add auto scripts

SCRIPTS/create_coordinates.sh

+cd $TDIR/NESTING
+
+
+ln -s $GFILE/DOMAIN/rotated/coordinates_ORCA_R12.nc $TDIR/NESTING/.
+cp $GFILE/DOMAIN/namelist.input $TDIR/NESTING/
+
+./agrif_create_coordinates.exe
+
+cp 1_coordinates_ORCA_R12.nc $DOMAIN/coordinates.nc
+
+
+#cp $START_FILES/GRIDO* $INPUTS/.
+#cp $START_FILES/namelist_reshape_bilin_gebco $INPUTS/.
+
+cd $WDIR

SCRIPTS/fix_elevation.sh

+cd $DOMAIN
+
+cp $GFILE/DOMAIN/$BATHY $DOMAIN
+
+
+
+ncks -d longitude,60.,110. -d latitude,0.,30. $BATHY cutdown_bathy.nc
+
+ncap2 -s 'where(depth > 0) depth=0' cutdown_bathy.nc tmp.nc
+
+ncflint --fix_rec_crd -w -1.0,0.0 tmp.nc tmp.nc bathy_in.nc
+
+rm tmp.nc
+rm $BATHY
+rm cutdown_bathy.nc
+
+cd $WDIR

SCRIPTS/load_modules_1.sh

+module unload nco cray-netcdf cray-hdf5
+module swap PrgEnv-cray PrgEnv-intel
+module load cray-netcdf-hdf5parallel
+module load cray-hdf5-parallel
+module load svn

SCRIPTS/load_modules_2.sh

+module unload cray-netcdf-hdf5parallel cray-hdf5-parallel
+module load cray-netcdf cray-hdf5
+module load nco/4.5.0
+

SCRIPTS/main1.sh

+echo "Making Paths"
+. ./make_paths.sh                                 > main_output.txt 2>&1
+echo "Making Directories"
+. ./make_directories.sh                          >> main_output.txt 2>&1
+echo "Loading modules (Intel)"
+. ./load_modules_1.sh                            >> main_output.txt 2>&1
+echo "Installing XIOS_2.0 - this will take 5-10 mins"
+. ./make_xios.sh                                 >> main_output.txt 2>&1
+echo "Installing NEMO - this will take a good 10/15 mins - make sure you have an NEMO account!"
+echo "WARNING - this automatically chooses OPA_SRC only"
+echo "If you want to choose anything else e.g. LIM_SRC, remove the echo in make_nemo.sh"
+. ./make_nemo.sh                                 >> main_output.txt 2>&1
+echo "Compiling various grid tools"
+. ./make_tools.sh                                >> main_output.txt 2>&1
+echo "Creating coordinate file"
+. ./create_coordinates.sh                        >> main_output.txt 2>&1
+echo "Loading other netcdf modules"
+. ./load_modules_2.sh                            >> main_output.txt 2>&1
+echo "Removing land"
+. ./fix_elevation.sh                             >> main_output.txt 2>&1
+echo "Interpolating GEBCO on to our domain"
+. ./interpolate_gebco.sh                         >> main_output.txt 2>&1
+echo "We stop here. Inspect bathy_meter.nc in "
+$DOMAIN
+echo "Before continuing to make domain_cfg.nc in the next step."

SCRIPTS/make_directories.sh

+mkdir $SBC
+mkdir $TIDE
+mkdir $OBC
+mkdir $RUND
+mkdir $EXP
+mkdir $DOMAIN
+mkdir $NEMO
+mkdir $ICS
+mkdir $ARCH1

SCRIPTS/make_domain_cfg.sh

+cp $DOMAIN/coordinates.nc     $TDIR/DOMAINcfg/.
+cp $DOMAIN/bathy_meter.nc     $TDIR/DOMAINcfg/.
+cp $GFILE/DOMAIN/namelist_cfg  $TDIR/DOMAINcfg/.
+cp $GFILE/DOMAIN/rs.pbs        $TDIR/DOMAINcfg/.
+cp $WDIR/make_paths.sh        $TDIR/DOMAINcfg/.
+
+cd $TDIR/DOMAINcfg
+qsub  rs.pbs

SCRIPTS/make_nemo.sh

+svn co http://forge.ipsl.jussieu.fr/nemo/svn/trunk/NEMOGCM@8395 $NEMO/trunk_NEMOGCM_r8395
+
+cp $ARCH/arch-XC_ARCHER_INTEL.fcm $CDIR/../ARCH/
+
+cd $CDIR
+
+printf 'y\nn\nn\nn\nn\nn\nn\nn\n' | ./makenemo -n $CONFIG -m XC_ARCHER_INTEL -j 10
+
+./makenemo -n $CONFIG -m XC_ARCHER_INTEL -j 10 clean
+
+
+cp $GFILE/f_files/* $CDIR/$CONFIG/MY_SRC/.
+cp $GFILE/cpp_file.fcm $CONFIG/cpp_$CONFIG.fcm
+
+./makenemo -n $CONFIG -m XC_ARCHER_INTEL -j 10
+
+cp  $XIOS_DIR/bin/xios_server.exe $EXP/xios_server.exe
+
+cd $WDIR

SCRIPTS/make_paths.sh

+export CONFIG=INDIAN_OCEAN_AUTO
+export WORK=/work/n01/n01/$USER
+export WDIR=$WORK/$CONFIG
+export NEMO=$WORK/NEMO/
+export DOMAIN=$WDIR/DOMAIN
+export SBC=$WDIR/SURFACE_FORCING
+export TIDE=$WDIR/TIDAL_FORCING
+export OBC=$WDIR/BOUNDARY_FORCING
+export ICS=$WDIR/INITIAL_CONDITIONS
+export CDIR=$NEMO/trunk_NEMOGCM_r8395/CONFIG
+export TDIR=$NEMO/trunk_NEMOGCM_r8395/TOOLS
+export RUND=$WDIR/RUN_DIRECTORY/
+export EXP=$RUND/$CONFIG
+export GFILE=$WORK/GENERIC_NEMO_FILES
+export ARCH=$GFILE/ARCH
+export XIOS_DIR=$WORK/xios-2.0_r1242
+export BATHY=global_merged2.nc
+export ARCH1=$WORK/ARCH

SCRIPTS/make_tools.sh

+cd $TDIR
+
+cp $ARCH/arch-XC_ARCHER_INTEL_NOXIOS.fcm ../ARCH/.
+cp $ARCH/arch-XC_ARCHER_INTEL_XIOS1.fcm  ../ARCH/.
+
+
+cd $TDIR/WEIGHTS/src
+
+patch -b < $GFILE/p_files/scripinterp_mod.patch
+patch -b < $GFILE/p_files/scripinterp.patch
+patch -b < $GFILE/p_files/scrip.patch
+patch -b < $GFILE/p_files/scripshape.patch
+patch -b < $GFILE/p_files/scripgrid.patch
+
+cd $TDIR
+
+./maketools -n NESTING -m XC_ARCHER_INTEL_NOXIOS -j 6
+./maketools -m XC_ARCHER_INTEL_XIOS1 -n DOMAINcfg
+./maketools -m XC_ARCHER_INTEL_XIOS1 -n REBUILD_NEMO
+./maketools -m XC_ARCHER_INTEL_XIOS1 -n WEIGHTS
+
+cd $WDIR
+

SCRIPTS/make_xios.sh

+cd $WORK
+
+svn co -r1242 http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk $XIOS_DIR
+cd $XIOS_DIR
+
+cp $ARCH/arch-XC30_ARCHER* arch/.
+
+./make_xios --full --prod --arch XC30_ARCHER --netcdf_lib netcdf4_par
+
+ln -s  $XIOS_DIR  $WORK/XIOS
+
+cd $WDIR

SCRIPTS/python_script.sh

+module unload anaconda
+module load anaconda/2.2.0-python2
+
+rm -rf ~/.conda
+yes | conda create --name nrct_env scipy=0.17.0 numpy matplotlib basemap netcdf4 libgfortran=1.0.0
+source activate nrct_env
+yes | conda install -c https://conda.anaconda.org/conda-forge seawater=3.3.4 # Note had to add https path
+yes | conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler
+yes | conda install -c https://conda.anaconda.org/srikanthnagella pyjnius
+
+#module load java
+LD_LIBRARY_PATH=/opt/java/jdk1.8.0_51/jre/lib/amd64/server/:$LD_LIBRARY_PATH
+
+
+
+cd $WORK/nrct/Python
+
+python setup.py build
+export PYTHONPATH=~/.conda/envs/nrct_env/lib/python2.7/site-packages/:$PYTHONPATH
+
+python setup.py install --prefix ~/.conda/envs/nrct_env
+
+#cd $TIDE
+#pynemo -s namelist.bdy
+
+
+

SCRIPTS/python_tide.sh

+cd $WORK/nrct/Python
+
+git checkout Generalise-tide-input
+
+python setup.py build
+export PYTHONPATH=~/.conda/envs/nrct_env/lib/python2.7/site-packages/:$PYTHONPATH
+
+python setup.py install --prefix ~/.conda/envs/nrct_

SCRIPTS/scri.sh

+module unload anaconda
+module load anaconda/2.2.0-python2
+
+git clone https://ashbre@bitbucket.org/jdha/nrct.git $WORK/nrct

SCRIPTS/setup_python_obc.sh

+module unload anaconda/2.2.0-python2
+
+module load anaconda
+
+git clone https://ashbre@bitbucket.org/jdha/nrct.git $WORK/nrct
+
+module unload anaconda
+
+module load anaconda/2.2.0-python2
+
+
+
+yes | conda create --name nrct_obc scipy=0.17.0 numpy matplotlib basemap netcdf4 libgfortran=1.0.0
+source activate nrct_obc
+
+yes | conda install -c https://conda.anaconda.org/conda-forge seawater=3.3.4 # Note had to add https path
+yes | conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler
+yes | conda install -c https://conda.anaconda.org/srikanthnagella pyjnius
+
+#module load java
+LD_LIBRARY_PATH=/opt/java/jdk1.8.0_51/jre/lib/amd64/server/:$LD_LIBRARY_PATH
+
+source deactivate nrct_obc
+
+git clone https://jpolton@bitbucket.org/jdha/nrct.git $WORK/nrct
+
+cd $WORK/nrct/Python
+
+git checkout ORCA0083
+
+python setup.py build
+export PYTHONPATH=~/.conda/envs/nrct_obc/lib/python2.7/site-packages/:$PYTHONPATH
+
+python setup.py install --prefix ~/.conda/envs/nrct_obc
+
+cd $WDIR

SCRIPTS/setup_python_tide.sh

+module unload anaconda/2.2.0-python2
+
+module load anaconda
+
+git clone https://ashbre@bitbucket.org/jdha/nrct.git $WORK/nrct
+
+module unload anaconda
+
+module load anaconda/2.2.0-python2
+
+
+yes | conda create --name nrct_tide scipy=0.17.0 numpy matplotlib basemap netcdf4 libgfortran=1.0.0
+source activate nrct_tide
+yes | conda install -c https://conda.anaconda.org/conda-forge seawater=3.3.4 # Note had to add https path
+yes | conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler
+yes | conda install -c https://conda.anaconda.org/srikanthnagella pyjnius
+
+#module load java
+LD_LIBRARY_PATH=/opt/java/jdk1.8.0_51/jre/lib/amd64/server/:$LD_LIBRARY_PATH
+
+source deactivate nrct_tide
+
+
+cd $WORK/nrct/Python
+
+git checkout Generalise-tide-input
+
+python setup.py build
+export PYTHONPATH=~/.conda/envs/nrct_tide/lib/python2.7/site-packages/:$PYTHONPATH
+
+python setup.py install --prefix ~/.conda/envs/nrct_tide
+
+cd $WDIR