From 7de31c4fec08b8618ac8c996a299ddc0e149ee68 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 2 Sep 2024 16:17:55 +1000 Subject: [PATCH] update doc - see https://github.com/COSIMA/access-om3/issues/224 --- doc/MOM_input | 13 ++++-- doc/README_doc.md | 1 + doc/config.yaml | 47 +++++++++++-------- doc/ice_in | 39 +++++++++++----- doc/nuopc.runconfig | 107 +++++++++++++++----------------------------- doc/nuopc.runseq | 2 +- 6 files changed, 104 insertions(+), 105 deletions(-) diff --git a/doc/MOM_input b/doc/MOM_input index 4e5df49..510ea63 100644 --- a/doc/MOM_input +++ b/doc/MOM_input @@ -71,7 +71,7 @@ NJGLOBAL = 300 ! ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time. ! === module MOM_fixed_initialization === -INPUTDIR = "./input/" ! default = "." +INPUTDIR = "./INPUT/" ! default = "." ! The directory in which input files are found. ! === module MOM_grid_init === @@ -141,6 +141,12 @@ DTFREEZE_DP = -7.75E-08 ! [deg C Pa-1] default = 0.0 ! When TFREEZE_FORM=LINEAR, this is the derivative of the freezing potential ! temperature with pressure. +EPS_OMESH = 1e-13 + ! "default = 0.0001 + ! An float which sets the allowable error (in degrees) between + ! grid angle defined in the ESMF mesh file used by CMEPS + ! and the ocean_hgrid file used by mom + ! === module MOM_tracer_flow_control === USE_IDEAL_AGE_TRACER = True ! [Boolean] default = False ! If true, use the ideal_age_example tracer package. @@ -201,6 +207,9 @@ Z_INIT_FILE_PTEMP_VAR = "temp" ! default = "ptemp" ! The name of the potential temperature variable in TEMP_Z_INIT_FILE. Z_INIT_ALE_REMAPPING = True ! [Boolean] default = False ! If True, then remap straight to model coordinate from file. +Z_INIT_REMAP_GENERAL = True ! [Boolean] default = False + ! If false, only initializes to z* coordinates. If true, allows initialization + ! directly to general coordinates. TEMP_SALT_INIT_VERTICAL_REMAP_ONLY = True ! [Boolean] default = False ! If true, initial conditions are on the model horizontal grid. Extrapolation ! over missing ocean values is done using an ICE-9 procedure with vertical ALE @@ -620,8 +629,6 @@ SALT_RESTORE_FILE = "salt_sfc_restore.nc" ! default = "salt_restore.nc" SRESTORE_AS_SFLUX = True ! [Boolean] default = False ! If true, the restoring of salinity is applied as a salt flux instead of as a ! freshwater flux. -MAX_DELTA_SRESTORE = 0.5 ! [PSU or g kg-1] default = 999.0 - ! The maximum salinity difference used in restoring terms. GUST_CONST = 0.02 ! [Pa] default = 0.0 ! The background gustiness in the winds. diff --git a/doc/README_doc.md b/doc/README_doc.md index f7d7b55..4ba1d01 100644 --- a/doc/README_doc.md +++ b/doc/README_doc.md @@ -7,3 +7,4 @@ The files in here should be the minimum required to support code search from lin ## Update history 1. Updated Mon 12 Feb 2024 14:22:51 AEDT from branch [1deg_jra55do_ryf](https://github.com/ACCESS-NRI/access-om3-configs/tree/1deg_jra55do_ryf) commit [a6829f9](https://github.com/ACCESS-NRI/access-om3-configs/tree/a6829f9) 1. Updated Wed 27 Mar 2024 12:59:33 AEDT from branch [1deg_jra55do_ryf](https://github.com/ACCESS-NRI/access-om3-configs/tree/1deg_jra55do_ryf) commit [c2585c7](https://github.com/ACCESS-NRI/access-om3-configs/tree/c2585c7) +1. Updated Mon 2 Sep 2024 16:14:36 AEST from branch [1deg_jra55do_ryf](https://github.com/ACCESS-NRI/access-om3-configs/tree/1deg_jra55do_ryf) commit [2bc6107](https://github.com/ACCESS-NRI/access-om3-configs/tree/2bc6107) diff --git a/doc/config.yaml b/doc/config.yaml index f24f6c6..a50eeef 100644 --- a/doc/config.yaml +++ b/doc/config.yaml @@ -2,41 +2,50 @@ # If submitting to a different project to your default, uncomment line below # and change project code as appropriate; also set shortpath below -project: x77 +# 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/v45 queue: normal -ncpus: 48 +ncpus: 240 jobfs: 10GB -mem: 192GB +mem: 960GB walltime: 01:00:00 jobname: 1deg_jra55do_ryf model: access-om3 -exe: /g/data/ik11/spack/0.20.1/opt/linux-rocky8-cascadelake/intel-2021.6.0/access-om3-main-lxbeca7/bin/access-om3-MOM6-CICE6 -input: - - /g/data/ik11/inputs/access-om3/0.x.0/1deg/share # shared grids and topography - - /g/data/ik11/inputs/access-om3/0.x.0/1deg/mom # grids, ICs etc - - /g/data/ik11/inputs/access-om3/0.x.0/1deg/cice # grids, ICs etc - - /g/data/ik11/inputs/access-om3/0.x.0/share/meshes/JRA55do-ESMFmesh.nc # mesh for JRA55-do stream - - /g/data/ik11/inputs/JRA-55/RYF/v1-4 # datm and drof JRA55-do streams data +exe: access-om3-MOM6-CICE6 +input: + - /g/data/vk83/experiments/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-ESMFmesh.nc + - /g/data/vk83/experiments/inputs/access-om3/share/meshes/global.1deg/2024.01.25/access-om2-1deg-nomask-ESMFmesh.nc + - /g/data/vk83/experiments/inputs/access-om3/share/meshes/share/2024.01.25/JRA55do-ESMFmesh.nc + - /g/data/vk83/experiments/inputs/access-om3/share/grids/global.1deg/2020.10.22/topog.nc + - /g/data/vk83/experiments/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc + - /g/data/vk83/experiments/inputs/access-om3/mom/grids/vertical/global.1deg/2023.07.28/ocean_vgrid.nc + - /g/data/vk83/experiments/inputs/access-om3/mom/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc + - /g/data/vk83/experiments/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc + - /g/data/vk83/experiments/inputs/access-om3/cice/grids/global.1deg/2024.05.14/grid.nc + - /g/data/vk83/experiments/inputs/access-om3/cice/grids/global.1deg/2024.05.14/kmt.nc + - /g/data/vk83/experiments/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/iced.1900-01-01-10800.nc + - /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data collate: false runlog: false +metadata: + enable: false userscripts: - setup: ./setup_cice_restarts.sh - archive: ./archive_cice_restarts.sh + 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/ik11/spack/0.20.1/modules/access-om3/0.x.0/linux-rocky8-cascadelake - load: - - intel-compiler/2021.6.0 - - openmpi/4.1.4 - - parallelio/2.5.10 + use: + - /g/data/ik11/spack/0.21.2/modules/access-om3/0.x.0/linux-rocky8-cascadelake + - /g/data/hh5/public/modules + load: + - access-om3/63ed4a4777aeac0c62720ddbe7f85e4ed16f82eb_main + - conda/analysis3-24.01 diff --git a/doc/ice_in b/doc/ice_in index 4d13bdc..687ef86 100644 --- a/doc/ice_in +++ b/doc/ice_in @@ -1,29 +1,32 @@ &setup_nml bfbflag = "off" conserv_check = .false. - debug_forcing = .true. - debug_model = .true. diagfreq = 960 dumpfreq = "y" dump_last = .true. histfreq = "d", "m", "x", "x", "x" + hist_suffix = "", "m", "x", "x", "x" !limited to one character due to https://github.com/COSIMA/access-om3/issues/201 + hist_time_axis = "middle" + history_deflate = 1 + history_chunksize = 180, 150 history_precision = 8 - ice_ic = "./input/iced.1900-01-01-10800.nc" + restart_deflate = 1 + ice_ic = "./INPUT/iced.1900-01-01-10800.nc" lcdf64 = .false. npt = 35040 pointer_file = './rpointer.ice' print_global = .false. / &grid_nml - bathymetry_file = "./input/topog.nc" + bathymetry_file = "./INPUT/topog.nc" grid_atm = "A" - grid_file = "./input/grid.nc" + grid_file = "./INPUT/grid.nc" grid_format = "nc" grid_ice = "B" grid_ocn = "A" grid_type = "tripole" kcatbound = 0 - kmt_file = "./input/kmt.nc" + kmt_file = "./INPUT/kmt.nc" nblyr = 1 ncat = 5 nfsd = 1 @@ -65,18 +68,18 @@ ustar_min = 0.0005 / &domain_nml - block_size_x = 16 - block_size_y = 15 + block_size_x = 15 + block_size_y = 20 distribution_type = "cartesian" distribution_wght = "latitude" maskhalo_bound = .true. maskhalo_dyn = .true. maskhalo_remap = .true. - max_blocks = 10 + max_blocks = 15 ns_boundary_type = "tripole" nx_global = 360 ny_global = 300 - processor_shape = "slenderX2" + processor_shape = "slenderX1" / &ice_prescribed_nml / @@ -123,12 +126,26 @@ f_fsurfn_ai = "m" f_hi = "md" f_hs = "md" + f_sifb = "md" f_snoice = "md" f_uvel = "md" , f_vvel = "md" f_vicen = "m" !----------------------------------- ! These fields are on by default (in ice_history_shared.F90) but lets turn them off !----------------------------------- + f_tlon = .false. , f_tlat = .false. + f_ulon = .false. , f_ulat = .false. + f_nlon = .false. , f_nlat = .false. + f_elon = .false. , f_elat = .false. + f_tmask = .false. , f_umask = .false. + f_nmask = .false. , f_emask = .false. + f_tarea = .false. , f_uarea = .false. + f_narea = .false. , f_earea = .false. + f_dxt = .false. , f_dyt = .false. + f_dxu = .false. , f_dyu = .false. + f_dxe = .false. , f_dye = .false. + f_dxn = .false. , f_dyn = .false. + f_HTN = .false. , f_HTE = .false. f_albpnd = 'x' f_atmdir = 'x' , f_atmspd = 'x' f_coszen = 'x' @@ -157,4 +174,4 @@ f_taubx = 'x' , f_tauby = 'x' f_Tref = 'x', f_Qref = 'x' f_uocn = 'x' , f_vocn = 'x' -/ \ No newline at end of file +/ diff --git a/doc/nuopc.runconfig b/doc/nuopc.runconfig index 595c4d8..5b4bd60 100644 --- a/doc/nuopc.runconfig +++ b/doc/nuopc.runconfig @@ -27,11 +27,11 @@ DRIVER_attributes:: :: PELAYOUT_attributes:: - atm_ntasks = 48 + atm_ntasks = 24 atm_nthreads = 1 atm_pestride = 1 atm_rootpe = 0 - cpl_ntasks = 48 + cpl_ntasks = 24 cpl_nthreads = 1 cpl_pestride = 1 cpl_rootpe = 0 @@ -40,31 +40,31 @@ PELAYOUT_attributes:: esp_nthreads = 1 esp_pestride = 1 esp_rootpe = 0 - glc_ntasks = 48 + glc_ntasks = 1 glc_nthreads = 1 glc_pestride = 1 glc_rootpe = 0 - ice_ntasks = 48 + ice_ntasks = 24 ice_nthreads = 1 ice_pestride = 1 ice_rootpe = 0 - lnd_ntasks = 48 + lnd_ntasks = 1 lnd_nthreads = 1 lnd_pestride = 1 lnd_rootpe = 0 ninst = 1 - ocn_ntasks = 48 + ocn_ntasks = 216 ocn_nthreads = 1 ocn_pestride = 1 - ocn_rootpe = 0 + ocn_rootpe = 24 pio_asyncio_ntasks = 0 pio_asyncio_rootpe = 1 pio_asyncio_stride = 0 - rof_ntasks = 48 + rof_ntasks = 24 rof_nthreads = 1 rof_pestride = 1 rof_rootpe = 0 - wav_ntasks = 48 + wav_ntasks = 1 wav_nthreads = 1 wav_pestride = 1 wav_rootpe = 0 @@ -116,12 +116,12 @@ ALLCOMP_attributes:: hostname = gadi ice_ncat = 5 mediator_present = true - mesh_atm = ./input/access-om2-1deg-nomask-ESMFmesh.nc + mesh_atm = ./INPUT/access-om2-1deg-nomask-ESMFmesh.nc mesh_glc = UNSET - mesh_ice = ./input/access-om2-1deg-ESMFmesh.nc + mesh_ice = ./INPUT/access-om2-1deg-ESMFmesh.nc mesh_lnd = UNSET - mesh_mask = ./input/access-om2-1deg-ESMFmesh.nc - mesh_ocn = ./input/access-om2-1deg-ESMFmesh.nc + mesh_mask = ./INPUT/access-om2-1deg-ESMFmesh.nc + mesh_ocn = ./INPUT/access-om2-1deg-ESMFmesh.nc model_version = unknown ocn2glc_coupling = .false. ocn2glc_levels = 1:10:19:26:30:33:35 @@ -278,19 +278,19 @@ MED_attributes:: :: CLOCK_attributes:: - atm_cpl_dt = 3600 + atm_cpl_dt = 99999 #not used calendar = NO_LEAP end_restart = .false. glc_avg_period = yearly - glc_cpl_dt = 86400 + glc_cpl_dt = 99999 #not used history_ymd = -999 - ice_cpl_dt = 3600 - lnd_cpl_dt = 3600 - ocn_cpl_dt = 3600 + ice_cpl_dt = 99999 #not used + lnd_cpl_dt = 99999 #not used + ocn_cpl_dt = 3600 #ignored (coupling timestep set by nuopc.runseq) unless stop_option is nsteps restart_n = 1 restart_option = nmonths restart_ymd = -999 - rof_cpl_dt = 3600 + rof_cpl_dt = 99999 #not used start_tod = 0 start_ymd = 19000101 stop_n = 1 @@ -300,7 +300,7 @@ CLOCK_attributes:: tprof_n = -999 tprof_option = never tprof_ymd = -999 - wav_cpl_dt = 3600 + wav_cpl_dt = 99999 #not used :: ATM_attributes:: @@ -311,6 +311,7 @@ ATM_attributes:: :: ICE_attributes:: + eps_imesh = 1e-13 # allowed error between angles in mesh file and cice grid Verbosity = off :: @@ -328,7 +329,7 @@ OCN_attributes:: ROF_attributes:: Verbosity = off - mesh_rof = ./input/access-om2-1deg-nomask-ESMFmesh.nc + mesh_rof = ./INPUT/access-om2-1deg-nomask-ESMFmesh.nc :: WAV_attributes:: @@ -360,18 +361,6 @@ ATM_modelio:: pio_typename = netcdf :: -LND_modelio:: - diro = ./log - logfile = lnd.log - pio_async_interface = .false. - pio_netcdf_format = 64bit_offset - pio_numiotasks = -99 - pio_rearranger = 2 - pio_root = 1 - pio_stride = 48 - pio_typename = netcdf -:: - ICE_modelio:: diro = ./log logfile = ice.log @@ -387,37 +376,25 @@ ICE_modelio:: OCN_modelio:: diro = ./log logfile = ocn.log - pio_async_interface = .false. - pio_netcdf_format = 64bit_offset - pio_numiotasks = -99 - pio_rearranger = 2 - pio_root = 1 - pio_stride = 48 - pio_typename = netcdf + pio_async_interface = .false. #not used + pio_netcdf_format = 64bit_offset #not used + pio_numiotasks = -99 #not used + pio_rearranger = 2 #not used + pio_root = 1 #not used + pio_stride = 48 #not used + pio_typename = netcdf #not used, set in input.nml :: ROF_modelio:: diro = ./log logfile = rof.log - pio_async_interface = .false. - pio_netcdf_format = 64bit_offset - pio_numiotasks = -99 - pio_rearranger = 2 - pio_root = 1 - pio_stride = 48 - pio_typename = netcdf -:: - -GLC_modelio:: - diro = ./log - logfile = glc/log - pio_async_interface = .false. - pio_netcdf_format = 64bit_offset - pio_numiotasks = -99 - pio_rearranger = 2 - pio_root = 1 - pio_stride = 48 - pio_typename = netcdf + pio_async_interface = .false. #not used + pio_netcdf_format = 64bit_offset #not used + pio_numiotasks = -99 #not used + pio_rearranger = 2 #not used + pio_root = 1 #not used + pio_stride = 48 #not used + pio_typename = netcdf #not used :: WAV_modelio:: @@ -432,18 +409,6 @@ WAV_modelio:: pio_typename = netcdf :: -ESP_modelio:: - diro = ./log - logfile = esp.log - pio_async_interface = .false. - pio_netcdf_format = 64bit_offset - pio_numiotasks = -99 - pio_rearranger = -99 - pio_root = -99 - pio_stride = -99 - pio_typename = nothing -:: - DRV_modelio:: diro = ./log logfile = drv.log diff --git a/doc/nuopc.runseq b/doc/nuopc.runseq index 9ce0aba..1349281 100644 --- a/doc/nuopc.runseq +++ b/doc/nuopc.runseq @@ -1,5 +1,5 @@ runSeq:: -@3600 +@3600 MED med_phases_aofluxes_run MED med_phases_prep_ocn_accum MED med_phases_ocnalb_run