Updated metadata. Experiment UUID: 30c57744-b9a8-48b3-8374-fb55efeb8405

payu archive: documentation of MOM6 run-time configuration

Author: angus-g

MOM_input

@@ -17,9 +17,18 @@ FATAL_UNUSED_PARAMS = True      !   [Boolean] default = False
 ! This section contains non default layout parameters which are set.
 ! ------------------------
 ! === module MOM_domains ===
-AUTO_MASKTABLE = True           !   [Boolean] default = False
+! AUTO_MASKTABLE = True          !   [Boolean] default = False
                                 ! Turn on automatic mask table generation to eliminate land blocks.
-AUTO_IO_LAYOUT_FAC = 6          ! default = 0
+! MASKTABLE = "mask_table.1193.48x36"
+! LAYOUT = 48, 36
+! IO_LAYOUT = 8, 6
+! MASKTABLE = "mask_table.2567.72x54"
+! LAYOUT = 72, 54
+! IO_LAYOUT = 8, 6
+MASKTABLE = "mask_table.4448.96x72"
+LAYOUT = 96, 72
+IO_LAYOUT = 12, 9
+! AUTO_IO_LAYOUT_FAC = 6          ! default = 0
                                 ! When AUTO_MASKTABLE is enabled, io layout is calculated by performing integer
                                 ! division of the runtime-determined domain layout with this factor. If the
                                 ! factor is set to 0 (default), the io layout is set to 1,1.
@@ -42,11 +51,11 @@ THICKNESSDIFFUSE = True         !   [Boolean] default = False
 THICKNESSDIFFUSE_FIRST = True   !   [Boolean] default = False
                                 ! If true, do thickness diffusion or interface height smoothing before dynamics.
                                 ! This is only used if THICKNESSDIFFUSE or APPLY_INTERFACE_FILTER is true.
-DT = 900.0                      !   [s]
+DT = 450.0                      !   [s]
                                 ! The (baroclinic) dynamics time step.  The time-step that is actually used will
                                 ! be an integer fraction of the forcing time-step (DT_FORCING in ocean-only mode
                                 ! or the coupling timestep in coupled mode.)
-DT_THERM = 7200.0               !   [s] default = 900.0
+DT_THERM = 3600.0               !   [s] default = 900.0
                                 ! The thermodynamic and tracer advection time step. Ideally DT_THERM should be
                                 ! an integer multiple of DT and less than the forcing or coupling time-step,
                                 ! unless THERMO_SPANS_COUPLING is true, in which case DT_THERM can be an integer
@@ -91,17 +100,17 @@ BAD_VAL_SST_MAX = 55.0          !   [deg C] default = 45.0
 BAD_VAL_SST_MIN = -3.0          !   [deg C] default = -2.1
                                 ! The value of SST below which a bad value message is triggered, if
                                 ! CHECK_BAD_SURFACE_VALS is true.
-SAVE_INITIAL_CONDS = True       !   [Boolean] default = False
+SAVE_INITIAL_CONDS = False       !   [Boolean] default = False
                                 ! If true, write the initial conditions to a file given by IC_OUTPUT_FILE.
 
 ! === module MOM_domains ===
 TRIPOLAR_N = True               !   [Boolean] default = False
                                 ! Use tripolar connectivity at the northern edge of the domain.  With
                                 ! TRIPOLAR_N, NIGLOBAL must be even.
-NIGLOBAL = 1440                 !
+NIGLOBAL = 4320                 !
                                 ! The total number of thickness grid points in the x-direction in the physical
                                 ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
-NJGLOBAL = 1142                 !
+NJGLOBAL = 3672                 !
                                 ! The total number of thickness grid points in the y-direction in the physical
                                 ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
 
@@ -559,7 +568,7 @@ KAPPA_H2_FACTOR = 0.84          !   [nondim] default = 1.0
 TKE_ITIDE_MAX = 0.1             !   [W m-2] default = 1000.0
                                 ! The maximum internal tide energy source available to mix above the bottom
                                 ! boundary layer with INT_TIDE_DISSIPATION.
-READ_TIDEAMP = True             !   [Boolean] default = False
+READ_TIDEAMP = False             !   [Boolean] default = False
                                 ! If true, read a file (given by TIDEAMP_FILE) containing the tidal amplitude
                                 ! with INT_TIDE_DISSIPATION.
 H2_FILE = "bottom_roughness.nc" !

config.yaml

@@ -1,74 +1,87 @@
 # Payu configuration
 
-# If submitting to a different project to your default, uncomment line below 
+# 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: g40
 # Force payu to always find, and save, files in this scratch project directory
-# shortpath: /scratch/v45
+shortpath: /scratch/x77
 
-# Using payu sync is recommend to copy data from ephemeral scratch space to 
+# Using payu sync is recommend to copy data from ephemeral scratch space to
 # longer term storage
 sync:
     enable: False # set path below and change to true
     path: null # Set to location on /g/data (e.g. /g/data/PROJECT/USER/EXPERIMENT)
     restart: True
 
 #Model software version
-modules:
-    use:
-        - /g/data/vk83/modules
-    load:
-        - access-om3/2025.05.001
+# modules:
+#     use:
+#         - /g/data/vk83/modules
+#     load:
+#         - access-om3/2025.05.001
 
 queue: normalsr
-ncpus: 1664
+#ncpus: 1664 # 16 nodes
+ncpus: 4992 # 48 nodes
+#ncpus: 3328 # 32 nodes
+#ncpus: 2912 # 28 nodes
 jobfs: 10GB
-mem: 8000GB
-walltime: 6:00:00
-jobname: 025km_jra_ryf
+#mem: 8000GB
+walltime: 05:00:00
+jobname: 8km_jra_ryf
 
 model: access-om3
-exe: access-om3-MOM6-CICE6
+exe: /g/data/x77/ahg157/inputs/mom6/global-8km/access-om3-MOM6-CICE6
 input:
-    - /g/data/vk83/configurations/inputs/access-om3/cice/grids/global.25km/2025.05.15/kmt.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/grids/mosaic/global.25km/2025.05.15/ocean_hgrid.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/grids/vertical/global.25km/2025.03.12/ocean_vgrid.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/initial_conditions/global.25km/2025.06.17/ocean_temp_salt.res.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/surface_salt_restoring/global.25km/2025.06.17/salt_sfc_restore.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/tidal_external_files/global.25km/2025.05.15/bottom_roughness.nc
-    - /g/data/vk83/configurations/inputs/access-om3/mom/tidal_external_files/global.25km/2025.05.15/tideamp.nc
-    - /g/data/vk83/configurations/inputs/access-om3/share/grids/global.25km/2025.05.15/topog.nc
-    - /g/data/vk83/configurations/inputs/access-om3/share/meshes/global.25km/2025.05.15/access-om3-25km-ESMFmesh.nc
-    - /g/data/vk83/configurations/inputs/access-om3/share/meshes/global.25km/2025.05.15/access-om3-25km-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/cmeps/remap_weights/global.25km/2025.05.15/access-om3-25km-rof-remap-weights.nc
-    - /g/data/vk83/configurations/inputs/JRA-55/RYF/v1-6/data
+  # - /g/data/x77/ahg157/inputs/mom6/global-8km/mask_table.2489.72x96
+  # - /g/data/x77/ahg157/inputs/mom6/global-8km/mask_table.1193.48x36
+  # - /g/data/x77/ahg157/inputs/mom6/global-8km/mask_table.2567.72x54
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/mask_table.4448.96x72
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/kmt.nc
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/ocean_hgrid.nc
+  - /g/data/vk83/configurations/inputs/access-om3/mom/grids/vertical/global.25km/2025.03.12/ocean_vgrid.nc
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/topog.nc
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/access-om3-8km-ESMFmesh.nc
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/access-om3-8km-nomask-ESMFmesh.nc
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/access-om3-8km-rof-remap-weights.nc
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/access-om3-8km-vmap-weights.nc
+  - /g/data/vk83/configurations/inputs/JRA-55/RYF/v1-6/data
+  - /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/x77/ahg157/inputs/mom6/global-8km/ocean_temp_salt.res.nc
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/salt_sfc_restore.nc
+  - /g/data/x77/ahg157/inputs/mom6/global-8km/bottom_roughness.nc
+  # - /g/data/vk83/configurations/inputs/access-om3/mom/tidal_external_files/global.25km/2025.05.15/tideamp.nc
 
 runlog: true
-metadata: 
+metadata:
     enable: true
-manifest:
-  reproduce:
-    exe: True
+# manifest:
+#   reproduce:
+#     exe: True
 
 platform:
     nodesize: 104
     nodemem: 512
 
-collate:
-  restart: true
-  mpi: true
-  walltime: 1:00:00
-  mem: 30GB
-  ncpus: 4
-  queue: expresssr
-  exe: /g/data/vk83/apps/mppnccombine-fast/0.2/bin/mppnccombine-fast
+storage:
+  gdata:
+    - x77
+
+collate: false
+# collate:
+#   restart: true
+#   mpi: true
+#   walltime: 1:00:00
+#   mem: 30GB
+#   ncpus: 4
+#   queue: expresssr
+#   exe: /g/data/vk83/apps/mppnccombine-fast/0.2/bin/mppnccombine-fast
 
 userscripts:
     archive: /usr/bin/bash /g/data/vk83/apps/om3-scripts/payu_config/archive.sh
 
 postscript: -v PROJECT,SCRIPTS_DIR=/g/data/vk83/apps/om3-scripts -lstorage=${PBS_NCI_STORAGE}+gdata/xp65 /g/data/vk83/apps/om3-scripts/payu_config/postscript.sh
 
-restart_freq: 1YS
+#restart_freq: 1YS
 payu_minimum_version: 1.1.7

datm_in

@@ -8,10 +8,10 @@
   flds_preso3 = .false.
   flds_wiso = .false.
   iradsw = 1
-  model_maskfile = "./INPUT/access-om3-25km-nomask-ESMFmesh.nc"
-  model_meshfile = "./INPUT/access-om3-25km-nomask-ESMFmesh.nc"
-  nx_global = 1440
-  ny_global = 1142
+  model_maskfile = "./INPUT/access-om3-8km-nomask-ESMFmesh.nc"
+  model_meshfile = "./INPUT/access-om3-8km-nomask-ESMFmesh.nc"
+  nx_global = 4320
+  ny_global = 3672
   restfilm = "null"
   skip_restart_read = .false.
 /

docs/MOM_parameter_doc.all

@@ -68,11 +68,11 @@ BATHYMETRY_AT_VEL = False       !   [Boolean] default = False
                                 ! If true, there are separate values for the basin depths at velocity points.
                                 ! Otherwise the effects of topography are entirely determined from thickness
                                 ! points.
-DT = 900.0                      !   [s]
+DT = 450.0                      !   [s]
                                 ! The (baroclinic) dynamics time step.  The time-step that is actually used will
                                 ! be an integer fraction of the forcing time-step (DT_FORCING in ocean-only mode
                                 ! or the coupling timestep in coupled mode.)
-DT_THERM = 7200.0               !   [s] default = 900.0
+DT_THERM = 3600.0               !   [s] default = 450.0
                                 ! The thermodynamic and tracer advection time step. Ideally DT_THERM should be
                                 ! an integer multiple of DT and less than the forcing or coupling time-step,
                                 ! unless THERMO_SPANS_COUPLING is true, in which case DT_THERM can be an integer
@@ -98,7 +98,7 @@ HFREEZE = 10.0                  !   [m] default = -1.0
 INTERPOLATE_P_SURF = False      !   [Boolean] default = False
                                 ! If true, linearly interpolate the surface pressure over the coupling time
                                 ! step, using the specified value at the end of the step.
-DTBT_RESET_PERIOD = 0.0         !   [s] default = 7200.0
+DTBT_RESET_PERIOD = 0.0         !   [s] default = 3600.0
                                 ! The period between recalculations of DTBT (if DTBT <= 0). If DTBT_RESET_PERIOD
                                 ! is negative, DTBT is set based only on information available at
                                 ! initialization.  If 0, DTBT will be set every dynamics time step. The default
@@ -165,7 +165,7 @@ SURFACE_ANSWER_DATE = 99991231  ! default = 99991231
 USE_DIABATIC_TIME_BUG = False   !   [Boolean] default = False
                                 ! If true, uses the wrong calendar time for diabatic processes, as was done in
                                 ! MOM6 versions prior to February 2018. This is not recommended.
-SAVE_INITIAL_CONDS = True       !   [Boolean] default = False
+SAVE_INITIAL_CONDS = False      !   [Boolean] default = False
                                 ! If true, write the initial conditions to a file given by IC_OUTPUT_FILE.
 IC_OUTPUT_FILE = "MOM_IC"       ! default = "MOM_IC"
                                 ! The file into which to write the initial conditions.
@@ -196,10 +196,10 @@ REENTRANT_Y = False             !   [Boolean] default = False
 TRIPOLAR_N = True               !   [Boolean] default = False
                                 ! Use tripolar connectivity at the northern edge of the domain.  With
                                 ! TRIPOLAR_N, NIGLOBAL must be even.
-NIGLOBAL = 1440                 !
+NIGLOBAL = 4320                 !
                                 ! The total number of thickness grid points in the x-direction in the physical
                                 ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
-NJGLOBAL = 1142                 !
+NJGLOBAL = 3672                 !
                                 ! The total number of thickness grid points in the y-direction in the physical
                                 ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
 NIHALO = 4                      ! default = 4
@@ -1834,14 +1834,9 @@ KAPPA_H2_FACTOR = 0.84          !   [nondim] default = 1.0
 TKE_ITIDE_MAX = 0.1             !   [W m-2] default = 1000.0
                                 ! The maximum internal tide energy source available to mix above the bottom
                                 ! boundary layer with INT_TIDE_DISSIPATION.
-READ_TIDEAMP = True             !   [Boolean] default = False
+READ_TIDEAMP = False            !   [Boolean] default = False
                                 ! If true, read a file (given by TIDEAMP_FILE) containing the tidal amplitude
                                 ! with INT_TIDE_DISSIPATION.
-TIDEAMP_FILE = "tideamp.nc"     ! default = "tideamp.nc"
-                                ! The path to the file containing the spatially varying tidal amplitudes with
-                                ! INT_TIDE_DISSIPATION.
-TIDEAMP_VARNAME = "tideamp"     ! default = "tideamp"
-                                ! The name of the tidal amplitude variable in the input file.
 H2_FILE = "bottom_roughness.nc" !
                                 ! The path to the file containing the sub-grid-scale topographic roughness
                                 ! amplitude with INT_TIDE_DISSIPATION.

docs/MOM_parameter_doc.layout

@@ -23,9 +23,9 @@ THIN_HALO_UPDATES = True        !   [Boolean] default = True
                                 ! statically determined at compile time.  Otherwise the sizes are not determined
                                 ! until run time. The STATIC option is substantially faster, but does not allow
                                 ! the PE count to be changed at run time.  This can only be set at compile time.
-AUTO_MASKTABLE = True           !   [Boolean] default = False
+AUTO_MASKTABLE = False          !   [Boolean] default = False
                                 ! Turn on automatic mask table generation to eliminate land blocks.
-MASKTABLE = "MOM_auto_mask_table" ! default = "MOM_mask_table"
+MASKTABLE = "mask_table.4448.96x72" ! default = "MOM_mask_table"
                                 ! A text file to specify n_mask, layout and mask_list. This feature masks out
                                 ! processors that contain only land points. The first line of mask_table is the
                                 ! number of regions to be masked out. The second line is the layout of the model
@@ -38,19 +38,15 @@ MASKTABLE = "MOM_auto_mask_table" ! default = "MOM_mask_table"
                                 !  4,6
                                 !  1,2
                                 !  3,6
-NIPROC = 36                     !
+NIPROC = 96                     !
                                 ! The number of processors in the x-direction. With STATIC_MEMORY_ this is set
                                 ! in MOM_memory.h at compile time.
-NJPROC = 48                     !
+NJPROC = 72                     !
                                 ! The number of processors in the y-direction. With STATIC_MEMORY_ this is set
                                 ! in MOM_memory.h at compile time.
-LAYOUT = 36, 48                 !
+LAYOUT = 96, 72                 !
                                 ! The processor layout that was actually used.
-AUTO_IO_LAYOUT_FAC = 6          ! default = 0
-                                ! When AUTO_MASKTABLE is enabled, io layout is calculated by performing integer
-                                ! division of the runtime-determined domain layout with this factor. If the
-                                ! factor is set to 0 (default), the io layout is set to 1,1.
-IO_LAYOUT = 6, 8                !
+IO_LAYOUT = 12, 9               ! default = 1
                                 ! The processor layout to be used, or 0,0 to automatically set the io_layout to
                                 ! be the same as the layout.