maint: bumping versions and updated install scripts

Signed-off-by: Nick Papior <[email protected]>

executables/compile_upload_siesta.sh

@@ -3,13 +3,15 @@
 # This small script will compile and upload the executables to the
 # website
 base=$(pwd)
-SIESTA_DIR=/home/nicpa/siesta/4.1
-year=18
+SIESTA_DIR=/home/nicpa/siesta/siesta
+year=20
 
 _obj=ObjTutorial$year
 
 # First download and compile NetCDF
-./install_netcdf4.bash
+_ncdf_prefix=/home/nicpa/siesta/netcdf-serial
+./install_netcdf4.bash -p $_ncdf_prefix --single-directory
+[ $? -ne 0 ] && exit 1
 
 pushd $SIESTA_DIR
 
@@ -19,7 +21,6 @@ mkdir -p $_obj
 cd $_obj
 
 # Ensure arch.make exists
-rm -f arch.make
 [ ! -e $base/static_gnu.make ] && echo "Failed to find static_gnu.make" && exit 1
 ln -s $base/static_gnu.make arch.make
 
@@ -31,7 +32,7 @@ function mmake {
     local suffix=$1
     shift
     make clean
-    make -j4 $@
+    make -j4 INSTALL_NCDF4_PATH=$_ncdf_prefix $@
     [ $? -ne 0 ] && exit 1
     scp $base tr:.p/sisl/workshop/$year/$base$suffix
     [ $? -ne 0 ] && exit 1

executables/install_netcdf4.bash

@@ -3,7 +3,7 @@
 # Installation script for zlib, hdf5, netcdf-c and netcdf-fortran
 # with complete CDF-4 support (in serial).
 # This installation script has been written by:
-#  Nick R. Papior, 2016-2018.
+#  Nick R. Papior, 2016-2020.
 #
 # The author takes no responsibility of damage done to your hardware or
 # software. It is up to YOU that the script executes the correct commands.
@@ -13,28 +13,89 @@
 # VERY BASIC installation script of required libraries
 # for installing these packages:
 #   zlib-1.2.11
-#   hdf5-1.8.21
-#   netcdf-c-4.6.1
-#   netcdf-fortran-4.4.4
+#   hdf5-1.12.0
+#   netcdf-c-4.7.2
+#   netcdf-fortran-4.5.2
 # If you want to change your compiler version you should define the
 # global variables that are used for the configure scripts to grab the
 # compiler, they should be CC and FC. Also if you want to compile with
 # different flags you should export those variables; CFLAGS, FFLAGS.
 
 # If you have downloaded other versions edit these version strings
 z_v=1.2.11
-h_v=1.8.21
-nc_v=4.6.1
-nf_v=4.4.4
+h_v=1.12.0
+nc_v=4.7.2
+nf_v=4.5.2
 
 # Install path, change accordingly
 # You can change this variable to control the installation path
 # If you want the installation path to be a "packages" folder in
 # your home directory, change to this:
 # ID=$HOME/packages
-ID=$(pwd)/static-libs
+if [ -z $PREFIX ]; then
+    ID=$(pwd)/build
+else
+    ID=$PREFIX
+fi
+# Decide whether everything is installed in 1 directory
+_single_dir=1
+
+while [ $# -gt 0 ]; do
+    opt=$1 ; shift
+    case $opt in
+	--prefix|-p)
+	    ID=$1 ; shift
+	    ;;
+	--libz-version|-libz-v)
+	    z_v=$1 ; shift
+	    ;;
+	--hdf5-version|-hdf5-v)
+	    h_v=$1 ; shift
+	    ;;
+	--netcdf-c-version|-nc-v)
+	    nc_v=$1 ; shift
+	    ;;
+	--netcdf-f-version|-nf-v)
+	    nf_v=$1 ; shift
+	    ;;
+	--single-directory)
+	    _single_dir=1
+	    ;;
+	--separate-directory)
+	    _single_dir=0
+	    ;;
+	--help|-h)
+	    echo " $0 --help shows this message"
+	    echo ""
+	    echo "These options are available:"
+	    echo ""
+	    echo "  --prefix|-p : specify the installation directory of the libraries"
+	    echo "  --libz-version|-libz-v : specify the libz version (default: $z_v)"
+	    echo "  --hdf5-version|-hdf5-v : specify the HDF5 version (default: $h_v)"
+	    echo "  --netcdf-c-version|-nc-v : specify the NetCDF-C version (default: $nc_v)"
+	    echo "  --netcdf-f-version|-nf-v : specify the NetCDF-fortran version (default: $nf_v)"
+	    echo "  --single-directory : all libraries are installed in --prefix/{bin,lib,include} (default: YES)"
+	    echo "  --separe-directory : all libraries are installed in --prefix/<package>/<version>/{bin,lib,include} (default: NO)"
+	    echo ""
+	    exit 0
+	    ;;
+    esac
+done
+
 
 echo "Installing libraries in folder: $ID"
+echo ""
+echo "Using these software versions:"
+echo "  libz    : $z_v"
+echo "  hdf5    : $h_v"
+echo "  netcdf-c: $nc_v"
+echo "  netcdf-f: $nf_v"
+echo ""
+echo "If you want other versions, please try $0 --help and check the options"
+echo "  Will wait 2 sec before proceeding"
+echo ""
+sleep 2
+
 mkdir -p $ID
 
 # First we check that the user have downloaded the files
@@ -47,12 +108,26 @@ function file_exists {
     fi
 }
 
-# First we check that the user have downloaded the files
-function dwn_file {
-    [ -e $2 ] && return 0
-    wget -O $2 $1
-    if [ $? -ne 0 ]; then
-	rm -f $2
+# Download a file, if able and the file does not exist
+which wget > /dev/null
+if [ $? -eq 0 ]; then
+    # success we can download using wget
+    function _dwn_file {
+	wget -O $1 $2
+    }
+else
+    function _dwn_file {
+	curl -o $1 $2
+    }
+fi
+
+# Use download function
+#  $1 is name of file
+#  $2 is URL
+function download_file {
+    if [ ! -e $(pwd)/$1 ] ; then
+	# Try and download
+	_dwn_file $1 $2
     fi
 }
 
@@ -68,117 +143,145 @@ function retval {
     fi
 }
 
-dwn_file http://zlib.net/zlib-${z_v}.tar.gz .zlib-${z_v}.tar.gz
-dwn_file https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-${h_v}/src/hdf5-${h_v}.tar.bz2 .hdf5-${h_v}.tar.bz2
-dwn_file https://github.com/Unidata/netcdf-c/archive/v${nc_v}.tar.gz .netcdf-c-${nc_v}.tar.gz
-dwn_file https://github.com/Unidata/netcdf-fortran/archive/v${nf_v}.tar.gz .netcdf-fortran-${nf_v}.tar.gz
-unset dwn_file
+# Download files if they can
+download_file zlib-${z_v}.tar.gz https://www.zlib.net/zlib-${z_v}.tar.gz
+download_file hdf5-${h_v}.tar.bz2 https://hdf-wordpress-1.s3.amazonaws.com/wp-content/uploads/manual/HDF5/HDF5_${h_v//./_}/source/hdf5-${h_v}.tar.bz2
+download_file netcdf-c-${nc_v}.tar.gz https://github.com/Unidata/netcdf-c/archive/v${nc_v}.tar.gz
+download_file netcdf-fortran-${nf_v}.tar.gz https://github.com/Unidata/netcdf-fortran/archive/v${nf_v}.tar.gz
 
-file_exists .zlib-${z_v}.tar.gz
-file_exists .hdf5-${h_v}.tar.bz2
-file_exists .netcdf-c-${nc_v}.tar.gz
-file_exists .netcdf-fortran-${nf_v}.tar.gz
+file_exists zlib-${z_v}.tar.gz
+file_exists hdf5-${h_v}.tar.bz2
+file_exists netcdf-c-${nc_v}.tar.gz
+file_exists netcdf-fortran-${nf_v}.tar.gz
 unset file_exists
 
 #################
 # Install z-lib #
 #################
-[ -e $ID/lib64/libz.a ] && zlib_lib=lib64 || zlib_lib=lib
-if [ ! -e $ID/$zlib_lib/libz.a ]; then
-    tar xfz .zlib-${z_v}.tar.gz
+if [ $_single_dir -eq 0 ]; then
+    zlib_dir=$ID/zlib/$z_v
+else
+    zlib_dir=$ID
+fi
+[ -d $zlib_dir/lib64 ] && zlib_lib=lib64 || zlib_lib=lib
+if [ ! -e $zlib_dir/$zlib_lib/libz.a ]; then
+    tar xfz zlib-${z_v}.tar.gz
     cd zlib-${z_v}
-    ./configure --prefix $ID
+    ./configure --prefix $zlib_dir/
     retval $? "zlib config"
-    make
+    make -j 2
     retval $? "zlib make"
     make test 2>&1 | tee zlib.test
     retval $? "zlib make test"
     make install
     retval $? "zlib make install"
-    mv zlib.test $ID/
+    mv zlib.test $zlib_dir/
     cd ../
     rm -rf zlib-${z_v}
     echo "Completed installing zlib"
-    [ -e $ID/lib64/libz.a ] && zlib_lib=lib64 || zlib_lib=lib
+    [ -d $zlib_dir/lib64 ] && zlib_lib=lib64 || zlib_lib=lib
 else
     echo "zlib directory already found."
 fi
 
 ################
 # Install hdf5 #
 ################
-[ -e $ID/lib64/libhdf5.a ] && hdf5_lib=lib64 || hdf5_lib=lib
-if [ ! -e $ID/$hdf5_lib/libhdf5.a ]; then
-    tar xfj .hdf5-${h_v}.tar.bz2
-    cd hdf5-${h_v}
+if [ $_single_dir -eq 0 ]; then
+    hdf_dir=$ID/hdf5/$h_v
+else
+    hdf_dir=$ID
+fi
+[ -d $hdf_dir/lib64 ] && hdf_lib=lib64 || hdf_lib=lib
+if [ ! -e $hdf_dir/$hdf_lib/libhdf5.a ]; then
+    rm -rf hdf5-$h_v
+    tar xfj hdf5-$h_v.tar.bz2
+    cd hdf5-$h_v
     mkdir build ; cd build
-    ../configure --prefix=$ID --enable-static \
-		 --enable-fortran --with-zlib=$ID
-		 LDFLAGS="-L$ID/$zlib_lib -Wl,-rpath=$ID/$zlib_lib"
+    ../configure --prefix=$hdf_dir \
+	--enable-shared --enable-static \
+	--enable-fortran --with-zlib=$zlib_dir \
+	LDFLAGS="-L$zlib_dir/$zlib_lib -Wl,-rpath=$zlib_dir/$zlib_lib"
     retval $? "hdf5 configure"
-    make
+    make -j 2
     retval $? "hdf5 make"
     make check-s 2>&1 | tee hdf5.test
     retval $? "hdf5 make check-s"
     make install
     retval $? "hdf5 make install"
-    mv hdf5.test $ID/
+    mv hdf5.test $hdf_dir/
     cd ../../
     rm -rf hdf5-${h_v}
     echo "Completed installing hdf5"
-    [ -e $ID/lib64/libhdf5.a ] && hdf5_lib=lib64 || hdf5_lib=lib
+    [ -d $hdf_dir/lib64 ] && hdf_lib=lib64 || hdf_lib=lib
 else
     echo "hdf5 directory already found."
 fi
 
 ####################
 # Install NetCDF-C #
 ####################
-[ -e $ID/lib64/libnetcdf.a ] && cdf_lib=lib64 || cdf_lib=lib
-if [ ! -e $ID/$cdf_lib/libnetcdf.a ]; then
-    tar xfz .netcdf-c-${nc_v}.tar.gz
-    cd netcdf-c-${nc_v}
+if [ $_single_dir -eq 0 ]; then
+    cdfc_dir=$ID/netcdf-c/$nc_v
+else
+    cdfc_dir=$ID
+fi
+[ -d $cdfc_dir/lib64 ] && cdfc_lib=lib64 || cdfc_lib=lib
+if [ ! -e $cdfc_dir/$cdfc_lib/libnetcdf.a ]; then
+    rm -rf netcdf-c-$nc_v
+    tar xfz netcdf-c-$nc_v.tar.gz
+    cd netcdf-c-$nc_v
     mkdir build ; cd build
-    ../configure --prefix=$ID --enable-static \
-		 --enable-netcdf-4 --disable-dap \
-		 CPPFLAGS="-I$ID/include" \
-		 LDFLAGS="-L$ID/$hdf5_lib -Wl,-rpath=$ID/$hdf5_lib -L$ID/$zlib_lib -Wl,-rpath=$ID/$zlib_lib"
+    ../configure --prefix=$cdfc_dir \
+	--enable-shared --enable-static \
+	--enable-netcdf-4 --disable-dap \
+	CPPFLAGS="-I$hdf_dir/include -I$zlib_dir/include" \
+	LDFLAGS="-L$hdf_dir/$hdf_lib -Wl,-rpath=$hdf_dir/$hdf_lib \
+-L$zlib_dir/$zlib_lib -Wl,-rpath=$zlib_dir/$zlib_lib"
     retval $? "netcdf configure"
-    make
+    make -j 2
     retval $? "netcdf make"
     make install
     retval $? "netcdf make install"
     cd ../../
-    rm -rf netcdf-c-${nc_v}
+    rm -rf netcdf-c-$nc_v
     echo "Completed installing C NetCDF library"
-    [ -e $ID/lib64/libnetcdf.a ] && cdf_lib=lib64 || cdf_lib=lib
+    [ -d $cdfc_dir/lib64 ] && cdfc_lib=lib64 || cdfc_lib=lib
 else
     echo "netcdf directory already found."
 fi
 
 ##########################
 # Install NetCDF-Fortran #
 ##########################
-if [ ! -e $ID/$cdf_lib/libnetcdff.a ]; then
-    tar xfz .netcdf-fortran-${nf_v}.tar.gz
-    cd netcdf-fortran-${nf_v}
+if [ $_single_dir -eq 0 ]; then
+    cdff_dir=$ID/netcdf-fortran/$nc_v
+else
+    cdff_dir=$ID
+fi
+[ -d $cdff_dir/lib64 ] && cdff_lib=lib64 || cdff_lib=lib
+if [ ! -e $cdff_dir/$cdff_lib/libnetcdff.a ]; then
+    rm -rf netcdf-fortran-$nf_v
+    tar xfz netcdf-fortran-$nf_v.tar.gz
+    cd netcdf-fortran-$nf_v
     mkdir build ; cd build
-    ../configure CPPFLAGS="-DgFortran -I$ID/include" \
-		 LIBS="-L$ID/$zlib_lib -Wl,-rpath=$ID/$zlib_lib \
-	-L$ID/$hdf5_lib -Wl,-rpath=$ID/$hdf5_lib \
-	-L$ID/$cdf_lib -Wl,-rpath=$ID/$cdf_lib \
+    ../configure CPPFLAGS="-DgFortran -I$zlib_dir/include \
+	-I$hdf_dir/include -I$cdfc_dir/include" \
+	LIBS="-L$zlib_dir/$zlib_lib -Wl,-rpath=$zlib_dir/$zlib_lib \
+	-L$hdf_dir/$hdf_lib -Wl,-rpath=$hdf_dir/$hdf_lib \
+	-L$cdfc_dir/$cdfc_lib -Wl,-rpath=$cdfc_dir/$cdfc_lib \
 	-lnetcdf -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz" \
-		 --prefix=$ID --enable-static
+	--prefix=$cdff_dir --enable-static --enable-shared
     retval $? "netcdf-fortran configure"
-    make
+    make -j 2
     retval $? "netcdf-fortran make"
     make check 2>&1 | tee check.fortran.serial
     retval $? "netcdf-fortran make check"
     make install
     retval $? "netcdf-fortran make install"
-    mv check.fortran.serial $ID/
+    mv check.fortran.serial $cdff_dir/
     cd ../../
-    rm -rf netcdf-fortran-${nf_v}
+    rm -rf netcdf-fortran-$nf_v
     echo "Completed installing Fortran NetCDF library"
 else
     echo "netcdf-fortran library already found."
@@ -199,13 +302,16 @@ echo ""
 
 echo "Please add the following to the BOTTOM of your arch.make file"
 echo ""
-echo "INCFLAGS += -I$ID/include"
-echo "LDFLAGS += -L$ID/$zlib_lib -Wl,-rpath=$ID/$zlib_lib"
-if [ $hdf5_lib != $zlib_lib ]; then
-    echo "LDFLAGS += -L$ID/$hdf5_lib -Wl,-rpath=$ID/$hdf5_lib"
-fi
-if [ $cdf_lib != $zlib_lib ]; then
-    echo "LDFLAGS += -L$ID/$cdf_lib -Wl,-rpath=$ID/$cdf_lib"
+# We only need the netcdf.mod file
+echo "INCFLAGS += -I$cdfc_dir/include"
+if [ $_single_dir -eq 0 ]; then
+    echo "LDFLAGS += -L$zlib_dir/$zlib_lib -Wl,-rpath=$zlib_dir/$zlib_lib"
+    echo "LDFLAGS += -L$hdf_dir/$hdf_lib -Wl,-rpath=$hdf_dir/$hdf_lib"
+    echo "LDFLAGS += -L$cdfc_dir/$cdfc_lib -Wl,-rpath=$cdfc_dir/$cdfc_lib"
+    echo "LDFLAGS += -L$cdff_dir/$cdff_lib -Wl,-rpath=$cdff_dir/$cdff_lib"
+else
+    # All have the same directory
+    echo "LDFLAGS += -L$ID/$zlib_lib -Wl,-rpath=$ID/$zlib_lib"
 fi
 echo "LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz"
 echo "COMP_LIBS += libncdf.a libfdict.a"