FESOM · ogurses · Apr 8, 2026 · Oct 15, 2024 · Nov 20, 2024 · Dec 10, 2024
diff --git a/.github/workflows/fesom2_recom.yml b/.github/workflows/fesom2_recom.yml
@@ -0,0 +1,95 @@
+
+name: "FESOM2: REcoM Biogeochemistry"
+# Controls when the action will run. Triggers the workflow on pull request only.
+on:
+  workflow_dispatch: {}
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+    branches:
+      - main
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  general_test:
+    # Containers must run in Linux based operating systems
+    runs-on: ubuntu-latest
+    # Docker Hub image that `container-job` executes in
+    container: ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master
+
+    # Service containers to run with `gfortran_ubuntu`
+    steps:
+      # NK: this changes working directory to fesom2
+      - uses: actions/checkout@v2
+
+      - name: Git safe directory
+        run: |
+          git config --global --add safe.directory ${PWD}
+
+      - name: Compile model with REcoM
+        run: |
+          ./configure.sh ubuntu -DRECOM_COUPLED=ON
+
+      - name: Create REcoM test run
+        run: |
+          mkrun recom test_pi_recom -m docker
+
+      - name: Add REcoM namelists
+        run: |
+          # mkrun doesn't create namelist.recom, so copy from config and patch
+          # Using 2p3z2d (30 tracers) - more complete/tested than 2p1z1d
+          cp config/bin_2p3z2d/namelist.recom work_recom/
+          cp config/bin_2p3z2d/namelist.tra work_recom/
+
+          # Patch namelist.recom
+          cd work_recom
+
+          # Remove nam_rsbc section (not used by code, causes parsing errors)
+          sed -i '/^&nam_rsbc/,/^\//d' namelist.recom
+
+          # Set REcoM_restart to false for initialization from climatology
+          sed -i "s|REcoM_restart.*=.*\.true\.|REcoM_restart         =.false.|" namelist.recom
+
+          # Patch tracer file list in namelist.tra  
+          sed -i "s|fe_pisces_opa_eq_init_3D_changed_name\.nc|fe5deg.nc|" namelist.tra
+          sed -i "s|woa18_all_o00_01_mmol_fesom2\.nc|oxy5deg.nc|" namelist.tra
+          sed -i "s|woa13_all_i00_01_fesom2\.nc|si5deg.nc|" namelist.tra
+          sed -i "s|GLODAPv2\.2016b\.TAlk_fesom2_mmol_fix_z_Fillvalue\.nc|talk5deg.nc|" namelist.tra
+          sed -i "s|GLODAPv2\.2016b\.TCO2_fesom2_mmol_fix_z_Fillvalue\.nc|tco2_5deg.nc|" namelist.tra
+          sed -i "s|woa13_all_n00_01_fesom2\.nc|din5deg.nc|" namelist.tra
+          sed -i "s|phc3\.0_winter\.nc|woa18_netcdf_5deg.nc|g" namelist.tra
+
+          # Enable atmospheric pressure forcing for REcoM CO2 flux calculation
+          sed -i "s|l_mslp *= *\.false\.|l_mslp=.true.|" namelist.forcing
+
+          echo "--- Verifying patches ---"
+          echo "REcoM restart: $(grep 'REcoM_restart' namelist.recom)"
+          echo "Atmospheric pressure: $(grep 'l_mslp' namelist.forcing)"
+          cd ..
+
+          # Copy REcoM input data files
+          cp test/input/recom/*.nc work_recom/
+
+          # Create dust file with expected name in the source directory
+          # (code reads from ClimateDataPath, not work directory)
+          cd test/input/recom
+          ln -s DustClimMonthlyAlbani_pimesh.nc DustClimMonthlyAlbani.nc
+          cd ../../..
+
+          # Copy forcing data files (from 1948)
+          cp test/input/global/*.1948.nc work_recom/
+          cp test/input/global/runoff.nc work_recom/
+          cp test/input/global/PHC2_salx.nc work_recom/
+
+      - name: FESOM2 REcoM test run
+        run: |
+          cd work_recom
+          echo "--- Running REcoM test (32 timesteps, 1 day) ---"
+          chmod +x job_docker_new
+          ./job_docker_new
+
+      - name: Check REcoM results
+        run: |-
+          cd work_recom
+          fcheck .
diff --git a/cmake/BuildLibfyaml.cmake b/cmake/BuildLibfyaml.cmake
@@ -46,7 +46,7 @@ ExternalProject_Add(libfyaml-external
     BUILD_COMMAND make -j${CMAKE_BUILD_PARALLEL_LEVEL} -C src libfyaml.la
     BUILD_IN_SOURCE ON
     BUILD_BYPRODUCTS ${LIBFYAML_INSTALL_PREFIX}/lib/libfyaml.so
-    INSTALL_COMMAND make -C src install-libLTLIBRARIES install-includeHEADERS && make install-pkgconfigDATA
+    INSTALL_COMMAND make -C src install-libLTLIBRARIES install-includeHEADERS install-libfyamlHEADERS && make install-pkgconfigDATA
     LOG_DOWNLOAD OFF
     LOG_CONFIGURE OFF
     LOG_BUILD OFF

diff --git a/config/bin_2p1z1d/job_albedo b/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

diff --git a/config/bin_2p1z1d/namelist.config b/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
+/
diff --git a/config/bin_2p1z1d/namelist.forcing b/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.
 /