ACCESS-NRI · anton-seaice · Aug 23, 2024 · Aug 7, 2024 · Aug 2, 2024 · Jul 29, 2024
diff --git a/MOM_input b/MOM_input
@@ -208,7 +208,7 @@ MINIMUM_DEPTH = 0.5
                                 ! MINIMUM_DEPTH."
 
 ! === module MOM_fixed_initialization ===
-INPUTDIR = "./input/"
+INPUTDIR = "./INPUT/"
                                 ! "The directory in which input files are found."
 
 CHANNEL_CONFIG = global_1deg

diff --git a/README.md b/README.md
@@ -14,4 +14,4 @@ information.
 
 ## Requirements
 
-This configuration requires payu v1.0.29 or greater to run correctly.
+This configuration requires [Payu](https://github.com/payu-org/payu) > v1.1.3 to run.
diff --git a/config.yaml b/config.yaml
@@ -19,8 +19,8 @@ jobname: 1deg_jra55do_iaf
 
 model: access-om3
 
-exe: /g/data/ik11/spack/0.21.2/opt/linux-rocky8-cascadelake/intel-2021.10.0/access-om3-69f719964a27e23deae3923d60af01a081cc3fc0_main-fkzzqnp/bin/access-om3-MOM6-CICE6-WW3
-input: 
+exe: access-om3-MOM6-CICE6-WW3
+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
@@ -51,3 +51,15 @@ 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/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/datm.streams.xml b/datm.streams.xml
diff --git a/datm_in b/datm_in
@@ -8,8 +8,8 @@
   flds_preso3 = .false.
   flds_wiso = .false.
   iradsw = 1
-  model_maskfile = "./input/access-om2-1deg-nomask-ESMFmesh.nc"
-  model_meshfile = "./input/access-om2-1deg-nomask-ESMFmesh.nc"
+  model_maskfile = "./INPUT/access-om2-1deg-nomask-ESMFmesh.nc"
+  model_meshfile = "./INPUT/access-om2-1deg-nomask-ESMFmesh.nc"
   nx_global = 360
   ny_global = 300
   restfilm = "null"

diff --git a/drof.streams.xml b/drof.streams.xml
diff --git a/drof_in b/drof_in
@@ -1,7 +1,7 @@
 &drof_nml
   datamode = "copyall"
-  model_maskfile = "./input/access-om2-1deg-nomask-ESMFmesh.nc"
-  model_meshfile = "./input/access-om2-1deg-nomask-ESMFmesh.nc"
+  model_maskfile = "./INPUT/access-om2-1deg-nomask-ESMFmesh.nc"
+  model_meshfile = "./INPUT/access-om2-1deg-nomask-ESMFmesh.nc"
   nx_global = 360
   ny_global = 300
   restfilm = "null"

diff --git a/ice_in b/ice_in
@@ -5,26 +5,27 @@
   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
   restart_deflate = 1
-  ice_ic = "./input/iced.1900-01-01-10800.nc"
+  ice_ic = "./INPUT/iced.1900-01-01-10800.nc"
   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 = 12
@@ -187,4 +188,4 @@
   f_taubx = 'x' , f_tauby = 'x'
   f_Tref = 'x', f_Qref = 'x'
   f_uocn = 'x' , f_vocn = 'x'
-/
+/
diff --git a/input.nml b/input.nml
@@ -20,3 +20,9 @@
     cf_compliance = .true.
 /
 
+&fms2_io_nml
+    ncchksz = 4194304
+    netcdf_default_format = "netcdf4"
+    deflate_level = 4
+    shuffle = .true.
+/
diff --git a/manifests/exe.yaml b/manifests/exe.yaml
@@ -2,7 +2,7 @@ format: yamanifest
 version: 1.0
 ---
 work/access-om3-MOM6-CICE6-WW3:
-  fullpath: /g/data/ik11/spack/0.21.2/opt/linux-rocky8-cascadelake/intel-2021.10.0/access-om3-69f719964a27e23deae3923d60af01a081cc3fc0_main-fkzzqnp/bin/access-om3-MOM6-CICE6-WW3
+  fullpath: /g/data/ik11/spack/0.21.2/opt/linux-rocky8-cascadelake/intel-2021.10.0/access-om3-63ed4a4777aeac0c62720ddbe7f85e4ed16f82eb_main-xekfuu4/bin/access-om3-MOM6-CICE6-WW3
   hashes:
-    binhash: b281583fa59e6b0ef755e24aee4303ee
-    md5: 2eb399f40b49a51cfaa0c621adfb381d
+    binhash: 9a04fbb06b2ced42c850e9f170c61b61
+    md5: 33fdb18891a41a2ac6202271331db65c
diff --git a/manifests/input.yaml b/manifests/input.yaml
diff --git a/nuopc.runconfig b/nuopc.runconfig
@@ -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
@@ -287,7 +287,7 @@ CLOCK_attributes::
      history_ymd = -999
      ice_cpl_dt = 99999 #not used
      lnd_cpl_dt = 99999 #not used
-     ocn_cpl_dt = 3600
+     ocn_cpl_dt = 3600 #ignored (coupling timestep set by nuopc.runseq) unless stop_option is nsteps
      restart_n = 1
      restart_option = ndays
      restart_ymd = -999
@@ -330,12 +330,12 @@ 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::
      Verbosity = off
-     mesh_wav = ./input/access-om2-1deg-nomask-ESMFmesh.nc
+     mesh_wav = ./INPUT/access-om2-1deg-nomask-ESMFmesh.nc
 ::
 
 MED_modelio::
@@ -362,64 +362,40 @@ 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
      pio_async_interface = .false.
      pio_netcdf_format = 64bit_offset
-     pio_numiotasks = -99
-     pio_rearranger = 2
+     pio_numiotasks = 1
+     pio_rearranger = 1
      pio_root = 1
      pio_stride = 48
-     pio_typename = netcdf
+     pio_typename = netcdf4p
 ::
 
 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::
@@ -436,18 +412,6 @@ WAV_modelio::
      history_option = ndays
 ::
 
-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/wav_in b/wav_in
@@ -3,7 +3,7 @@
   dtcfli = 300.
   dtmax = 600.
   dtmin = 50.
-  initfile = "./input/restart.ww3"
+  initfile = "./INPUT/restart.ww3"
 /
 &input_nml
   input%forcing%water_levels = 'T'