rebase to head

.gitignore

@@ -5,6 +5,16 @@ cfgs/GLOBAL_QCO_MEDUSA/MY_SRC/*.F90
 head/
 ISSUE.md
 
+data/INPUT_eORCA025
+data/INPUT_eORCA1
+data/INPUT_eORCA12
+scripts/compile_nemo
+scripts/compile_tools
+scripts/python/mkslurm_NPD
+tools/INITIAL_CONDITIONS/dev
+tools/INITIAL_CONDITIONS/data
+
+
 # Created by https://www.toptal.com/developers/gitignore/api/jupyternotebooks,fortran,svn,matlab,python,emacs,vim
 # Edit at https://www.toptal.com/developers/gitignore?templates=jupyternotebooks,fortran,svn,matlab,python,emacs,vim
 

arch/NOC/arch-Anemone-ifort-xios3.fcm

@@ -32,7 +32,7 @@
 #
 %NCDF_HOME           $EBROOTNETCDF
 %HDF5_HOME           $EBROOTHDF5
-%XIOS_HOME           /home/acc/xios3-trunk-head
+%XIOS_HOME           /dssgfs01/working/atb299/XIOS3
 #%OASIS_HOME          /not/defined
 
 %NCDF_INC            -I%NCDF_HOME/include 
@@ -45,7 +45,7 @@
 #%OASIS_LIB           -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
 
 %CPP	             cpp 
-%FC                  mpiifort -c -fpp -fpp-name:/opt/software/eb/software/GCCcore/11.2.0/bin/cpp -Dkey_xios3 -Wp,-P,-traditional
+%FC                  mpiifort -c -fpp -fpp-name:/opt/software/rocky9/eb/software/GCCcore/12.3.0/bin/cpp -Dkey_xios3 -Wp,-P,-traditional
 %FCFLAGS             -i4 -r8 -O3 -fp-model precise -fno-alias
 %FFLAGS              %FCFLAGS
 %LD                  mpiifort 

arch/NOC/arch-Anemone-ifort.fcm

@@ -32,7 +32,7 @@
 #
 %NCDF_HOME           $EBROOTNETCDF
 %HDF5_HOME           $EBROOTHDF5
-%XIOS_HOME           /home/acc/xios-trunk
+%XIOS_HOME           /dssgfs01/working/atb299/XIOS3
 #%OASIS_HOME          /not/defined
 
 %NCDF_INC            -I%NCDF_HOME/include 
@@ -45,7 +45,7 @@
 #%OASIS_LIB           -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
 
 %CPP	             cpp 
-%FC                  mpiifort -c -fpp -fpp-name:/opt/software/eb/software/GCCcore/11.2.0/bin/cpp -Wp,-P,-traditional
+%FC                  mpiifort -c -fpp -fpp-name:/opt/software/rocky9/eb/software/GCCcore/12.3.0/bin/cpp -Wp,-P,-traditional
 %FCFLAGS             -i4 -r8 -O3 -fp-model precise -fno-alias
 %FFLAGS              %FCFLAGS
 %LD                  mpiifort 

cfgs/GLOBAL_QCO/MY_SRC/icethd_pnd.F90

@@ -686,8 +686,8 @@ SUBROUTINE pnd_TOPO
                         ! differential growth of base of surface floating ice layer
                         zdTice = MAX( - ( t_su(ji,jj,jl) - zTd ) , 0._wp ) ! > 0
                         zomega = rcnd_i * zdTice / zrhoi_L
-                        zdHui  = SQRT( 2._wp * zomega * rDt_ice + ( v_il(ji,jj,jl) / a_i(ji,jj,jl) )**2 ) &
-                               - v_il(ji,jj,jl) / a_i(ji,jj,jl)
+                        zdHui  = SQRT( 2._wp * zomega * rDt_ice + ( v_il(ji,jj,jl) / a_ip(ji,jj,jl) )**2 ) &
+                               - v_il(ji,jj,jl) / a_ip(ji,jj,jl)
                         zdvice = min( zdHui*a_ip(ji,jj,jl) , v_ip(ji,jj,jl) )
 
                         IF ( zdvice > epsi10 ) THEN

cfgs/GLOBAL_QCO/eORCA025/iodef.xml

@@ -24,21 +24,29 @@
     </variable_definition>
     <pool_definition>
      <pool name="Opool" nprocs="96">
-      <service name="t1dwriter" nprocs="4"  type="writer"/>
+      <service name="t1dwriter" nprocs="3"  type="writer"/>
+      <service name="s1dwriter" nprocs="1"  type="writer"/>
       <service name="t5dwriter" nprocs="4"  type="writer"/>
-      <service name="w5dwriter" nprocs="4"  type="writer"/>
+      <service name="w5dwriter" nprocs="3"  type="writer"/>
+      <service name="s5dwriter" nprocs="1"  type="writer"/>
       <service name="iwriter"   nprocs="4"  type="writer"/>
       <service name="t1mwriter" nprocs="4"  type="writer"/>
-      <service name="w1mwriter" nprocs="4"  type="writer"/>
-      <service name="u1dwriter" nprocs="4"  type="writer"/>
-      <service name="u5dwriter" nprocs="4"  type="writer"/>
-      <service name="u1mwriter" nprocs="4"  type="writer"/>
+      <service name="w1mwriter" nprocs="3"  type="writer"/>
+      <service name="s1mwriter" nprocs="1"  type="writer"/>
+      <service name="u1dwriter" nprocs="2"  type="writer"/>
+      <service name="u5dwriter" nprocs="2"  type="writer"/>
+      <service name="u1mwriter" nprocs="2"  type="writer"/>
+      <service name="v1dwriter" nprocs="2"  type="writer"/>
+      <service name="v5dwriter" nprocs="2"  type="writer"/>
+      <service name="v1mwriter" nprocs="2"  type="writer"/>
       <service name="tgatherer" nprocs="24" type="gatherer"/>
       <service name="igatherer" nprocs="8"  type="gatherer"/>
       <service name="ugatherer" nprocs="16" type="gatherer"/>
       <service name="t1ywriter" nprocs="4"  type="writer"/>
-      <service name="w1ywriter" nprocs="4"  type="writer"/>
-      <service name="u1ywriter" nprocs="4"  type="writer"/>
+      <service name="w1ywriter" nprocs="3"  type="writer"/>
+      <service name="s1ywriter" nprocs="1"  type="writer"/>
+      <service name="u1ywriter" nprocs="2"  type="writer"/>
+      <service name="v1ywriter" nprocs="2"  type="writer"/>
      </pool>
     </pool_definition>
   </context>

cfgs/GLOBAL_QCO/eORCA025/namelist_cfg

@@ -37,9 +37,9 @@
 &namtsd
     cn_dir = './INPUT/',
 	ln_tsd_init = .false.,
-    sn_tem = 'EN.4.1.1.f.analysis.g10.1995-2014.eORCA025_v4.2.teos10.nc', -1, 'temperature', .true., .true., 'yearly',
+    sn_tem = 'woa23_decav71A0_TS_TEOS10_eORCA025.nc', -1, 'temperature', .true., .true., 'yearly',
              '', '', '',
-    sn_sal = 'EN.4.1.1.f.analysis.g10.1995-2014.eORCA025_v4.2.teos10.nc', -1, 'salinity', .true., .true., 'yearly',
+    sn_sal = 'woa23_decav71A0_TS_TEOS10_eORCA025.nc', -1, 'salinity', .true., .true., 'yearly',
              '', '', '',
 /
 
@@ -67,6 +67,8 @@
     sn_tair    = 'tas',  3, 'tas',  .true.,  .false., 'yearly', 'weights_grid_jra_bilin_e025_nohaloes_full.nc', '', ''
     sn_wndi    = 'uas',  3, 'uas',  .true.,  .false., 'yearly', 'weights_grid_jra_bicubic_e025_nohaloes_full.nc', 'Ume', ''
     sn_wndj    = 'vas',  3, 'vas',  .true.,  .false., 'yearly', 'weights_grid_jra_bicubic_e025_nohaloes_full.nc', 'Vme', ''
+    sn_uoatm   = 'uos', -12, 'uos', .false., .true.,  'yearly', 'weights_grid_jra_bicubic_e025_nohaloes_full.nc', 'Uoceatm', ''
+    sn_voatm   = 'vos', -12, 'vos', .false., .true.,  'yearly', 'weights_grid_jra_bicubic_e025_nohaloes_full.nc', 'Voceatm', ''
 /
 
 &namtra_qsr
@@ -82,7 +84,7 @@
     nn_sssr = 2,
     rn_deds = -33.3333333,
     cn_dir = './INPUT/',
-    sn_sss = 'sss_1m_teos10_v4.2.nc', -1, 'salinity', .true., .true., 'yearly',
+    sn_sss = 'woa23_decav91C0_sss_TEOS10_eORCA025.nc', -1, 'salinity', .true., .true., 'yearly',
              '', '', '',
 /
 
@@ -232,3 +234,6 @@
     ln_diacfl = .true.,
 /
 
+&namtrd
+    ln_tra_trd = .true.,
+/

cfgs/GLOBAL_QCO/eORCA025/namelist_cfg_ERA5

@@ -71,6 +71,9 @@
     sn_tair    = 't2m',      1, 't2m',      .true.,  .false., 'monthly', 'weights_ERA5_eORCA025_bilin.nc', '', ''
     sn_wndi    = 'u10',      1, 'u10',      .true.,  .false., 'monthly', 'weights_ERA5_eORCA025_bicub.nc', 'Ume', ''
     sn_wndj    = 'v10',      1, 'v10',      .true.,  .false., 'monthly', 'weights_ERA5_eORCA025_bicub.nc', 'Vme', ''
+! ATB: Need to check whether uos,vos are required for ERA5, and if so what fields to use.
+!   sn_uoatm   = 'uos', -12, 'uos', .false., .true.,  'yearly', 'weights_ERA5_eORCA025_bicub.nc', 'Uoceatm', ''
+!   sn_voatm   = 'vos', -12, 'vos', .false., .true.,  'yearly', 'weights_ERA5_eORCA025_bicub.nc', 'Voceatm', ''
 /
 
 &namtra_qsr

cfgs/GLOBAL_QCO/eORCA025/namelist_cfg_JRA55

@@ -14,6 +14,8 @@
     cn_ocerst_outdir = './RESTARTS',
     nn_stock = 70128,
     ln_mskland = .true.,
+    ln_rst_list = .false.
+    nn_stocklist = 0,0,0,0,0,0,0,0,0,0
 /
 
 &namdom
@@ -65,6 +67,8 @@
     sn_tair    = 'tas',  3, 'tas',  .true.,  .false., 'yearly', 'weights_grid_jra_bilin_e025_nohaloes_full.nc', '', ''
     sn_wndi    = 'uas',  3, 'uas',  .true.,  .false., 'yearly', 'weights_grid_jra_bicubic_e025_nohaloes_full.nc', 'Ume', ''
     sn_wndj    = 'vas',  3, 'vas',  .true.,  .false., 'yearly', 'weights_grid_jra_bicubic_e025_nohaloes_full.nc', 'Vme', ''
+    sn_uoatm   = 'uos', -12, 'uos', .false., .true.,  'yearly', 'weights_grid_jra_bicubic_e025_nohaloes_full.nc', 'Uoceatm', ''
+    sn_voatm   = 'vos', -12, 'vos', .false., .true.,  'yearly', 'weights_grid_jra_bicubic_e025_nohaloes_full.nc', 'Voceatm', ''
 /
 
 &namtra_qsr
@@ -134,7 +138,6 @@
 &nambbl
     ln_trabbl = .true.,
     nn_bbl_adv  =  1,
-
 /
 
 &nameos
@@ -162,7 +165,6 @@
     nn_aei_ijk_t = 21,
     ln_ldfeiv_dia = .true.,
     nn_ldfeiv_shape = 2,
-
 /
 
 &namdyn_adv

cfgs/GLOBAL_QCO/eORCA025/run_nemo1326_96x_26n.slurm

@@ -13,17 +13,19 @@
 # time units used here for restart frequency and simulaion length
   TIME_UNITS=0 # 0=years ; 1=days ; 2=hours
 # Restart/resubmission frequency (in TIME_UNITS)
-  FREQRST=1 
+  FREQRST=1
 # job-step initial time step (0: infer from time.step)
 # IT000 != 0 -> auto-resubmission is switched OFF
-  IT000=1
+  IT000=0
 #
 # Simulation original starting time step (unchanged for LENGTHxTIME_UNITS)
   ITBEGIN=1
 # Simulation length (in TIME_UNITS) 
-  LENGTH=1   
+  LENGTH=3   
 # Name of this script (to resubmit)
   SCRIPTNAME=run_nemo1326_96x_26n.slurm
+# If conducting the repeat and reset T and S spinup set SPIN to 1, else set to 0
+  SPIN=0
 #
 # Use of nn_stocklist to trigger end-of-year restarts regardless of leap- or non-leap-
 # years, means job-steps have to be limited to no more than 10 years. Force this if
@@ -34,8 +36,9 @@ if [ "$TIME_UNITS" -eq 0 ] ; then
 fi
 # ========================================================
 ## modules load
-
+module purge
 module load NEMO/prg-env
+module load libfabric/1.18.0-GCCcore-12.3.0
 
 # ========================================================
 # Define useful functions
@@ -136,6 +139,21 @@ if [ "$IT000" -gt 1 ]; then
       RST_FILE=$RST_DIR/${OCERST_IN}_0000.nc
     fi
     read -r RST_YR START_MTH START_DAY START_YR <<< "$(date_from_restart $RST_FILE )"
+
+    if [ $SPIN = 1 ] ; then
+      START_YR=$RST_YR
+      edit_var ln_reset_ts ".true." ./namelist_cfg
+      edit_var nn_rstctl "0" ./namelist_cfg
+    elif [ $SPIN = 0 ] ; then
+      edit_var ln_reset_ts ".false." ./namelist_cfg
+      edit_var nn_rstctl "2" ./namelist_cfg
+    else
+      echo "Error: it is unclear whether this is a spinup with T and S reset, or a normal simulation"
+      exit 1
+    fi
+
+    echo "Start year is: " $START_YR
+
 else
     # Start from rest
     edit_var ln_rstart ".false." ./namelist_cfg
@@ -170,12 +188,16 @@ if [ "$TIME_UNITS" -eq 0 ]; then
     EXP_LENGTH=$(greg_length $EXP_START_YR )
     LT=$(( LENGTH - 1 ))
     if [ "$LT" -gt 0 ] ; then
-      for y in `seq 1 1 $LT`
-       do
-        EXP_START_YR=$(( EXP_START_YR + 1 ))
-        YL=$( greg_length $EXP_START_YR )
-        EXP_LENGTH=$(( EXP_LENGTH + YL ))
-       done
+      if [ $SPIN = 1 ] ; then
+        EXP_LENGTH=$(( EXP_LENGTH * LENGTH ))
+      else
+        for y in `seq 1 1 $LT`
+        do
+          EXP_START_YR=$(( EXP_START_YR + 1 ))
+          YL=$( greg_length $EXP_START_YR )
+          EXP_LENGTH=$(( EXP_LENGTH + YL ))
+        done
+      fi
     fi
     # convert from days to hours
     EXP_LENGTH=$(( EXP_LENGTH * 24 ))
@@ -190,15 +212,15 @@ if [ "$TIME_UNITS" -eq 0 ]; then
     LT=$(( FREQRST - 1 ))
     if [ "$LT" -gt 0 ] ; then
       for y in `seq 1 1 $LT`
-       do
+      do
         START_YR=$(( START_YR + 1 ))
         YL=$( greg_length $START_YR )
         NEXT_STOCK="$(( NEXT_STOCK + YL * 24 * 60 * 60 / DT ))"
         # stocklist is limited to length 10
         if [ "$y" -lt 10 ] ; then
           STOCK_LIST="${STOCK_LIST},${NEXT_STOCK}"
         fi
-       done
+      done
     fi
     ITEND=$NEXT_STOCK
     edit_var nn_stocklist "$STOCK_LIST" ./namelist_cfg
@@ -232,7 +254,7 @@ mkdir -p {RESTARTS,OUTPUT}
 # Link nemo
 ln -fs ../BLD/bin/nemo.exe nemo
 
-export XIO_HOME=/home/acc/xios3-trunk-head
+export XIO_HOME=/dssgfs01/working/atb299/XIOS3
 #
 export OMP_NUM_THREADS=1
 export I_MPI_SHM=off

cfgs/GLOBAL_QCO/eORCA1/INPUT

@@ -0,0 +1 @@
+../../../data/INPUT_eORCA1/

cfgs/GLOBAL_QCO/eORCA1/axis_def_nemo.xml

@@ -0,0 +1 @@
+../../SHARED/axis_def_nemo.xml

cfgs/GLOBAL_QCO/eORCA1/bfr_coef.nc

@@ -0,0 +1 @@
+INPUT/bfr_coef01.nc

cfgs/GLOBAL_QCO/eORCA1/context_nemo.xml

@@ -0,0 +1,46 @@
+<!--
+ ============================================================================================== 
+    NEMO context
+============================================================================================== 
+-->
+<context id="nemo">
+    <!-- $id$ -->
+    <variable_definition>
+       <!-- Year/Month/Day of time origin for NetCDF files; defaults to 1800-01-01 -->
+       <variable id="ref_year"  type="int"> 1900 </variable>
+       <variable id="ref_month" type="int"> 01 </variable>
+       <variable id="ref_day"   type="int"> 01 </variable>
+       <variable id="rho0"      type="float" > 1026.0 </variable>
+       <variable id="cpocean"   type="float" > 3991.86795711963 </variable>
+       <variable id="convSpsu"  type="float" > 0.99530670233846  </variable>
+       <variable id="rhoic"     type="float" > 917.0 </variable>
+       <variable id="rhosn"     type="float" > 330.0 </variable>
+       <variable id="missval"   type="float" > 1.e20 </variable>
+    </variable_definition>
+
+<!-- Fields definition -->
+    <field_definition src="./field_def_nemo-oce.xml"/>       <!--  NEMO ocean dynamics                     -->
+    <field_definition src="./field_def_nemo-ice.xml"/>       <!--  NEMO ocean sea ice                      -->
+
+
+<!-- Files definition -->
+    <file_definition src="file_def_nemo-oce_1d_C6.xml"/>     <!--  NEMO ocean dynamics                     -->
+    <file_definition src="file_def_nemo-oce_5d_C6.xml"/>     <!--  NEMO ocean dynamics                     -->
+    <file_definition src="file_def_nemo-oce_1m_C6.xml"/>     <!--  NEMO ocean dynamics                     -->
+    <file_definition src="file_def_nemo-oce_1y_C6.xml"/>     <!--  NEMO ocean dynamics                     -->
+
+    <file_definition src="./file_def_nemo-ice_5d_C6.xml"/>   <!--  NEMO ocean sea ice                      -->
+    <file_definition src="./file_def_nemo-ice_1m_C6.xml"/>   <!--  NEMO ocean sea ice                      -->
+    <file_definition src="./file_def_nemo-ice_1y_C6.xml"/>   <!--  NEMO ocean sea ice                      -->
+
+<!-- Axis definition -->
+    <axis_definition src="./axis_def_nemo.xml"/>
+
+<!-- Domain definition -->
+    <domain_definition src="./domain_def_nemo.xml"/>
+
+<!-- Grids definition -->
+    <grid_definition   src="./grid_def_nemo.xml"/>
+
+
+</context>

cfgs/GLOBAL_QCO/eORCA1/domain_def_nemo.xml

@@ -0,0 +1 @@
+../../SHARED/domain_def_nemo.xml

cfgs/GLOBAL_QCO/eORCA1/eddy_viscosity_3D.nc

@@ -0,0 +1 @@
+INPUT/eddy_viscosity_3D_eORCA1.nc

cfgs/GLOBAL_QCO/eORCA1/field_def_nemo-ice.xml

@@ -0,0 +1 @@
+../../SHARED/field_def_nemo-ice.xml

cfgs/GLOBAL_QCO/eORCA1/field_def_nemo-oce.xml

@@ -0,0 +1 @@
+../../SHARED/field_def_nemo-oce.xml

cfgs/GLOBAL_QCO/eORCA1/file_def_nemo-ice_1m_C6.xml

@@ -0,0 +1 @@
+../../SHARED/file_def_nemo-ice_1m_C6.xml

cfgs/GLOBAL_QCO/eORCA1/file_def_nemo-ice_1y_C6.xml

@@ -0,0 +1 @@
+../../SHARED/file_def_nemo-ice_1y_C6.xml

cfgs/GLOBAL_QCO/eORCA1/file_def_nemo-ice_5d_C6.xml

@@ -0,0 +1 @@
+../../SHARED/file_def_nemo-ice_5d_C6.xml

cfgs/GLOBAL_QCO/eORCA1/file_def_nemo-oce_1d_C6.xml

@@ -0,0 +1 @@
+../../SHARED/file_def_nemo-oce_1d_C6.xml

cfgs/GLOBAL_QCO/eORCA1/file_def_nemo-oce_1m_C6.xml

@@ -0,0 +1 @@
+../../SHARED/file_def_nemo-oce_1m_C6.xml

cfgs/GLOBAL_QCO/eORCA1/file_def_nemo-oce_1y_C6.xml

@@ -0,0 +1 @@
+../../SHARED/file_def_nemo-oce_1y_C6.xml

cfgs/GLOBAL_QCO/eORCA1/file_def_nemo-oce_5d_C6.xml

@@ -0,0 +1 @@
+../../SHARED/file_def_nemo-oce_5d_C6.xml

cfgs/GLOBAL_QCO/eORCA1/grid_def_nemo.xml

@@ -0,0 +1 @@
+../../SHARED/grid_def_nemo.xml