add Cgrid-related fixes for nuopc/cmeps

.github/workflows/test-cice.yml

@@ -0,0 +1,135 @@
+name: GHActions
+
+# This workflow is triggered on pushes, pull-requeust, and releases
+# ghactions* branch names will trigger this to support development testing
+# To Do: get it working with bash and ubuntu
+
+on:
+  push:
+    branches:
+      - master
+      - 'CICE*'
+      - 'ghactions*'
+  pull_request:
+  release:
+    types:
+      - created
+
+defaults:
+  run:
+    shell: /bin/csh {0}
+
+jobs:
+  build:
+    name: "CICETesting"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+#        os: [macos-latest, ubuntu-latest]
+        os: [macos-latest]
+#        os: [ubuntu-latest]
+        include: 
+          - os: macos-latest
+            envdef: macos
+            minicond: Miniconda3-latest-MacOSX-x86_64.sh
+#          - os: ubuntu-latest
+#            envdef: linux
+#            minicond: Miniconda3-latest-Linux-x86_64.sh
+    steps:
+      - name: reset macos toolchain to commandlinetools
+        shell: /bin/bash {0}
+        if: contains( matrix.envdef, 'macos')
+        run: |
+          sudo xcode-select -r
+          sudo xcode-select -s /Library/Developer/CommandLineTools
+          echo "xcrun --show-sdk-path: $(xcrun --show-sdk-path)"
+          echo "xcode-select -p: $(xcode-select -p)"
+      - name: system info
+        shell: /bin/bash {0}
+        run: |
+          type wget
+          type curl
+          type csh
+          echo "readlink \$(which csh): $(python -c 'import os, sys; print os.path.realpath(sys.argv[1])' $(which csh))"
+          echo "csh --version: $(csh --version)"
+          echo "uname -a: $(uname -a)"
+          echo "sw_vers: $(sw_vers)"
+          echo "HOME: $HOME"
+          echo "GITHUB_WORKSPACE: $GITHUB_WORKSPACE"
+          echo "OS: ${{ matrix.os }}"
+          echo "ENVDEF: ${{ matrix.envdef }}"
+          echo "MINICOND: ${{ matrix.minicond }}"
+      - name : install miniconda
+        shell: /bin/bash {0}
+        run: |
+          wget https://repo.anaconda.com/miniconda/${{ matrix.minicond }} -O ~/miniconda.sh
+          bash ~/miniconda.sh -b -p $HOME/miniconda
+      - name: clone
+        uses: actions/checkout@v2
+        with:
+          submodules: 'recursive'
+      - name: link
+        run: |
+           ln -s ${GITHUB_WORKSPACE}/../CICE ${HOME}/cice
+#           ls -al ${HOME}/
+#           ls -al ${GITHUB_WORKSPACE}/
+      - name: setup conda env
+        shell: /bin/bash {0}
+        run: |
+          cd $HOME && mkdir -p cice-dirs/runs cice-dirs/baseline cice-dirs/input
+          source $HOME/miniconda/bin/activate
+          conda init tcsh
+          cd $HOME/cice
+          conda env create -f configuration/scripts/machines/environment.yml
+      - name: check conda env
+        run: |
+          conda activate cice && which mpicc && which mpifort && which make
+          mpifort --version
+          mpicc --version
+          make --version
+      - name: check setup case
+        run: |
+          cd $HOME/cice
+          ./cice.setup -m conda -e ${{ matrix.envdef }} -c case0 --pes 1x1 -s diag1
+      - name: check setup test
+        run: |
+          cd $HOME/cice
+          ./cice.setup -m conda -e ${{ matrix.envdef }} --test smoke --testid c0
+#      - name: compile case
+#        run: |
+#          cd $HOME/cice
+#          ./cice.setup -m conda -e ${{ matrix.envdef }} -c case1
+#          cd case1
+#          ./cice.build
+      - name: download input data
+        run: |
+          cd $HOME/cice-dirs/input
+          wget https://zenodo.org/record/3728358/files/CICE_data_gx3_grid_ic-20200320.tar.gz && tar xvfz CICE_data_gx3_grid_ic-20200320.tar.gz
+          wget https://zenodo.org/record/3728362/files/CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz && tar xvfz CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz
+          wget https://zenodo.org/record/3728364/files/CICE_data_gx3_forcing_JRA55-20200320.tar.gz && tar xvfz CICE_data_gx3_forcing_JRA55-20200320.tar.gz
+          pwd
+          ls -alR
+#      - name: run case
+#        run: |
+#          cd $HOME/cice
+#          cd case1
+#          ./cice.run
+      - name: run suite
+        run: |
+          cd $HOME/cice
+          ./cice.setup -m conda -e ${{ matrix.envdef }} --suite travis_suite --testid ${{ matrix.os }}
+      - name: write output
+        run: |
+          cd $HOME/cice
+          ./.github/workflows/write_logfiles.csh
+          cd testsuite.${{ matrix.os }}
+          ./results.csh
+      - name: successful run
+        if: ${{ success() }}
+        run: |
+          echo "${{ job.name }} PASSED"
+      - name: trap failure
+        if: ${{ failure() }}
+        run: |
+          echo "${{ job.name }} FAILED"
+          exit 99

.github/workflows/write_logfiles.csh

@@ -0,0 +1,10 @@
+#!/bin/csh 
+
+#echo "hello"
+
+foreach logfile (case*/logs/cice.runlog* testsuite.*/*/logs/cice.runlog*)
+  echo "### ${logfile} ###"
+  tail -20 $logfile
+  echo " "
+end
+

.travis.yml

@@ -25,7 +25,11 @@ install:
 
   # Fetch forcing data
   - "wget https://zenodo.org/record/3728362/files/CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz &&
-    tar xvfz CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz -C ~"
+    tar xvfz CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz -C ~" 
+
+  # Fetch jra55_gx3 forcing data
+  - "wget https://zenodo.org/record/3728364/files/CICE_data_gx3_forcing_JRA55-20200320.tar.gz &&
+    tar xvfz CICE_data_gx3_forcing_JRA55-20200320.tar.gz -C ~" 
 
   # Mirror entire data folder
   #- "lftp ftp://anonymous:travis@travis-ci.org@ftp.cgd.ucar.edu 

README.md

@@ -1,4 +1,5 @@
-[![Build Status](https://travis-ci.org/CICE-Consortium/CICE.svg?branch=master)](https://travis-ci.org/CICE-Consortium/CICE)
+[![Travis-CI](https://travis-ci.org/CICE-Consortium/CICE.svg?branch=master)](https://travis-ci.org/CICE-Consortium/CICE)
+[![GHActions](https://github.com/CICE-Consortium/CICE/workflows/GHActions/badge.svg)](https://github.com/CICE-Consortium/CICE/actions)
 [![Documentation Status](https://readthedocs.org/projects/cice-consortium-cice/badge/?version=master)](http://cice-consortium-cice.readthedocs.io/en/master/?badge=master)
 [![lcov](https://img.shields.io/endpoint?url=https://apcraig.github.io/coverage.json)](https://apcraig.github.io)
 

cicecore/cicedynB/analysis/ice_diagnostics.F90

@@ -1561,11 +1561,11 @@ subroutine print_state(plabel,i,j,iblk)
 
       real (kind=dbl_kind) :: &
            eidebug, esdebug, &
-           qi, qs, Tsnow, &
+           qi, qs, Tsnow, si, &
            rad_to_deg, puny, rhoi, lfresh, rhos, cp_ice
 
       integer (kind=int_kind) :: n, k, nt_Tsfc, nt_qice, nt_qsno, nt_fsd, &
-           nt_isosno, nt_isoice
+           nt_isosno, nt_isoice, nt_sice
 
       logical (kind=log_kind) :: tr_fsd, tr_iso
 
@@ -1576,7 +1576,7 @@ subroutine print_state(plabel,i,j,iblk)
 
       call icepack_query_tracer_flags(tr_fsd_out=tr_fsd, tr_iso_out=tr_iso)
       call icepack_query_tracer_indices(nt_Tsfc_out=nt_Tsfc, nt_qice_out=nt_qice, &
-           nt_qsno_out=nt_qsno, nt_fsd_out=nt_fsd, &
+           nt_qsno_out=nt_qsno, nt_sice_out=nt_sice, nt_fsd_out=nt_fsd, &
            nt_isosno_out=nt_isosno, nt_isoice_out=nt_isoice)
       call icepack_query_parameters( &
            rad_to_deg_out=rad_to_deg, puny_out=puny, rhoi_out=rhoi, lfresh_out=lfresh, &
@@ -1621,7 +1621,6 @@ subroutine print_state(plabel,i,j,iblk)
 
       enddo                     ! n
 
-
       eidebug = c0
       do n = 1,ncat
          do k = 1,nilyr
@@ -1654,6 +1653,14 @@ subroutine print_state(plabel,i,j,iblk)
       write(nu_diag,*) 'qsnow(i,j)',esdebug
       write(nu_diag,*) ' '
 
+      do n = 1,ncat
+         do k = 1,nilyr
+            si = trcrn(i,j,nt_sice+k-1,n,iblk)
+            write(nu_diag,*) 'sice, cat ',n,' layer ',k, si
+         enddo
+      enddo
+      write(nu_diag,*) ' '
+
       write(nu_diag,*) 'uvel(i,j)',uvel(i,j,iblk)
       write(nu_diag,*) 'vvel(i,j)',vvel(i,j,iblk)
 

cicecore/cicedynB/analysis/ice_history.F90

@@ -925,12 +925,12 @@ subroutine init_hist (dt)
              ns1, f_strinty)
 
          call define_hist_field(n_taubx,"taubx","N/m^2",ustr2D, ucstr,   &
-             "basal (seabed) stress (x)",                                &
+             "seabed (basal) stress (x)",                                &
              "positive is x direction on U grid", c1, c0,                &
              ns1, f_taubx)
 
          call define_hist_field(n_tauby,"tauby","N/m^2",ustr2D, ucstr,   &
-             "basal (seabed) stress (y)",                                &
+             "seabed (basal) stress (y)",                                &
              "positive is y direction on U grid", c1, c0,                &
              ns1, f_tauby)
 

cicecore/cicedynB/analysis/ice_history_bgc.F90

@@ -267,7 +267,7 @@ module ice_history_bgc
       subroutine init_hist_bgc_2D
 
       use ice_broadcast, only: broadcast_scalar
-      use ice_calendar, only: nstreams
+      use ice_calendar, only: nstreams, histfreq
       use ice_communicate, only: my_task, master_task
       use ice_history_shared, only: tstr2D, tcstr, define_hist_field, &
           f_fsalt, f_fsalt_ai, f_sice
@@ -781,6 +781,7 @@ subroutine init_hist_bgc_2D
     if (tr_iso .or. tr_aero .or. tr_brine .or. solve_zsal .or. skl_bgc) then
 
     do ns = 1, nstreams
+       if (histfreq(ns) /= 'x') then
 
       if (f_iso(1:1) /= 'x') then
          do n=1,n_iso
@@ -1780,6 +1781,7 @@ subroutine init_hist_bgc_2D
              "distance from ice bottom to brine surface", c1, c0,       &
              ns, f_hbri)
 
+       endif ! histfreq(ns) /= 'x'
     enddo ! nstreams
 
     endif ! tr_aero, etc 
@@ -1790,7 +1792,7 @@ end subroutine init_hist_bgc_2D
 
       subroutine init_hist_bgc_3Dc
 
-      use ice_calendar, only: nstreams
+      use ice_calendar, only: nstreams, histfreq
       use ice_history_shared, only: tstr3Dc, tcstr, define_hist_field
 
       integer (kind=int_kind) :: ns
@@ -1802,26 +1804,27 @@ subroutine init_hist_bgc_3Dc
       if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
          file=__FILE__, line=__LINE__)
 
-    if (tr_brine) then
+      if (tr_brine) then
 
       ! 3D (category) variables must be looped separately
       do ns = 1, nstreams
-        if (f_fbri(1:1) /= 'x') &
-         call define_hist_field(n_fbri,"fbrine","1",tstr3Dc, tcstr, &
+         if (histfreq(ns) /= 'x') then
+           if (f_fbri(1:1) /= 'x') &
+           call define_hist_field(n_fbri,"fbrine","1",tstr3Dc, tcstr, &
              "brine tracer fraction of ice volume, cat",             &
-             "none", c1, c0,       &
-             ns, f_fbri)
+             "none", c1, c0, ns, f_fbri)
+         endif ! histfreq /= 'x'
       enddo ! ns
 
-    endif
+      endif ! tr_brine
 
       end subroutine init_hist_bgc_3Dc
 
 !=======================================================================
 
       subroutine init_hist_bgc_3Db
 
-      use ice_calendar, only: nstreams
+      use ice_calendar, only: nstreams,histfreq
       use ice_history_shared, only: tstr3Db, tcstr, define_hist_field
 
       integer (kind=int_kind) :: ns
@@ -1841,6 +1844,7 @@ subroutine init_hist_bgc_3Db
     if (z_tracers .or. solve_zsal) then
 
       do ns = 1, nstreams
+         if (histfreq(ns) /= 'x') then
 
          if (f_bTin(1:1) /= 'x') &
             call define_hist_field(n_bTin,"bTizn","C",tstr3Db, tcstr, &
@@ -1873,6 +1877,7 @@ subroutine init_hist_bgc_3Db
                 "internal ice PAR", "on bio interface grid", c1, c0, &
                 ns, f_zfswin)
 
+         endif ! histfreq(ns) /= 'x'
       enddo  ! ns
 
     endif  ! z_tracers or solve_zsal
@@ -2012,9 +2017,10 @@ subroutine accum_hist_bgc (iblk)
       ! increment field
       !---------------------------------------------------------------
 
-    if (tr_iso .or. tr_aero .or. tr_brine .or. solve_zsal .or. skl_bgc) then
-      ! 2d bgc fields
+    ! 2d bgc fields
+    if (allocated(a2D)) then
 
+    if (tr_iso .or. tr_aero .or. tr_brine .or. solve_zsal .or. skl_bgc) then
 
       ! zsalinity
       if (f_fzsal  (1:1) /= 'x') &  
@@ -2635,19 +2641,22 @@ subroutine accum_hist_bgc (iblk)
          call accum_hist_field(n_hbri,     iblk, &
                         hbri(:,:,iblk), a2D)
 
-    endif  ! 2d bgc tracers, tr_aero, tr_brine, solve_zsal, skl_bgc
-
+    endif ! 2d bgc tracers, tr_aero, tr_brine, solve_zsal, skl_bgc
+    endif ! allocated(a2D)
 
       ! 3D category fields
 
+    if (allocated(a3Dc)) then
     if (tr_brine) then
       ! 3Dc bgc category fields
 
       if (f_fbri   (1:1) /= 'x') &
          call accum_hist_field(n_fbri-n2D, iblk, ncat_hist, &
                                trcrn(:,:,nt_fbri,1:ncat_hist,iblk), a3Dc)
     endif
+    endif ! allocated(a3Dc)
 
+    if (allocated(a3Db)) then
     if (z_tracers .or. solve_zsal) then
       ! 3Db category fields
 
@@ -2754,8 +2763,10 @@ subroutine accum_hist_bgc (iblk)
                                   workz(:,:,1:nzblyr), a3Db)
       endif
 
-    endif  ! 3Db fields
+    endif ! 3Db fields
+    endif ! allocated(a3Db)
 
+    if (allocated(a3Da)) then
     if (z_tracers) then
       ! 3Da category fields
 
@@ -3189,15 +3200,16 @@ subroutine accum_hist_bgc (iblk)
                                   workz2(:,:,1:nzalyr), a3Da)
       endif
 
-    endif   ! z_tracers, 3Da tracers
+      endif ! z_tracers, 3Da tracers
+      endif ! allocated(a3Da)
 
       end subroutine accum_hist_bgc
 
 !=======================================================================
 
       subroutine init_hist_bgc_3Da
 
-      use ice_calendar, only: nstreams
+      use ice_calendar, only: nstreams, histfreq
       use ice_history_shared, only: tstr3Da, tcstr, define_hist_field
 
       integer (kind=int_kind) :: ns, n
@@ -3216,6 +3228,7 @@ subroutine init_hist_bgc_3Da
     if (z_tracers) then
 
     do ns = 1, nstreams
+       if (histfreq(ns) /= 'x') then
 
 !----------------------------------------------------------------------------
 ! snow+bio grid ==>
@@ -3439,6 +3452,7 @@ subroutine init_hist_bgc_3Da
                 "other bulk nitrogen pool in cat 1", "snow+bio grid", c1, c0, &
                 ns, f_bgc_PON_cat1)
 
+       endif ! histfreq(ns) /= 'x'
     enddo  !ns
 
     endif ! z_tracers