From b568539bc7f6b52fac4c453d4b00e73c84abca6a Mon Sep 17 00:00:00 2001 From: jpolton <jelt@noc.ac.uk> Date: Thu, 21 Mar 2019 21:09:00 +0000 Subject: [PATCH] add auto scripts --- SCRIPTS/create_coordinates.sh | 15 +++++++++++++++ SCRIPTS/fix_elevation.sh | 17 +++++++++++++++++ SCRIPTS/load_modules_1.sh | 5 +++++ SCRIPTS/load_modules_2.sh | 4 ++++ SCRIPTS/main1.sh | 25 ++++++++++++++++++++++++ SCRIPTS/make_directories.sh | 9 +++++++++ SCRIPTS/make_domain_cfg.sh | 8 ++++++++ SCRIPTS/make_nemo.sh | 19 ++++++++++++++++++ SCRIPTS/make_paths.sh | 18 ++++++++++++++++++ SCRIPTS/make_tools.sh | 23 ++++++++++++++++++++++ SCRIPTS/make_xios.sh | 12 ++++++++++++ SCRIPTS/python_script.sh | 27 ++++++++++++++++++++++++++ SCRIPTS/python_tide.sh | 8 ++++++++ SCRIPTS/scri.sh | 4 ++++ SCRIPTS/setup_python_obc.sh | 36 +++++++++++++++++++++++++++++++++++ SCRIPTS/setup_python_tide.sh | 33 ++++++++++++++++++++++++++++++++ 16 files changed, 263 insertions(+) create mode 100755 SCRIPTS/create_coordinates.sh create mode 100755 SCRIPTS/fix_elevation.sh create mode 100755 SCRIPTS/load_modules_1.sh create mode 100755 SCRIPTS/load_modules_2.sh create mode 100755 SCRIPTS/main1.sh create mode 100755 SCRIPTS/make_directories.sh create mode 100755 SCRIPTS/make_domain_cfg.sh create mode 100755 SCRIPTS/make_nemo.sh create mode 100755 SCRIPTS/make_paths.sh create mode 100755 SCRIPTS/make_tools.sh create mode 100755 SCRIPTS/make_xios.sh create mode 100755 SCRIPTS/python_script.sh create mode 100755 SCRIPTS/python_tide.sh create mode 100644 SCRIPTS/scri.sh create mode 100755 SCRIPTS/setup_python_obc.sh create mode 100755 SCRIPTS/setup_python_tide.sh diff --git a/SCRIPTS/create_coordinates.sh b/SCRIPTS/create_coordinates.sh new file mode 100755 index 0000000..b07f9bd --- /dev/null +++ b/SCRIPTS/create_coordinates.sh @@ -0,0 +1,15 @@ +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 diff --git a/SCRIPTS/fix_elevation.sh b/SCRIPTS/fix_elevation.sh new file mode 100755 index 0000000..1e4acc8 --- /dev/null +++ b/SCRIPTS/fix_elevation.sh @@ -0,0 +1,17 @@ +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 $WDIR diff --git a/SCRIPTS/load_modules_1.sh b/SCRIPTS/load_modules_1.sh new file mode 100755 index 0000000..c39cbef --- /dev/null +++ b/SCRIPTS/load_modules_1.sh @@ -0,0 +1,5 @@ +module unload nco cray-netcdf cray-hdf5 +module swap PrgEnv-cray PrgEnv-intel +module load cray-netcdf-hdf5parallel +module load cray-hdf5-parallel +module load svn diff --git a/SCRIPTS/load_modules_2.sh b/SCRIPTS/load_modules_2.sh new file mode 100755 index 0000000..fb2253c --- /dev/null +++ b/SCRIPTS/load_modules_2.sh @@ -0,0 +1,4 @@ +module unload cray-netcdf-hdf5parallel cray-hdf5-parallel +module load cray-netcdf cray-hdf5 +module load nco/4.5.0 + diff --git a/SCRIPTS/main1.sh b/SCRIPTS/main1.sh new file mode 100755 index 0000000..9ed7c6e --- /dev/null +++ b/SCRIPTS/main1.sh @@ -0,0 +1,25 @@ +echo "Making Paths" +. ./make_paths.sh > main_output.txt 2>&1 +echo "Making Directories" +. ./make_directories.sh >> main_output.txt 2>&1 +echo "Loading modules (Intel)" +. ./load_modules_1.sh >> main_output.txt 2>&1 +echo "Installing XIOS_2.0 - this will take 5-10 mins" +. ./make_xios.sh >> main_output.txt 2>&1 +echo "Installing NEMO - this will take a good 10/15 mins - make sure you have an NEMO account!" +echo "WARNING - this automatically chooses OPA_SRC only" +echo "If you want to choose anything else e.g. LIM_SRC, remove the echo in make_nemo.sh" +. ./make_nemo.sh >> main_output.txt 2>&1 +echo "Compiling various grid tools" +. ./make_tools.sh >> main_output.txt 2>&1 +echo "Creating coordinate file" +. ./create_coordinates.sh >> main_output.txt 2>&1 +echo "Loading other netcdf modules" +. ./load_modules_2.sh >> main_output.txt 2>&1 +echo "Removing land" +. ./fix_elevation.sh >> main_output.txt 2>&1 +echo "Interpolating GEBCO on to our domain" +. ./interpolate_gebco.sh >> main_output.txt 2>&1 +echo "We stop here. Inspect bathy_meter.nc in " +$DOMAIN +echo "Before continuing to make domain_cfg.nc in the next step." diff --git a/SCRIPTS/make_directories.sh b/SCRIPTS/make_directories.sh new file mode 100755 index 0000000..e113a36 --- /dev/null +++ b/SCRIPTS/make_directories.sh @@ -0,0 +1,9 @@ +mkdir $SBC +mkdir $TIDE +mkdir $OBC +mkdir $RUND +mkdir $EXP +mkdir $DOMAIN +mkdir $NEMO +mkdir $ICS +mkdir $ARCH1 diff --git a/SCRIPTS/make_domain_cfg.sh b/SCRIPTS/make_domain_cfg.sh new file mode 100755 index 0000000..feebab7 --- /dev/null +++ b/SCRIPTS/make_domain_cfg.sh @@ -0,0 +1,8 @@ +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 diff --git a/SCRIPTS/make_nemo.sh b/SCRIPTS/make_nemo.sh new file mode 100755 index 0000000..0f38c9b --- /dev/null +++ b/SCRIPTS/make_nemo.sh @@ -0,0 +1,19 @@ +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 $WDIR diff --git a/SCRIPTS/make_paths.sh b/SCRIPTS/make_paths.sh new file mode 100755 index 0000000..c762a26 --- /dev/null +++ b/SCRIPTS/make_paths.sh @@ -0,0 +1,18 @@ +export CONFIG=INDIAN_OCEAN_AUTO +export WORK=/work/n01/n01/$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 diff --git a/SCRIPTS/make_tools.sh b/SCRIPTS/make_tools.sh new file mode 100755 index 0000000..018ced4 --- /dev/null +++ b/SCRIPTS/make_tools.sh @@ -0,0 +1,23 @@ +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 + diff --git a/SCRIPTS/make_xios.sh b/SCRIPTS/make_xios.sh new file mode 100755 index 0000000..7f19a95 --- /dev/null +++ b/SCRIPTS/make_xios.sh @@ -0,0 +1,12 @@ +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 $WDIR diff --git a/SCRIPTS/python_script.sh b/SCRIPTS/python_script.sh new file mode 100755 index 0000000..80eb75e --- /dev/null +++ b/SCRIPTS/python_script.sh @@ -0,0 +1,27 @@ +module unload anaconda +module load anaconda/2.2.0-python2 + +rm -rf ~/.conda +yes | conda create --name nrct_env scipy=0.17.0 numpy matplotlib basemap netcdf4 libgfortran=1.0.0 +source activate nrct_env +yes | conda install -c https://conda.anaconda.org/conda-forge seawater=3.3.4 # Note had to add https path +yes | conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler +yes | conda install -c https://conda.anaconda.org/srikanthnagella pyjnius + +#module load java +LD_LIBRARY_PATH=/opt/java/jdk1.8.0_51/jre/lib/amd64/server/:$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 + + + diff --git a/SCRIPTS/python_tide.sh b/SCRIPTS/python_tide.sh new file mode 100755 index 0000000..648088d --- /dev/null +++ b/SCRIPTS/python_tide.sh @@ -0,0 +1,8 @@ +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_ diff --git a/SCRIPTS/scri.sh b/SCRIPTS/scri.sh new file mode 100644 index 0000000..ee61c23 --- /dev/null +++ b/SCRIPTS/scri.sh @@ -0,0 +1,4 @@ +module unload anaconda +module load anaconda/2.2.0-python2 + +git clone https://ashbre@bitbucket.org/jdha/nrct.git $WORK/nrct diff --git a/SCRIPTS/setup_python_obc.sh b/SCRIPTS/setup_python_obc.sh new file mode 100755 index 0000000..6218bed --- /dev/null +++ b/SCRIPTS/setup_python_obc.sh @@ -0,0 +1,36 @@ +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 diff --git a/SCRIPTS/setup_python_tide.sh b/SCRIPTS/setup_python_tide.sh new file mode 100755 index 0000000..e0170a4 --- /dev/null +++ b/SCRIPTS/setup_python_tide.sh @@ -0,0 +1,33 @@ +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 -- GitLab