ocean.nml diffs

[PaulSpence]

Hi Folks,

I am validating ocean/input.nml inputs for wombat enabled https://github.com/hakaseh/025deg_jra55_ryf/ with
/g/data/ik11/outputs/access-om2-025/025deg_jra55_ryf9091_gadi/output324/ocean/

Its really hard to tell the differences since the files are scrambled a bit relative to each other :) (if only there was a handy Kiss tool!)

Some subtle differences (no wombat vs wombat) where only differing values are retained below:

1. &ocean_barotropic_nml
   barotropic_time_stepping_A = .true.
   barotropic_time_stepping_B = .false. vs

&ocean_barotropic_nml
barotropic_time_stepping_a = .true.
barotropic_time_stepping_b = .false.

Fortran is not case sensitive, I think. So no problem here.

2. &ocean_bbc_nml
   uresidual = 0.05

vs

&ocean_bbc_nml
cdbot_hi = 0.007

/

3. &ocean_nphysics_util_nml
   agm=200.0
   drhodz_smooth_horz=.false.
   drhodz_smooth_vert=.false.
   tracer_mix_micom=.false.
   vel_micom=0.0
   agm_closure_length_fixed=.false.
   agm_closure_length_rossby=.false.
   agm_closure_length_bczone=.false.
   agm_closure_eden_greatbatch=.false.
   agm_closure_eden_gamma=0.0
   agm_smooth_space=.false.
   agm_smooth_time=.false.
   agm_damping_time=45.0
   rossby_radius_max=100e3
   rossby_radius_min=10e3
   /

vs

&ocean_nphysics_util_nml
agm_closure_buoy_freq = 0.004
/

Should I just upgrade the https://github.com/hakaseh/025deg_jra55_ryf/ocean/input.nml to /g/data/ik11/outputs/access-om2-025/025deg_jra55_ryf9091_gadi/output324/ocean/input.nml?

Andrew, can we use your *.nml diff tool here?

Thank you,
Paul

[PaulSpence]

@aekiss Andrew, can we use your *.nml diff tool here? The evaluation above isn;t complete.

[PaulSpence]

The wombat 025 RYF simulation is grinding here:
/home/561/pas561/access-om2/025deg_jra55_ryf

[aekiss]

try https://github.com/aekiss/nmltab

[aekiss]

FYI Hakase and I are still straightening out some updates to the executables... COSIMA/1deg_jra55_iaf#11

[PaulSpence]

yeah, i turned the bgc off in the sea ice module.

[aekiss]

BTW as well as comparing existing disorganised namelists, https://github.com/aekiss/nmltab can also put the namelists into a consistent format using --tidy_overwrite so that they are easier to compare with diff

[aekiss]

run it from the command line, not python

[PaulSpence]

Hi Folks,

The 025/ryf with wombat in the ocean (wombat off in sea ice) runs smoothly (output00[0-2]) using Hakase's original ocean/input.nml file, here:
/home/561/pas561/access-om2/025deg_jra55_ryf/ocean/input_orig.nml

It fails in first couple days when the file is updated to follow
/g/data/ik11/outputs/access-om2-025/025deg_jra55_ryf9091_gadi/output324/ocean/input.nml

I love nmltab.py --tidy_overwrite :)

The relevant differences between these two files are: diff input_orig.nml input_updated.nml
./../../../nmltab/nmltab.py -d --format markdown input_orig.nml input_updated.nml

File	&monin_obukhov_nml neutral	&mpp_io_nml deflate_level	&ocean_albedo_nml ocean_albedo_option	&ocean_barotropic_nml debug_this_module	&ocean_bbc_nml cdbot	&ocean_bbc_nml cdbot_roughness_length	&ocean_bbc_nml use_geothermal_heating	&ocean_nphysics_util_nml agm	&ocean_nphysics_util_nml agm_closure_eden_gamma	&ocean_nphysics_util_nml agm_closure_eden_greatbatch	&ocean_nphysics_util_nml agm_closure_length_bczone	&ocean_nphysics_util_nml agm_closure_length_fixed	&ocean_nphysics_util_nml agm_closure_length_rossby	&ocean_nphysics_util_nml agm_damping_time	&ocean_nphysics_util_nml agm_smooth_space	&ocean_nphysics_util_nml agm_smooth_time	&ocean_nphysics_util_nml drhodz_smooth_horz	&ocean_nphysics_util_nml drhodz_smooth_vert	&ocean_nphysics_util_nml rossby_radius_max	&ocean_nphysics_util_nml rossby_radius_min	&ocean_nphysics_util_nml tracer_mix_micom	&ocean_nphysics_util_nml vel_micom	&ocean_nphysicsc_nml debug_this_module	&ocean_pressure_nml zero_pressure_force	&ocean_rivermix_nml debug_this_module	&ocean_sbc_nml ocean_ice_salt_limit	&ocean_shortwave_gfdl_nml debug_this_module	&ocean_submesoscale_nml debug_this_module	&ocean_tempsalt_nml debug_this_module	&ocean_thickness_nml debug_this_module	&ocean_tracer_diag_nml diag_step	&ocean_tracer_nml debug_this_module
input_orig.nml		5																								0.006					4320
input_updated.nml	True	-1	2	False	0.001	False	False	200.0	0.0	False	False	False	False	45.0	False	False	False	False	100000.0	10000.0	False	0.0	False	False	False		False	False	False	False	48	False

[PaulSpence]

The differences between the working input.nml from Hakase (input_orig.nml) and Andrew Kisss current ice-BGC 1deg case (https://github.com/COSIMA/1deg_jra55_iaf/tree/bgc-mdppm-run) are quite extensive:

./../../../nmltab/nmltab.py -d --format markdown input_orig.nml ../../1deg_jra55_iaf/ocean/input.nml

File	&auscom_ice_nml redsea_gulfbay_sfix	&fms_nml domains_stack_size	&mom_oasis3_interface_nml fields_in	&mom_oasis3_interface_nml fields_out	&mom_oasis3_interface_nml num_fields_in	&mom_oasis3_interface_nml num_fields_out	&mpp_io_nml deflate_level	&ocean_bihgen_friction_nml bottom_5point	&ocean_bihgen_friction_nml ncar_boundary_scaling	&ocean_bihgen_friction_nml vel_micom_bottom	&ocean_bihgen_friction_nml vel_micom_iso	&ocean_bihgen_friction_nml visc_crit_scale	&ocean_lapgen_friction_nml bottom_5point	&ocean_lapgen_friction_nml k_smag_aniso	&ocean_lapgen_friction_nml k_smag_iso	&ocean_lapgen_friction_nml restrict_polar_visc	&ocean_lapgen_friction_nml restrict_polar_visc_lat	&ocean_lapgen_friction_nml restrict_polar_visc_ratio	&ocean_lapgen_friction_nml use_this_module	&ocean_lapgen_friction_nml vel_micom_iso	&ocean_lapgen_friction_nml viscosity_ncar	&ocean_lapgen_friction_nml viscosity_ncar_2007	&ocean_lapgen_friction_nml viscosity_scale_by_rossby	&ocean_lapgen_friction_nml viscosity_scale_by_rossby_power	&ocean_mixdownslope_nml mixdownslope_mask_gfdl	&ocean_mixdownslope_nml mixdownslope_npts	&ocean_mixdownslope_nml read_mixdownslope_mask	&ocean_mixdownslope_nml use_this_module	&ocean_model_nml io_layout	&ocean_model_nml layout	&ocean_nphysics_util_nml agm_closure_length	&ocean_nphysics_util_nml agm_closure_max	&ocean_nphysics_util_nml agm_closure_min	&ocean_nphysics_util_nml aredi	&ocean_nphysics_util_nml aredi_diffusivity_grid_scaling	&ocean_sbc_nml do_bitwise_exact_sum	&ocean_sbc_nml max_delta_salinity_restore	&ocean_sbc_nml ocean_ice_salt_limit	&ocean_sigma_transport_nml use_this_module	&ocean_submesoscale_nml smooth_advect_transport_num	&ocean_submesoscale_nml smooth_psi_num	&ocean_vert_mix_nml j09_bgmax	&ocean_vert_mix_nml j09_bgmin	&ocean_vert_mix_nml j09_diffusivity	&ocean_vert_mix_nml j09_lat
input_orig.nml			['u_flux', 'v_flux', 'lprec', 'fprec', 'salt_flx', 'mh_flux', 'sw_flux', 'q_flux', 't_flux', 'lw_flux', 'runof', 'p', 'aice', 'wfimelt', 'wfiform', 'licefw', 'liceht', 'wnd_io', 'iof_nit', 'iof_alg']	['t_surf', 's_surf', 'u_surf', 'v_surf', 'dssldx', 'dssldy', 'frazil', 'n_surf', 'alg_surf']	20	9	5	False	False	0.0	0.0	1.0							False									False	[6, 5]	[48, 40]	20000.0	200.0	1.0	200.0	True	False	0.5	0.006	False	4	3
../../1deg_jra55_iaf/ocean/input.nml	False	115200	['u_flux', 'v_flux', 'lprec', 'fprec', 'salt_flx', 'mh_flux', 'sw_flux', 'q_flux', 't_flux', 'lw_flux', 'runof', 'p', 'aice', 'wfimelt', 'wfiform', 'licefw', 'liceht']	['t_surf', 's_surf', 'u_surf', 'v_surf', 'dssldx', 'dssldy', 'frazil']	17	7	-1	True	True	0.01	0.04	0.25	True	0.0	0.0	True	60.0	0.35	True	0.1	False	False	True	4.0	False	4	False	True	[4, 3]	[16, 15]	50000.0	600.0	50.0	600.0		True	-0.5		True	2	2	5e-06	1e-06	True	20.0

[aekiss]

Hi @PaulSpence

It would be easier to make sense of these diffs if you did something like

nmltab.py -d --format markdown file1.nml file2.nml ... fileN.nml

If you paste the resulting markdown into a comment on this issue it should make a nice table. You can diff multiple files at once to get a single table for everything.

[PaulSpence]

Awesome functionality :) Tables updated above, below is a sanity check on the diffs between my my updated input.nml (that doesn;t work) with its source /g/data/ik11/outputs/access-om2-025/025deg_jra55_ryf9091_gadi/output324/ocean/

It looks clean to me.

./../../../nmltab/nmltab.py -d --format markdown input_updated.nml input_updated_nowombat.nml

File	&diag_manager_nml max_axes	&diag_manager_nml max_files	&diag_manager_nml max_num_axis_sets	&mom_oasis3_interface_nml fields_in	&mom_oasis3_interface_nml fields_out	&mom_oasis3_interface_nml num_fields_in	&mom_oasis3_interface_nml num_fields_out	&ocean_frazil_nml debug_this_module	&ocean_grids_nml debug_this_module	&ocean_nphysics_nml debug_this_module	&ocean_operators_nml use_legacy_div_ud	&ocean_overexchange_nml debug_this_module	&ocean_overexchange_nml overexch_npts	&ocean_overexchange_nml overexch_weight_far	&ocean_overexchange_nml overflow_umax	&ocean_polar_filter_nml use_this_module	&ocean_tracer_advect_nml debug_this_module	&ocean_tracer_diag_nml diag_step	&ocean_velocity_diag_nml debug_this_module	&ocean_vert_kpp_iow_nml use_this_module
input_updated.nml	400	200	200	['u_flux', 'v_flux', 'lprec', 'fprec', 'salt_flx', 'mh_flux', 'sw_flux', 'q_flux', 't_flux', 'lw_flux', 'runof', 'p', 'aice', 'wfimelt', 'wfiform', 'licefw', 'liceht', 'wnd_io', 'iof_nit', 'iof_alg']	['t_surf', 's_surf', 'u_surf', 'v_surf', 'dssldx', 'dssldy', 'frazil', 'n_surf', 'alg_surf']	20	9											48
input_updated_nowombat.nml				['u_flux', 'v_flux', 'lprec', 'fprec', 'salt_flx', 'mh_flux', 'sw_flux', 'q_flux', 't_flux', 'lw_flux', 'runof', 'p', 'aice', 'wfimelt', 'wfiform']	['t_surf', 's_surf', 'u_surf', 'v_surf', 'dssldx', 'dssldy', 'frazil']	15	7	False	False	False	False	False	4	False	5.0	False	False	4320	False	False

[PaulSpence]

Hi Folks, I still need to work on getting the 0.25 bgc simulation working (I haven't spent much time on it lately). Perhaps, we can have a quick chat about how to proceed? Should I wait until the sea ice bgc is working? I'll try to play around with the namelist issues a bit. Thank you, Paul

…

On Thu, Sep 23, 2021 at 7:13 PM Andrew Kiss ***@***.***> wrote: Hi @PaulSpence <https://github.com/PaulSpence> It would be easier to make sense of these diffs if you did something like nmltab.py -d --format markdown file1.nml file2.nml ... fileN.nml If you paste the resulting markdown into a comment on this issue it should make a nice table. You can diff multiple files at once to get a single table for everything. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABSWJXCOM4O2C3HNJ7NXE63UDLVS3ANCNFSM5ENMZLAA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- *I’m sending this message at a time that suits me. I don’t expect you to reply outside of your own work hours.* Paul Spence, Assoc. Prof. ARC Future Fellow Institute for Marine and Antarctic Studies <https://www.imas.utas.edu.au/> University of Tasmania, Hobart, Australia https://paulspence.github.io/