Update cice5 package.py

packages/cice5/package.py

@@ -0,0 +1,215 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# Copyright 2023 ACCESS-NRI
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import install, join_path, mkdirp
+
+# https://spack.readthedocs.io/en/latest/build_systems/makefilepackage.html
+class Cice5(MakefilePackage):
+    """The Los Alamos sea ice model (CICE) is the result of an effort to develop a computationally efficient sea ice component for a fully coupled atmosphere-land global climate model."""
+
+    homepage = "https://www.access-nri.org.au"
+    git = "https://github.com/ACCESS-NRI/cice5.git"
+    # NOTE: URL definition required for CI
+    # Spack needs tarball URL to be defined to access github branches
+    url = "https://github.com/ACCESS-NRI/cice5/tarball/master"
+
+    maintainers = ["harshula"]
+
+    version("master", branch="master")
+
+    # Depend on virtual package "mpi".
+    depends_on("mpi")
+    depends_on("oasis3-mct")
+    depends_on("datetime-fortran")
+    depends_on("[email protected]:")
+    depends_on("[email protected]:")
+    # TODO: For initial verification we are going to use static pio.
+    #       Eventually we plan to move to shared pio
+    # ~shared requires: https://github.com/spack/spack/pull/34837
+    depends_on("parallelio~pnetcdf~timing~shared")
+    depends_on("libaccessom2")
+
+    phases = ["edit", "build", "install"]
+
+    _buildscript = "spack-build.sh"
+    _buildscript_path = join_path("bld", _buildscript)
+
+    # The integer represents environment variable NTASK
+    __targets = {24: {}, 480: {}, 722: {}, 1682: {}}
+    __targets[24]["driver"] = "auscom"
+    __targets[24]["grid"] = "360x300"
+    __targets[24]["blocks"] = "24x1"
+
+    __targets[480]["driver"] = "auscom"
+    __targets[480]["grid"] = "1440x1080"
+    __targets[480]["blocks"] = "48x40"
+
+    # Comment from bld/config.nci.auscom.3600x2700:
+    # Recommendations:
+    #   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.
+    __targets[722]["driver"] = "auscom"
+    __targets[722]["grid"] = "3600x2700"
+    __targets[722]["blocks"] = "90x90"
+
+    __targets[1682]["driver"] = "auscom"
+    __targets[1682]["grid"] = "3600x2700"
+    __targets[1682]["blocks"] = "200x180"
+
+    def edit(self, spec, prefix):
+
+        srcdir = self.stage.source_path
+        buildscript_dest = join_path(srcdir, self._buildscript_path)
+        makeinc_path = join_path(srcdir, "bld", "Macros.spack")
+
+        copy(join_path(self.package_dir, self._buildscript), buildscript_dest)
+
+        config = {}
+
+        istr = join_path((spec["oasis3-mct"].headers).cpp_flags, "psmile.MPI1")
+        ideps = ["parallelio", "oasis3-mct", "libaccessom2", "netcdf-fortran"]
+        incs = " ".join([istr] + [(spec[d].headers).cpp_flags for d in ideps])
+
+        lstr = " ".join(
+                    ["-L" + join_path(spec["parallelio"].prefix, "lib"),
+                    "-lpiof",
+                    "-lpioc"]
+                   )
+        # NOTE: The order of the libraries matter during the linking step!
+        # NOTE: datetime-fortran is a dependency of libaccessom2.
+        ldeps = ["oasis3-mct", "libaccessom2", "netcdf-c", "netcdf-fortran", "datetime-fortran"]
+        libs = " ".join([lstr] + [(spec[d].libs).ld_flags for d in ldeps])
+
+        # Copied from bld/Macros.nci
+        config["pre"] = f"""
+INCLDIR    := -I. {incs}
+SLIBS      := {libs}
+ULIBS      :=
+CPP        := cpp
+FC         := mpifort
+
+CPPFLAGS   := -P -traditional
+CPPDEFS    := -DLINUX -DPAROPT
+CFLAGS     := -c -O2
+FIXEDFLAGS := -132
+FREEFLAGS  :=
+"""
+
+        config["gcc"] = f"""
+# TODO: removed -std=f2008 due to compiler errors
+FFLAGS = -Wall -fdefault-real-8 -fdefault-double-8 -ffpe-trap=invalid,zero,overflow -fallow-argument-mismatch
+"""
+
+        # module load intel-compiler/2019.5.281
+        config["intel"] = f"""
+NCI_INTEL_FLAGS := -r8 -i4 -traceback -w -fpe0 -ftz -convert big_endian -assume byterecl -check noarg_temp_created
+NCI_REPRO_FLAGS := -fp-model precise -fp-model source -align all
+ifeq ($(DEBUG), 1)
+    NCI_DEBUG_FLAGS := -g3 -O0 -debug all -check all -no-vec -assume nobuffered_io
+    FFLAGS          := $(NCI_INTEL_FLAGS) $(NCI_REPRO_FLAGS) $(NCI_DEBUG_FLAGS)
+    CPPDEFS         := $(CPPDEFS) -DDEBUG=$(DEBUG)
+else
+    NCI_OPTIM_FLAGS := -g3 -O2 -axCORE-AVX2 -debug all -check none -qopt-report=5 -qopt-report-annotate -assume buffered_io
+    FFLAGS          := $(NCI_INTEL_FLAGS) $(NCI_REPRO_FLAGS) $(NCI_OPTIM_FLAGS)
+endif
+"""
+
+        # Copied from bld/Macros.nci
+        config["post"] = """
+MOD_SUFFIX := mod
+LD         := $(FC)
+LDFLAGS    := $(FFLAGS) -v
+
+CPPDEFS :=  $(CPPDEFS) -DNXGLOB=$(NXGLOB) -DNYGLOB=$(NYGLOB) \
+            -DNUMIN=$(NUMIN) -DNUMAX=$(NUMAX) \
+            -DTRAGE=$(TRAGE) -DTRFY=$(TRFY) -DTRLVL=$(TRLVL) \
+            -DTRPND=$(TRPND) -DNTRAERO=$(NTRAERO) -DTRBRI=$(TRBRI) \
+            -DNBGCLYR=$(NBGCLYR) -DTRBGCS=$(TRBGCS) \
+            -DNICECAT=$(NICECAT) -DNICELYR=$(NICELYR) \
+            -DNSNWLYR=$(NSNWLYR) \
+            -DBLCKX=$(BLCKX) -DBLCKY=$(BLCKY) -DMXBLCKS=$(MXBLCKS)
+
+ifeq ($(COMMDIR), mpi)
+   SLIBS   :=  $(SLIBS) -lmpi
+endif
+
+ifeq ($(DITTO), yes)
+   CPPDEFS :=  $(CPPDEFS) -DREPRODUCIBLE
+endif
+ifeq ($(BARRIERS), yes)
+   CPPDEFS :=  $(CPPDEFS) -Dgather_scatter_barrier
+endif
+
+ifeq ($(IO_TYPE), netcdf)
+   CPPDEFS :=  $(CPPDEFS) -Dncdf
+endif
+
+ifeq ($(IO_TYPE), pio)
+   CPPDEFS :=  $(CPPDEFS) -Dncdf -DPIO
+endif
+
+# TODO: Do we want to delete this conditional?
+#ifeq ($(USE_ESMF), yes)
+#   CPPDEFS :=  $(CPPDEFS) -Duse_esmf
+#   INCLDIR :=  $(INCLDIR) -I ???
+#   SLIBS   :=  $(SLIBS) -L ??? -lesmf -lcprts -lrt -ldl
+#endif
+
+ifeq ($(AusCOM), yes)
+   CPPDEFS := $(CPPDEFS) -DAusCOM -Dcoupled
+endif
+
+ifeq ($(UNIT_TESTING), yes)
+   CPPDEFS := $(CPPDEFS) -DUNIT_TESTING
+endif
+ifeq ($(ACCESS), yes)
+   CPPDEFS := $(CPPDEFS) -DACCESS
+endif
+# standalone CICE with AusCOM mods
+ifeq ($(ACCICE), yes)
+   CPPDEFS := $(CPPDEFS) -DACCICE
+endif
+# no MOM just CICE+UM
+ifeq ($(NOMOM), yes)
+   CPPDEFS := $(CPPDEFS) -DNOMOM
+endif
+ifeq ($(OASIS3_MCT), yes)
+   CPPDEFS := $(CPPDEFS) -DOASIS3_MCT
+endif
+"""
+        with open(makeinc_path, "w") as makeinc:
+            makeinc.write(
+                config["pre"]
+                + config[self.compiler.name]
+                + config["post"]
+            )
+
+    def build(self, spec, prefix):
+
+        build = Executable(
+                    join_path(self.stage.source_path, self._buildscript_path)
+                )
+
+        for k in self.__targets:
+            build(self.__targets[k]["driver"],
+                    self.__targets[k]["grid"],
+                    self.__targets[k]["blocks"],
+                    str(k))
+
+    def install(self, spec, prefix):
+
+        mkdirp(prefix.bin)
+        for k in self.__targets:
+            name = "_".join([self.__targets[k]["driver"],
+                                self.__targets[k]["grid"],
+                                self.__targets[k]["blocks"],
+                                str(k) + "p"])
+            install(join_path("build_" + name, "cice_" + name + ".exe"),
+                    prefix.bin)

packages/cice5/spack-build.sh

@@ -0,0 +1,153 @@
+#! /bin/csh -f
+
+set echo on
+
+if ( $#argv < 4 ) then
+  echo '*** Please issue the command like ***'
+  echo '> ./bld/build.sh <driver> <grid> <blocks> <ntask> [<debug>]'
+  echo 'e.g. bld/build.sh auscom 1440x1080 48x40 480'
+  echo 'driver: which driver to use.'
+  echo 'grid: grid resolution longitude by latitude.'
+  echo 'blocks: grid split into the number of blocks longitude by latitude.'
+  echo 'ntask: number of tasks.'
+  echo 'debug: if this is a unit testing or debug build. Valid options are \'debug\' or \'unit_testing\''
+  exit
+else
+  set driver = $1
+  set grid = $2
+  set blocks = $3
+  set ntask = $4
+  set debug = $5
+endif
+
+# Location of this model
+setenv SRCDIR $cwd
+setenv CBLD   $SRCDIR/bld
+
+if ($debug == 'debug') then
+    setenv DEBUG 1
+else
+    setenv DEBUG 0
+endif
+if ($debug == 'unit_testing') then
+    setenv DEBUG 1
+    setenv UNIT_TESTING yes
+endif
+
+### 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  pio       # set to none if netcdf library is unavailable
+setenv DITTO    no        # reproducible diagnostics
+setenv THRD     no        # set to yes for OpenMP threading
+if ( $THRD == 'yes') setenv OMP_NUM_THREADS 2 # positive integer 
+setenv BARRIERS yes       # set -Dgather_scatter_barrier, prevents hangs on raijin
+setenv AusCOM   yes
+if ($driver == 'access') then
+    setenv ACCESS   yes
+else
+    setenv ACCESS   no
+endif
+setenv OASIS3_MCT yes	  # oasis3-mct version
+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
+
+### 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
+
+### Where this model is compiled
+setenv OBJDIR $SRCDIR/build_${driver}_${grid}_${blocks}_${ntask}p
+if !(-d $OBJDIR) mkdir -p $OBJDIR
+
+setenv NTASK $ntask
+setenv RES $grid
+set NXGLOB = `echo $RES | sed s/x.\*//`
+set NYGLOB = `echo $RES | sed s/.\*x//`
+set NXBLOCK = `echo $blocks | sed s/x.\*//`
+set NYBLOCK = `echo $blocks | sed s/.\*x//`
+setenv BLCKX `expr $NXGLOB / $NXBLOCK` # x-dimension of blocks ( not including )
+setenv BLCKY `expr $NYGLOB / $NYBLOCK` # y-dimension of blocks (  ghost cells  )
+
+@ a = $NXGLOB * $NYGLOB ; @ b = $BLCKX * $BLCKY * $NTASK
+@ m = $a / $b ; setenv MXBLCKS $m ; if ($MXBLCKS == 0) setenv MXBLCKS 1
+echo Autimatically generated: MXBLCKS = $MXBLCKS
+
+###########################################
+# ars599: 24032014
+#	copy from /short/p66/ars599/CICE.v5.0/accice.v504_csiro
+#	solo_ice_comp
+###########################################
+### Tracers               # match ice_in tracer_nml to conserve memory
+setenv TRAGE   1          # set to 1 for ice age tracer
+setenv TRFY    1          # set to 1 for first-year ice area tracer
+setenv TRLVL   1          # set to 1 for level and deformed ice tracers
+setenv TRPND   1          # set to 1 for melt pond tracers
+setenv NTRAERO 0          # number of aerosol tracers 
+                          # (up to max_aero in ice_domain_size.F90) 
+                          # CESM uses 3 aerosol tracers
+setenv TRBRI   1          # set to 1 for brine height tracer
+setenv NBGCLYR 0          # number of zbgc layers
+setenv TRBGCS  2          # number of skeletal layer bgc tracers 
+                          # TRBGCS=0 or 2<=TRBGCS<=9)
+
+### File unit numbers
+setenv NUMIN 11           # minimum file unit number
+setenv NUMAX 99           # maximum file unit number
+
+if ($IO_TYPE == 'netcdf') then
+  setenv IODIR io_netcdf
+else if ($IO_TYPE == 'pio') then
+  setenv IODIR io_pio
+else
+  setenv IODIR io_binary
+endif
+
+
+
+cp -f $CBLD/Makefile.std $CBLD/Makefile
+
+if ($NTASK == 1) then
+   setenv COMMDIR serial
+else
+   setenv COMMDIR mpi
+endif
+echo COMMDIR: $COMMDIR
+
+setenv DRVDIR $driver
+
+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
+
+cc -o makdep $CBLD/makdep.c || exit 2
+
+make VPFILE=Filepath EXEC=cice_${driver}_${grid}_${blocks}_${ntask}p.exe \
+           NXGLOB=$NXGLOB NYGLOB=$NYGLOB \
+           BLCKX=$BLCKX BLCKY=$BLCKY MXBLCKS=$MXBLCKS \
+           -f  $CBLD/Makefile MACFILE=$CBLD/Macros.spack || 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