install_netcdf

#!/bin/bash
set -e
prog=$(basename $0)
dprog=$(dirname $0)
pid="$$"
# --------------------------------------------------------------------
#
# Bash script for installing the programs working with netcdf.
#
# Set parameters in Setup section below. Set also dictories to already installed packages.
#
# Prerequisites:          curl, c, c++, compilers (e.g., g++)
# Optional prerequisites: fortran compiler (e.g. gfortran), java compiler
#
# The following software versions were tested on Ubuntu 12.04 LTS Precise Pangolin
# and Mac OS X 10.7.5 and 10.9.1:
#   szip=2.1
#   hdf5=1.8.12
#   netcdf4=4.3.0
#   netcdf4_fortran=4.2
#   udunits=2.1.24
#   netcdf3=3.6.3
#   libpng=1.6.8
#   tiff=3.8.2
#   proj4=4.8.0
#   jasper=1.900.1
#   grip_api=1.11.0
#   cdo=1.6.2
#   ncview=2.1.2
#   gsl=1.12
#   antlr=2.7.7
#   nco=4.4.2
#
# Dependencies are:
#   hdf5            <- zlib, szip
#   netcdf4         <- hdf5
#   netcdf4_fortran <- netcdf4
#   grip_api        <- netcdf4, jasper, libpng
#   cdo             <- netcdf4, proj4, grip_api, udunits
#   nco             <- netcdf4, antlr v2 (not v3/4), gsl, udunits
#   ncview          <- netcdf4, udunits
#
# The websites to check for the latest versions are:
#   szip              - http://www.hdfgroup.org/ftp/lib-external/szip/
#   hdf5              - http://www.hdfgroup.org/ftp/HDF5/releases/
#   netcdf3/4_fortran - ftp://ftp.unidata.ucar.edu/pub/netcdf/
#   proj4             - http://download.osgeo.org/proj/
#   libpng            - http://sourceforge.net/projects/libpng/files/
#   jasper            - http://www.ece.uvic.ca/~frodo/jasper/
#   grip_api          - https://software.ecmwf.int/wiki/display/GRIB/Releases
#   udunits           - ftp://ftp.unidata.ucar.edu/pub/udunits/
#   cdo               - https://code.zmaw.de/projects/cdo/files
#   ncview            - ftp://cirrus.ucsd.edu/pub/ncview/
#   gsl               - ftp://ftp.gnu.org/gnu/gsl/
#   antlr             - http://www.antlr2.org/download.html
#   nco               - http://nco.sourceforge.net/src/
#   tiff              - http://download.osgeo.org/libtiff/
#
# Note
# - If some libraries are already installed such as png, set dolibpng=0 below.
#   One can set EXTRA_CPPFLAGS and EXTRA_LDFLAGS if the compilers do not find it automatically,
#   for example: EXTRA_LDFLAGS='-L/opt/local'
# - Do not untabify this script because the netcdf_fortran 4.2 patch will not work anymore.
# - UBUNTU
#   install the following software from package management via the command line
#   by typing sudo apt-get install <PACKAGE>
#   The package name is given in < > below
#     zlib=1.2.3.4 [installed by default]
#     libpng=1.2.46 <libpng12-dev>
#     tiff=3.9.5    <libtiff4-dev>
#     antlr=2.7.7   <libantlr-dev>
#   Do not forget to unselect the packages below
#     dolibpng=0
#     dotiff=0
#     doantlr=0
#
# authors: Stephan Thober, Matthias Cuntz
# created: Feb 2014
#
# --------------------------------------------------------------------

# --------------------------------------------------------------------
# Setup

# Where to install
prefix=/usr/local

# Which steps to do
# steps are: 1. download, 2. unpack, 3. configure, make, install, 4. clean-up
download=1   # 1: curl sources, 0: skip
docheck=1    # 1: make check, 2: make check but do not exit on errors, 0: skip
dormtar=1    # 1: rm downloaded sources, 0: skip
dosudo=1     # 1: install in ${prefix} with sudo, 0: install as user

# What is to be installed in which version (setup list)
doszip=1
  szip=2.1
dohdf5=1
  hdf5=1.8.12
donetcdf4=1
  netcdf4=4.3.0
donetcdf4_fortran=1
  netcdf4_fortran=4.2
doudunits=1
  udunits=2.1.24
donetcdf3=1
  netcdf3=3.6.3
dolibpng=0
  libpng=1.6.9
dotiff=0
  tiff=3.8.2 # 4.0.3 did not work on Mac OS X 10.7.5
doproj4=1
  proj4=4.8.0
dojasper=1
  jasper=1.900.1
dogrib_api=1
  grib_api=1.11.0
docdo=1
  cdo=1.6.2
doncview=1
  ncview=2.1.2
dogsl=1
  gsl=1.12 # > 1.12 has some strange chmod a-w for gsl-config and gsl.pc
doantlr=0
  antlr=2.7.7
donco=1
  nco=4.4.2

# Install netcdf-fortran for which Fortran compilers
fortran_compilers="gfortran"
#fortran_compilers="nagfor"

# Extra CPPFLAGS and LDFLAGS, for example for libs in non-default path such as /opt/lib
EXTRA_CPPFLAGS="-I/usr/include"
EXTRA_LDFLAGS="-L/usr/lib"

# Path to zlib's include/ lib/ directories
ZPATH=/usr

# Path to curl lib (libcurl.*) for cdo
CURLLIB=/usr/lib

# Path to X-devel for ncview. Searches for example checking X11/Intrinsic.h and X11/Xaw/Simple.h
XPATH=/usr
XLIB=${XPATH}/lib/X11
XINC=${XPATH}/include/X11
SYSTEM_DIR=/usr
SYSTEM_LIBDIR=/usr/lib/x86_64-linux-gnu

# --------------------------------------------------------------------
# Function

function download_unpack () {
    base=${1}
    zbase=${2}
    http=${3}
    # download
    if [[ ${download} -eq 1 ]] ; then curl -L ${http}/${zbase} -o ${zbase} ; fi
    # extract
    case "${zbase#${base}}" in
        ".tar")     tar -xvf  ${zbase} ;;
        ".tar.bz")  tar -xvjf ${zbase} ;;
        ".tar.bz2") tar -xvjf ${zbase} ;;
        ".tar.gz")  tar -xvzf ${zbase} ;;
        ".tar.z")   tar -xvZf ${zbase} ;;
        ".tar.Z")   tar -xvZf ${zbase} ;;
        ".zip")     unzip     ${zbase} ;;
        *) printf "Error: compression not known ${zbase#${base}}\n\n" 1>&2; exit 1;;
    esac
}

function make_install () {
    base=${1}
    zbase=${2}
    bconf=${3}
    aconf=${4}
    # cd
    cd ${base}
    # configure
    eval "${bconf}" LDFLAGS=\"-L${prefix}/lib ${EXTRA_LDFLAGS}\" \
        CPPFLAGS=\"-I${prefix}/include ${EXTRA_CPPFLAGS}\" \
        ./configure --prefix=${iprefix} ${aconf}
    # make
    make
    # check
    case ${docheck} in
        1) make check ;;
        2) set +e ; make check ; set -e ;;
        *) : ;;
    esac
    # install
    if [[ ${dosudo} -eq 1 ]] ; then
        echo ${supw} | sudo -S make install
    else
        make install
    fi
}

function cleanup () {
    base=${1}
    zbase=${2}
    # clean up
    rm -r ${base}
    if [[ ${dormtar} -eq 1 ]] ; then rm ${zbase} ; fi
}

function download_make_install () {
    base=${1}
    zbase=${2}
    http=${3}
    bconf=${4}
    aconf=${5}
    download_unpack ${base} ${zbase} ${http}
    make_install ${base} ${zbase} "${bconf}" "${aconf}"
    cd ..
    cleanup ${base} ${zbase}
}


# --------------------------------------------------------------------
# Start

# System: darwin, ...
sys=$(uname -s | tr [A-Z] [a-z])
iprefix=${prefix}

# get sudo password
if [[ ${dosudo} -eq 1 ]] ; then
    printf "\n"
    read -rs -p "sudo password for make install into ${prefix}: " supw
    printf "\n\n"
fi

# build szip
if [[ ${doszip} -eq 1 ]] ; then
    printf 'Build szip\n'
    base=szip-${szip}
    zbase=${base}.tar.gz
    http=http://www.hdfgroup.org/ftp/lib-external/szip/${szip}/src
    download_make_install ${base} ${zbase} ${http}
fi

# build hdf5 # Jude was building the hdf5 also with nagfor
if [[ ${dohdf5} -eq 1 ]] ; then
    printf 'Build hdf5\n'
    base=hdf5-${hdf5}
    zbase=${base}.tar.gz
    http=http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-${hdf5}/src
    download_make_install ${base} ${zbase} ${http} " " "--with-zlib=${ZPATH} --with-szlib=${prefix}"
fi

# build netcdf4 C
if [[ ${donetcdf4} -eq 1 ]] ; then
    printf 'build netcdf4-C\n'
    base=netcdf-${netcdf4}
    zbase=${base}.tar.gz
    http=ftp://ftp.unidata.ucar.edu/pub/netcdf
    download_unpack ${base} ${zbase} ${http}
    if [[ "${sys}" == "darwin" ]] ; then
	sed -e '/<stdio.h>/a\
#include <config.h>/' ${base}/ncgen3/load.c > load.c.${pid}
	mv load.c.${pid} ${base}/ncgen3/load.c
    fi
    make_install ${base} ${zbase} " " "--disable-dap-remote-tests"
fi

# build netcdf4-fortran
if [[ ${donetcdf4_fortran} -eq 1 ]] ; then
    printf 'Build netcdf4-fortran\n'
    base=netcdf-fortran-${netcdf4_fortran}
    zbase=${base}.tar.gz
    http=ftp://ftp.unidata.ucar.edu/pub/netcdf
    download_unpack ${base} ${zbase} ${http}
    # patch libtool for netcdf4.2
    if [[ "${netcdf4_fortran}" == "4.2" ]] ; then
        # sed -n -e "/begin.netcdf${netcdf4_fortran}.patch/,/end.netcdf${netcdf4_fortran}.patch/p" ${dprog}/${prog} \
        #     > patchit.${pid}
        # patch ${base}/m4/libtool.m4 patchit.${pid}
        sed -n -e "/nagbegin.netcdf${netcdf4_fortran}.patch/,/nagend.netcdf${netcdf4_fortran}.patch/p" \
	    ${dprog}/${prog} > patchit.${pid}
        patch -R ${base}/m4/libtool.m4 patchit.${pid}
        rm patchit.${pid}
    fi
    # configure / make / check / install for all fortran compilers
    for f_comp in ${fortran_compilers} ; do
        case ${f_comp} in
            *gfortran*)
                printf "Build ${base}-${f_comp}\n"
		EXTRA_CPPFLAGS="${EXTRA_CPPFLAGS} -DgFortran"
		iprefix=${prefix}/${base}-${f_comp}
		make_install ${base} ${zbase} "FC=${f_comp}"
		EXTRA_CPPFLAGS="${EXTRA_CPPFLAGS% ?*}"
		iprefix=${prefix}
                ;;
            *nag*)
                printf "Build ${base}-${f_comp}\n"
		# EXTRA_CPPFLAGS="${EXTRA_CPPFLAGS}"
		iprefix=${prefix}/${base}-${f_comp}
		make_install ${base} ${zbase} "FC=${f_comp} FCFLAGS='-O3 -fpp -mismatch_all -kind=byte -ieee=stop' FFLAGS='-O3 -fpp -mismatch_all -kind=byte -ieee=stop'" " "
		# EXTRA_CPPFLAGS="${EXTRA_CPPFLAGS% ?*}"
		iprefix=${prefix}
	        # patch libtool on Gnu/Linux systems
	        if [[ "${sys}" == "linux" ]] ; then
                    sed -n -e "/nagbegin.netcdf${netcdf4_fortran}.patch/,/nagend.netcdf${netcdf4_fortran}.patch/p" \
	    ${dprog}/${prog} > patchit.${pid}
		    patch libtool patchit.${pid}
		    rm patchit.${pid}
		fi
                ;;
            *)
                printf "${prog}: Fortran compiler not known: ${f_comp}.\n\n"
                continue
                ;;
        esac
        # clean for next fortran compiler
        make clean
	cd ..
    done
    cleanup ${base} ${zbase}
fi

# build netcdf3
if [[ ${donetcdf3} -eq 1 ]] ; then
    printf 'Build netcdf3\n'
    base=netcdf-${netcdf3}
    zbase=${base}.tar.gz
    http=ftp://ftp.unidata.ucar.edu/pub/netcdf
    download_unpack ${base} ${zbase} ${http}
    # configure / make / check / install for all fortran compilers
    for f_comp in ${fortran_compilers} ; do
        case ${f_comp} in
            *gfortran*)
                printf "Build ${base}-${f_comp}\n"
		EXTRA_CPPFLAGS="${EXTRA_CPPFLAGS} -DgFortran"
		iprefix=${prefix}/${base}-${f_comp}
		make_install ${base} ${zbase} "FC=${f_comp}" "--enable-shared --enable-f90"
		EXTRA_CPPFLAGS="${EXTRA_CPPFLAGS% ?*}"
		iprefix=${prefix}
                ;;
            *nag*)
                printf "Build ${base}-${f_comp}\n"
		EXTRA_CPPFLAGS="${EXTRA_CPPFLAGS} -DNAGf90Fortran"
		iprefix=${prefix}/${base}-${f_comp}
		make_install ${base} ${zbase} "FC=${f_comp} F77=${f_comp} FCFLAGS='-O3 -fpp -mismatch_all -kind=byte -unsharedf95 -ieee=full' FFLAGS='-O3 -fpp -mismatch_all -kind=byte -unsharedf95 -ieee=full -fixed -dusty'" "--enable-shared --enable-f90"
		EXTRA_CPPFLAGS="${EXTRA_CPPFLAGS% ?*}"
		iprefix=${prefix}
                ;;
            *)
                printf "${prog}: Fortran compiler not known: ${f_comp}.\n\n"
                continue
                ;;
        esac
        # clean for next fortran compiler
        make clean
	cd ..
    done
    cleanup ${base} ${zbase}
fi

# build udunits
if [[ ${doudunits} -eq 1 ]] ; then
    printf 'build udunits\n'
    base=udunits-${udunits}
    zbase=${base}.tar.gz
    http=ftp://ftp.unidata.ucar.edu/pub/udunits
    download_make_install ${base} ${zbase} ${http}
fi

# build libpng
if [[ ${dolibpng} -eq 1 ]] ; then
    printf 'build libpng\n'
    base=libpng-${libpng}
    zbase=${base}.tar.gz
    http=http://downloads.sourceforge.net/project/libpng/libpng16/${libpng}
    download_make_install ${base} ${zbase} ${http}
fi

# build tiff
if [[ ${dotiff} -eq 1 ]] ; then
    printf 'build tiff\n'
    base=tiff-${tiff}
    zbase=${base}.tar.gz
    http=http://download.osgeo.org/libtiff
    download_make_install ${base} ${zbase} ${http}
fi

# build proj4
if [[ ${doproj4} -eq 1 ]] ; then
    printf 'build proj4\n'
    base=proj-${proj4}
    zbase=${base}.tar.gz
    http=http://download.osgeo.org/proj
    download_make_install ${base} ${zbase} ${http}
fi

# build jasper
if [[ ${dojasper} -eq 1 ]] ; then
    printf 'build jasper\n'
    base=jasper-${jasper}
    zbase=${base}.zip
    http=http://www.ece.uvic.ca/~frodo/jasper/software
    download_make_install ${base} ${zbase} ${http}
fi

# build grib_api
if [[ ${dogrib_api} -eq 1 ]] ; then
    printf 'build grib_api\n'
    base=grib_api-${grib_api}
    zbase=${base}.tar.gz
    http=https://software.ecmwf.int/wiki/download/attachments/3473437
    download_unpack ${base} ${zbase} ${http}
    # change all files to be writeable, otherwise rm asks to override -r--r--r on Mac OS X
    chmod -R u+w ${base}
    # make install
    make_install ${base} ${zbase}
    cd ..
    cleanup ${base} ${zbase}
fi

# build cdo
if [[ ${docdo} -eq 1 ]] ; then
    printf 'build cdo\n'
    base=cdo-${cdo}
    zbase=${base}.tar.gz
    http=https://code.zmaw.de/attachments/download/6764
    download_unpack ${base} ${zbase} ${http}
    # patch cdo 
    if [[ (${cdo} == '1.6.2')  ]]; then
    	# patch grid reference.c
    	printf '23d22\n< #include <curl/types.h>\n' | patch --input=- ${base}/src/gridreference.c
    	# patch job.c
    	printf '352d351\n< #  include <curl/types.h>\n' | patch --input=- ${base}/src/job.c
    fi
    make_install ${base} ${zbase} " " "--prefix=${prefix} --with-szlib=${prefix} --with-hdf5=${SYSTEM_DIR} --with-jasper=${SYSTEM_DIR} --with-grib_api=${SYSTEM_DIR} --with-proj=${SYSTEM_DIR} --with-udunits2=${SYSTEM_LIBDIR} --with-curl=${SYSTEM_DIR} --with-netcdf=${SYSTEM_DIR}"
fi

# build gsl
if [[ ${dogsl} -eq 1 ]] ; then
    printf 'build gsl\n'
    base=gsl-${gsl}
    zbase=${base}.tar.gz
    http=ftp://ftp.gnu.org/gnu/gsl
    download_make_install ${base} ${zbase} ${http}
fi

# build antlr
if [[ ${doantlr} -eq 1 ]] ; then
    printf 'build antlr\n'
    base=antlr-${antlr}
    zbase=${base}.tar.gz
    http=http://www.antlr2.org/download
    download_make_install ${base} ${zbase} ${http}
fi

# build nco
if [[ ${donco} -eq 1 ]] ; then
    printf 'build nco\n'
    base=nco-${nco}
    zbase=${base}.tar.gz
    http=http://nco.sourceforge.net/src
    download_unpack ${base} ${zbase} ${http}
    # change some unknown LaTeX
    sed -e '/textdegree/d' ${base}/doc/nco.texi > tmp.${pid}
    mv tmp.${pid} ${base}/doc/nco.texi
    # make install
    make_install ${base} ${zbase} "GSL_ROOT=${prefix} ANTLR_ROOT=${SYSTEM_DIR} PATH_TO_NCGEN=${SYSTEM_DIR}/bin/ncgen NETCDF_INC=${SYSTEM_DIR}/include NETCDF_LIB=${SYSTEM_DIR}/lib NETCDF4_ROOT=${SYSTEM_DIR} UDUNITS2_PATH=${SYSTEM_DIR}" "--enable-dap-netcdf --enable-gsl"
    cd ..
    cleanup ${base} ${zbase}
fi

# build ncview
if [[ ${doncview} -eq 1 ]] ; then
    printf 'build ncview\n'
    base=ncview-${ncview}
    zbase=${base}.tar.gz
    http=ftp://cirrus.ucsd.edu/pub/ncview
    download_unpack ${base} ${zbase} ${http}
    # change some defaults in code
    sed -e '/^#define DEFAULT_BLOWUP[[:blank:]]/s/DEFAULT_BLOWUP.*/DEFAULT_BLOWUP 8/' \
        -e '/^#define DEFAULT_MIN_MAX_METHOD[[:blank:]]/s/DEFAULT_MIN_MAX_METHOD.*/DEFAULT_MIN_MAX_METHOD MIN_MAX_METHOD_EXHAUST/' \
        -e '/^#define DEFAULT_BLOWUP_TYPE[[:blank:]]/s/DEFAULT_BLOWUP_TYPE.*/DEFAULT_BLOWUP_TYPE BLOWUP_REPLICATE/' \
        -e '/^#define DEFAULT_AUTO_OVERLAY[[:blank:]]/s/DEFAULT_AUTO_OVERLAY.*/DEFAULT_AUTO_OVERLAY FALSE/' \
        -e '/options.blowup[[:blank:]]\{1,\}=/s/blowup[[:blank:]]\{1,\}=.*/blowup = DEFAULT_BLOWUP;/' \
        -e '/options.beep_on_restart[[:blank:]]\{1,\}=/s/beep_on_restart[[:blank:]]\{1,\}=.*/beep_on_restart = TRUE;/' \
        ${base}/src/ncview.c > tmp.${pid}
    mv tmp.${pid} ${base}/src/ncview.c
    # Mac OS X uses .dylib for shared libraries, .so hardcoded in configure
    if [[ "${sys}" == "darwin" ]] ; then
	sed -e 's/\.so/.dylib/' -e '/RPDIR=/s/RPDIR=.*/RPDIR=${word:2}/' ${base}/configure > tmp.${pid}
	mv tmp.${pid} ${base}/configure
	chmod +x ${base}/configure
    fi
    # make install
    make_install ${base} ${zbase} " " "--prefix=${prefix} --with-nc_config=${NC_DIR}/bin/nc-config --with-udunits2_incdir=${PNG_INCDIR}/include --with-udunits2_libdir=${PNG_LIBDIR} --x-libraries=${XLIB} --x-includes=${XINC} --with-png_incdir=${PNG_INCDIR}/include --with-png_libdir=${PNG_LIBDIR}"
    cd ..
    cleanup ${base} ${zbase}
fi

# --------------------------------------------------------------------
# Finish

exit 0

# --------------------------------------------------------------------
# netcdf4.2 patch for nagfor found on Unidata website
# begin.netcdf4.2.patch
# 4054,4058d4053
# *** netcdf-fortran-4.2/m4/libtool.m4	2011-09-27 08:17:58.000000000 -0600
# --- netcdf-fortran-4.2.new/m4/libtool.m4	2012-10-30 20:00:55.000000000 -0600
# ***************
# *** 4051,4056 ****
# --- 4051,4062 ----
#   	_LT_TAGVAR(lt_prog_compiler_pic, $1)='--shared'
#   	_LT_TAGVAR(lt_prog_compiler_static, $1)='--static'
#   	;;
# +       # NAG 5.3.1
# +       nag*)
# + 	_LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,-Wl,,'
# + 	_LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
# + 	_LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
# + 	;;
#         pgcc* | pgf77* | pgf90* | pgf95* | pgfortran*)
#           # Portland Group compilers (*not* the Pentium gcc compiler,
#   	# which looks to be a dead project)
# ***************
# *** 4477,4482 ****
# --- 4483,4491 ----
#   	lf95*)				# Lahey Fortran 8.1
#   	  _LT_TAGVAR(whole_archive_flag_spec, $1)=
#   	  tmp_sharedflag='--shared' ;;
# + 	nag*)				# NAG 5.3.1
# +           _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience ${wl}$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive'
# + 	  tmp_sharedflag='-pic -Wl,-shared' ;;
#   	xl[[cC]]* | bgxl[[cC]]* | mpixl[[cC]]*) # IBM XL C 8.0 on PPC (deal with xlf below)
#   	  tmp_sharedflag='-qmkshrobj'
#   	  tmp_addflag= ;;
# # end.netcdf4.2.patch

# # --------------------------------------------------------------------
# # netcdf4.2 patch for nagfor from NAG support - attention wrong way round, use patch -R
# # nagbegin.netcdf4.2.patch
# 4054,4058d4053
# <       nagfor*)
# <         _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,-Wl,,'
# <         _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
# <         _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
# <         ;;
# 4485,4488d4479
# <       nagfor*) # NAG Fortran 5.3
# <         _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"`,-Wl,,--no-whole-archive'
# <         tmp_sharedflag='-Wl,-shared'
# <           ;;
# 4515,4517d4505
# <       nagfor*) # NAG Fortran 5.3
# <         _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag"' $libobjs $deplibs $compiler_flags ${wl}-soname,,$soname -o $lib'
# <           ;;
# nagend.netcdf4.2.patch