Fesom2.6 recom tra diags and CI test

config/bin_2p1z1d/job_albedo

@@ -1,16 +1,15 @@
 #!/bin/bash
-#SBATCH --account=nwg_hauck.maresys # edit your account
-#SBATCH --job-name=recom
+#SBATCH --account=biogeo_model.biogeo_model
+#SBATCH --job-name=2p1z1d
 #SBATCH --partition=mpp
-#SBATCH --time=01:30:00
-####SBATCH --constraint="[rack1|rack3]"
+#SBATCH -N 9
+#SBATCH --cpus-per-task=1
+#SBATCH --time=08:00:00
 #SBATCH --qos=12h
-#SBATCH --nodes=9            # Number of tasks (MPI) tasks to be launched
-#SBATCH --tasks-per-node 96 #8 #4  # using all 128CPus we exceed the maxload limit (>130) of many used nodes when us parallel I/O
-#SBATCH --cpus-per-task 1
+#SBATCH --tasks-per-node 96  # using all 128CPus we exceed the maxload limit (>130) of many used nodes when us parallel I/O
 
-#SBATCH -o fesom2o.out
-#SBATCH -e fesom2e.out
+#SBATCH -o slurm-out.out
+#SBATCH -e slurm-err.out
 
 # disable hyperthreading
 #SBATCH --hint=nomultithread
@@ -23,35 +22,33 @@ ulimit -s unlimited
 # determine JOBID
 JOBID=`echo $SLURM_JOB_ID |cut -d"." -f1`
 
-ln -s ../bin/fesom.x .           # cp -n ../bin/fesom.x
-cp -n ../config/namelist.config  .
-cp -n ../config/namelist.forcing .
-cp -n ../config/namelist.oce     .
-cp -n ../config/namelist.dyn     .
-cp -n ../config/namelist.tra     .
-cp -n ../config/namelist.ice     .
-cp -n ../config/namelist.io      .
-cp -n ../config/namelist.icepack .
+#ln -s ../bin/fesom.x .           # cp -n ../bin/fesom.x
+#cp -n ../config/namelist.config  .
+#cp -n ../config/namelist.forcing .
+#cp -n ../config/namelist.oce     .
+#cp -n ../config/namelist.dyn     .
+#cp -n ../config/namelist.tra     .
+#cp -n ../config/namelist.ice     .
+#cp -n ../config/namelist.io      .
+#cp -n ../config/namelist.icepack .
 
 #___DETERMINE SLURM JOBID+OUTPUTFILE____________________________________________
 jobid=$(echo $SLURM_JOB_ID | cut -d"." -f1)
-fname="fesom2_${SLURM_JOB_NAME}_${jobid}.out"
+fname="fesom2.0.out"
 
 #___PUT JOB IN QUEUE____________________________________________________________
 date
-####srun --mpi=pmi2 ./fesom.x >> ${fname}
 srun --mpi=pmi2 ./fesom.x > fesom2.0.out
 date
 
 #qstat -f $PBS_JOBID
 #export EXITSTATUS=$?
 #if [ ${EXITSTATUS} -eq 0 ] || [ ${EXITSTATUS} -eq 127 ] ; then
-#sbatch job_ollie
+#sbatch job_albedo
 #fi
 
-#Resultpath='/albedo/scratch/user/ogurses/ocean_only/'
-Resultpath='/albedo/scratch/user/ogurses/fesom2.5_recom_st1_vsink_vben_diags/'
-test -d $Resultpath/fesom.2019.oce.restart && exit
+Resultpath='/albedo/work/user/...'
+test -e $Resultpath/fesom.xxxxx.oce.restart && exit
 
 IsInFile=$( tail -3 fesom2.0.out | grep -c timesteps)
 if (( IsInFile > 0 )); then

config/bin_2p1z1d/namelist.config

@@ -6,8 +6,8 @@ runid='fesom'
 
 &timestep
 step_per_day=32 !96 !96 !72 !72 !45 !72 !96
-run_length=1 !62 !62 !62 !28
-run_length_unit='y'		! y, m, d, s
+run_length= 1 !62 !62 !62 !28
+run_length_unit='y' ! y, m, d, s
 /
 
 &clockinit              ! the model starts at
@@ -18,8 +18,8 @@ yearnew=1958
 
 &paths
 MeshPath='/albedo/work/projects/p_recompdaf/frbunsen/FESOM2/meshes/core2/'
-ClimateDataPath='/albedo/work/projects/MarESys/ogurses/input/corrected_input/' 
-ResultPath='/albedo/scratch/user/ogurses/fesom2.5_recom_st1_vsink_vben_diags/'
+ClimateDataPath='/albedo/work/projects/MarESys/ogurses/input/corrected_input/'
+ResultPath='/albedo/work/user/...'
 /
 
 &restart_log
@@ -29,7 +29,7 @@ raw_restart_length=1        ! --> do core dump restart
 raw_restart_length_unit='off' ! e.g. y, d, h, s, off
 bin_restart_length=1        ! --> do derived type binary restart 
 bin_restart_length_unit='off' ! e.g. y, d, h, s, off
-logfile_outfreq=960     !in logfile info. output frequency, # steps
+logfile_outfreq=960         !in logfile info. output frequency, # steps
 /
 
 &ale_def
@@ -59,9 +59,18 @@ use_cavity_partial_cell=.false.
 use_floatice = .false.
 use_sw_pene=.true.
 flag_debug=.false.
+use_transit=.false.
 /
 
 &machine
 n_levels=2
 n_part= 12, 36          ! 432 number of partitions on each hierarchy level
 /
+
+&icebergs
+use_icesheet_coupling=.false.
+ib_num=1
+use_icebergs=.false.
+steps_per_ib_step=8
+ib_async_mode=0
+/

config/bin_2p1z1d/namelist.forcing

@@ -23,11 +23,23 @@ ncar_bulk_z_shum=10.0 ! height at which humi forcing is located (CORE, JRA-do: 1
 use_landice_water=.false.
 landice_start_mon=5
 landice_end_mon=10
+fwf_path='./mesh/'
+
+/
+
+&age_tracer
+use_age_tracer=.false.
+use_age_mask=.false.
+age_tracer_path='./mesh/'
+age_start_year=2000
+
 /
 
 &nam_sbc
    nm_xwind_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/uas.clim61'        ! name of file with winds, if nm_sbc=2
    nm_ywind_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/vas.clim61'        ! name of file with winds, if nm_sbc=2
+   nm_xstre_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/uas.clim61'        ! name of file with winds, if nm_sbc=2
+   nm_ystre_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/vas.clim61'        ! name of file with winds, if nm_sbc=2
    nm_humi_file  = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/huss.clim61'        ! name of file with humidity
    nm_qsr_file   = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/rsds.clim61'    ! name of file with solar heat
    nm_qlw_file   = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/rlds.clim61'    ! name of file with Long wave
@@ -37,24 +49,32 @@ landice_end_mon=10
    nm_mslp_file  = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/psl.clim61'         ! air_pressure_at_sea_level
    nm_xwind_var  = 'uas'   ! name of variable in file with wind
    nm_ywind_var  = 'vas'   ! name of variable in file with wind
-   nm_humi_var   = 'huss'   ! name of variable in file with humidity
-   nm_qsr_var    = 'rsds'   ! name of variable in file with solar heat
-   nm_qlw_var    = 'rlds'   ! name of variable in file with Long wave
+   nm_xstre_var  = 'uas'   ! name of variable in file with wind
+   nm_ystre_var  = 'vas'   ! name of variable in file with wind
+   nm_humi_var   = 'huss'  ! name of variable in file with humidity
+   nm_qsr_var    = 'rsds'  ! name of variable in file with solar heat
+   nm_qlw_var    = 'rlds'  ! name of variable in file with Long wave
    nm_tair_var   = 'tas'   ! name of variable in file with 2m air temperature
-   nm_prec_var   = 'prra'       ! name of variable in file with total precipitation
-   nm_snow_var   = 'prsn'       ! name of variable in file with total precipitation
-   nm_mslp_var   = 'psl'        ! name of variable in file with air_pressure_at_sea_level
+   nm_prec_var   = 'prra'  ! name of variable in file with total precipitation
+   nm_snow_var   = 'prsn'  ! name of variable in file with total precipitation
+   nm_mslp_var   = 'psl'   ! name of variable in file with air_pressure_at_sea_level
    nm_nc_iyear   = 1900
    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    = 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)
    y_perpetual=.true.
-   l_xwind=.true. l_ywind=.true. l_humi=.true. l_qsr=.true. l_qlw=.true. l_tair=.true. l_prec=.true. l_mslp=.true. l_cloud=.false. l_snow=.true.
+   l_xwind=.true. l_ywind=.true. l_xstre=.false. l_ystre=.false. l_humi=.true. l_qsr=.true. l_qlw=.true. l_tair=.true. l_prec=.true. l_mslp=.true. l_cloud=.false. l_snow=.true.
    nm_runoff_file      ='/albedo/pool/FESOM/forcing/CORE2/runoff.nc'
    runoff_data_source ='CORE2'	!Dai09, CORE2
    !runoff_data_source ='Dai09'  !Dai09, CORE2, JRA55
    !runoff_climatology =.true.
-   nm_sss_data_file    ='/albedo/pool/FESOM/forcing/CORE2/PHC2_salx.nc'
    sss_data_source    ='CORE2'
+   nm_sss_data_file   ='/albedo/pool/FESOM/forcing/CORE2/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   ='/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/Sweeney/Sweeney_2005.nc'
+   chl_const          = 0.1
+   use_runoff_mapper  = .FALSE.
+   runoff_basins_file = 'runoff_maps_regular.nc'
+   runoff_radius      = 500000.
 /

config/bin_2p1z1d/namelist.icepack.cesm.ponds

@@ -0,0 +1,144 @@
+&env_nml                    ! In the original release these variables are defined in the icepack.settings
+    nicecat   = 5           ! number of ice thickness categories
+    nfsdcat   = 1           ! number of floe size categories
+    nicelyr   = 4           ! number of vertical layers in the ice
+    nsnwlyr   = 4           ! number of vertical layers in the snow
+    ntraero   = 0           ! number of aerosol tracers (up to max_aero in ice_domain_size.F90)
+    trzaero   = 0           ! number of z aerosol tracers (up to max_aero = 6)
+    tralg     = 0           ! number of algal tracers (up to max_algae = 3)
+    trdoc     = 0           ! number of dissolve organic carbon (up to max_doc = 3)
+    trdic     = 0           ! number of dissolve inorganic carbon (up to max_dic = 1)
+    trdon     = 0           ! number of dissolve organic nitrogen (up to max_don = 1)
+    trfed     = 0           ! number of dissolved iron tracers (up to max_fe  = 2)
+    trfep     = 0           ! number of particulate iron tracers (up to max_fe  = 2)
+    nbgclyr   = 0           ! number of zbgc layers
+    trbgcz    = 0           ! set to 1 for zbgc tracers (needs TRBGCS = 0 and TRBRI = 1)
+    trzs      = 0           ! set to 1 for zsalinity tracer (needs TRBRI = 1)
+    trbri     = 0           ! set to 1 for brine height tracer
+    trage     = 0           ! set to 1 for ice age tracer
+    trfy      = 0           ! set to 1 for first-year ice area tracer
+    trlvl     = 0           ! set to 1 for level and deformed ice tracers
+    trpnd     = 1           ! set to 1 for melt pond tracers
+    trbgcs    = 0           ! set to 1 for skeletal layer tracers (needs TRBGCZ = 0)
+    ndtd      = 1           ! dynamic time steps per thermodynamic time step
+/
+
+&grid_nml
+    kcatbound    = 1
+/
+
+&tracer_nml
+    tr_iage      = .false.
+    tr_FY        = .false.
+    tr_lvl       = .false.
+    tr_pond_cesm = .true.
+    tr_pond_topo = .false.
+    tr_pond_lvl  = .false.
+    tr_aero      = .false.
+    tr_fsd       = .false.
+/
+
+&thermo_nml
+    kitd              = 1
+    ktherm            = 1
+    conduct           = 'bubbly'
+    a_rapid_mode      =  0.5e-3
+    Rac_rapid_mode    =    10.0
+    aspect_rapid_mode =     1.0
+    dSdt_slow_mode    = -5.0e-8
+    phi_c_slow_mode   =    0.05
+    phi_i_mushy       =    0.85
+/
+
+&shortwave_nml
+    shortwave       = 'dEdd'
+    albedo_type     = 'ccsm3'
+    albicev         = 0.78
+    albicei         = 0.36
+    albsnowv        = 0.98
+    albsnowi        = 0.70
+    ahmax           = 0.3
+    R_ice           = 0.
+    R_pnd           = 0.
+    R_snw           = 1.5
+    dT_mlt          = 1.5
+    rsnw_mlt        = 1500.
+    kalg            = 0.6
+/
+
+&ponds_nml
+    hp1             = 0.01
+    hs0             = 0.
+    hs1             = 0.03
+    dpscale         = 1.e-3
+    frzpnd          = 'hlid'
+    rfracmin        = 0.15
+    rfracmax        = 1.
+    pndaspect       = 0.8
+/
+
+&forcing_nml
+    formdrag        = .false.
+    atmbndy         = 'default'
+    calc_strair     = .true.
+    calc_Tsfc       = .true.
+    highfreq        = .false.
+    natmiter        = 5
+    ustar_min       = 0.0005
+    emissivity      = 0.95
+    fbot_xfer_type  = 'constant'
+    update_ocn_f    = .false.
+    l_mpond_fresh   = .false.
+    tfrz_option     = 'linear_salt'
+    oceanmixed_ice  = .true.
+    wave_spec_type  = 'none'
+/
+
+&dynamics_nml
+    kstrength       = 1
+    krdg_partic     = 1
+    krdg_redist     = 1
+    mu_rdg          = 3
+    Cf              = 17.
+    P_star          = 27000.
+    C_star          = 20.
+/
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!                Icepack output namelist                    !!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+&nml_list_icepack
+io_list_icepack =  'aicen     ',1, 'm', 4, ! Sea ice concentration
+                   'vicen     ',1, 'm', 4, ! Volume per unit area of ice
+                   'vsnon     ',1, 'm', 4, ! Volume per unit area of snow
+                   !'Tsfcn     ',1, 'm', 4, ! Sea ice surf. temperature
+                   !'iagen     ',1, 'm', 4, ! Sea ice age
+                   !'FYn       ',1, 'm', 4, ! First year ice
+                   !'lvln      ',1, 'm', 4, ! Ridged sea ice area and volume
+                   !'pond_cesmn',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
+                   !'pond_topon',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
+                   !'pond_lvln ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
+                   !'brinen    ',1, 'm', 4, ! Volume fraction of ice with dynamic salt
+                   !'qicen     ',1, 'm', 4, ! Sea ice enthalpy
+                   !'sicen     ',1, 'm', 4, ! Sea ice salinity
+                   !'qsnon     ',1, 'm', 4, ! Snow enthalpy
+                   ! Average over thicknes classes
+                   !'aice      ',1, 'm', 4, ! Sea ice concentration
+                   !'vice      ',1, 'm', 4, ! Volume per unit area of ice
+                   !'vsno      ',1, 'm', 4, ! Volume per unit area of snow
+                   !'Tsfc      ',1, 'm', 4, ! Sea ice surf. temperature
+                   !'iage      ',1, 'm', 4, ! Sea ice age
+                   !'FY        ',1, 'm', 4, ! First year ice
+                   !'lvl       ',1, 'm', 4, ! Ridged sea ice area and volume
+                   !'pond_cesm ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
+                   !'pond_topo ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
+                   !'pond_lvl  ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
+                   !'brine     ',1, 'm', 4, ! Volume fraction of ice with dynamic salt
+                   !'qice      ',1, 'm', 4, ! Sea ice enthalpy
+                   !'sice      ',1, 'm', 4, ! Sea ice salinity
+                   !'qsno      ',1, 'm', 4, ! Snow enthalpy
+                   ! Other variables
+                   !'uvel      ',1, 'm', 4, ! x-component of sea ice velocity
+                   !'vvel      ',1, 'm', 4, ! y-component of sea ice velocity                   
+/

config/bin_2p1z1d/namelist.io

@@ -12,7 +12,7 @@ ldiag_extflds    =.false.
 /
 
 &nml_general
-io_listsize    =100 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list
+io_listsize    =150 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list
 vec_autorotate =.false.
 /
 
@@ -40,11 +40,11 @@ io_list =  'sst       ',1, 'm', 4,
            'otracers  ',1, 'm', 4,
            'N2        ',1, 'y', 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,
+           'u         ',1, 'm', 4,
+           'v         ',1, 'm', 4,
+           'unod      ',1, 'm', 4,
+           'vnod      ',1, 'm', 4,
+           'w         ',1, 'm', 4,
            'Av        ',1, 'y', 4,
            'bolus_u   ',1, 'y', 4,
            'bolus_v   ',1, 'y', 4,