NOAA operations and research computers

.gitignore

@@ -7,3 +7,6 @@ doc/build
 
 # Ignore macOS cache files
 .DS_Store
+
+# Ignore testsuite directories
+testsuite.*

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "icepack"]
 	path = icepack
-	url = https://github.com/cice-consortium/icepack.git
+	url = https://github.com/cice-consortium/Icepack
 	branch = master

cicecore/cicedynB/infrastructure/ice_domain.F90

@@ -478,12 +478,12 @@ subroutine init_domain_distribution(KMTG,ULATG)
             if (this_block%j_glob(j) > 0) then
                do i=this_block%ilo,this_block%ihi
                   if (this_block%i_glob(i) > 0) then
-	             ig = this_block%i_glob(i)
+                     ig = this_block%i_glob(i)
                      jg = this_block%j_glob(j)
                      if (KMTG(ig,jg) > puny .and.                      &
                         (ULATG(ig,jg) < shlat/rad_to_deg .or.          &
                          ULATG(ig,jg) > nhlat/rad_to_deg) )            & 
- 	                 nocn(n) = nocn(n) + flat(ig,jg)
+                          nocn(n) = nocn(n) + flat(ig,jg)
                   endif
                end do
             endif

cicecore/shared/ice_arrays_column.F90

@@ -268,7 +268,7 @@ module ice_arrays_column
       real (kind=dbl_kind), dimension(:), allocatable, public :: &
          R_C2N     ,      & ! algal C to N (mole/mole)
          R_chl2N   ,      & ! 3 algal chlorophyll to N (mg/mmol)
-	 R_Si2N             ! silica to nitrogen mole ratio for algal groups
+         R_Si2N             ! silica to nitrogen mole ratio for algal groups
 
 !=======================================================================
 

cicecore/shared/ice_constants.F90

@@ -60,7 +60,7 @@ module ice_constants
         c180 = 180.0_dbl_kind, &
         c360 = 360.0_dbl_kind, &
         c365 = 365.0_dbl_kind, &
-	c400 = 400.0_dbl_kind, &
+        c400 = 400.0_dbl_kind, &
         c1000= 1000.0_dbl_kind, &
         c3600= 3600.0_dbl_kind, &
         p001 = 0.001_dbl_kind, &

cicecore/shared/ice_spacecurve.F90

@@ -31,7 +31,7 @@ module ice_spacecurve
 ! !PUBLIC MEMBER FUNCTIONS: 
 
    public :: GenSpaceCurve,     &
-	     IsLoadBalanced
+             IsLoadBalanced
 
    public :: Factor,            &
              IsFactorable,      &
@@ -41,24 +41,24 @@ module ice_spacecurve
 
 ! !PRIVATE MEMBER FUNCTIONS:
 
-   private :: map,    		&
-	      PeanoM, 		&
-	      Hilbert, 		&
-	      Cinco,  		&
+   private :: map,            	&
+              PeanoM,         	&
+              Hilbert,         	&
+              Cinco,          	&
               GenCurve
 
    private :: FirstFactor,      &
               FindandMark
 
    integer(int_kind), dimension(:,:), allocatable ::  &
-	dir,      &! direction to move along each level
+        dir,      &! direction to move along each level
         ordered    ! the ordering 
    integer(int_kind), dimension(:), allocatable ::  &
-	pos        ! position along each of the axes
+        pos        ! position along each of the axes
 
    integer(int_kind) ::  &
-	maxdim,	  &! dimensionality of entire space
-	vcnt       ! visitation count
+        maxdim,	  &! dimensionality of entire space
+        vcnt       ! visitation count
 
    logical           :: verbose=.FALSE. 
 
@@ -80,7 +80,7 @@ recursive function Cinco(l,type,ma,md,ja,jd) result(ierr)
 ! !DESCRIPTION:
 !  This subroutine implements a Cinco space-filling curve.
 !  Cinco curves connect a Nb x Nb block of points where 
-!  		
+!
 !        Nb = 5^p 
 !
 ! !REVISION HISTORY:
@@ -91,12 +91,12 @@ recursive function Cinco(l,type,ma,md,ja,jd) result(ierr)
 ! !INPUT PARAMETERS 
 
    integer(int_kind), intent(in) ::  &
-	l, 	& ! level of the space-filling curve 
+        l, 	& ! level of the space-filling curve 
         type,   & ! type of SFC curve
-	ma,     & ! Major axis [0,1]
-	md,  	& ! direction of major axis [-1,1]
-	ja,	& ! joiner axis [0,1]
-	jd	  ! direction of joiner axis [-1,1]
+        ma,     & ! Major axis [0,1]
+        md,  	& ! direction of major axis [-1,1]
+        ja,	& ! joiner axis [0,1]
+        jd	  ! direction of joiner axis [-1,1]
 
 ! !OUTPUT PARAMETERS
 
@@ -111,12 +111,12 @@ recursive function Cinco(l,type,ma,md,ja,jd) result(ierr)
 !-----------------------------------------------------------------------
 
    integer(int_kind) :: &
-	lma,		&! local major axis (next level)
-	lmd,		&! local major direction (next level)
-	lja,		&! local joiner axis (next level)
-	ljd,		&! local joiner direction (next level)
-	ltype,          &! type of SFC on next level 
-        ll		 ! next level down 
+        lma,        	&! local major axis (next level)
+        lmd,        	&! local major direction (next level)
+        lja,        	&! local joiner axis (next level)
+        ljd,        	&! local joiner direction (next level)
+        ltype,          &! type of SFC on next level 
+        ll        	 ! next level down 
 
    logical     :: debug = .FALSE.
 
@@ -963,8 +963,8 @@ function IncrementCurve(ja,jd) result(ierr)
 
 ! !INPUT PARAMETERS:
      integer(int_kind)  :: &
-	ja, 	&! axis to increment
-	jd	 ! direction along axis
+        ja, 	&! axis to increment
+        jd	 ! direction along axis
 
 ! !OUTPUT PARAMETERS:
      integer(int_kind) :: ierr ! error return code
@@ -975,7 +975,7 @@ function IncrementCurve(ja,jd) result(ierr)
      ! mark the newly visited point
      !-----------------------------
      ordered(pos(0)+1,pos(1)+1) = vcnt
-	
+
      !------------------------------------
      ! increment curve and update position
      !------------------------------------
@@ -1064,20 +1064,20 @@ function  IsLoadBalanced(nelem,npart)
 ! !INTPUT PARAMETERS:
 
    integer(int_kind), intent(in) ::  &
-	nelem,		&  ! number of blocks/elements to partition
-	npart              ! size of partition
+        nelem,		&  ! number of blocks/elements to partition
+        npart              ! size of partition
 
 ! !OUTPUT PARAMETERS:
    logical        :: IsLoadBalanced   ! .TRUE. if a perfectly load balanced 
-				      ! partition is possible
+                                      ! partition is possible
 !EOP
 !BOC
 !-----------------------------------------------------------------------
 !
 !  local variables
 !
 !-----------------------------------------------------------------------
-	
+
    integer(int_kind)   :: tmp1 ! temporary int
 
    character(len=*),parameter :: subname='(IsLoadBalanced)'
@@ -1086,7 +1086,7 @@ function  IsLoadBalanced(nelem,npart)
    tmp1 = nelem/npart
 
    if(npart*tmp1 == nelem ) then 
-	IsLoadBalanced=.TRUE.
+        IsLoadBalanced=.TRUE.
    else
         IsLoadBalanced=.FALSE.
    endif
@@ -1285,7 +1285,7 @@ function Factor(num) result(res)
 !-----------------------------------------------------------------------
 
    integer(int_kind)   ::  &
-	tmp,tmp2,tmp3,tmp5   ! tempories for the factorization algorithm
+        tmp,tmp2,tmp3,tmp5   ! tempories for the factorization algorithm
    integer(int_kind)   :: i,n    ! loop tempories
    logical             :: found  ! logical temporary
    character(len=*),parameter :: subname='(Factor)'
@@ -1437,9 +1437,9 @@ subroutine map(l)
 !-----------------------------------------------------------------------
 
    integer(int_kind)  :: &
-	d, 		 & ! dimension of curve only 2D is supported
-	type,		 & ! type of space-filling curve to start off
-        ierr   		   ! error return code
+        d,         	 & ! dimension of curve only 2D is supported
+        type,        	 & ! type of space-filling curve to start off
+        ierr           	   ! error return code
    character(len=*),parameter :: subname='(map)'
 
    d = SIZE(pos)
@@ -1485,7 +1485,7 @@ subroutine PrintCurve(Mesh)
 !-----------------------------------------------------------------------
      integer(int_kind) ::  &
         gridsize,	   &! order of space-filling curve
-        i		    ! loop temporary
+        i        	    ! loop temporary
      character(len=*),parameter :: subname='(PrintCurve)'
 
 !-----------------------------------------------------------------------
@@ -1523,7 +1523,7 @@ subroutine PrintCurve(Mesh)
         write (*,*) "------------------------------------------"
         do i=1,gridsize
            write(*,6) Mesh(1,i),Mesh(2,i),Mesh(3,i), &
-	    	      Mesh(4,i),Mesh(5,i),Mesh(6,i)
+            	      Mesh(4,i),Mesh(5,i),Mesh(6,i)
         enddo
      else if(gridsize == 8) then
         write (*,*) "A Level 3 Hilbert Curve:"
@@ -1615,7 +1615,7 @@ subroutine PrintCurve(Mesh)
                        Mesh(13,i),Mesh(14,i),Mesh(15,i),Mesh(16,i), &
                        Mesh(17,i),Mesh(18,i),Mesh(19,i),Mesh(20,i), &
                        Mesh(21,i),Mesh(22,i),Mesh(23,i),Mesh(24,i), &
-		       Mesh(25,i)
+                       Mesh(25,i)
         enddo
      else if(gridsize == 27) then
         write (*,*) "A Level 3 Peano Meandering Curve:"
@@ -1683,7 +1683,7 @@ subroutine  GenSpaceCurve(Mesh)
 
 ! !INPUT/OUTPUT PARAMETERS:
    integer(int_kind), target,intent(inout) :: &
-	Mesh(:,:)		! The SFC ordering in 2D array
+        Mesh(:,:)        	! The SFC ordering in 2D array
 
 !EOP
 !BOC
@@ -1694,7 +1694,7 @@ subroutine  GenSpaceCurve(Mesh)
 !-----------------------------------------------------------------------
 
    integer(int_kind) ::  &
-	level,   &! Level of space-filling curve		
+        level,   &! Level of space-filling curve
 	dim       ! dimension of SFC... currently limited to 2D
 
    integer(int_kind) :: gridsize   ! number of points on a side

configuration/scripts/cice.batch.csh

@@ -165,6 +165,34 @@ cat >> ${jobfile} << EOFB
 #SBATCH --qos=standby
 EOFB
 
+else if (${ICE_MACHINE} =~ theia*) then
+cat >> ${jobfile} << EOFB
+#SBATCH -J ${ICE_CASENAME}
+#SBATCH -t ${batchtime}
+#SBATCH -q batch
+#SBATCH -A marine-cpu
+#SBATCH -N ${nnodes}
+#SBATCH -e slurm%j.err
+#SBATCH -o slurm%j.out
+#SBATCH --mail-type END,FAIL
+#SBATCH [email protected]
+EOFB
+
+else if (${ICE_MACHINE} =~ phase2*) then
+cat >> ${jobfile} << EOFB
+# nothing to do
+EOFB
+
+else if (${ICE_MACHINE} =~ phase3*) then
+cat >> ${jobfile} << EOFB
+# nothing to do
+EOFB
+
+else if (${ICE_MACHINE} =~ high_Sierra*) then
+cat >> ${jobfile} << EOFB
+# nothing to do
+EOFB
+
 else if (${ICE_MACHINE} =~ testmachine*) then
 cat >> ${jobfile} << EOFB
 # nothing to do

configuration/scripts/cice.launch.csh

@@ -153,6 +153,33 @@ mpirun -np ${ntasks} ./cice >&! \$ICE_RUNLOG_FILE
 EOFR
 endif
 
+#=======
+else if (${ICE_MACHINE} =~ theia*) then
+cat >> ${jobfile} << EOFR
+#mpirun -np ${ntasks} ./cice >&! \$ICE_RUNLOG_FILE
+srun -n ${ntasks} -c ${nthrds} ./cice >&! \$ICE_RUNLOG_FILE
+#./cice >&! \$ICE_RUNLOG_FILE
+EOFR
+#=======
+else if (${ICE_MACHINE} =~ high_Sierra*) then
+cat >> ${jobfile} << EOFR
+mpirun -np ${ntasks} ./cice >&! \$ICE_RUNLOG_FILE
+#./cice >&! \$ICE_RUNLOG_FILE
+EOFR
+
+#=======
+else if (${ICE_MACHINE} =~ phase2*) then
+cat >> ${jobfile} << EOFR
+mpirun -np ${ntasks} ./cice >&! \$ICE_RUNLOG_FILE
+#./cice >&! \$ICE_RUNLOG_FILE
+EOFR
+
+#=======
+else if (${ICE_MACHINE} =~ phase3*) then
+cat >> ${jobfile} << EOFR
+mpirun -np ${ntasks} ./cice >&! \$ICE_RUNLOG_FILE
+#./cice >&! \$ICE_RUNLOG_FILE
+EOFR
 #=======
 else if (${ICE_MACHINE} =~ testmachine*) then
 cat >> ${jobfile} << EOFR

configuration/scripts/machines/Macros.high_Sierra_gnu

@@ -0,0 +1,47 @@
+#==============================================================================
+# Makefile macros for Travis-CI - GCC and openmpi compilers
+#==============================================================================
+
+CPP        := cpp
+CPPDEFS    := -DFORTRANUNDERSCORE -DNO_R16 -DHAVE_F2008_CONTIGUOUS -DLINUX -DCPRINTEL ${ICE_CPPDEFS}
+CFLAGS     := -c -O2 
+
+FIXEDFLAGS := -132
+FFLAGS     :=  -O2 -ffree-line-length-none -fconvert=big-endian -finit-real=nan
+FFLAGS_NOOPT:= -O0
+
+ifeq ($(ICE_BLDDEBUG), true)
+    #FFLAGS     += -O0 -g -Wextra -fbacktrace -fbounds-check -ffpe-trap=zero,overflow
+    FFLAGS     += -O0 -g -std=f2008 -fbacktrace -fbounds-check -ffpe-trap=zero,overflow
+else
+    FFLAGS     += -O2
+endif
+
+FC := mpif90
+
+MPICC:= 
+
+MPIFC:= mpif90
+LD:= $(FC)
+
+NETCDF_PATH := $(NETCDF)
+
+ifeq ($(ICE_IOTYPE), netcdf)
+    NETCDF_PATH := $(shell nc-config --prefix)
+    INCLDIR := $(INCLDIR) -I$(NETCDF_PATH)/include
+    LIB_NETCDF := $(NETCDF_PATH)/lib
+    LIB_PNETCDF := 
+    SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff
+else
+    SLIBS   := 
+endif
+
+LIB_MPI := 
+SCC:=gcc 
+SFC:= 
+
+#ifeq ($(ICE_THREADED), true) 
+#   LDFLAGS += -fopenmp
+#   CFLAGS += -fopenmp
+#   FFLAGS += -fopenmp
+#endif