Merge remote-tracking branch 'Consortium/master' into feature/updcice

.github/workflows/test-icepack.yml

@@ -115,7 +115,7 @@ jobs:
       - name: run suite
         run: |
           cd $HOME/icepack
-          ./icepack.setup -m conda -e ${{ matrix.envdef }} --suite travis_suite --testid ${{ matrix.os }}
+          ./icepack.setup -m conda -e ${{ matrix.envdef }} --suite travis_suite,io_suite --testid ${{ matrix.os }}
       - name: write output
         run: |
           cd $HOME/icepack

.travis.yml

@@ -31,7 +31,7 @@ script:
   - "./icepack.setup --case trcase --mach travisCI --env gnu --pes 1x1 -s diag1 && sleep 4"
   - "./icepack.setup --test smoke --testid trtest --mach travisCI --env gnu 
     --pes 1x1 -s diag1 && sleep 4"
-  - "./icepack.setup --suite travis_suite --testid travisCItest 
+  - "./icepack.setup --suite travis_suite,io_suite --testid travisCItest 
     --mach travisCI --env gnu &&
     cd testsuite.travisCItest &&
     ./results.csh"

columnphysics/version.txt

@@ -1 +1 @@
-ICEPACK 1.2.5
+ICEPACK 1.3.0

configuration/driver/icedrv_RunMod.F90

@@ -35,6 +35,7 @@ subroutine icedrv_run
       use icedrv_forcing, only: get_forcing, get_wave_spec
       use icedrv_forcing_bgc, only: faero_default, fiso_default, get_forcing_bgc
       use icedrv_flux, only: init_flux_atm_ocn
+      use icedrv_history, only: history_cdf, history_close
 
       logical (kind=log_kind) :: skl_bgc, z_tracers, tr_aero, tr_zaero, &
                                  wave_spec, tr_fsd, tr_iso
@@ -61,7 +62,10 @@ subroutine icedrv_run
 
          call calendar(time)    ! at the end of the timestep
 
-         if (stop_now >= 1) exit timeLoop
+         if (stop_now >= 1) then
+            if (history_cdf) call history_close()
+            exit timeLoop
+         endif
 
          call icepack_query_parameters(skl_bgc_out=skl_bgc, z_tracers_out=z_tracers,&
                                        wave_spec_out=wave_spec)
@@ -97,6 +101,7 @@ subroutine ice_step
       use icedrv_diagnostics_bgc, only: hbrine_diags, zsal_diags, bgc_diags
       use icedrv_flux, only: init_history_therm, init_history_bgc, &
           daidtt, daidtd, dvidtt, dvidtd, dagedtt, dagedtd, init_history_dyn
+      use icedrv_history, only: history_cdf, history_write
       use icedrv_restart, only: dumpfile, final_restart
       use icedrv_restart_bgc, only: write_restart_bgc
       use icedrv_step, only: prep_radiation, step_therm1, step_therm2, &
@@ -219,6 +224,10 @@ subroutine ice_step
          if (skl_bgc .or. z_tracers)  call bgc_diags
          if (tr_brine)                call hbrine_diags
       endif
+
+      if (history_cdf) then
+         call history_write()
+      endif
 
       if (write_restart == 1) then
          call dumpfile     ! core variables for restarting

configuration/driver/icedrv_calendar.F90

@@ -72,6 +72,7 @@ module icedrv_calendar
       real (kind=dbl_kind), public :: &
          dt             , & ! thermodynamics timestep (s)
          dt_dyn         , & ! dynamics/transport/ridging timestep (s)
+         time0          , & ! total elapsed time at istep0 for idate0 (s)
          time           , & ! total elapsed time (s)
          time_forc      , & ! time of last forcing update (s)
          yday           , & ! day of the year
@@ -123,6 +124,7 @@ subroutine init_calendar
       !-----------------------------------------------------------------
 
       istep = 0         ! local timestep number
+      time0=istep0*dt   ! start time
       time=istep0*dt    ! s
       yday=c0           ! absolute day number
       mday=0            ! day of the month

configuration/driver/icedrv_init.F90

@@ -62,6 +62,7 @@ subroutine input_data
       use icedrv_calendar, only: year_init, istep0
       use icedrv_calendar, only: dumpfreq, diagfreq, dump_last
       use icedrv_calendar, only: npt, dt, ndtd, days_per_year, use_leap_years
+      use icedrv_history, only: history_cdf
       use icedrv_restart_shared, only: restart, restart_dir, restart_file
       use icedrv_flux, only: update_ocn_f, l_mpond_fresh, cpl_bgc
       use icedrv_flux, only: default_season
@@ -129,7 +130,7 @@ subroutine input_data
         dt,             npt,            ndtd,            dump_last,     &
         ice_ic,         restart,        restart_dir,     restart_file,  &
         dumpfreq,       diagfreq,       diag_file,       cpl_bgc,       &
-        conserv_check
+        conserv_check,  history_cdf
 
       namelist /grid_nml/ &
         kcatbound
@@ -248,6 +249,7 @@ subroutine input_data
       restart = .false.      ! if true, read restart files for initialization
       restart_dir  = './'    ! write to executable dir for default
       restart_file = 'iced'  ! restart file name prefix
+      history_cdf = .false.  ! history netcdf file flag
       ice_ic       = 'default'      ! initial conditions are specified in the code
                                     ! otherwise, the filename for reading restarts
       ndtd = 1               ! dynamic time steps per thermodynamic time step
@@ -292,55 +294,111 @@ subroutine input_data
 
       open (nu_nml, file=nml_filename, status='old',iostat=nml_error)
       if (nml_error /= 0) then
-         nml_error = -1
-      else
-         nml_error =  1
+         write(ice_stdout,*) 'error opening namelist file '//trim(nml_filename)
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
       endif
+      close(nu_nml)
 
-      do while (nml_error > 0)
-         print*,'Reading namelist file   ',nml_filename
+      print*,'Reading namelist file   ',nml_filename
 
-         print*,'Reading setup_nml'
+      open (nu_nml, file=nml_filename, status='old',iostat=nml_error)
+      nml_error =  1
+      print*,'Reading setup_nml'
+      do while (nml_error > 0)
          read(nu_nml, nml=setup_nml,iostat=nml_error)
-         if (nml_error /= 0) exit
+      end do
+      if (nml_error /= 0) then
+         write(ice_stdout,*) 'error reading namelist'
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
+      endif
+      close(nu_nml)
 
-         print*,'Reading grid_nml'
+      open (nu_nml, file=nml_filename, status='old',iostat=nml_error)
+      nml_error =  1
+      print*,'Reading grid_nml'
+      do while (nml_error > 0)
          read(nu_nml, nml=grid_nml,iostat=nml_error)
-         if (nml_error /= 0) exit
+      end do
+      if (nml_error /= 0) then
+         write(ice_stdout,*) 'error reading namelist'
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
+      endif
+      close(nu_nml)
 
-         print*,'Reading tracer_nml'
+      open (nu_nml, file=nml_filename, status='old',iostat=nml_error)
+      nml_error =  1
+      print*,'Reading tracer_nml'
+      do while (nml_error > 0)
          read(nu_nml, nml=tracer_nml,iostat=nml_error)
-         if (nml_error /= 0) exit
+      end do
+      if (nml_error /= 0) then
+         write(ice_stdout,*) 'error reading namelist'
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
+      endif
+      close(nu_nml)
 
-         print*,'Reading thermo_nml'
+      open (nu_nml, file=nml_filename, status='old',iostat=nml_error)
+      nml_error =  1
+      print*,'Reading thermo_nml'
+      do while (nml_error > 0)
          read(nu_nml, nml=thermo_nml,iostat=nml_error)
-         if (nml_error /= 0) exit
+      end do
+      if (nml_error /= 0) then
+         write(ice_stdout,*) 'error reading namelist'
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
+      endif
+      close(nu_nml)
 
-         print*,'Reading shortwave_nml'
+      open (nu_nml, file=nml_filename, status='old',iostat=nml_error)
+      nml_error =  1
+      print*,'Reading shortwave_nml'
+      do while (nml_error > 0)
          read(nu_nml, nml=shortwave_nml,iostat=nml_error)
-         if (nml_error /= 0) exit
+      end do
+      if (nml_error /= 0) then
+         write(ice_stdout,*) 'error reading namelist'
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
+      endif
+      close(nu_nml)
 
-         print*,'Reading ponds_nml'
+      open (nu_nml, file=nml_filename, status='old',iostat=nml_error)
+      nml_error =  1
+      print*,'Reading ponds_nml'
+      do while (nml_error > 0)
          read(nu_nml, nml=ponds_nml,iostat=nml_error)
-         if (nml_error /= 0) exit
+      end do
+      if (nml_error /= 0) then
+         write(ice_stdout,*) 'error reading namelist'
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
+      endif
+      close(nu_nml)
 
-         if (tr_snow) then
-            print*,'Reading snow_nml'
+      if (tr_snow) then
+         open (nu_nml, file=nml_filename, status='old',iostat=nml_error)
+         nml_error =  1
+         print*,'Reading snow_nml'
+         do while (nml_error > 0)
             read(nu_nml, nml=snow_nml,iostat=nml_error)
-            if (nml_error /= 0) exit
+         end do
+         if (nml_error /= 0) then
+            write(ice_stdout,*) 'error reading namelist'
+            call icedrv_system_abort(file=__FILE__,line=__LINE__)
          endif
+         close(nu_nml)
+      endif
 
-         print*,'Reading forcing_nml'
+      open (nu_nml, file=nml_filename, status='old',iostat=nml_error)
+      nml_error =  1
+      print*,'Reading forcing_nml'
+      do while (nml_error > 0)
          read(nu_nml, nml=forcing_nml,iostat=nml_error)
-         if (nml_error /= 0) exit
       end do
-      if (nml_error == 0) close(nu_nml)
       if (nml_error /= 0) then
          write(ice_stdout,*) 'error reading namelist'
          call icedrv_system_abort(file=__FILE__,line=__LINE__)
       endif
       close(nu_nml)
-      
+
       !-----------------------------------------------------------------
       ! set up diagnostics output and resolve conflicts
       !-----------------------------------------------------------------
@@ -558,6 +616,7 @@ subroutine input_data
                                trim(restart_dir)
          write(nu_diag,*)    ' restart_file              = ', &
                                trim(restart_file)
+         write(nu_diag,1010) ' history_cdf               = ', history_cdf
          write(nu_diag,*)    ' ice_ic                    = ', &
                                trim(ice_ic)
          write(nu_diag,1010) ' conserv_check             = ', conserv_check

configuration/driver/icedrv_init_column.F90

@@ -1008,20 +1008,20 @@ subroutine init_zbgc
 
       open (nu_nml, file=trim(nml_filename), status='old',iostat=nml_error)
       if (nml_error /= 0) then
-         nml_error = -1
-      else
-         nml_error =  1
+         print*,'error opening zbgc namelist file '//trim(nml_filename)
+         call icedrv_system_abort(file=__FILE__,line=__LINE__)
       endif 
 
+      nml_error =  1
       print*,'Reading zbgc_nml'
       do while (nml_error > 0)
          read(nu_nml, nml=zbgc_nml,iostat=nml_error)
       end do
-      if (nml_error == 0) close(nu_nml)
       if (nml_error /= 0) then
          print*,'error reading zbgc namelist'
          call icedrv_system_abort(file=__FILE__,line=__LINE__)
       endif
+      close(nu_nml)
 
       !-----------------------------------------------------------------
       ! resolve conflicts

configuration/scripts/Makefile

@@ -68,6 +68,7 @@ OBJS  := $(addsuffix .o, $(sort $(basename $(notdir $(SRCS)))))
 DEPS  := $(addsuffix .d, $(sort $(basename $(notdir $(SRCS)))))
 INCS  := $(patsubst %,-I%, $(VPATH) )
 RM    := rm
+MODDIR:= -I.
 
 .SUFFIXES:
 .SUFFIXES: .F90 .F .c .o
@@ -95,15 +96,16 @@ db_files:
 	@echo "* VPATH   := $(VPATH)"
 	@echo "* SRCFILE := $(SRCFILE)"
 	@echo "* INCS    := $(INCS)"
+	@echo "* MODDIR  := $(MODDIR)"
 	@echo "* SRCS    := $(SRCS)"
 	@echo "* OBJS    := $(OBJS)"
 	@echo "* DEPS    := $(DEPS)"
 db_flags:
 	@echo " "
-	@echo "* cpp     := $(CPP) $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR)"
-	@echo "* cc      := cc -c $(CFLAGS) $(INCS) $(INCLDIR)"
-	@echo "* .F.o    := $(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(INCS) $(INCLDIR)"
-	@echo "* .F90.o  := $(FC) -c $(FFLAGS) $(FREEFLAGS) $(INCS) $(INCLDIR)"
+	@echo "* cpp     := $(CPP) $(CPPFLAGS) $(CPPDEFS) $(INCLDIR)"
+	@echo "* cc      := $(CC) -c $(CFLAGS) $(INCLDIR)"
+	@echo "* .F.o    := $(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(INCLDIR)"
+	@echo "* .F90.o  := $(FC) -c $(FFLAGS) $(FREEFLAGS) $(MODDIR) $(INCLDIR)"
 
 #-------------------------------------------------------------------------------
 # build rule for makdep: MACFILE, cmd-line, or env vars must provide
@@ -121,13 +123,13 @@ $(EXEC): $(OBJS)
 	$(LD) -o $(EXEC) $(LDFLAGS) $(OBJS) $(ULIBS) $(SLIBS)
 
 .c.o:
-	cc $(CFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $<
+	$(CC) $(CFLAGS) $(CPPDEFS) $(INCLDIR) $<
 
 .F.o:
-	$(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $<
+	$(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(CPPDEFS) $(INCLDIR) $<
 
 .F90.o:
-	$(FC) -c $(FFLAGS) $(FREEFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $<
+	$(FC) -c $(FFLAGS) $(FREEFLAGS) $(CPPDEFS) $(MODDIR) $(INCLDIR) $<
 
 mostlyclean:
 	$(RM) -f *.f *.f90 

configuration/scripts/icepack.build

@@ -26,6 +26,10 @@ cd ${ICE_OBJDIR}
 
 setenv ICE_CPPDEFS "${ICE_CPPDEFS} -DNXGLOB=${ICE_NXGLOB} -DNICELYR=${NICELYR} -DNSNWLYR=${NSNWLYR} -DNICECAT=${NICECAT} -DNFSDCAT=${NFSDCAT} -DTRAGE=${TRAGE} -DTRFY=${TRFY} -DTRLVL=${TRLVL} -DTRPND=${TRPND} -DTRSNOW=${TRSNOW} -DTRBRI=${TRBRI} -DNTRISO=${NTRISO} -DNTRAERO=${NTRAERO}  -DTRZS=${TRZS} -DNBGCLYR=${NBGCLYR} -DTRALG=${TRALG} -DTRBGCZ=${TRBGCZ} -DTRDOC=${TRDOC} -DTRDOC=${TRDOC} -DTRDIC=${TRDIC} -DTRDON=${TRDON} -DTRFED=${TRFED} -DTRFEP=${TRFEP} -DTRZAERO=${TRZAERO} -DTRBGCS=${TRBGCS} "
 
+if (${ICE_IOTYPE} == 'netcdf') then
+  setenv ICE_CPPDEFS "${ICE_CPPDEFS} -DUSE_NETCDF"
+endif
+
 ### List of source code directories (in order of importance).
 cat >! Filepath << EOF
 ${ICE_SANDBOX}/configuration/driver

configuration/scripts/icepack_in

@@ -13,6 +13,7 @@
     dump_last      = .false.
     diagfreq       = 24
     diag_file      = 'ice_diag'
+    history_cdf    = .false.
     cpl_bgc        = .false.
     conserv_check  = .false.
 /

configuration/scripts/machines/Macros.badger_intel

@@ -24,28 +24,23 @@ CC := $(SCC)
 FC := $(SFC)
 LD := $(FC)
 
-# set in Macros file
-NETCDF_PATH := /usr/projects/climate/SHARED_CLIMATE/software/conejo/netcdf/3.6.3/intel-13.0.1
-PNETCDF_PATH := /usr/projects/climate/SHARED_CLIMATE/software/conejo/parallel-netcdf/1.3.1/intel-13.0.1/openmpi-1.6.3
-#LAPACK_LIBDIR := /glade/apps/opt/lapack/3.4.2/intel/12.1.5/lib
+NETCDF_PATH := /usr/projects/hpcsoft/toss3/common/netcdf/4.4.0_intel-18.0.5
+PNETCDF_PATH := /usr/projects/hpcsoft/toss3/badger/netcdf/4.4.0_intel-18.0.5_openmpi-2.1.2
 
 PIO_CONFIG_OPTS:= --enable-filesystem-hints=gpfs 
 
 ifeq ($(ICE_IOTYPE), netcdf)
-  INCLDIR := $(INCLDIR) -I$(NETCDF_PATH)/include
-#  INCLDIR := $(INCLDIR) -I/usr/projects/climate/SHARED_CLIMATE/software/conejo/netcdf/3.6.3/intel-13.0.1/include
+  INCLDIR := $(INCLDIR) -I$(NETCDF_PATH)/include -I$(PNETCDF_PATH)/include
 
   LIB_NETCDF := $(NETCDF_PATH)/lib
   LIB_PNETCDF := $(PNETCDF_PATH)/lib
   LIB_MPI := $(IMPILIBDIR)
 
-  #SLIBS   := -L$(LIB_NETCDF) -lnetcdf -L$(LIB_PNETCDF) -lpnetcdf -L$(LAPACK_LIBDIR) -llapack -lblas
-  SLIBS   := -L$(LIB_NETCDF) -lnetcdf -L$(LIB_PNETCDF) -lpnetcdf 
+  SLIBS   := -L$(LIB_NETCDF) -lnetcdf -L$(LIB_PNETCDF) -lnetcdff 
 else
   SLIBS   := 
 endif
 
-
 ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -qopenmp
    CFLAGS += -qopenmp

configuration/scripts/machines/Macros.conda_macos

@@ -26,6 +26,9 @@ CC := $(SCC)
 FC := $(SFC)
 LD := $(FC)
 
+# Location of the compiled Fortran modules (NetCDF)
+MODDIR  += -I$(CONDA_PREFIX)/include
+
 # Location of the system C header files (required on recent macOS to compile makdep)
 SDKPATH = $(shell xcrun --show-sdk-path)
 ifeq ($(strip $(SDKPATH)),)
@@ -35,6 +38,9 @@ else
   LD += -L$(SDKPATH)/usr/lib
 endif
 
+# Libraries to be passed to the linker
+SLIBS   := -L$(CONDA_PREFIX)/lib -lnetcdf -lnetcdff
+
 # Necessary flag to compile with OpenMP support
 ifeq ($(ICE_THREADED), true)
    LDFLAGS += -fopenmp