Update toolchain to newer versions of packages (alongside oneAPI upgrade)

[manodeep]

When creating the new oneAPI build, we should move to the latest versions of module/external packages whenever possible. Specifically, these are:

• openmpi 4.0.2 -> 5.0.5 (see module avail openmpi on gadi)
• netcdf-c 4.7.4 -> 4.9.2 (see this link)
• netcdf-fortran 4.5.2 -> 4.6.1 (see this link)
• hdf5 1.10.11 -> 1.14.3 (see this link).^

^: This is assuming we do install the netcdf package and hdf5 comes along as a dependency. netcdf/4.9.2 on gadi seems to be installed with hdf5/1.12.1

[/apps/netcdf/4.9.2/lib/Intel @gadi06] ldd libnetcdff.so
        linux-vdso.so.1 (0x00007fff445d3000)
        libnetcdf.so.19 => /apps/netcdf/4.9.2/lib/libnetcdf.so.19 (0x00007f2ae61df000)
        libmfhdf.so.0 => /apps/hdf4/4.2.14/lib/libmfhdf.so.0 (0x00007f2ae5fb4000)
        libdf.so.0 => /apps/hdf4/4.2.14/lib/libdf.so.0 (0x00007f2ae5d02000)
        libtirpc.so.3 => /lib64/libtirpc.so.3 (0x00007f2ae5ace000)
        libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00007f2ae5865000)
        libhdf5_hl.so.200 => /apps/hdf5/1.12.1/lib/libhdf5_hl.so.200 (0x00007f2ae5644000)
        libhdf5.so.200 => /apps/hdf5/1.12.1/lib/libhdf5.so.200 (0x00007f2ae501d000)

[manodeep]

All of these version upgrades are in addition to the compiler update to oneAPI 2025.0.4

[manodeep]

Noting one set of updates that spack installed fully:

[+] /g/data/tm70/ms2335/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/oneapi-2025.0.4/access-esm1p6-latest-soyimp7aguwsxts24ad4li3jsjadobtq
==> Updating view at /g/data/tm70/ms2335/spack/0.22/environments/esm1p6-dev/.spack-env/view

real    43m33.119s
user    55m15.564s
sys     14m56.015s
[esm1p6-dev] [~/codes/access-nri/ACCESS-ESM1.6 @gadi06] spack find
==> In environment esm1p6-dev
==> 1 root specs
[+] access-esm1p6@latest

==> Installed packages
-- linux-rocky8-x86_64_v4 / [email protected] --------------------------
[email protected]

-- linux-rocky8-x86_64_v4 / [email protected] ---------------------
access-esm1p6@latest                                [email protected]                                                     [email protected]
[email protected]_2025.02.1=2025.02.2              [email protected]=access-esm1.5  [email protected]
[email protected]=2025.02.1  [email protected]                                                        [email protected]=access-esm1.5
[email protected]=2017.12.0                [email protected]                                                       [email protected]
[email protected]                                         [email protected]                                                      [email protected]
[email protected]                                      [email protected]                                     [email protected]
[email protected]=access-esm1.5   [email protected]                                                      [email protected]=access-esm1.6
[email protected]                                        [email protected]                                                     [email protected]
[email protected]                                      [email protected]                                                         [email protected]
[email protected]                                       [email protected]=access-esm1.6
==> 30 installed packages

[manodeep]

Updating all of the listed package versions works (updated here: netcdf-fortran + hdf5)

[+] /g/data/tm70/ms2335/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/oneapi-2025.0.4/mom5-git.dev-2025.03.001_access-esm1.6-pqo47puj5dmxaipqzqhsxzez2kv54nml
==> Installing access-esm1p6-latest-lajrvssialpfr3jsvab4bbh7sthvivju [27/27]
==> No patches needed for access-esm1p6
==> access-esm1p6: Executing phase: 'install'
==> access-esm1p6: Successfully installed access-esm1p6-latest-lajrvssialpfr3jsvab4bbh7sthvivju
  Stage: 0.00s.  Install: 0.00s.  Post-install: 0.63s.  Total: 3.59s
[+] /g/data/tm70/ms2335/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/oneapi-2025.0.4/access-esm1p6-latest-lajrvssialpfr3jsvab4bbh7sthvivju
==> Updating view at /g/data/tm70/ms2335/spack/0.22/environments/esm1p6-dev/.spack-env/view

real    19m3.733s
user    28m15.193s
sys     6m57.759s
[esm1p6-dev] [~/codes/access-nri/ACCESS-ESM1.6 @gadi03] spack find
==> In environment esm1p6-dev
==> 1 root specs
[+] access-esm1p6@latest

==> Installed packages
-- linux-rocky8-x86_64_v4 / [email protected] --------------------------
[email protected]

-- linux-rocky8-x86_64_v4 / [email protected] ---------------------
access-esm1p6@latest                                [email protected]                                                    [email protected]                                                           [email protected]
[email protected]_2025.02.1=2025.02.2              [email protected]                                                     [email protected]                                                          [email protected]
[email protected]=2025.02.1  [email protected]                                                     [email protected]                                                              [email protected]=access-esm1.6
[email protected]=2017.12.0                [email protected]=access-esm1.5  [email protected]=access-esm1.6                                 [email protected]
[email protected]                                         [email protected]                                                        [email protected]                                                         [email protected]
[email protected]                                      [email protected]                                                       [email protected]
[email protected]=access-esm1.5   [email protected]                                                       [email protected]=access-esm1.5
[email protected]                                        [email protected]                                     [email protected]
==> 30 installed packages
[esm1p6-dev] [~/codes/access-nri/ACCESS-ESM1.6 @gadi03]