Skip to content

Commit 26df848

Browse files
ogursesogurses
committed
feat(recom): ! FESOM2.6-REcoM3.1 Stable Release
Stable FESOM2.6-REcoM3.1 release version. Tested with 2p3z2d and 4p3z2d setups. BREAKING CHANGE: f2.6r3.1 tagged stable version
1 parent 4408f0e commit 26df848

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

41 files changed

+11302
-3160
lines changed

‎CMakeLists.txt‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -10,17 +10,17 @@ project(FESOM2.0)
1010

1111
set(BUILD_SHARED_LIBS ON CACHE BOOL "Default to using shared libs")
1212
set(TOPLEVEL_DIR ${CMAKE_CURRENT_LIST_DIR})
13-
set(FESOM_COUPLED OFF CACHE BOOL "compile fesom standalone or with oasis support (i.e. coupled)")
14-
set(OIFS_COUPLED OFF CACHE BOOL "compile fesom coupled to OpenIFS. (Also needs FESOM_COUPLED to work)")
15-
set(CRAY OFF CACHE BOOL "compile with cray ftn")
16-
set(USE_ICEPACK OFF CACHE BOOL "compile fesom with the Iceapck modules for sea ice column physics.")
13+
set(FESOM_COUPLED OFF CACHE BOOL "compile fesom standalone or with oasis support (i.e. coupled)")
14+
set(OIFS_COUPLED OFF CACHE BOOL "compile fesom coupled to OpenIFS. (Also needs FESOM_COUPLED to work)")
15+
set(CRAY OFF CACHE BOOL "compile with cray ftn")
16+
set(USE_ICEPACK OFF CACHE BOOL "compile fesom with the Iceapck modules for sea ice column physics.")
1717
set(OPENMP_REPRODUCIBLE OFF CACHE BOOL "serialize OpenMP loops that are critical for reproducible results")
18-
set(RECOM_COUPLED ON CACHE BOOL "compile fesom including biogeochemistry, REcoM3")
19-
set(CISO_COUPLED OFF CACHE BOOL "compile ciso coupled to REcoM3. RECOM_COUPLED has to be active")
20-
set(USE_MULTIO OFF CACHE BOOL "Use MULTIO for IO, either grib or binary for now. This also means path to MULTIO installation has to provided using env MULTIO_INSTALL_PATH='..' and multio configuration yamls must be present to run the model with MULTIO")
21-
set(OASIS_WITH_YAC OFF CACHE BOOL "Useing a version of OASIS compiled with YAC instead of SCRIP for interpolation?")
22-
set(ASYNC_ICEBERGS ON CACHE BOOL "compile fesom with or without support for asynchronous iceberg computations")
23-
set(VERBOSE OFF CACHE BOOL "toggle debug output")
18+
set(RECOM_COUPLED ON CACHE BOOL "compile fesom including biogeochemistry, REcoM3")
19+
set(CISO_COUPLED OFF CACHE BOOL "compile ciso coupled to REcoM3. RECOM_COUPLED has to be active")
20+
set(USE_MULTIO OFF CACHE BOOL "Use MULTIO for IO, either grib or binary for now. This also means path to MULTIO installation has to provided using env MULTIO_INSTALL_PATH='..' and multio configuration yamls must be present to run the model with MULTIO")
21+
set(OASIS_WITH_YAC OFF CACHE BOOL "Useing a version of OASIS compiled with YAC instead of SCRIP for interpolation?")
22+
set(ASYNC_ICEBERGS ON CACHE BOOL "compile fesom with or without support for asynchronous iceberg computations")
23+
set(VERBOSE OFF CACHE BOOL "toggle debug output")
2424
#add_subdirectory(oasis3-mct/lib/psmile)
2525
add_subdirectory(src)
2626

‎config/bin_2p1z1d/job_albedo‎

Lines changed: 16 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,12 @@
11
#!/bin/bash
2-
#SBATCH --account=nwg_hauck.maresys # edit your account
2+
#SBATCH --account=biogeo_model.biogeo_model
33
#SBATCH --job-name=recom
44
#SBATCH --partition=mpp
55
#SBATCH --time=01:30:00
66
####SBATCH --constraint="[rack1|rack3]"
77
#SBATCH --qos=12h
8-
#SBATCH --nodes=9 # Number of tasks (MPI) tasks to be launched
9-
#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
8+
#SBATCH --nodes=9
9+
#SBATCH --tasks-per-node 96 # using all 128CPus we exceed the maxload limit (>130) of many used nodes when us parallel I/O
1010
#SBATCH --cpus-per-task 1
1111

1212
#SBATCH -o fesom2o.out
@@ -23,35 +23,32 @@ ulimit -s unlimited
2323
# determine JOBID
2424
JOBID=`echo $SLURM_JOB_ID |cut -d"." -f1`
2525

26-
ln -s ../bin/fesom.x . # cp -n ../bin/fesom.x
27-
cp -n ../config/namelist.config .
28-
cp -n ../config/namelist.forcing .
29-
cp -n ../config/namelist.oce .
30-
cp -n ../config/namelist.dyn .
31-
cp -n ../config/namelist.tra .
32-
cp -n ../config/namelist.ice .
33-
cp -n ../config/namelist.io .
34-
cp -n ../config/namelist.icepack .
26+
#ln -s ../bin/fesom.x . # cp -n ../bin/fesom.x
27+
#cp -n ../config/namelist.config .
28+
#cp -n ../config/namelist.forcing .
29+
#cp -n ../config/namelist.oce .
30+
#cp -n ../config/namelist.dyn .
31+
#cp -n ../config/namelist.tra .
32+
#cp -n ../config/namelist.ice .
33+
#cp -n ../config/namelist.io .
34+
#cp -n ../config/namelist.icepack .
3535

3636
#___DETERMINE SLURM JOBID+OUTPUTFILE____________________________________________
3737
jobid=$(echo $SLURM_JOB_ID | cut -d"." -f1)
38-
fname="fesom2_${SLURM_JOB_NAME}_${jobid}.out"
38+
fname="fesom2.0.out"
3939

40-
#___PUT JOB IN QUEUE____________________________________________________________
4140
date
42-
####srun --mpi=pmi2 ./fesom.x >> ${fname}
4341
srun --mpi=pmi2 ./fesom.x > fesom2.0.out
4442
date
4543

4644
#qstat -f $PBS_JOBID
4745
#export EXITSTATUS=$?
4846
#if [ ${EXITSTATUS} -eq 0 ] || [ ${EXITSTATUS} -eq 127 ] ; then
49-
#sbatch job_ollie
47+
#sbatch job_albedo
5048
#fi
5149

52-
#Resultpath='/albedo/scratch/user/ogurses/ocean_only/'
53-
Resultpath='/albedo/scratch/user/ogurses/fesom2.5_recom_st1_vsink_vben_diags/'
54-
test -d $Resultpath/fesom.2019.oce.restart && exit
50+
Resultpath='/albedo/scratch/user/'
51+
test -d $Resultpath/fesom.2024.oce.restart && exit
5552

5653
IsInFile=$( tail -3 fesom2.0.out | grep -c timesteps)
5754
if (( IsInFile > 0 )); then

‎config/bin_2p1z1d/namelist.config‎

Lines changed: 11 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ yearnew=1958
1919
&paths
2020
MeshPath='/albedo/work/projects/p_recompdaf/frbunsen/FESOM2/meshes/core2/'
2121
ClimateDataPath='/albedo/work/projects/MarESys/ogurses/input/corrected_input/'
22-
ResultPath='/albedo/scratch/user/ogurses/fesom2.5_recom_st1_vsink_vben_diags/'
22+
ResultPath='/albedo/scratch/user/'
2323
/
2424

2525
&restart_log
@@ -50,6 +50,7 @@ gammaEuler=-90. ![degree] then around new z.
5050

5151
&calendar
5252
include_fleapyear=.false.
53+
use_flpyrcheck =.true.
5354
/
5455

5556
&run_config
@@ -59,9 +60,18 @@ use_cavity_partial_cell=.false.
5960
use_floatice = .false.
6061
use_sw_pene=.true.
6162
flag_debug=.false.
63+
use_transit=.false.
6264
/
6365

6466
&machine
6567
n_levels=2
6668
n_part= 12, 36 ! 432 number of partitions on each hierarchy level
6769
/
70+
71+
&icebergs
72+
use_icesheet_coupling=.false.
73+
ib_num=1
74+
use_icebergs=.false.
75+
steps_per_ib_step=8
76+
ib_async_mode=0
77+
/

‎config/bin_2p1z1d/namelist.forcing‎

Lines changed: 27 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -23,11 +23,23 @@ ncar_bulk_z_shum=10.0 ! height at which humi forcing is located (CORE, JRA-do: 1
2323
use_landice_water=.false.
2424
landice_start_mon=5
2525
landice_end_mon=10
26+
fwf_path='./mesh/'
27+
28+
/
29+
30+
&age_tracer
31+
use_age_tracer=.false.
32+
use_age_mask=.false.
33+
age_tracer_path='./mesh/'
34+
age_start_year=2000
35+
2636
/
2737

2838
&nam_sbc
2939
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
3040
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
41+
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
42+
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
3143
nm_humi_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/huss.clim61' ! name of file with humidity
3244
nm_qsr_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/rsds.clim61' ! name of file with solar heat
3345
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
3749
nm_mslp_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/psl.clim61' ! air_pressure_at_sea_level
3850
nm_xwind_var = 'uas' ! name of variable in file with wind
3951
nm_ywind_var = 'vas' ! name of variable in file with wind
40-
nm_humi_var = 'huss' ! name of variable in file with humidity
41-
nm_qsr_var = 'rsds' ! name of variable in file with solar heat
42-
nm_qlw_var = 'rlds' ! name of variable in file with Long wave
52+
nm_xstre_var = 'uas' ! name of variable in file with wind
53+
nm_ystre_var = 'vas' ! name of variable in file with wind
54+
nm_humi_var = 'huss' ! name of variable in file with humidity
55+
nm_qsr_var = 'rsds' ! name of variable in file with solar heat
56+
nm_qlw_var = 'rlds' ! name of variable in file with Long wave
4357
nm_tair_var = 'tas' ! name of variable in file with 2m air temperature
44-
nm_prec_var = 'prra' ! name of variable in file with total precipitation
45-
nm_snow_var = 'prsn' ! name of variable in file with total precipitation
46-
nm_mslp_var = 'psl' ! name of variable in file with air_pressure_at_sea_level
58+
nm_prec_var = 'prra' ! name of variable in file with total precipitation
59+
nm_snow_var = 'prsn' ! name of variable in file with total precipitation
60+
nm_mslp_var = 'psl' ! name of variable in file with air_pressure_at_sea_level
4761
nm_nc_iyear = 1900
4862
nm_nc_imm = 1 ! initial month of time axis in netCDF
4963
nm_nc_idd = 1 ! initial day of time axis in netCDF
5064
nm_nc_freq = 1 ! data points per day (i.e. 86400 if the time axis is in seconds)
5165
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)
5266
y_perpetual=.true.
53-
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.
67+
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.
5468
nm_runoff_file ='/albedo/pool/FESOM/forcing/CORE2/runoff.nc'
5569
runoff_data_source ='CORE2' !Dai09, CORE2
5670
!runoff_data_source ='Dai09' !Dai09, CORE2, JRA55
5771
!runoff_climatology =.true.
5872
nm_sss_data_file ='/albedo/pool/FESOM/forcing/CORE2/PHC2_salx.nc'
5973
sss_data_source ='CORE2'
74+
chl_data_source ='None' !'Sweeney' monthly chlorophyll climatology or 'NONE' for constant chl_const (below). Make use_sw_pene=.TRUE. in namelist.config!
75+
nm_chl_data_file ='/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/Sweeney/Sweeney_2005.nc'
76+
chl_const = 0.1
77+
use_runoff_mapper = .FALSE.
78+
runoff_basins_file = 'runoff_maps_regular.nc'
79+
runoff_radius = 500000.
6080
/

‎config/bin_2p1z1d/namelist.io‎

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ ldiag_extflds =.false.
1212
/
1313

1414
&nml_general
15-
io_listsize =100 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list
15+
io_listsize =150 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list
1616
vec_autorotate =.false.
1717
/
1818

@@ -40,11 +40,11 @@ io_list = 'sst ',1, 'm', 4,
4040
'otracers ',1, 'm', 4,
4141
'N2 ',1, 'y', 4,
4242
'Kv ',1, 'y', 4,
43-
'u ',1, 'y', 4,
44-
'v ',1, 'y', 4,
45-
'unod ',1, 'y', 4,
46-
'vnod ',1, 'y', 4,
47-
'w ',1, 'y', 4,
43+
'u ',1, 'm', 4,
44+
'v ',1, 'm', 4,
45+
'unod ',1, 'm', 4,
46+
'vnod ',1, 'm', 4,
47+
'w ',1, 'm', 4,
4848
'Av ',1, 'y', 4,
4949
'bolus_u ',1, 'y', 4,
5050
'bolus_v ',1, 'y', 4,
@@ -70,6 +70,8 @@ io_list = 'sst ',1, 'm', 4,
7070
'NPPn ',1, 'm', 4,
7171
'PAR ',1, 'm', 4,
7272
'respmeso',1, 'm', 4,
73+
'respmacro',1, 'm', 4,
74+
'respmicro',1, 'm', 4,
7375
'calcdiss',1, 'm', 4,
7476
'calcif',1, 'm', 4,
7577
'aggn',1, 'm', 4,

0 commit comments

Comments
 (0)