DRAFT: Refactoring

.github/workflows/fesom2_icepack.yml → .github/inactive_workflows/fesom2_icepack.yml

@@ -1,18 +1,18 @@
 
 name: FESOM2_icepack
 
-# Controls when the action will run. Triggers the workflow on push or pull request.
+# Controls when the action will run. Triggers the workflow on push or pull request. 
 
 on: [push, pull_request]
 
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  gfortran_ubuntu:
+  icepack_test:
     # Containers must run in Linux based operating systems
     runs-on: ubuntu-latest
     # Docker Hub image that `container-job` executes in
-    container: koldunovn/fesom2_test:fesom2.1
+    container: koldunovn/fesom2_test:refactoring2
 
     # Service containers to run with `gfortran_ubuntu`
     steps:

.github/workflows/fesom2.1.yml

@@ -1,31 +1,40 @@
 
 name: FESOM2 main test
 
-# Controls when the action will run. Triggers the workflow on push or pull request.
+# Controls when the action will run. Triggers the workflow on push or pull request. 
 
 on: [push, pull_request]
 
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  gfortran_ubuntu:
+  general_test:
     # Containers must run in Linux based operating systems
     runs-on: ubuntu-latest
     # Docker Hub image that `container-job` executes in
-    container: koldunovn/fesom2_test:fesom2.1
+    container: koldunovn/fesom2_test:refactoring2
 
     # Service containers to run with `gfortran_ubuntu`
     steps:
     # NK: this changes working directory to fesom2
     - uses: actions/checkout@v2
 
-    - name: Compile model
+    - name: Compile model (binary)
       run: |
         bash -l configure.sh ubuntu
-
+
+    - name: Compile model (library)
+      run: |
+        bash ./test/ifs_interface/configure_lib.sh -l
+
+    - name: Library exists
+      run: |
+        bash ./test/ifs_interface/check_exist.sh
+
     - name: Create global test run
       run: |
         mkrun pi test_pi -m docker
+
     - name: FESOM2 global test run
       run: |    
         cd work_pi
@@ -35,15 +44,22 @@ jobs:
       run: |
         cd work_pi
         fcheck .
-
+
+    - name: Check restarts
+      run: |
+        cd work_pi
+        ./job_docker_new
+
     - name: Create channel test run
       run: |
         mkrun souf test_souf -m docker
+
     - name: FESOM2 channel test run
       run: |    
         cd work_souf
         chmod +x job_docker_new
         ./job_docker_new
+
     - name: Check channel  results
       run: |
         cd work_souf
@@ -53,6 +69,7 @@ jobs:
       run: |
         cd mesh_part
         bash -l configure.sh ubuntu
+
     - name: Run partitioner
       run: |
         cd work_pi

.github/workflows/fesom2_openmp.yml

@@ -0,0 +1,49 @@
+
+name: FESOM2 OpenMP test
+
+# Controls when the action will run. Triggers the workflow on push or pull request. 
+
+on: [push, pull_request]
+
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  openmp_test:
+    # Containers must run in Linux based operating systems
+    runs-on: ubuntu-latest
+    # Docker Hub image that `container-job` executes in
+    container: koldunovn/fesom2_test:refactoring2
+
+    # Service containers to run with `gfortran_ubuntu`
+    steps:
+    # NK: this changes working directory to fesom2
+    - uses: actions/checkout@v2
+
+    - name: switch OpenMP ON
+      run: |
+        cd ./src/
+        sed -i 's/with OpenMP\" OFF/with OpenMP\" ON/g' CMakeLists.txt
+        cd ../
+
+    - name: Compile model
+      run: |
+        bash -l configure.sh ubuntu
+
+    - name: Create global test run with 4 OpenMP threads
+      run: |
+        mkrun pi test_pi -m docker
+        cd work_pi
+        sed -i 's/THREADS=1/THREADS=4/g' job_docker_new
+        cd ../
+
+    - name: FESOM2 global test run
+      run: |    
+        cd work_pi
+        chmod +x job_docker_new
+        ./job_docker_new
+
+
+
+
+
+

.gitignore

@@ -1,10 +1,14 @@
 /build
+/build.lib
 *.o
 *.mod
 *.x
 #*.out
 *~
 *.swp
 src/icepack_drivers/Icepack
+lib/*.a
+lib/*.so
 /work_*
 Makefile.in
+mesh_part/build

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.4)
+cmake_minimum_required(VERSION 3.9)
 
 # set default build type cache entry (do so before project(...) is called, which would create this cache entry on its own)
 if(NOT CMAKE_BUILD_TYPE)
@@ -7,11 +7,13 @@ if(NOT CMAKE_BUILD_TYPE)
 endif()
 
 project(FESOM2.0)
+option(BUILD_SHARED_LIBS "Build using shared libraries" OFF) # cmake-internal switch to toggle if library targets are being build as STATIC or SHARED, see https://cmake.org/cmake/help/latest/guide/tutorial/Selecting%20Static%20or%20Shared%20Libraries.html
 set(TOPLEVEL_DIR ${CMAKE_CURRENT_LIST_DIR})
 set(FESOM_COUPLED OFF CACHE BOOL "compile fesom standalone or with oasis support (i.e. coupled)")
 set(OIFS_COUPLED OFF CACHE BOOL "compile fesom coupled to OpenIFS. (Also needs FESOM_COUPLED to work)")
 set(CRAY OFF CACHE BOOL "compile with cray ftn")
 set(USE_ICEPACK OFF CACHE BOOL "compile fesom with the Iceapck modules for sea ice column physics.")
+set(OPENMP_REPRODUCIBLE OFF CACHE BOOL "serialize OpenMP loops that are critical for reproducible results")
 #set(VERBOSE OFF CACHE BOOL "toggle debug output")
 #add_subdirectory(oasis3-mct/lib/psmile)
 add_subdirectory(src)

README.md

@@ -27,3 +27,12 @@ References
 * **[Version coupled with ECHAM6 atmosphere]** Sidorenko, D., Goessling, H. F., Koldunov, N. V., Scholz, P., Danilov, S., Barbi, D., et al ( 2019). Evaluation of FESOM2.0 coupled to ECHAM6.3: Pre‐industrial and HighResMIP simulations. Journal of Advances in Modeling Earth Systems, 11. https://doi.org/10.1029/2019MS001696
 
 * **[Version with ICEPACK sea ice thermodynamics]** Zampieri, Lorenzo, Frank Kauker, Jörg Fröhle, Hiroshi Sumata, Elizabeth C. Hunke, and Helge Goessling. Impact of Sea-Ice Model Complexity on the Performance of an Unstructured-Mesh Sea-ice/ocean Model Under Different Atmospheric Forcings. Washington: American Geophysical Union, 2020. https://dx.doi.org/10.1002/essoar.10505308.1.
+
+Documentation for FESOM2
+************************
+
+Here lives FESOM2 documentation
+
+Rendered version: https://fesom2.readthedocs.io/en/latest/
+
+

config/namelist.config

@@ -23,8 +23,12 @@ ResultPath='../result_tmp/'
 /
 
 &restart_log
-restart_length=1        !only required for d,h,s cases,  y, m take 1
-restart_length_unit='y' !output period: y,  d, h, s 
+restart_length=1            ! --> do netcdf restart ( only required for d,h,s cases, y, m take 1)
+restart_length_unit='y'     !output period: y, d, h, s, off
+raw_restart_length=1        ! --> do core dump restart
+raw_restart_length_unit='y' ! e.g. y, d, h, s, off
+bin_restart_length=1        ! --> do derived type binary restart 
+bin_restart_length_unit='y' ! e.g. y, d, h, s, off
 logfile_outfreq=960     !in logfile info. output frequency, # steps
 /
 
@@ -54,6 +58,7 @@ use_cavity=.false.              !
 use_cavity_partial_cell=.false. 
 use_floatice = .false.
 use_sw_pene=.true.
+flag_debug=.false.
 /
 
 &machine

config/namelist.config.toy_soufflet

@@ -54,6 +54,7 @@ use_floatice = .false.
 use_sw_pene=.false.
 toy_ocean=.true.
 which_toy="soufflet"
+flag_debug=.true.
 /
 
 &machine

config/namelist.cvmix

@@ -13,15 +13,16 @@ tke_min            = 1.0e-6
 ! tke_mxl_choice ... Can only be 1 or 2, choice of calculation of mixing 
 ! length; currently only Blanke, B., P. Delecluse option is implemented
 tke_mxl_choice     = 2     
+tke_dolangmuir     = .false.    
 /
 
-! namelist for IDEMIX
+! namelist for IDEMIX von Pollman et al. (2017)
 &param_idemix
-idemix_tau_v       = 86400.0    ! time scale for vertical symmetrisation (sec)
-idemix_tau_h       = 1296000.0  ! time scale for horizontal symmetrisation
+idemix_tau_v       = 172800.0   ! 2days ! time scale for vertical symmetrisation (sec)
+idemix_tau_h       = 1296000.0  !15days ! time scale for horizontal symmetrisation
 idemix_gamma       = 1.570      ! constant of order one derived from the shape of the spectrum in m space (dimensionless)
-idemix_jstar       = 10.0       ! spectral bandwidth in modes (dimensionless)
-idemix_mu0         = 1.33333333 ! dissipation parameter (dimensionless)
+idemix_jstar       = 5.0        ! spectral bandwidth in modes (dimensionless)
+idemix_mu0         = 0.33333333 ! dissipation parameter (dimensionless)
 idemix_sforcusage  = 0.2
 idemix_n_hor_iwe_prop_iter = 5  ! iterations for contribution from horiz. wave propagation
 idemix_surforc_file = '/work/ollie/clidyn/forcing/IDEMIX/fourier_smooth_2005_cfsr_inert_rgrid.nc'

config/namelist.dyn

@@ -0,0 +1,23 @@
+&dynamics_visc
+visc_gamma0  = 0.003 ! [m/s],   backgroung viscosity= gamma0*len, it should be as small a s possible (keep it < 0.01 m/s).
+visc_gamma1  = 0.1   ! [nodim], for computation of the flow aware viscosity
+visc_gamma2  = 0.285 ! [s/m],   is only used in easy backscatter option
+visc_easybsreturn= 1.5
+
+opt_visc     = 5          
+! 5=Kinematic (easy) Backscatter
+! 6=Biharmonic flow aware (viscosity depends on velocity Laplacian)
+! 7=Biharmonic flow aware (viscosity depends on velocity differences)
+! 8=Dynamic Backscatter
+
+use_ivertvisc= .true.  
+/
+
+&dynamics_general
+momadv_opt   = 2       ! option for momentum advection in moment only =2
+use_freeslip = .false. ! Switch on free slip
+use_wsplit   = .false. ! Switch for implicite/explicte splitting of vert. velocity
+wsplit_maxcfl= 1.0     ! maximum allowed CFL criteria in vertical (0.5 < w_max_cfl < 1.) 
+                       ! in older FESOM it used to be w_exp_max=1.e-3
+/
+

config/namelist.forcing

@@ -50,11 +50,14 @@ landice_end_mon=10
    nm_nc_freq    = 1            ! data points per day (i.e. 86400 if the time axis is in seconds)
    nm_nc_tmid    = 0            ! 1 if the time stamps are given at the mid points of the netcdf file, 0 otherwise (i.e. 1 in CORE1, CORE2; 0 in JRA55)
    l_xwind=.true. l_ywind=.true. l_humi=.true. l_qsr=.true. l_qlw=.true. l_tair=.true. l_prec=.true. l_mslp=.false. l_cloud=.false. l_snow=.true.
-   nm_runoff_file     ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/CORE2_runoff.nc'
    runoff_data_source ='CORE2'	!Dai09, CORE2
+   nm_runoff_file     ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/CORE2_runoff.nc'
    !nm_runoff_file     ='/work/ollie/qwang/FESOM2_input/mesh/CORE2_finaltopo_mean/forcing_data_on_grid/runoff_clim.nc'
    !runoff_data_source ='Dai09'  !Dai09, CORE2, JRA55
    !runoff_climatology =.true.
-   nm_sss_data_file   ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/PHC2_salx.nc'
    sss_data_source    ='CORE2'
+   nm_sss_data_file   ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/PHC2_salx.nc'
+   chl_data_source    ='None' !'Sweeney' monthly chlorophyll climatology or 'NONE' for constant chl_const (below). Make use_sw_pene=.TRUE. in namelist.config!
+   nm_chl_data_file   ='/work/ollie/clidyn/forcing/Sweeney/Sweeney_2005.nc'
+   chl_const          = 0.1
 /

config/namelist.forcing.ncep2

@@ -0,0 +1,56 @@
+! This is the namelist file for forcing
+
+&forcing_exchange_coeff
+Ce_atm_oce=0.00175 ! exchange coeff. of latent heat over open water
+Ch_atm_oce=0.00175 ! exchange coeff. of sensible heat over open water
+Cd_atm_oce=0.001  ! drag coefficient between atmosphere and water
+Ce_atm_ice=0.00175 ! exchange coeff. of latent heat over ice
+Ch_atm_ice=0.00175 ! exchange coeff. of sensible heat over ice
+Cd_atm_ice=0.0012  ! drag coefficient between atmosphere and ice 
+Swind     =0.0     ! parameterization for coupled current feedback
+/
+
+&forcing_bulk
+AOMIP_drag_coeff=.false.
+ncar_bulk_formulae=.true.
+ncar_bulk_z_wind=10.0 ! height at which wind forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m)
+ncar_bulk_z_tair=2.0 ! height at which temp forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m)
+ncar_bulk_z_shum=2.0 ! height at which humi forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m)
+/
+
+&land_ice
+use_landice_water=.false.
+landice_start_mon=5
+landice_end_mon=10
+/
+
+&nam_sbc
+   nm_xwind_file = '/work/ollie/clidyn/forcing/NCEP2/uwnd.10m.gauss.'   ! name of file with winds, if nm_sbc=2
+   nm_ywind_file = '/work/ollie/clidyn/forcing/NCEP2/vwnd.10m.gauss.'   ! name of file with winds, if nm_sbc=2
+   nm_humi_file  = '/work/ollie/clidyn/forcing/NCEP2/shum.2m.gauss.'    ! name of file with 2m specific humidity
+   nm_qsr_file   = '/work/ollie/clidyn/forcing/NCEP2/dswrf.sfc.gauss.'  ! name of file with solar heat
+   nm_qlw_file   = '/work/ollie/clidyn/forcing/NCEP2/dlwrf.sfc.gauss.'  ! name of file with Long wave
+   nm_tair_file  = '/work/ollie/clidyn/forcing/NCEP2/air.2m.gauss.'     ! name of file with 2m air temperature
+   nm_prec_file  = '/work/ollie/clidyn/forcing/NCEP2/prate.sfc.gauss.'  ! name of file with rain fall
+   nm_snow_file  = ''                                                   ! name of file with snow fall
+   nm_mslp_file  = ''                                                   ! air_pressure_at_sea_level
+   nm_xwind_var  = 'uwnd'   	! name of variable in file with wind
+   nm_ywind_var  = 'vwnd'   	! name of variable in file with wind
+   nm_humi_var   = 'shum'   	! name of variable in file with humidity
+   nm_qsr_var    = 'dswrf'  	! name of variable in file with solar heat
+   nm_qlw_var    = 'dlwrf'  	! name of variable in file with Long wave
+   nm_tair_var   = 'air'    	! name of variable in file with 2m air temperature
+   nm_prec_var   = 'prate'  	! name of variable in file with total precipitation
+   nm_snow_var   = ''       	! name of variable in file with total precipitation
+   nm_mslp_var   = ''       	! name of variable in file with air_pressure_at_sea_level
+   nm_nc_iyear   = 1800
+   nm_nc_imm     = 1            ! initial month of time axis in netCDF
+   nm_nc_idd     = 1            ! initial day of time axis in netCDF
+   nm_nc_freq    = 24           ! data points per day (i.e. 86400 if the time axis is in seconds)
+   nm_nc_tmid    = 0            ! 1 if the time stamps are given at the mid points of the netcdf file, 0 otherwise (i.e. 1 in CORE1, CORE2; 0 in JRA55)
+   l_xwind=.true., l_ywind=.true., l_humi=.true., l_qsr=.true., l_qlw=.true., l_tair=.true., l_prec=.true., l_mslp=.false., l_cloud=.false., l_snow=.false.
+   nm_runoff_file     ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/CORE2_runoff.nc'
+   runoff_data_source ='CORE2'  !Dai09, CORE2, JRA55
+   nm_sss_data_file   ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/PHC2_salx.nc'
+   sss_data_source    ='CORE2'
+/

config/namelist.io

@@ -9,8 +9,9 @@ ldiag_DVD        =.false.
 ldiag_forc       =.false.
 /
 
-&nml_listsize
-io_listsize=100 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list
+&nml_general
+io_listsize    =100 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list
+vec_autorotate =.false.
 /
 
 ! for sea ice related variables use_ice should be true, otherewise there will be no output
@@ -22,8 +23,8 @@ io_listsize=100 !number of streams to allocate. shallbe large or equal to the nu
 io_list =  'sst       ',1, 'm', 4,
            'sss       ',1, 'm', 4,
     	   'ssh       ',1, 'm', 4,
-           'uice      ',1, 'm', 4,
-           'vice      ',1, 'm', 4,
+           'uice      ',1, 'd', 4,
+           'vice      ',1, 'd', 4,
            'a_ice     ',1, 'm', 4,
            'm_ice     ',1, 'm', 4,
            'm_snow    ',1, 'm', 4,
@@ -37,6 +38,8 @@ io_list =  'sst       ',1, 'm', 4,
            'Kv        ',1, 'y', 4,
            'u         ',1, 'y', 4,
            'v         ',1, 'y', 4,
+           'unod      ',1, 'y', 4,
+           'vnod      ',1, 'y', 4,
            'w         ',1, 'y', 4,
            'Av        ',1, 'y', 4,
            'bolus_u   ',1, 'y', 4,