COSIMA · anton-seaice · Aug 22, 2016 · Aug 31, 2016 · Nov 10, 2016 · Nov 28, 2016
diff --git a/.github/workflows/model-build-test-ci.yml b/.github/workflows/model-build-test-ci.yml
@@ -0,0 +1,15 @@
+name: Test model build
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - "master"
+
+jobs:
+  build:
+    name: Build ${{ github.repository }} via spack
+    uses: access-nri/build-ci/.github/workflows/model-1-build.yml@main
+    permissions:
+      packages: read
diff --git a/.gitmodules b/.gitmodules
diff --git a/LICENSE.pdf b/LICENSE.pdf
diff --git a/ParallelIO b/ParallelIO
diff --git a/README.md b/README.md
@@ -1,10 +1,14 @@
 ## Overview
-This repository contains the trunk from the subversion (svn) repository of the Los Alamos Sea Ice Model, CICE, including release tags through version 5.1.2. 
+This repository contains the access/auscom fork of cice5 used in the ACCESS-ESM1.6 and ACCESS-OM2. It was forked from https://github.com/CICE-Consortium/CICE-svn-trunk/ which in turn captured the trunk from the subversion (svn) repository of the Los Alamos Sea Ice Model, CICE, including release tags through version 5.1.2.
+
+ACCESS-ESM1.6 related code came from https://code.metoffice.gov.uk/trac/cice/browser/main/branches/pkg/Config/vn5.1.2_GSI8.1_package_branch/cice?order=name&rev=334#source (MOSRS account required)
 
 More recent versions are found in the [CICE](https://github.com/CICE-Consortium/CICE) and [Icepack](https://github.com/CICE-Consortium/Icepack) repositories, which are maintained by the CICE Consortium.  
 
 If you expect to make any changes to the code, we recommend that you work in the CICE and Icepack repositories.  Changes made to code in this repository will not be accepted, other than critical bug fixes.
 
+There is [PDF documentation](https://github.com/ACCESS-NRI/cice5/blob/master/doc/cicedoc.pdf) available for CICE 5.1.2, however some changes were made to this fork to support coupling with ACCESS-OM2 and ACCESS-ESM1.6, Parallel IO, ERA5 Forcing, BGC modelling and for other updates. Some of these changes are described in the [ACCESS-OM2 Technical Report](https://github.com/COSIMA/ACCESS-OM2-1-025-010deg-report).
+
 ## Useful links
 * **Wiki**: https://github.com/CICE-Consortium/CICE-svn-trunk/wiki
 
@@ -16,4 +20,4 @@ If you expect to make any changes to the code, we recommend that you work in the
 
 * **Resource Index**: https://github.com/CICE-Consortium/About-Us/wiki/Resource-Index
 
-   List of resources for information about the Consortium and its repositories as well as model documentation, testing, and development.    
+   List of resources for information about the Consortium and its repositories as well as model documentation, testing, and development.
diff --git a/bld/Macros.Linux.raijin-185 b/bld/Macros.Linux.raijin-185
@@ -26,7 +26,7 @@ FC         := mpifort
 ifeq ($(DEBUG), yes)
     FFLAGS     := -r8 -i4 -O0 -g -align all -w -ftz -convert big_endian -assume byterecl -no-vec -mcmodel=medium -xHost -fp-model precise
 else
-    FFLAGS     := -r8 -i4 -O2 -align all -w -ftz -convert big_endian -assume byterecl -no-vec -mcmodel=medium -xHost -fp-model precise
+    FFLAGS     := -r8 -i4 -O2 -align all -w -ftz -convert big_endian -assume byterecl -no-vec -mcmodel=medium -xHost -fp-model precise -assume buffered_io -check noarg_temp_created
 endif
 MOD_SUFFIX := mod
 LD         := $(FC)

diff --git a/bld/Makefile b/bld/Makefile
@@ -113,11 +113,11 @@ $(EXEC): $(OBJS)
 	cc $(CFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $<
 
 .F.o:
-	$(CPP) $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $< > $*.f 
+	$(FC) -P $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $< -o $*.f
 	$(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(INCS) $(INCLDIR) $*.f  
 
 .F90.o:
-	$(CPP) $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $< > $*.f90
+	$(FC) -P $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $< -o $*.f90
 	$(FC) -c $(FFLAGS) $(FREEFLAGS) $(INCS) $(INCLDIR) $*.f90  
 
 mostlyclean:

diff --git a/bld/Makefile.std b/bld/Makefile.std
@@ -113,11 +113,11 @@ $(EXEC): $(OBJS)
 	cc $(CFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $<
 
 .F.o:
-	$(CPP) $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $< > $*.f 
+	$(FC) -P $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $< -o $*.f
 	$(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(INCS) $(INCLDIR) $*.f  
 
 .F90.o:
-	$(CPP) $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $< > $*.f90
+	$(FC) -P $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $< -o $*.f90
 	$(FC) -c $(FFLAGS) $(FREEFLAGS) $(INCS) $(INCLDIR) $*.f90  
 
 mostlyclean:

diff --git a/bld/build.sh b/bld/build.sh
@@ -78,17 +78,10 @@ if ( $AusCOM == 'yes' ) then
     setenv CPL_INCS '-I$(CPLINCDIR)/include -I$(OASISDIR)/psmile.MPI1 -I$(OASISDIR)/mct -I$(SRCDIR)/ParallelIO/build/include/'
 endif
 
-### Setup the version string, this is the git hash of the commit used to build
-### the code. The version of an executable can be found with the following
-### command: strings <executable> | grep 'CICE_COMMIT_HASH='
-setenv GIT_CONFIG_NOGLOBAL 'yes'
-
-set old_hash=`grep 'public :: CICE_COMMIT_HASH =' $SRCDIR/drivers/$driver/version.F90 | cut -d '"' -f 2 | cut -d '=' -f 2`
-set new_hash=`git rev-parse HEAD`
-
-if ( $old_hash != $new_hash ) then
-    sed -e "s/{CICE_COMMIT_HASH}/$new_hash/g" $SRCDIR/drivers/$driver/version.F90.template > $SRCDIR/drivers/$driver/version.F90
-endif
+### The version of an executable can be found with the following
+### command: strings <executable> | grep 'CICE_VERSION='
+set version='202301'
+sed -e "s/{CICE_VERSION}/$version/g" $SRCDIR/drivers/$driver/version.F90.template > $SRCDIR/drivers/$driver/version_mod.F90
 
 ### Location and name of the generated exectuable
 setenv EXE cice_${driver}_${resolution}_${NTASK}p.exe

diff --git a/bld/makdep.c b/bld/makdep.c
@@ -51,7 +51,7 @@ static struct node *suffix_list;      /* List of Fortran suffixes to look for */
 static void check (char *, struct node *, char *, int);
 static int already_found (char *, struct node *);
 
-main (int argc, char **argv)
+int main (int argc, char **argv)
 {
   int lastdot;             /* points to the last . in fname */
   int c;                   /* return from getopt */

diff --git a/compile/comp_access-cm1440-185_ac330 b/compile/comp_access-cm1440-185_ac330
@@ -0,0 +1,238 @@
+#! /bin/csh -f
+
+set echo on
+#setenv DEBUG   yes       # set to yes for debug
+
+if ( $1 == '') then
+  echo '*** Please issue the command like ***'
+  echo '     > ./comp_auscom_cice.RJ.nP #nproc    ' 
+  echo 'here #proc is the number of cpu to be used for CICE5 (e.g. 1, 2, 4, 6...)'
+  set nproc = 192
+  echo *** $nproc processors will be used to run CICE5... ***
+  sleep 3
+  #exit
+else
+  set nproc = $1
+  echo *** $nproc processors will be used to run CICE5... ***
+endif
+
+### Change these to your own site and user directory! 
+### You will need to create a Makefile Macro in bld
+### Platform and its architecture ($HOST = xe)
+setenv ARCH raijin-185
+
+# Set AusCOM home:
+setenv AusCOMHOME $cwd:h:h:h
+
+#----------------------------------------------------------------------
+
+### Specialty code
+setenv CAM_ICE  no        # set to yes for CAM runs (single column)
+setenv SHRDIR   csm_share # location of CCSM shared code
+setenv IO_TYPE  netcdf    # set to none if netcdf library is unavailable
+                          # set to pio for parallel netcdf
+setenv DITTO    no        # reproducible diagnostics
+setenv THRD     no        # set to yes for OpenMP threading
+if ( $THRD == 'yes') setenv OMP_NUM_THREADS 2 # positive integer 
+
+setenv ACCESS   yes       # set to yes for ACCESS
+setenv AusCOM   yes       # set to yes for AusCOM
+setenv OASIS3_MCT yes	  # oasis3-mct version
+setenv CHAN     MPI1	  # MPI1 or MPI2 (always MPI1!)
+setenv NICELYR    4       # number of vertical layers in the ice
+setenv NSNWLYR    1       # number of vertical layers in the snow
+setenv NICECAT    5       # number of ice thickness categories
+
+### Location of ACCESS system
+setenv SYSTEMDIR $AusCOMHOME
+echo SYSTEMDIR: $SYSTEMDIR
+
+### Location of this model (source)
+setenv SRCDIR $cwd:h  #$SYSTEMDIR/submodels/cice5.0.4
+echo SRCDIR: $SRCDIR
+
+source ${SRCDIR}/compile/environs.$ARCH  # environment variables and loadable modules
+
+### Location and names of coupling libraries and inclusions
+### Location and names of coupling libraries
+#setenv CPLLIBDIR ~access/access-cm2/prebuild/oasis3-mct/Linux-182/lib
+setenv CPLLIBDIR /projects/access/apps/oasis3-mct/ompi185/lib
+setenv CPLLIBS '-L$(CPLLIBDIR) -lpsmile.${CHAN} -lmct -lmpeu -lscrip'
+#echo CPLLIBS: ${CPLLIBS}
+
+### Location of coupling inclusions
+#setenv CPLINCDIR ~access/access-cm2/prebuild/oasis3-mct/Linux-182/build/lib
+setenv CPLINCDIR /projects/access/apps/oasis3-mct/ompi185/include
+setenv CPL_INCS '-I$(CPLINCDIR)/psmile.$(CHAN) -I$(CPLINCDIR)/pio -I$(CPLINCDIR)/mct'
+#echo CPL_INCS: $CPL_INCS
+
+### For multi-Layer ice (standard) configuration
+setenv N_ILYR 1                # 4 for standard multi-layer ice. for ktherm=0, zero-layer thermodynamics
+
+### Location and name of the generated exectuable
+setenv DATESTR `date +%Y%m%d`
+setenv BINDIR $SYSTEMDIR/bin
+setenv EXE cice_GC3GA7-cm1440-185.${DATESTR}_${nproc}p_${NICELYR}lyr
+
+### Where this model is compiled
+setenv OBJDIR $SRCDIR/compile/build_${CHAN}_{$nproc}p-mct-185
+if !(-d $OBJDIR) mkdir -p $OBJDIR
+#/bin/rm $OBJDIR/*
+#
+
+### Grid resolution
+#setenv GRID gx3 ; setenv RES 100x116
+#setenv GRID gx1 ; setenv RES 320x384
+#setenv GRID tx1 ; setenv RES 360x240
+#setenv GRID tp1 ; setenv RES 360x300
+setenv GRID tp1 ; setenv RES 1440x1080
+
+set NXGLOB = `echo $RES | sed s/x.\*//`
+set NYGLOB = `echo $RES | sed s/.\*x//`
+echo NXGLOB: $NXGLOB
+echo NYGLOB: $NYGLOB
+
+# Recommendations:
+#   NTASK equals nprocs in ice_in
+#   use processor_shape = slenderX1 or slenderX2 in ice_in
+#   one per processor with distribution_type='cartesian' or
+#   squarish blocks with distribution_type='rake'
+# If BLCKX (BLCKY) does not divide NXGLOB (NYGLOB) evenly, padding
+# will be used on the right (top) of the grid.
+setenv NTASK      $nproc
+#setenv BLCKX     45       # x-dimension of blocks ( not including )
+#setenv BLCKY     38       # y-dimension of blocks (  ghost cells  )
+setenv BLCKX     `expr $NXGLOB / $nproc`
+setenv BLCKY     `expr $NYGLOB` 
+echo BLCKX: $BLCKX
+echo BLCKY: $BLCKY
+
+echo
+#24 : 12x2 
+setenv BLCKX     120 
+setenv BLCKY     540 
+#144 : 16x9
+setenv BLCKX     90
+setenv BLCKY     120
+#16 : 8x2 
+setenv BLCKX     180 
+setenv BLCKY     540 
+#16 : 4x4 
+setenv BLCKX     360 
+setenv BLCKY     270 
+##216 : 24x9 
+#setenv BLCKX     60 
+#setenv BLCKY     120 
+#192 : 16x12 -->square-ice 
+setenv BLCKX     90 
+setenv BLCKY     90 
+#192 : 96x2 
+setenv BLCKX     15 
+setenv BLCKY     540 
+
+# may need to increase MXBLCKS with rake distribution or padding
+@ a = $NXGLOB * $NYGLOB ; @ b = $BLCKX * $BLCKY * $NTASK
+@ m = $a / $b ; setenv MXBLCKS $m ; if ($MXBLCKS == 0) setenv MXBLCKS 1
+echo Autimatically generated: MXBLCKS = $MXBLCKS
+##setenv MXBLCKS 8 # if necessary (code will print proper value)
+#20110830: increase it to 12 as required by code:
+#          (but no clue why it never happened before!)
+#setenv MXBLCKS 12 # if necessary (code will print proper value)
+
+###########################################
+# ars599: 24032014
+#	copy from /short/p66/ars599/CICE.v5.0/accice.v504_csiro
+#	solo_ice_comp
+###########################################
+### Tracers               # match ice_in tracer_nml to conserve memory
+setenv TRAGE   1          # set to 1 for ice age tracer
+setenv TRFY    0          # set to 1 for first-year ice area tracer
+setenv TRLVL   0          # set to 1 for level and deformed ice tracers
+setenv TRPND   1          # set to 1 for melt pond tracers
+setenv NTRAERO 0          # number of aerosol tracers 
+                          # (up to max_aero in ice_domain_size.F90) 
+                          # CESM uses 3 aerosol tracers
+setenv TRBRI   0          # set to 1 for brine height tracer
+setenv NBGCLYR 0          # number of zbgc layers
+setenv TRBGCS  0          # number of skeletal layer bgc tracers 
+                          # TRBGCS=0 or 2<=TRBGCS<=9)
+
+### File unit numbers
+setenv NUMIN 11           # minimum file unit number
+setenv NUMAX 99           # maximum file unit number
+
+if ($IO_TYPE == 'netcdf') then
+  setenv IODIR io_netcdf
+else if ($IO_TYPE == 'pio') then
+  setenv IODIR io_pio
+else
+  setenv IODIR io_binary
+endif
+
+###########################################
+
+setenv CBLD   $SRCDIR/bld
+
+if ( $ARCH == 'UNICOS/mp') setenv ARCH UNICOS
+if ( $ARCH == 'UNICOS') then
+   cp -f $CBLD/Makefile.$ARCH $CBLD/Makefile
+else
+   cp -f $CBLD/Makefile.std $CBLD/Makefile
+endif
+
+if ($NTASK == 1) then
+   setenv COMMDIR serial
+else
+   setenv COMMDIR mpi
+endif
+echo COMMDIR: $COMMDIR
+
+if ($ACCESS == 'yes') then
+  setenv DRVDIR access
+else  
+  setenv DRVDIR cice
+endif
+echo DRVDIR: $DRVDIR
+
+cd $OBJDIR
+
+### List of source code directories (in order of importance).
+cat >! Filepath << EOF
+$SRCDIR/drivers/$DRVDIR
+$SRCDIR/source
+$SRCDIR/$COMMDIR
+$SRCDIR/$IODIR
+$SRCDIR/$SHRDIR
+EOF
+
+if ( $ARCH == 'UNICOS.ORNL.phoenix' ) then
+   ### use -h command for phoenix
+   cc -o makdep -h command $CBLD/makdep.c           || exit 2
+else if ( $ARCH == 'Linux.ORNL.jaguar' ) then
+   gcc -g -o makdep $CBLD/makdep.c                  || exit 2
+else
+   cc -o makdep $CBLD/makdep.c                      || exit 2
+endif
+
+setenv MACFILE $CBLD/Macros.Linux.${ARCH}
+
+gmake VPFILE=Filepath EXEC=$BINDIR/$EXE \
+           NXGLOB=$NXGLOB NYGLOB=$NYGLOB \
+           BLCKX=$BLCKX BLCKY=$BLCKY MXBLCKS=$MXBLCKS \
+      -f  $CBLD/Makefile MACFILE=$MACFILE || exit 2
+
+cd ..
+pwd
+echo NTASK = $NTASK
+echo "global N, block_size" 
+echo "x    $NXGLOB,    $BLCKX"
+echo "y    $NYGLOB,    $BLCKY"
+echo max_blocks = $MXBLCKS
+echo $TRAGE   = TRAGE,   iage tracer
+echo $TRFY    = TRFY,    first-year ice tracer
+echo $TRLVL   = TRLVL,   level-ice tracers
+echo $TRPND   = TRPND,   melt pond tracers
+echo $NTRAERO = NTRAERO, number of aerosol tracers
+echo $TRBRI   = TRBRI,   brine height tracer
+echo $NBGCLYR = NBGCLYR, number of bio grid layers
+echo $TRBGCS  = TRBGCS,  number of BGC tracers