updated installation scripts so it is self-contained

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

executables/compile_upload_siesta.sh

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+#!/bin/bash
+
+# This small script will compile and upload the executables to the
+# website
+base=$(pwd)
+SIESTA_DIR=/home/nicpa/siesta/4.1
+year=18
+
+_obj=ObjTutorial$year
+
+# First download and compile NetCDF
+./install_netcdf4.bash
+
+pushd $SIESTA_DIR
+
+# Prepare directory (ensure it is clean)
+rm -rf $_obj
+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
+
+../Src/obj_setup.sh
+
+function mmake {
+    local base=$1
+    shift
+    local suffix=$1
+    shift
+    make clean
+    make -j4 $@
+    [ $? -ne 0 ] && exit 1
+    scp $base tr:.p/sisl/workshop/$year/$base$suffix
+    [ $? -ne 0 ] && exit 1
+}
+
+mmake siesta ""
+mmake siesta _sse USE_SSE=1
+mmake siesta _avx USE_AVX=1
+mmake siesta _avx2 USE_AVX2=1
+
+cd ../Util/TS/TBtrans
+
+mmake tbtrans "" OBJDIR=$_obj
+mmake tbtrans _sse OBJDIR=$_obj USE_SSE=1
+mmake tbtrans _avx OBJDIR=$_obj USE_AVX=1
+mmake tbtrans _avx2 OBJDIR=$_obj USE_AVX2=1
+
+popd
+

executables/install_netcdf4.bash

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+#!/bin/bash
+
+# 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.
+#
+# 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.
+#
+# This script is released under the LGPL license.
+
+# 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
+# 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
+
+# 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
+
+echo "Installing libraries in folder: $ID"
+mkdir -p $ID
+
+# First we check that the user have downloaded the files
+function file_exists {
+    if [ ! -e $(pwd)/$1 ]; then
+	echo "I could not find file $1..."
+	echo "Please download the file and place it in this folder:"
+	echo " $(pwd)"
+	exit 1
+    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
+    fi
+}
+
+# Check for function $?
+function retval {
+    local ret=$1
+    local info="$2"
+    shift 2
+    if [ $ret -ne 0 ]; then
+	echo "Error: $ret"
+	echo "$info"
+	exit 1
+    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-${nf_v}.tar.gz
+unset dwn_file
+
+file_exists .zlib-${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-${z_v}.tar.gz
+    cd zlib-${z_v}
+    ./configure --prefix $ID
+    retval $? "zlib config"
+    make
+    retval $? "zlib make"
+    make test 2>&1 | tee zlib.test
+    retval $? "zlib make test"
+    make install
+    retval $? "zlib make install"
+    mv zlib.test $ID/
+    cd ../
+    rm -rf zlib-${z_v}
+    echo "Completed installing zlib"
+    [ -e $ID/lib64/libz.a ] && 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}
+    mkdir build ; cd build
+    ../configure --prefix=$ID --enable-static \
+		 --enable-fortran --with-zlib=$ID
+		 LDFLAGS="-L$ID/$zlib_lib -Wl,-rpath=$ID/$zlib_lib"
+    retval $? "hdf5 configure"
+    make
+    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 $ID/
+    cd ../../
+    rm -rf hdf5-${h_v}
+    echo "Completed installing hdf5"
+    [ -e $ID/lib64/libhdf5.a ] && hdf5_lib=lib64 || hdf5_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}
+    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"
+    retval $? "netcdf configure"
+    make
+    retval $? "netcdf make"
+    make install
+    retval $? "netcdf make install"
+    cd ../../
+    rm -rf netcdf-c-${nc_v}
+    echo "Completed installing C NetCDF library"
+    [ -e $ID/lib64/libnetcdf.a ] && cdf_lib=lib64 || cdf_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}
+    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/$cdf_lib \
+	-lnetcdf -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz" \
+		 --prefix=$ID --enable-static
+    retval $? "netcdf-fortran configure"
+    make
+    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 $ID/
+    cd ../../
+    rm -rf netcdf-fortran-${nf_v}
+    echo "Completed installing Fortran NetCDF library"
+else
+    echo "netcdf-fortran library already found."
+fi
+
+##########################
+# Completed installation #
+##########################
+
+echo ""
+echo "##########################"
+echo "# Completed installation #"
+echo "#   of NetCDF package    #"
+echo "#  and its dependencies  #"
+echo "##########################"
+echo ""
+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"
+fi
+echo "LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz"
+echo "COMP_LIBS += libncdf.a libfdict.a"
+echo "FPPFLAGS += -DCDF -DNCDF -DNCDF_4"
+echo ""

executables/static_gnu.make

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+### Notes
+# Compilation of static OpenBLAS with dynamic architecture may be
+# done like this:
+#   make clean
+#   make DYNAMIC_ARCH=1 USE_THREAD=1 NUM_THREADS=4 USE_OPENMP=1 BINARY=64 SANITY_CHECK=1 MAX_STACK_ALLOC=2048 NO_LAPACK=0 CC=gcc FC=gfortran libs
+# To install the NetCDF suite, simply do:
+#   ./install_netcdf4.bash
+
+# Define whether the program should be compiled with SSE/AVX/AVX2
+USE_SSE ?= 0
+USE_AVX ?= 0
+USE_AVX2 ?= 0
+
+.SUFFIXES:
+.SUFFIXES: .f .F .c .o .a .f90 .F90
+
+SIESTA_ARCH=x86_64-gfortran-serial-static
+FPP = gfortran
+FPP_OUTPUT=
+FC = gfortran
+FC_SERIAL = gfortran
+AR = gcc-ar
+RANLIB = gcc-ranlib
+SYS  = nag
+SP_KIND = 4
+DP_KIND = 8
+KINDS = $(SP_KIND) $(DP_KIND)
+
+# Generic paths
+#INC_PATH = -I/usr/local/include/ -I/usr/include/
+#LIB_PATH = -L/usr/local/lib -L/usr/lib
+
+# Add local paths for NetCDF4 installation and OpenBLAS
+INSTALL_NCDF4_PATH = /home/nicpa/siesta/ts-tbt-sisl-tutorial/executables/static-libs
+INC_PATH = -I$(INSTALL_NCDF4_PATH)/include
+LIB_PATH = -L$(INSTALL_NCDF4_PATH)/lib -L$(INSTALL_NCDF4_PATH)/lib64
+
+FFLAGS = -m64 -fPIC -O2 -ftree-vectorize -fexpensive-optimizations -fno-second-underscore $(INC_PATH)
+
+ifeq ($(USE_AVX2),1)
+  FFLAGS += -mavx2
+  USE_AVX := 1
+endif
+ifeq ($(USE_AVX),1)
+  FFLAGS += -mavx
+  USE_SSE := 1
+endif
+ifeq ($(USE_SSE),1)
+  FFLAGS += -msse2
+endif
+
+INCFLAGS += $(INC_PATH)
+
+FPPFLAGS = -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DNCDF -DNCDF_4
+COMP_LIBS = libncdf.a libfdict.a
+COMP_LIBS += libsiestaLAPACK.a libsiestaBLAS.a
+
+LDFLAGS = $(LIB_PATH)
+
+# These two flags should work:
+NETCDF_LIBS = -lnetcdff -lnetcdf
+
+# The hdf5 libraries may have different names
+#NETCDF_LIBS += -lhdf5 -lhdf5_serial 
+# Or
+#NETCDF_LIBS += -lhdf5
+NETCDF_LIBS += -lhdf5_hl -lhdf5
+
+# Finally add zlib (and dl which is needed for HDF5, but ain't used)
+NETCDF_LIBS += -lz -ldl
+
+LIBS += $(NETCDF_LIBS)
+
+# Ensure the executable is static
+FFLAGS += -static
+LDFLAGS += -static
+
+#Dependency rules are created by autoconf according to whether
+#discrete preprocessing is necessary or not.
+.F.o:
+	$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F)  $< 
+.F90.o:
+	$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $< 
+.f.o:
+	$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f)  $<
+.f90.o:
+	$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90)  $<