclusive -A pawsey0889`

Adding setonix to ssh config

```bash
Host setonix
    Hostname setonix.pawsey.org.au
    User cbull
    ForwardX11 true
    ForwardX11Trusted yes
    IdentityFile ~/.ssh/id_rsa
    AddKeysToAgent yes
    ForwardAgent yes

```

---

<div class="post-metadata">

**Author:** ![cbull](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/cbull/32/2203_2.png) [@cbull](https://forum.access-hive.org.au/u/cbull)\
**Post date:** [17 November 2025 00:21 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523/6 "2025-11-17T00:21:42Z")

</div>

### Installing and using Payu

- Regarding payu:

> - I mentioned this to Angus Gibson last week, but our (Chris C and myself) Payu scripts on Setonix are quite hacked together to solve past issues - but I’m fairly sure if I grab the latest Payu there might only be 2 or 3 lines that need changing. I can have a go at this sometime this week and get back to you. There is a specific module set required though - as the default versions cause issues with Payu. This is what I’m currently loading:

```bash
module load pawseyenv/2024.05
module load gcc/12.2.0
module load libfabric/1.15.2.0
module load rclone/1.63.1
module load netcdf-c/4.9.2
module load netcdf-fortran/4.6.1
module load python/3.11.6 py-pip/23.1.2-py3.11.6

```

> Regarding JRA  
> I’ve got the JRA forcing (padded at each end temporally for IAF runs) on ACACIA. This can be accessed using RCLONE once you’ve set up the keys; E.g.,

```bash
Rclone copy acacia:pawsey0410-jra-iaf-padded/<YEAR> /scratch/pawseyXXXX/<username>/

```

### Installing Payu

This was installing @Aidan’s old branch which I didn’t get to work…

```bash
[cbull.setonix-02: /home/cbull]$ git clone https://github.com/payu-org/payu
Cloning into 'payu'...
remote: Enumerating objects: 6972, done.
remote: Counting objects: 100% (1822/1822), done.
remote: Compressing objects: 100% (540/540), done.
remote: Total 6972 (delta 1597), reused 1287 (delta 1282), pack-reused 5150 (from 3)
Receiving objects: 100% (6972/6972), 3.31 MiB | 8.88 MiB/s, done.
Resolving deltas: 100% (4942/4942), done.
[681][cbull.setonix-02: /home/cbull]$ cd payu
[682][cbull.setonix-02: /home/cbull/payu]$ git switch pawsey
branch 'pawsey' set up to track 'origin/pawsey'.
Switched to a new branch 'pawsey'
[683][cbull.setonix-02: /home/cbull/payu]$ pip install . --user
Processing /home/cbull/payu
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting f90nml>=0.16 (from payu==1.0.19)
  Obtaining dependency information for f90nml>=0.16 from https://files.pythonhosted.org/packages/21/f2/4454eefc15cc326b46530d230c58cc0bb91a1e9797f2842b2a1720cbb233/f90nml-1.5.0-py2.py3-none-any.whl.metadata
  Downloading f90nml-1.5.0-py2.py3-none-any.whl.metadata (6.4 kB)
Collecting yamanifest>=0.3.4 (from payu==1.0.19)
  Obtaining dependency information for yamanifest>=0.3.4 from https://files.pythonhosted.org/packages/2a/5a/91816ff3c7f589f027168218fe53bc79c5e6baa76086d6e90fefc0679681/yamanifest-0.3.14-py3-none-any.whl.metadata
  Downloading yamanifest-0.3.14-py3-none-any.whl.metadata (15 kB)
Collecting PyYAML (from payu==1.0.19)
  Obtaining dependency information for PyYAML from https://files.pythonhosted.org/packages/8b/9d/b3589d3877982d4f2329302ef98a8026e7f4443c765c46cfecc8858c6b4b/pyyaml-6.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata
  Downloading pyyaml-6.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
Collecting requests[security] (from payu==1.0.19)
  Obtaining dependency information for requests[security] from https://files.pythonhosted.org/packages/1e/db/4254e3eabe8020b458f1a747140d32277ec7a271daf1d235b70dc0b4e6e3/requests-2.32.5-py3-none-any.whl.metadata
  Downloading requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
Collecting python-dateutil (from payu==1.0.19)
  Obtaining dependency information for python-dateutil from https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting tenacity!=7.0.0 (from payu==1.0.19)
  Obtaining dependency information for tenacity!=7.0.0 from https://files.pythonhosted.org/packages/e5/30/643397144bfbfec6f6ef821f36f33e57d35946c44a2352d3c9f0ae847619/tenacity-9.1.2-py3-none-any.whl.metadata
  Downloading tenacity-9.1.2-py3-none-any.whl.metadata (1.2 kB)
Collecting six (from yamanifest>=0.3.4->payu==1.0.19)
  Obtaining dependency information for six from https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl.metadata
  Downloading six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting xxhash (from yamanifest>=0.3.4->payu==1.0.19)
  Obtaining dependency information for xxhash from https://files.pythonhosted.org/packages/11/4f/426f91b96701ec2f37bb2b8cec664eff4f658a11f3fa9d94f0a887ea6d2b/xxhash-3.6.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata
  Downloading xxhash-3.6.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (13 kB)
Collecting charset_normalizer<4,>=2 (from requests[security]->payu==1.0.19)
  Obtaining dependency information for charset_normalizer<4,>=2 from https://files.pythonhosted.org/packages/c0/10/d20b513afe03acc89ec33948320a5544d31f21b05368436d580dec4e234d/charset_normalizer-3.4.4-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata
  Downloading charset_normalizer-3.4.4-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (37 kB)
Collecting idna<4,>=2.5 (from requests[security]->payu==1.0.19)
  Obtaining dependency information for idna<4,>=2.5 from https://files.pythonhosted.org/packages/0e/61/66938bbb5fc52dbdf84594873d5b51fb1f7c7794e9c0f5bd885f30bc507b/idna-3.11-py3-none-any.whl.metadata
  Downloading idna-3.11-py3-none-any.whl.metadata (8.4 kB)
Collecting urllib3<3,>=1.21.1 (from requests[security]->payu==1.0.19)
  Obtaining dependency information for urllib3<3,>=1.21.1 from https://files.pythonhosted.org/packages/a7/c2/fe1e52489ae3122415c51f387e221dd0773709bad6c6cdaa599e8a2c5185/urllib3-2.5.0-py3-none-any.whl.metadata
  Downloading urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests[security]->payu==1.0.19)
  Obtaining dependency information for certifi>=2017.4.17 from https://files.pythonhosted.org/packages/70/7d/9bc192684cea499815ff478dfcdc13835ddf401365057044fb721ec6bddb/certifi-2025.11.12-py3-none-any.whl.metadata
  Downloading certifi-2025.11.12-py3-none-any.whl.metadata (2.5 kB)
Downloading f90nml-1.5.0-py2.py3-none-any.whl (51 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.0/52.0 kB 12.8 MB/s eta 0:00:00
Downloading tenacity-9.1.2-py3-none-any.whl (28 kB)
Downloading yamanifest-0.3.14-py3-none-any.whl (20 kB)
Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 229.9/229.9 kB 41.1 MB/s eta 0:00:00
Downloading pyyaml-6.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (807 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 807.9/807.9 kB 84.9 MB/s eta 0:00:00
Downloading certifi-2025.11.12-py3-none-any.whl (159 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 159.4/159.4 kB 33.9 MB/s eta 0:00:00
Downloading charset_normalizer-3.4.4-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (153 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 153.5/153.5 kB 31.4 MB/s eta 0:00:00
Downloading idna-3.11-py3-none-any.whl (71 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 71.0/71.0 kB 13.8 MB/s eta 0:00:00
Downloading six-1.17.0-py2.py3-none-any.whl (11 kB)
Downloading urllib3-2.5.0-py3-none-any.whl (129 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 129.8/129.8 kB 28.2 MB/s eta 0:00:00
Downloading requests-2.32.5-py3-none-any.whl (64 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.7/64.7 kB 15.6 MB/s eta 0:00:00
Downloading xxhash-3.6.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (193 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 193.9/193.9 kB 39.3 MB/s eta 0:00:00
Building wheels for collected packages: payu
  Building wheel for payu (pyproject.toml) ... done
  Created wheel for payu: filename=payu-1.0.19-py2.py3-none-any.whl size=80914 sha256=c32be0ca68cf4625298aa0d1d3bd0acabc516d4c186d47bd86dad26b407289e1
  Stored in directory: /tmp/pip-ephem-wheel-cache-2xn7ydcb/wheels/de/b6/3b/9e30c8c57505b9a124ae5dbce71f4febecf120aa3bdc831fcb
Successfully built payu
Installing collected packages: f90nml, xxhash, urllib3, tenacity, six, PyYAML, idna, charset_normalizer, certifi, yamanifest, requests, python-dateutil, payu
  WARNING: The script f90nml is installed in '/home/cbull/.local/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script normalizer is installed in '/home/cbull/.local/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script yamf is installed in '/home/cbull/.local/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts payu, payu-collate, payu-profile and payu-run are installed in '/home/cbull/.local/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed PyYAML-6.0.3 certifi-2025.11.12 charset_normalizer-3.4.4 f90nml-1.5.0 idna-3.11 payu-1.0.19 python-dateutil-2.9.0.post0 requests-2.32.5 six-1.17.0 tenacity-9.1.2 urllib3-2.5.0 xxhash-3.6.0 yamanifest-0.3.14

```

This was installing the latest version which did work, need to `module load python/3.11.6`

```bash
[cbull.setonix-05: cbull]$ git clone https://github.com/payu-org/payu
Cloning into 'payu'...
remote: Enumerating objects: 6972, done.
remote: Counting objects: 100% (1824/1824), done.
remote: Compressing objects: 100% (542/542), done.
remote: Total 6972 (delta 1598), reused 1287 (delta 1282), pack-reused 5148 (from 3)
Receiving objects: 100% (6972/6972), 3.31 MiB | 8.52 MiB/s, done.
Resolving deltas: 100% (4942/4942), done.
Updating files: 100% (133/133), done.
[703][cbull.setonix-05: cbull]$ cd payu
[704][cbull.setonix-05: payu]$ pip install . --user
Processing /scratch/pawsey0889/cbull/payu
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting f90nml>=0.16 (from payu==1.2.0)
  Obtaining dependency information for f90nml>=0.16 from https://files.pythonhosted.org/packages/21/f2/4454eefc15cc326b46530d230c58cc0bb91a1e9797f2842b2a1720cbb233/f90nml-1.5.0-py2.py3-none-any.whl.metadata
  Using cached f90nml-1.5.0-py2.py3-none-any.whl.metadata (6.4 kB)
Collecting yamanifest>=0.3.4 (from payu==1.2.0)
  Obtaining dependency information for yamanifest>=0.3.4 from https://files.pythonhosted.org/packages/2a/5a/91816ff3c7f589f027168218fe53bc79c5e6baa76086d6e90fefc0679681/yamanifest-0.3.14-py3-none-any.whl.metadata
  Using cached yamanifest-0.3.14-py3-none-any.whl.metadata (15 kB)
Collecting PyYAML (from payu==1.2.0)
  Obtaining dependency information for PyYAML from https://files.pythonhosted.org/packages/8b/9d/b3589d3877982d4f2329302ef98a8026e7f4443c765c46cfecc8858c6b4b/pyyaml-6.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata
  Using cached pyyaml-6.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
Collecting requests (from payu==1.2.0)
  Obtaining dependency information for requests from https://files.pythonhosted.org/packages/1e/db/4254e3eabe8020b458f1a747140d32277ec7a271daf1d235b70dc0b4e6e3/requests-2.32.5-py3-none-any.whl.metadata
  Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
Collecting python-dateutil (from payu==1.2.0)
  Obtaining dependency information for python-dateutil from https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting tenacity>=8.0.0 (from payu==1.2.0)
  Obtaining dependency information for tenacity>=8.0.0 from https://files.pythonhosted.org/packages/e5/30/643397144bfbfec6f6ef821f36f33e57d35946c44a2352d3c9f0ae847619/tenacity-9.1.2-py3-none-any.whl.metadata
  Using cached tenacity-9.1.2-py3-none-any.whl.metadata (1.2 kB)
Collecting cftime (from payu==1.2.0)
  Obtaining dependency information for cftime from https://files.pythonhosted.org/packages/d1/fd/a7266970312df65e68b5641b86e0540a739182f5e9c62eec6dbd29f18055/cftime-1.6.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata
  Using cached cftime-1.6.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (8.7 kB)
Collecting GitPython>=3.1.40 (from payu==1.2.0)
  Obtaining dependency information for GitPython>=3.1.40 from https://files.pythonhosted.org/packages/01/61/d4b89fec821f72385526e1b9d9a3a0385dda4a72b206d28049e2c7cd39b8/gitpython-3.1.45-py3-none-any.whl.metadata
  Using cached gitpython-3.1.45-py3-none-any.whl.metadata (13 kB)
Collecting ruamel.yaml>=0.18.5 (from payu==1.2.0)
  Obtaining dependency information for ruamel.yaml>=0.18.5 from https://files.pythonhosted.org/packages/0f/73/bb1bc2529f852e7bf64a2dec885e89ff9f5cc7bbf6c9340eed30ff2c69c5/ruamel.yaml-0.18.16-py3-none-any.whl.metadata
  Using cached ruamel.yaml-0.18.16-py3-none-any.whl.metadata (25 kB)
Collecting packaging (from payu==1.2.0)
  Obtaining dependency information for packaging from https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl.metadata
  Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting netCDF4 (from payu==1.2.0)
  Obtaining dependency information for netCDF4 from https://files.pythonhosted.org/packages/97/1a/78b19893197ed7525edfa7f124a461626541e82aec694a468ba97755c24e/netcdf4-1.7.3-cp311-abi3-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata
  Using cached netcdf4-1.7.3-cp311-abi3-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.9 kB)
Collecting jsonschema (from payu==1.2.0)
  Obtaining dependency information for jsonschema from https://files.pythonhosted.org/packages/bf/9c/8c95d856233c1f82500c2450b8c68576b4cf1c871db3afac5c34ff84e6fd/jsonschema-4.25.1-py3-none-any.whl.metadata
  Using cached jsonschema-4.25.1-py3-none-any.whl.metadata (7.6 kB)
Collecting gitdb<5,>=4.0.1 (from GitPython>=3.1.40->payu==1.2.0)
  Obtaining dependency information for gitdb<5,>=4.0.1 from https://files.pythonhosted.org/packages/a0/61/5c78b91c3143ed5c14207f463aecfc8f9dbb5092fb2869baf37c273b2705/gitdb-4.0.12-py3-none-any.whl.metadata
  Using cached gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)
Collecting ruamel.yaml.clib>=0.2.7 (from ruamel.yaml>=0.18.5->payu==1.2.0)
  Obtaining dependency information for ruamel.yaml.clib>=0.2.7 from https://files.pythonhosted.org/packages/61/62/150c841f24cda9e30f588ef396ed83f64cfdc13b92d2f925bb96df337ba9/ruamel_yaml_clib-0.2.15-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata
  Using cached ruamel_yaml_clib-0.2.15-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (3.5 kB)
Collecting six (from yamanifest>=0.3.4->payu==1.2.0)
  Obtaining dependency information for six from https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl.metadata
  Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting xxhash (from yamanifest>=0.3.4->payu==1.2.0)
  Obtaining dependency information for xxhash from https://files.pythonhosted.org/packages/11/4f/426f91b96701ec2f37bb2b8cec664eff4f658a11f3fa9d94f0a887ea6d2b/xxhash-3.6.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata
  Using cached xxhash-3.6.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (13 kB)
Collecting numpy>=1.21.2 (from cftime->payu==1.2.0)
  Obtaining dependency information for numpy>=1.21.2 from https://files.pythonhosted.org/packages/b6/23/2a1b231b8ff672b4c450dac27164a8b2ca7d9b7144f9c02d2396518352eb/numpy-2.3.5-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata
  Using cached numpy-2.3.5-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
Collecting attrs>=22.2.0 (from jsonschema->payu==1.2.0)
  Obtaining dependency information for attrs>=22.2.0 from https://files.pythonhosted.org/packages/3a/2a/7cc015f5b9f5db42b7d48157e23356022889fc354a2813c15934b7cb5c0e/attrs-25.4.0-py3-none-any.whl.metadata
  Using cached attrs-25.4.0-py3-none-any.whl.metadata (10 kB)
Collecting jsonschema-specifications>=2023.03.6 (from jsonschema->payu==1.2.0)
  Obtaining dependency information for jsonschema-specifications>=2023.03.6 from https://files.pythonhosted.org/packages/41/45/1a4ed80516f02155c51f51e8cedb3c1902296743db0bbc66608a0db2814f/jsonschema_specifications-2025.9.1-py3-none-any.whl.metadata
  Using cached jsonschema_specifications-2025.9.1-py3-none-any.whl.metadata (2.9 kB)
Collecting referencing>=0.28.4 (from jsonschema->payu==1.2.0)
  Obtaining dependency information for referencing>=0.28.4 from https://files.pythonhosted.org/packages/2c/58/ca301544e1fa93ed4f80d724bf5b194f6e4b945841c5bfd555878eea9fcb/referencing-0.37.0-py3-none-any.whl.metadata
  Using cached referencing-0.37.0-py3-none-any.whl.metadata (2.8 kB)
Collecting rpds-py>=0.7.1 (from jsonschema->payu==1.2.0)
  Obtaining dependency information for rpds-py>=0.7.1 from https://files.pythonhosted.org/packages/04/4c/f9b8a05faca3d9e0a6397c90d13acb9307c9792b2bff621430c58b1d6e76/rpds_py-0.29.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Using cached rpds_py-0.29.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB)
Collecting certifi (from netCDF4->payu==1.2.0)
  Obtaining dependency information for certifi from https://files.pythonhosted.org/packages/70/7d/9bc192684cea499815ff478dfcdc13835ddf401365057044fb721ec6bddb/certifi-2025.11.12-py3-none-any.whl.metadata
  Using cached certifi-2025.11.12-py3-none-any.whl.metadata (2.5 kB)
Collecting charset_normalizer<4,>=2 (from requests->payu==1.2.0)
  Obtaining dependency information for charset_normalizer<4,>=2 from https://files.pythonhosted.org/packages/c0/10/d20b513afe03acc89ec33948320a5544d31f21b05368436d580dec4e234d/charset_normalizer-3.4.4-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata
  Using cached charset_normalizer-3.4.4-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (37 kB)
Collecting idna<4,>=2.5 (from requests->payu==1.2.0)
  Obtaining dependency information for idna<4,>=2.5 from https://files.pythonhosted.org/packages/0e/61/66938bbb5fc52dbdf84594873d5b51fb1f7c7794e9c0f5bd885f30bc507b/idna-3.11-py3-none-any.whl.metadata
  Using cached idna-3.11-py3-none-any.whl.metadata (8.4 kB)
Collecting urllib3<3,>=1.21.1 (from requests->payu==1.2.0)
  Obtaining dependency information for urllib3<3,>=1.21.1 from https://files.pythonhosted.org/packages/a7/c2/fe1e52489ae3122415c51f387e221dd0773709bad6c6cdaa599e8a2c5185/urllib3-2.5.0-py3-none-any.whl.metadata
  Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->GitPython>=3.1.40->payu==1.2.0)
  Obtaining dependency information for smmap<6,>=3.0.1 from https://files.pythonhosted.org/packages/04/be/d09147ad1ec7934636ad912901c5fd7667e1c858e19d355237db0d0cd5e4/smmap-5.0.2-py3-none-any.whl.metadata
  Using cached smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)
Collecting typing-extensions>=4.4.0 (from referencing>=0.28.4->jsonschema->payu==1.2.0)
  Obtaining dependency information for typing-extensions>=4.4.0 from https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl.metadata
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Using cached smmap-5.0.2-py3-none-any.whl (24 kB)
Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
Building wheels for collected packages: payu
  Building wheel for payu (pyproject.toml) ... done
  Created wheel for payu: filename=payu-1.2.0-py3-none-any.whl size=138743 sha256=01a7bd9f55d46b6c64d70fbf69d519e84207eb07b67739444afa84ef1bd30f85
  Stored in directory: /tmp/pip-ephem-wheel-cache-6knf0lww/wheels/dc/2b/0d/0a9e5a2ea73680c251c2c3fe52dd6bf042940ba47f4382be98
Successfully built payu
Installing collected packages: f90nml, xxhash, urllib3, typing-extensions, tenacity, smmap, six, ruamel.yaml.clib, rpds-py, PyYAML, packaging, numpy, idna, charset_normalizer, certifi, attrs, yamanifest, ruamel.yaml, requests, referencing, python-dateutil, gitdb, cftime, netCDF4, jsonschema-specifications, GitPython, jsonschema, payu
Successfully installed GitPython-3.1.45 PyYAML-6.0.3 attrs-25.4.0 certifi-2025.11.12 cftime-1.6.5 charset_normalizer-3.4.4 f90nml-1.5.0 gitdb-4.0.12 idna-3.11 jsonschema-4.25.1 jsonschema-specifications-2025.9.1 netCDF4-1.7.3 numpy-2.3.5 packaging-25.0 payu-1.2.0 python-dateutil-2.9.0.post0 referencing-0.37.0 requests-2.32.5 rpds-py-0.29.0 ruamel.yaml-0.18.16 ruamel.yaml.clib-0.2.15 six-1.17.0 smmap-5.0.2 tenacity-9.1.2 typing-extensions-4.15.0 urllib3-2.5.0 xxhash-3.6.0 yamanifest-0.3.14
[705][cbull.setonix-05: payu]$

```

### Rsync tips

From @john_reilly

> - Rsync jobs timing out: Typically use the _data-mover_ nodes for longer transfers (or any transfers really). E.g., from gadi:

```bash
* Rsync <gadi path> <username>@ **data-mover**.pawsey.org.au:<pawsey path>

```

With discussion with @joshuatorrance we figured out this works. Using screen on setonix

```bash
rsync -avz --progress cyb561@gadi-dm.nci.org.au:/g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0 /scratch/pawsey0889/cbull/

```

---

<div class="post-metadata">

**Author:** ![cbull](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/cbull/32/2203_2.png) [@cbull](https://forum.access-hive.org.au/u/cbull)\
**Post date:** [19 November 2025 00:55 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523/7 "2025-11-19T00:55:53Z")

</div>

### Running OM3 `dev-MC_100km_jra_iaf` (`ceaabe3`)!

Modified config.yaml for  
`ceaabe3077382e5d6201791cdd21e1a4b039e964`

Using payu to setup run dir

```bash
module load python/3.11.6
[cbull.setonix-05: access-om3-configs]$ payu setup
laboratory path: /scratch/pawsey0889/cbull/cbull/access-om3
binary path: /scratch/pawsey0889/cbull/cbull/access-om3/bin
input path: /scratch/pawsey0889/cbull/cbull/access-om3/input
work path: /scratch/pawsey0889/cbull/cbull/access-om3/work
archive path: /scratch/pawsey0889/cbull/cbull/access-om3/archive
Metadata and UUID generation is disabled. Experiment name used for archival: access-om3-configs
payu: Found modules in /opt/cray/pe/lmod/lmod
Loading input manifest: manifests/input.yaml
Loading restart manifest: manifests/restart.yaml
Loading exe manifest: manifests/exe.yaml
Setting up access-om3
Checking exe, input and restart manifests
Writing manifests/input.yaml
Writing manifests/restart.yaml
Writing manifests/exe.yaml

```

Note the `config.yaml` needed to be modified

```yaml
# PBS configuration

# If submitting to a different project to your default, uncomment line below
# and change project code as appropriate; also set shortpath below
# project: x77

# Force payu to always find, and save, files in this scratch project directory
# (you may need to add the corresponding PBS -l storage flag in sync_data.sh)
# shortpath: /scratch/v45
shortpath: /scratch/pawsey0889/cbull

queue: normal
ncpus: 240
jobfs: 10GB
mem: 960GB

walltime: 02:00:00
jobname: 1deg_jra55do_iaf

model: access-om3

exe: /software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3_take2/.spack-env/view/bin/access-om3-MOM6-CICE6
input:

    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-ESMFmesh.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-nomask-ESMFmesh.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-datm-ESMFmesh.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-drof-ESMFmesh.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/share/grids/global.1deg/2020.10.22/topog.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/prerelease/configurations/inputs/access-om3/mom/grids/vertical/share/2025.03.12/ocean_vgrid.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/mom/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/cice/grids/global.1deg/2024.05.14/kmt.nc
    - /scratch/pawsey0889/cbull/om3forcing/vk83/configurations/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/iced.1900-01-01-10800.nc
    #- /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0
    - /scratch/pawsey0889/cbull/om3forcing/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0

collate: false
runlog: false
metadata:
    enable: false

#userscripts:
# setup: /usr/bin/bash /g/data/vk83/apps/om3-scripts/payu_config/setup.sh
# archive: /usr/bin/bash /g/data/vk83/apps/om3-scripts/payu_config/archive.sh
#
#modules:
# use:
# - /g/data/vk83/modules
# load:
# - access-om3/2025.01.2
# - nco/5.0.5

payu_minimum_version: 1.1.6

```

Now running:

```bash
[cbull.setonix-05: cbull]$ salloc -p work -n 256 -N 2 --exclusive -A pawsey0889
salloc: Pending job allocation 35030705
salloc: job 35030705 queued and waiting for resources
salloc: job 35030705 has been allocated resources
salloc: Granted job allocation 35030705
salloc: Waiting for resource configuration
salloc: Nodes nid[001515,001526] are ready for job
[680][cbull.nid001515: cbull]$ /scratch/pawsey0889/cbull/access-om3-configs/work
bash: /scratch/pawsey0889/cbull/access-om3-configs/work: Is a directory
[681][cbull.nid001515: cbull]$ cd /scratch/pawsey0889/cbull/access-om3-configs/work
[682][cbull.nid001515: work]$ ls
access-om3-MOM6-CICE6 datm_in diag_table drof.streams.xml fd.yaml INPUT log MOM_input nuopc.runconfig RESTART
config.yaml datm.streams.xml drof_in drv_in ice_in input.nml manifests MOM_override nuopc.runseq timing
[683][cbull.nid001515: work]$ ls -lah access-om3-MOM6-CICE6
lrwxrwxrwx 1 cbull pawsey0889 116 Nov 19 08:41 access-om3-MOM6-CICE6 -> /software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3_take2/.spack-env/view/bin/access-om3-MOM6-CICE6
[684][cbull.nid001515: work]$ srun -N 2 -n 256 /software/projects/pawsey0889/cbull/setonix/2025.08/environments/om3_take2/.spack-env/view/bin/access-om3-MOM6-CICE6
 (t_initf) Read in prof_inparm namelist from: drv_in
 (t_initf) Using profile_disable= F
 (t_initf) profile_timer= 4
 (t_initf) profile_depth_limit= 4
 (t_initf) profile_detail_limit= 2
 (t_initf) profile_barrier= F
 (t_initf) profile_outpe_num= 1
 (t_initf) profile_outpe_stride= 0
 (t_initf) profile_single_file= F
 (t_initf) profile_global_stats= T
 (t_initf) profile_ovhd_measurement= F
 (t_initf) profile_add_detail= F
 (t_initf) profile_papi_enable= F
NOTE from PE 0: MPP_DOMAINS_SET_STACK_SIZE: stack size set to 32768.
NOTE from PE 0: MPP_DOMAINS_SET_STACK_SIZE: stack size set to 5000000.
NOTE from PE 0: field_manager_init:: You are using the legacy version of the field_table

 Dumping coupler_mod/types tree
types/
      air_sea_gas_flux_generic/
            implementation/
                  ocmip2/
                        num_parameters = 2
                  duce/
                        num_parameters = 1
                  johnson/
                        num_parameters = 2
            num_flags = 0
            use_atm_pressure = T
            use_10m_wind_speed = T
            pass_through_ice = F
            atm/
                  name[1] = 'pcair'
                  name[2] = 'u10'
                  name[3] = 'psurf'
                  long_name[1] = 'Atmospheric concentration'
                  long_name[2] = 'Wind speed at 10 m'
                  long_name[3] = 'Surface atmospheric pressure'
                  units[1] = 'mol/mol'
                  units[2] = 'm/s'
                  units[3] = 'Pa'
            ice/
                  name[1] = 'alpha'
                  name[2] = 'csurf'
                  name[3] = 'sc_no'
                  long_name[1] = 'Solubility w.r.t. atmosphere'
                  long_name[2] = 'Ocean concentration'
                  long_name[3] = 'Schmidt number'
                  units[1] = 'mol/m^3/atm'
                  units[2] = 'mol/m^3'
                  units[3] = 'dimensionless'
            flux/
                  name[1] = 'flux'
                  name[2] = 'deltap'
                  name[3] = 'kw'
                  name[4] = 'flux0'
                  long_name[1] = 'Surface flux'
                  long_name[2] = 'Ocean-air delta pressure'
                  long_name[3] = 'Piston velocity'
                  long_name[4] = 'Surface flux no atm'
                  units[1] = 'mol/m^2/s'
                  units[2] = 'uatm'
                  units[3] = 'm/s'
                  units[4] = 'mol/m^2/s'
      air_sea_gas_flux/
            implementation/
                  ocmip2/
                        num_parameters = 2
                  ocmip2_data/
                        num_parameters = 2
                  linear/
                        num_parameters = 3
            num_flags = 0
            use_atm_pressure = T
            use_10m_wind_speed = T
            pass_through_ice = F
            atm/
                  name[1] = 'pcair'
                  name[2] = 'u10'
                  name[3] = 'psurf'
                  long_name[1] = 'Atmospheric concentration'
                  long_name[2] = 'Wind speed at 10 m'
                  long_name[3] = 'Surface atmospheric pressure'
                  units[1] = 'mol/mol'
                  units[2] = 'm/s'
                  units[3] = 'Pa'
            ice/
                  name[1] = 'alpha'
                  name[2] = 'csurf'
                  long_name[1] = 'Solubility from atmosphere times Schmidt number term'
                  long_name[2] = 'Ocean concentration times Schmidt number term'
                  units[1] = 'mol/m^3/atm'
                  units[2] = 'mol/m^3'
            flux/
                  name = 'flux'
                  long_name = 'Surface flux'
                  units = 'mol/m^2/s'
      air_sea_deposition/
            implementation/
                  dry/
                        num_parameters = 1
                  wet/
                        num_parameters = 1
            num_flags = 0
            use_atm_pressure = F
            use_10m_wind_speed = F
            pass_through_ice = T
            atm/
                  name = 'deposition'
                  long_name = 'Atmospheric deposition'
                  units = 'kg/m^2/s'
            ice/
                  name = NULL
                  long_name = NULL
                  units = NULL
            flux/
                  name = 'flux'
                  long_name = 'Surface deposition'
                  units = 'mol/m^2/s'
      land_sea_runoff/
            implementation/
                  river/
                        num_parameters = 1
            num_flags = 0
            use_atm_pressure = F
            use_10m_wind_speed = F
            pass_through_ice = T
            atm/
                  name = 'runoff'
                  long_name = 'Concentration in land runoff'
                  units = 'mol/m^3'
            ice/
                  name = NULL
                  long_name = NULL
                  units = NULL
            flux/
                  name = 'flux'
                  long_name = 'Concentration in land runoff'
                  units = 'mol/m^3'
NOTE from PE 0: open_param_file: MOM_input has been opened successfully.
NOTE from PE 0: open_param_file: MOM_override has been opened successfully.
NOTE from PE 0: close_param_file: MOM_input has been closed successfully.
NOTE from PE 0: close_param_file: MOM_override has been closed successfully.
 ==>Note from atmos_ocean_fluxes_mod(atmos_ocean_fluxes_init): No gas fluxes
NOTE from PE 0: callTree: ---> ocean_model_init(), ocean_model_MOM.F90
NOTE from PE 0: open_param_file: MOM_input has been opened successfully.
NOTE from PE 0: open_param_file: MOM_override has been opened successfully.
NOTE from PE 0: Found the optimum layout for auto-masking. Terminating iteration...
NOTE from PE 0: MOM_domains_init: reading maskmap information from MOM_auto_mask_table
 MOM_in domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 30 30 30 30 30 30 30 30 30 30 30 30
  Y-AXIS = 17 17 17 17 17 17 16 16 16 16 16 16 17 17 17 17 17 17
 MOM_inc domain decomposition
whalo = 2, ehalo = 2, shalo = 2, nhalo = 2
  X-AXIS = 15 15 15 15 15 15 15 15 15 15 15 15
  Y-AXIS = 9 9 9 8 8 8 8 8 8 8 8 8 8 8 8 9 9 9
 parse_mask_table: Number of domain regions masked in MOM_in = 22
 MOM_in domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 22 22 21 21 21 21 21 21 20 21 21 21 21 21 21 22 22
  Y-AXIS = 22 22 22 21 21 21 21 21 21 21 21 22 22 22
 MOM_inc domain decomposition
whalo = 2, ehalo = 2, shalo = 2, nhalo = 2
  X-AXIS = 11 11 11 11 11 10 10 10 10 10 10 10 11 11 11 11 11
  Y-AXIS = 11 11 11 11 11 10 10 10 10 11 11 11 11 11
NOTE from PE 0: diag_manager_mod::diag_manager_init: prepend_date only supported when diag_manager_init is called with time_init present.
NOTE from PE 0: diag_manager_mod::diag_manager_init: You are using the legacy version of the diag table
 MOM_in domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 22 22 21 21 21 21 21 21 20 21 21 21 21 21 21 22 22
  Y-AXIS = 22 22 22 21 21 21 21 21 21 21 21 22 22 22
 MOM_in domain decomposition
whalo = 2, ehalo = 2, shalo = 2, nhalo = 2
  X-AXIS = 11 11 11 11 11 10 10 10 10 10 10 10 11 11 11 11 11
  Y-AXIS = 11 11 11 11 11 10 10 10 10 11 11 11 11 11
 MOM_MOSAIC domain decomposition
whalo = 9, ehalo = 9, shalo = 9, nhalo = 9
  X-AXIS = 44 44 42 42 42 42 42 42 40 42 42 42 42 42 42 44 44
  Y-AXIS = 44 44 44 42 42 42 42 42 42 42 42 44 44 44
 MOM_MOSAIC domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 22 22 21 21 21 21 21 21 20 21 21 21 21 21 21 22 22
  Y-AXIS = 22 22 22 21 21 21 21 21 21 21 21 22 22 22
 MOM_in domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 30 30 30 30 30 30 30 30 30 30 30 30
  Y-AXIS = 17 17 17 17 17 17 16 16 16 16 16 16 17 17 17 17 17 17
 MOM_in domain decomposition
whalo = 2, ehalo = 2, shalo = 2, nhalo = 2
  X-AXIS = 15 15 15 15 15 15 15 15 15 15 15 15
  Y-AXIS = 9 9 9 8 8 8 8 8 8 8 8 8 8 8 8 9 9 9
 MOM_MOSAIC domain decomposition
whalo = 9, ehalo = 9, shalo = 9, nhalo = 9
  X-AXIS = 60 60 60 60 60 60 60 60 60 60 60 60
  Y-AXIS = 34 34 34 34 34 34 32 32 32 32 32 32 34 34 34 34 34 34
 MOM_MOSAIC domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 30 30 30 30 30 30 30 30 30 30 30 30
  Y-AXIS = 17 17 17 17 17 17 16 16 16 16 16 16 17 17 17 17 17 17
 MOM_in domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 30 30 30 30 30 30 30 30 30 30 30 30
  Y-AXIS = 17 17 17 17 17 17 16 16 16 16 16 16 17 17 17 17 17 17
 MOM_in domain decomposition
whalo = 2, ehalo = 2, shalo = 2, nhalo = 2
  X-AXIS = 15 15 15 15 15 15 15 15 15 15 15 15
  Y-AXIS = 9 9 9 8 8 8 8 8 8 8 8 8 8 8 8 9 9 9

WARNING from PE 0: Open_file is appending .nc to the filename ./ocean_geometry

WARNING from PE 0: Open_file is appending .nc to the filename ./ocean_geometry

 MOM_in domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 22 22 21 21 21 21 21 21 20 21 21 21 21 21 21 22 22
  Y-AXIS = 22 22 22 21 21 21 21 21 21 21 21 22 22 22
 MOM_in domain decomposition
whalo = 2, ehalo = 2, shalo = 2, nhalo = 2
  X-AXIS = 11 11 11 11 11 10 10 10 10 10 10 10 11 11 11 11 11
  Y-AXIS = 11 11 11 11 11 10 10 10 10 11 11 11 11 11

WARNING from PE 0: MEKE_init: Initializing MEKE with a local equilibrium balance.

NOTE from PE 0: MOM_restart: Unable to find MEKE_Le queried by pointer, probably because of the suspect comparison of pointers by ASSOCIATED.
NOTE from PE 0: MOM_restart: Unknown restart variable MEKE_Le queried for initialization.

WARNING from PE 0: MEKE_init: Initializing MEKE with a local equilibrium balance.

NOTE from PE 0: MOM_vert_friction: updateCFLtruncationValue set CFL limit to 0.000E+00
 MOM_in domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 22 22 21 21 21 21 21 21 20 21 21 21 21 21 21 22 22
  Y-AXIS = 22 22 22 21 21 21 21 21 21 21 21 22 22 22
 MOM_in domain decomposition
whalo = 2, ehalo = 2, shalo = 2, nhalo = 2
  X-AXIS = 11 11 11 11 11 10 10 10 10 10 10 10 11 11 11 11 11
  Y-AXIS = 11 11 11 11 11 10 10 10 10 11 11 11 11 11
 MOM_in domain decomposition
whalo = 0, ehalo = 0, shalo = 0, nhalo = 0
  X-AXIS = 22 22 21 21 21 21 21 21 20 21 21 21 21 21 21 22 22
  Y-AXIS = 22 22 22 21 21 21 21 21 21 21 21 22 22 22
NOTE from PE 0: data_override_init: You are using the legacy version of the data table.
NOTE from PE 0: data_override_mod: File data_table does not exist.
NOTE from PE 0: data_table is empty, not doing any data_overrides
NOTE from PE 0: data_override_init: You are using the legacy version of the data table.
NOTE from PE 0: data_override_mod: File data_table does not exist.
NOTE from PE 0: data_table is empty, not doing any data_overrides
 MOM_in domain decomposition
whalo = 4, ehalo = 4, shalo = 4, nhalo = 4
  X-AXIS = 22 22 21 21 21 21 21 21 20 21 21 21 21 21 21 22 22
  Y-AXIS = 22 22 22 21 21 21 21 21 21 21 21 22 22 22
 MOM_in domain decomposition
whalo = 2, ehalo = 2, shalo = 2, nhalo = 2
  X-AXIS = 11 11 11 11 11 10 10 10 10 10 10 10 11 11 11 11 11
  Y-AXIS = 11 11 11 11 11 10 10 10 10 11 11 11 11 11
NOTE from PE 0: MOM_vert_friction: updateCFLtruncationValue set CFL limit to 2.188E-01
NOTE from PE 0: MOM_vert_friction: updateCFLtruncationValue set CFL limit to 3.750E-01
NOTE from PE 0: MOM_vert_friction: updateCFLtruncationValue set CFL limit to 4.688E-01
NOTE from PE 0: MOM_vert_friction: updateCFLtruncationValue set CFL limit to 5.000E-01
 ERROR: 1 nans found in Fioi_meltw
 ABORTING JOB, see PET file for details
MPICH ERROR [Rank 0] [job id 35030705.0] [Wed Nov 19 08:45:40 2025] [nid001515] - Abort(1) (rank 0 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 0

srun: error: nid001526: tasks 128-255: Exited with exit code 1
srun: Terminating StepId=35030705.0
slurmstepd: error: ***STEP 35030705.0 ON nid001515 CANCELLED AT 2025-11-19T08:45:41***
srun: error: nid001515: tasks 0-127: Exited with exit code 1

```

---

<div class="post-metadata">

**Author:** ![cbull](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/cbull/32/2203_2.png) [@cbull](https://forum.access-hive.org.au/u/cbull)\
**Post date:** [28 November 2025 00:19 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523/8 "2025-11-28T00:19:20Z")

</div>

@helen / @harshula as I’ve now started [keeping notes / issues / errors on GitHub](https://github.com/ACCESS-NRI/access-om3-configs/issues/893). I think I’m inclined to delete my posts above (might make a backup offline). That ok?

---

<div class="post-metadata">

**Author:** ![helen](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/helen/32/2840_2.png) [@helen](https://forum.access-hive.org.au/u/helen)\
**Post date:** [28 November 2025 00:32 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om3-on-setonix/5523/9 "2025-11-28T00:32:45Z")

</div>

That works for me. Please keep @harshula’s first post though.