Singularity.jupyter3rttov

BootStrap: localimage
From: jupyter3.sif
# Bootstrap: shub
# From: MBlaschek/singularity-jupyter:jupyter3


%help
Container Centos 6.10 (docker)

Jupyter Notebook/Lab Server
Options:
  --NotebookApp.token='super-secret'  	Token when not using a password
  --ip=0.0.0.0   						port forwarding from VirtualBox
  --NotebookApp.base_url='/ipython/'	Directory path
  --port=????							Server port

Create Notebook Password (HOME/.jupyter/jupyter_notebook_config.json):
	jupyter notebook password

Check Jupyter paths:
	jupyter --paths

Anaconda Python 3 (Xarray, cfgrib, eccodes)
Eccodes and CFgrib are Software from ECMWF

Run RTTOV 12.3 inside a container
Download Rttov from https://www.nwpsaf.eu/site/software/rttov/download/#Software
into rttov directory (local)

RTTOV apps:
rthelp [execute] 	Creates a rtdoc directory and copies Documentation there.
rtcoef [execute]	Download RTTOV coeficient files (interactive)
atlas  [execute]	Download some Emissivity atlas data and BRDF atlas data
rttest [options]	Run RTTOV test suite (reuqires coefficient files), options: fwd, hires, solar, ...

%setup
	mkdir -p ${SINGULARITY_ROOTFS}/rttov
	mkdir -p ${SINGULARITY_ROOTFS}/rtcoef
	mkdir -p ${SINGULARITY_ROOTFS}/rtdoc

%files
	# DOC
	rttov/rttov-wrapper-python.pdf /rtdoc/RTTOV_Python_wrapper.pdf
	rttov/users_guide_rttov12_v1.3.pdf /rtdoc/RTTOV_User_guide_v12_v1.3.pdf
	# SRC
	# RTTOV Source is not available like this
	rttov/rttov123.tar.gz /rttov/rttov123.tar.gz
	rttov/Makefile.local /rttov/Makefile.local
	rttov/gfortran-anaconda /rttov/gfortran-anaconda
	run.sh /usr/bin

%apprun rthelp
	echo "RTTOV User guide and Python wrapper"
	echo "Supply execute as Argument to copy to ./rtdoc"
	echo "$@" | grep execute > /dev/null
	if [ $? -eq 0 ]; then
		mkdir -vp ./rtdoc
		cp -ruv /rtdoc/* ./rtdoc/
	fi

%apprun rtcoef
	echo "Download RTTOV coefficient files to your host"
	[ -z "$SINGULARITY_BIND" ] && echo -e "Bind /rtcoef to the container (RW) \n BASH ENV e.g.:    export SINGULARITY_BIND=\"${PWD}/rtcoef:/rtcoef\""
	echo "Supply execute as argument to run rttov_coef_download.sh"
	echo "$@" | grep execute > /dev/null
	if [ $? -eq 0 ]; then
		mkdir -vp ./rtcoef
		cp -nruv /rttov/rtcoef_backup/* ./rtcoef
		cd ./rtcoef
		# comment out directory check
		sed -i '159,174 {s/^/#/}' rttov_coef_download.sh
		exec ./rttov_coef_download.sh
	fi

%apprun atlas
	echo "Download Emissivity/ BRDF Atlas data"
	echo "Goto: https://www.nwpsaf.eu/site/software/rttov/download/ and Download Emis data"
	echo "Here only: UW IR atlas data and BRDF atlas data are downloaded"
	[ -z "$SINGULARITY_BIND" ] && echo -e "Bind /emis_data to the container (RW) \n BASH ENV e.g.:    export SINGULARITY_BIND=\"${PWD}/emis_data:/emis_data\""
	echo "Supply execute as argument to run rttov_coef_download.sh"
	echo "$@" | grep execute > /dev/null
	if [ $? -eq 0 ]; then
		if [ ! -d /emis_data ]; then
			mkdir -f /emis_data
		fi
		cd /emis_data
		wget https://www.nwpsaf.eu/downloads/emis_data/uw_ir_emis_atlas_hdf5.tar
		tar xvf *.tar
		wget https://nwp-saf.eumetsat.int/downloads/emis_data/telsem2_mw_atlas.tar.bz2
		# wget https://www.nwpsaf.eu/downloads/emis_data/telsem2_mw_atlas.tbz
		tar xjvf *.bz2
		if [ ! -d /brdf_data ]; then
			mkdir -f /brdf_data
		fi
		cd /brdf_data
		wget https://www.nwpsaf.eu/downloads/brdf_data/cms_brdf_atlas_hdf5.tar
		tar xvf *.tar
	fi

%apprun rttest
	echo "Running the test suite"
	cat <<EOF
Options:
	Default (no options) runs test_rttov12.sh
	fwd  	: forward model
	hires	: hires IR sounders
	solar	: visible/near-IR solar
	multi	: multiple instruments together
	pc		: principal components
	htfrtc	: HTFRTC
EOF
	[ -z "$SINGULARITY_BIND" ] && echo -e "Bind /rtcoef to the container \n e.g.:    export SINGULARITY_BIND=\"${PWD}/rtcoef:/rtcoef\""
	[ -z "$SINGULARITY_BIND" ] || echo "Found Bind: $SINGULARITY_BIND"
	#
	# Make Test directory
	# /tmp/rttest
	# /tmp/rttest/rttov_test
	# /tmp/rttest/rtcoef_rttov??
	#
	mkdir -p /tmp/rttest
	cd /tmp/rttest
	#
	# Copy tests
	#
	cp -urf /rttov/rttov_test . && echo "Tests copied to /tmp/rttest"
	# Link Coefficients
	ln -fvs /rtcoef rtcoef_rttov${RTTOV_VERSION} && echo "Coefficients linked"
	ln -fvs /emis_data . && echo "Emis Atlas linked"
	ln -fvs /brdf_data . && echo "BDRF Atlas linked"
	cd rttov_test
	echo
	echo "#####################################################"
	echo "Testting: "
	echo "$@" | grep fwd > /dev/null
	if [ $? -eq 0 ]; then
		./test_fwd.sh ARCH=gfortran-anaconda BIN=../../usr/local/bin
	fi
	echo "$@" | grep hires > /dev/null
	if [ $? -eq 0 ]; then
		./test_rttov12_hires.sh ARCH=gfortran-anaconda BIN=../../usr/local/bin
	fi

	echo "$@" | grep solar > /dev/null
	if [ $? -eq 0 ]; then
		./test_solar.sh ARCH=gfortran-anaconda BIN=../../usr/local/bin
	fi
	echo "$@" | grep multi > /dev/null
	if [ $? -eq 0 ]; then
		./test_multi_instrument.sh ARCH=gfortran-anaconda BIN=../../usr/local/bin
	fi
	echo "$@" | grep pc > /dev/null
	if [ $? -eq 0 ]; then
		./test_pc.sh ARCH=gfortran-anaconda BIN=../../usr/local/bin
	fi
	if [ $# -eq 0 ]; then
		./test_rttov12.sh ARCH=gfortran-anaconda BIN=../../usr/local/bin
	fi

	echo "rttest used /tmp/rttest"
	echo "Finished"

%runscript
	# mkdir -p $JUPYTER_RUNTIME_DIR
	# mkdir -p $JUPYTER_DATA_DIR
	# mkdir -p $JUPYTERLAB_DIR
	exec /usr/bin/run.sh "$@"

%post
	# Additonal
	yum check-update && yum -y update
	# gfortran
	yum groupinstall -y "Development Tools"
	yum install -y cmake doxygen graphviz chrpath
	# install gfortran from anaconda
	/opt/conda/bin/conda install gfortran_linux-64 gxx_linux-64 sphinx -y
	# conda install libgfortran -y
	# need netcdf.mod
	/opt/conda/bin/conda install -c conda-forge netcdf-fortran -y
	# Clean
	yum clean all

	# required for CMAKE
	export PATH=/opt/conda/bin:$PATH
	export LD_LIBRARY_PATH=/opt/conda/lib:$LD_LIBRARY_PATH
	export RTTOV_VERSION=12
	#
	# Compile
	#
	cd /rttov
	if [ ! -e rttov123.tar.gz ]; then
		echo "Error, Download RTTOV https://www.nwpsaf.eu/site/software/rttov/download/#Software"
		echo "Save into rttov/ directory"
		exit 1
	    # wget ftp://srvx1.img.univie.ac.at/pub/upload/mblaschek/rttov123.tar.gz
	fi
	tar -xzf rttov*.tar.gz
	#
	# Potentiall add bug fixes tar's here end overwrite
	#
	if false; then
		echo "No Bug fixes yet"
	fi
	#
	# Copy Makefile.local (HDF, Netcdf libs from Conda)
	#
	mv Makefile.local ./build
	mv gfortran-anaconda ./build/arch
	#
	# Compile using conda gfortran + hdf, netcdf, f2py
	#
	cd src/
	../build/Makefile.PL RTTOV_HDF=1 RTTOV_F2PY=1 RTTOV_USER_LAPACK=0
	make ARCH=gfortran-anaconda INSTALLDIR=../usr/local
	#
	# Backup std coef-files and make links
	# Host can bind coef-files to container (/rtcoef)
	#
	cd ..
	mv rtcoef_rttov${RTTOV_VERSION} rtcoef_backup
	rm -rf rtcoef_rttov*
	ln -s /rtcoef/ rtcoef_rttov${RTTOV_VERSION}
	cp -rfv rtcoef_backup/* /rtcoef
	# emis
	mkdir /emis_data
	rm -rf emis_data/
	ln -s /emis_data/ emis_data
	mkdir /brdf_data
	rm -rf brdf_data/
	ln -s /brdf_data brdf_data
	#
	# Fix links of F2py libs
	#
	cd wrapper
	ln -sf /usr/local/lib/rttov_wrapper_f2py.so .
	cd ../gui
	ln -sf /usr/local/lib/rttov_gui_f2py.so .
	cd ..
	#
	# Python Wrapper
	#
	cd wrapper
	#
	# make library accessable from python
	#
	echo "/rttov/wrapper" > /opt/conda/lib/python3.7/site-packages/rttov.pth
	#
	# Documentation of Python Interface
	#
	doxygen doxygen_config_wrapper
	mv doxygen_doc_wrapper/html /rtdoc/wrapper
	cd pyrttov_doc
	make html
	mv _build/html /rtdoc/pyrttov
	cd ..
	mkdir -p /rtdoc/pyexamples
	cp *.py /rtdoc/pyexamples/
	cd ..
	mv *.pdf /rtdoc
	# Clean
	/opt/conda/bin/conda clean -a -y

%environment
	# important part otherwise the server will try to access /run/user and fail
	export JUPYTER_RUNTIME_DIR=$PWD/.runtime
	# Make sure we use container kernels
	export JUPYTER_DATA_DIR=$PWD/.kernels
	# Development
	export JUPYTERLAB_DIR=$PWD/.lab
	#
	export PATH=/opt/conda/bin:$PATH
	export LD_LIBRARY_PATH=/opt/conda/lib:/usr/local/lib:$LD_LIBRARY_PATH
	# RTTOV Options
	export RTTOV_VERSION=12
	export OMP_STACKSIZE=1000M
	export RTTOV_DIR=/rttov
	export RTTOV_COEF=/rtcoef