Helpful instructions for installing libraries to support ASCAT_sir processing

In theory, standard system libraries should be used.  These instructions are 
for installing these libraries locally.  For convenience, downloads of 
recent linux version are included.

hdf5-1.10.1.tar.gz
netcdf-c-4.5.0.tar.gz
netcdf-fortran-4.4.4.tar.gz
lloyd-yajl-2.1.0-0-ga0ecdde.zip
gsl-2.4.tar.gz

First locally install HDF5, then netcdf-c, then netcdf-fortran using w/gcc 
and gfortran support.  Finally create yajl and gsl.

Note: png, jpeg, z, and curl libraries are also used, but they usually part
of a standard linux install so are not separately included.

#####################
# set default compiler flags
CC="gcc"
CFLAGS="-m64 -O2"
LDFLAGS=""
LIBS=""
CPPFLAGS=""
CPP=""
# note: including the -ff2c interfaces g77 and gfortran but breaks hdf4 
# testing, so not used
F77="gfortran"  
FFLAGS="-m64 -O2" # "-ffixed-line-length-255 -frecord-marker=4 -ff2c"
F90="gfortran"  
F90FLAGS="-m64 -O2" # "-ffixed-line-length-255 -frecord-marker=4 -ff2c"
F90LIBS=""
export CC CFLAGS LDFLAGS LIBS CPPFLAGS CPP F77 FFLAGS F90 F90FLAGS F90LIBS

# define install location
HDFDIR="/home/long/src/linux/ascat/current_sir_practice/ascat_sir/libs"
export HDFDIR

NOTE: For this "local" install, the shared libraries have been disabled.
However, this is not, in general, required.

# HDF5
gunzip hdf5-1.10.1.tar.gz
tar xvf hdf5-1.10.1.tar
cd hdf5-1.10.1
./configure --disable-shared --enable-static-exec --prefix=${HDFDIR} --enable-fortran
make clean
make
make check
make install
cd ..

# NETCDF4-C
gunzip netcdf-c-4.5.0.tar.gz
tar xf netcdf-c-4.5.0.tar
cd netcdf-c-4.5.0
# modify flags to point to hdf4 and hdf5 libraries
CFLAGS="-m64 -O2 -I${HDFDIR}/include"
LDFLAGS="-L${HDFDIR}/lib -L/usr/lib64/"
#LIBS="-lhdf5 -lhdf5_hl -lhdf5_fortran -lhdf5hl_fortran -lmfhdf -ldf -ljpeg -lm"
LIBS="-lhdf5 -lhdf5_hl -lhdf5_fortran -lhdf5hl_fortran -ljpeg -lm"
export CFLAGS LDFLAGS LIBS
## Note: --enable-hdf4 does not work -- does not pass checks
#configure --disable-shared --prefix=${HDFDIR} --enable-fortran --enable-hdf4
./configure --disable-shared --prefix=${HDFDIR} --enable-fortran # --enable-hdf4
make clean
make
make install
# note: got some errors when doing testing, install anywaq
make check
cd ..

# NETCDF4-fortran
gunzip netcdf-fortran-4.4.4.tar.gz
tar xf netcdf-fortran-4.4.4.tar
cd netcdf-fortran-4.4.4
CFLAGS="-m64 -O2 -I${HDFDIR}/include"
LDFLAGS="-L${HDFDIR}/lib -L/usr/lib64/"
#LIBS="-lhdf5 -lhdf5_hl -lhdf5_fortran -lhdf5hl_fortran -lmfhdf -ldf -ljpeg -lm"
LIBS="-lhdf5 -lhdf5_hl -lhdf5_fortran -lhdf5hl_fortran -ljpeg -lnetcdf -lm"
export CFLAGS LDFLAGS LIBS
./configure --enable-static --disable-shared --prefix=${HDFDIR} # --disable-f03 
make clean
make
make install
make check
cd ..

# YAJL
unzip lloyd-yajl-2.1.0-0-ga0ecdde.zip
cd lloyd-yajl-66cb08c
# Unfortunately, yajl requires cmake, which requires installing it from 
# http://cmake.org  
# I found that on my system, I could edit the configure file to change
# line 41 from "cmake -DCMAKE..." to "cmake3 -DCMAKE..." and then 
# execute configure
./configure --enable-static --disable-shared --prefix=${HDFDIR}
make
# make install
# note: yajl does not recognize the local install prefix flag and tries 
# to create its sharable output in /usr/local/lib/, which causes an error.
# Instead, we can do a manual "install" (copy) of key files into
# our local library area
cp build/yajl-2.1.0/lib/libyajl_s.a ${HDFDIR}/lib/
cp -R build/yajl-2.1.0/include/yajl ${HDFDIR}/include/


# GSL
gunzip gsl-2.4.tar.gz
tar xf gsl-2.4.tar
cd gsl-2.4
./configure --enable-static --disable-shared --prefix=${HDFDIR}
make
# note: I got a "fail" error on one part of the checking, but this
# does not seem to affect the results
make check
make install