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README.txt
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README.txt
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+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Nicolas Jourdain, IGE-CNRS, Feb. 2017
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Pre-processing tools to build a regional NEMO configuration laterally forced by a global ocean simulation.
Tested with NEMO-3.6 but should work with previous NEMO-3.x versions.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Before you start, make sure your system has the following:
- a fortran compiler
- netcdf and fortran-netcdf libraries.
To download NEMO, you need to register on http://www.nemo-ocean.eu/user/register
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Last updates:
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#########################################################################################################
#########################################################################################################
## 0-- First of all, choose a configuration name, e.g. WED12, AMU12, PERIANT025, etc, and save it.
export CONFIG='WED12' ## NB: to redo if you start a new session along the following steps !!
#########################################################################################################
#########################################################################################################
## 1-- Get and install NEMO and XIOS (required for the preprocessing to build the mesh_mask file)
## NB: on froggy (Grenoble), you will need to run this command to enable svn functions:
export ftp_proxy=http://www-cache.ujf-grenoble.fr:3128
cd $WORKDIR
mkdir models
cd models
## Choose if you install XIOS-1 or XIOS-2 :
svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0 XIOS ## XIOS-1
svn co -r 1011 http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk XIOS ## XIOS-2
## Install XIOS :
cd XIOS
chmod +x make_xios
./make_xios --avail ## find your architecture if it exists (e.g. X64_ADA)
## or create a new one in the arch directory.
time ./make_xios --prod --full --arch X64_ADA --jobs 8 &> compil.log &
tail -f compil.log ## to follow the compilation
ls bin/xios_server.exe ## to check that it went ok
cd ..
## Choose one of these NEMO releases (or any other branch and version) :
svn co http://forge.ipsl.jussieu.fr/nemo/svn/trunk MY_NEMO ## for the last trunk version
svn co -r 6402 http://forge.ipsl.jussieu.fr/nemo/svn/trunk MY_NEMO ## for version 6402 of the trunk
svn co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2015/nemo_v3_6_STABLE MY_NEMO ## NEMO3.6 STABLE
## Compile for a new configuration, e.g. the WED12 configuration (you can have several ones)
cd MY_NEMO/NEMOGCM/CONFIG
echo "$CONFIG OPA_SRC LIM_SRC_3" >> cfg.txt ## here for OPA+LIM3 (see cfg.txt for other options)
./makenemo -h ## find your architecture if it exists (e.g. X64_ADA)
## or create a new one in the MY_NEMO/NEMOGCM/ARCH directory.
vi ../ARCH/arch-X64_ADA.fcm ## adapt XIOS pathway accordingly with the previous installation.
mkdir $CONFIG
## Choose fppkeys prior to compilation (see NEMO documentations or examples in existing configurations,
## e.g. MY_NEMO/NEMOGCM/CONFIG/AMM12/cpp_AMM12.fcm), e.g. :
echo " bld::tool::fppkeys key_bdy key_dynspg_ts key_lim3 key_ldfslp key_iomput key_mpp_mpi" > AMU12/cpp_${CONFIG}.fcm
time ./makenemo -n $CONFIG -m X64_ADA -j 8 &> compile.log &
tail -f compile.log ## to follow the compilation
ls -al ${CONFIG}/BLD/bin/nemo.exe ## to check that everything went fine
## if you recompile, it is recommended to remove these directories: rm -rf ${CONFIG}/WORK ${CONFIG}/BLD
cd ..
## Compile REBUILD_NEMO (used to recombine outputs at the end of the jobs):
cd TOOLS
./maketools -h ## use same architecture as for NEMO's compilation (e.g. X64_ADA)
./maketools -m X64_ADA -n REBUILD_NEMO
ls -al REBUILD_NEMO/BLD/bin/ ## to check that everything went fine
cd ..
#########################################################################################################
#########################################################################################################
## 2-- Prepare the pre-processing tools:
##### GSW TOOLBOX #####
# First you may need the TEOS10 toolbox to convert from EOS80 to TEOS10.
# To avoid issues with updates on the GSW-Fortran tools, I've cloned the 2016 GSW-Fortran
# in this repository. In case you want to check for updates (not recommended), you can still do:
# git clone https://github.com/TEOS-10/GSW-Fortran.git
cd GSW-Fortran/test
# edit makefile (in particular fill the FC and NETCDF_INCDIR variables)
make
./gsw_check ## to check (some have to work, maybe not all of them)
cd ../..
# The gsw_data_v3_0.nc file provided in this repository should be fine, but in case you start again
# from the original file (i.e. from github.com/TEOS-10/GSW-Fortran.git), you will need to modify it
# to avoid NaN in some places (otherwise, skip the next 4 lines):
./compile.sh remove_NaN_from_gsw_data_v3_0.f90
./remove_NaN_from_gsw_data_v3_0
ncks -x -v ocean_ref,ndepth_ref,deltaSA_ref,SA_ref,SAAR_ref GSW-Fortran/test/gsw_data_v3_0.nc gsw_data_v3_0.nc
ncks -A gsw_data_v3_0_to_be_ncks-A.nc gsw_data_v3_0.nc
# Edit your own namelist, e.g. namelist_WED12, and link namelist_pre to it:
vi namelist_${CONFIG}
ln -s -v namelist_${CONFIG} namelist_pre
# Edit compile_ALL.sh, adapt fortran compiler (and maybe netcdf path), then execute it:
./compile_ALL.sh
# Create a directory where you will store all the netcdf files created along the following steps, e.g.:
mkdir $WORKDIR/input/nemo_${CONFIG} # WARNING: this must correspond to the namelist entry "config_dir"
#########################################################################################################
#########################################################################################################
## 3-- Build the bathymetry (and ice shelf draft if needed) and coordinates files for the regional domain.
./submit.sh extract_bathy_coord 01 ## -> should create the bathy and coordinate files,
## e.g. bathy_meter_WED12.nc and coordinates_WED12.nc
## (stored in directory defined as config_dir in the namelist)
#########################################################################################################
#########################################################################################################
## 4- Create mesh_mask file.
cd xxxxx ## TO BE IMPROVED
## NB: set jpni=jpnj=jpnij=0 in the &nammpp section of NEMO's namelist.
## and use the same &namdom parameters as in the simulation used as BDYs.
qsub run_nemo.sh ## this will create mesh_mask_${CONFIG}.nc before crashing
./rebuild_mesh_mask.sh 0
mv mesh_mask.nc $WORKDIR/input/nemo_${CONFIG}/mesh_mask_${CONFIG}.nc ## directory defined as config_dir
#########################################################################################################
#########################################################################################################
## 5- Create the initial state (temperature and salinity)
./submit.sh extract_istate 01 ## -> should create the initial state for temperature and salinity
## e.g. dta_temp_WED12.nc and dta_sal_WED12.nc
## (stored in directory defined as config_dir in the namelist)
#########################################################################################################
#########################################################################################################
## 5- Create the lateral boundary conditions (u, v, T, S, SSH, sea-ice thic, sea-ice frac)
./submit.sh build_coordinates_bdy 01 ## -> creates the coordinate file for lateral boundaries
## e.g. coordinates_bdy_WED12.nc
./submit.sh extract_bdy_gridT 01 15 ## -> creates T,S bdy files and store them in a BDY folder
## itself located in directory defined as config_dir
./submit.sh extract_bdy_gridU 01 15 ## -> creates U bdy files and store them in a BDY folder
./submit.sh extract_bdy_gridV 01 15 ## -> creates V bdy files and store them in a BDY folder
./submit.sh extract_bdy_icemod 01 ## -> creates ice bdy files and store them in a BDY folder
./submit.sh extract_bdy_ssh 01 ## -> creates SSH bdy files and store them in a BDY folder
./concatenate_yearly_BDY.sh ## Edit this file first.
## -> concatenate the bdy files into yearly files
./submit.sh extract_bdy_tides 01 ## if you want to put tidal signals along the BDYs
#########################################################################################################
#########################################################################################################
## 6- Other files (SSS for restoring, runoff, chlorophyll)
./submit.sh extract_SSS_restoring 01 15 ## -> creates SSS files and store them in a SSS folder
./concatenate_yearly_SSS.sh ## Edit this file first.
## -> concatenate the bdy files into yearly files
./submit.sh extract_runoff_icebergs 01 ## -> creates iceberg runoff file
## (stored in config_dir defined in the namelist)
./submit.sh extract_chloro 01 ## -> creates chlorophyll file
## (stored in config_dir defined in the namelist)
#########################################################################################################
#########################################################################################################
## 7- Weights for the interpolation of atmospheric forcing
# here it is assumed that you have NEMO downloaded and installed as explained in step #1
cd $WORKDIR/models/MY_NEMO/NEMOGCM/TOOLS
maketools -m X64_ADA -n WEIGHTS ## Adapt for any machine different from ADA (try makenemo -h)
cd WEIGHTS ## See nice README file in this directoy.
cp -p nocsutil/namelist_example_bilin namelist_WEIGHTS_${CONFIG}_bilin ## Edit this namelist
#NB: you may have to increase char_len in src/kinds_mod.f90 if you include long path for file names.
## Below is an example for namelist_WEIGHTS_${CONFIG}_bilin :
##
## &grid_inputs
## input_file = 'drowned_precip_DFS5.2_y1993.nc'
## nemo_file = 'coordinates_WED12.nc'
## datagrid_file = 'remap_data_grid.nc'
## nemogrid_file = 'remap_nemo_grid.nc'
## method = 'regular'
## input_lon = 'lon'
## input_lat = 'lat'
## nemo_lon = 'glamt'
## nemo_lat = 'gphit'
## nemo_mask = 'none'
## nemo_mask_value = 10
## input_mask = 'none'
## input_mask_value = 10
## /
##
## &remap_inputs
## num_maps = 1
## grid1_file = 'remap_data_grid.nc'
## grid2_file = 'remap_nemo_grid.nc'
## interp_file1 = 'data_nemo_bilin.nc'
## interp_file2 = 'nemo_data_bilin.nc'
## map1_name = 'data to nemo bilin Mapping'
## map2_name = 'nemo to data bilin Mapping'
## map_method = 'bilinear'
## normalize_opt = 'frac'
## output_opt = 'scrip'
## restrict_type = 'latitude'
## num_srch_bins = 90
## luse_grid1_area = .false.
## luse_grid2_area = .false.
## /
##
## &interp_inputs
## input_file = "drowned_precip_DFS5.2_y1993.nc"
## interp_file = "data_nemo_bilin.nc"
## input_name = "snow"
## input_start = 1,1,1,1
## input_stride = 1,1,1,1
## input_stop = 0,0,0,1
## input_vars = 'initial_time0_hours'
## /
##
## &interp_outputs
## output_file = "snow_orca.nc"
## output_mode = "create"
## output_dims = 'x', 'y', 'time_counter'
## output_scaling = "snow|1.0", "time_counter|86400.0"
## output_name = 'snow'
## output_lon = 'x'
## output_lat = 'y'
## output_vars = 'time_counter'
## output_attributes = 'time_counter|units|seconds since 1995-00-00 00:00:00',
## 'time_counter|calendar|noleap',
## 'snow|units|mm/s'
## /
##
## Then, execute these things:
./scripgrid.exe ## namelist_${CONFIG}_bilin
./scrip.exe ## namelist_${CONFIG}_bilin
./scripshape.exe ## namelist_${CONFIG}_bilin
## Then create another namelist: namelist_${CONFIG}_bicub and just change these parameters:
## interp_file1 = 'data_nemo_bicubic.nc'
## interp_file2 = 'nemo_data_bicubic.nc'
## map1_name = 'data to nemo bicubic Mapping'
## map2_name = 'nemo to data bicubic Mapping'
## map_method = 'bicubic'
## interp_file = "data_nemo_bicubic.nc"
## interp_file = 'data_nemo_bicubic.nc'
## output_file = 'weights_bicubic.nc'
## Then execute :
./scrip.exe ## namelist_${CONFIG}_bicub
./scripshape.exe ## namelist_${CONFIG}_bicub