Updating fork to latest rcps version

CPMD_Intel_MPI_install

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+#!/usr/bin/env bash
+
+###############################################
+# Installing CPMD: MPI with Intel compilers
+#
+# by Brian Alston, May 2017 
+#
+# Using Ian's require function to load modules
+#
+# Will need modules: see list of modules below.
+
+VERSION=${VERSION:-4.1}
+PLATFORM=${PLATFORM:-INTEL-MPI}
+INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/CPMD/$VERSION/Intel-MPI}
+SRC_ARCHIVE_CPMD=${SRC_ARCHIVE_CPMD:-cpmd-v$VERSION.tar.gz}
+SRC_ARCHIVE_CPMD2CUBE=${SRC_ARCHIVE_CPMD2CUBE:-cpmd2cube.tar.gz}
+SRC_ARCHIVE_LOCATION=${SRC_ARCHIVE_LOCATION:-/shared/ucl/apps/CPMD/sources/}
+PATCHES="patch_3808-3812.txt patch_3812-3813.txt patch_3815-3816.txt"
+LOG_LOCATION=${LOG_LOCATION:-~/Software/CPMD}
+
+export PATH=$INSTALL_PREFIX/bin:$PATH
+
+dirname=$(dirname $0 2>/dev/null || pwd)
+INCLUDES_DIR=${INCLUDES_DIR:-${dirname}/includes}
+source ${INCLUDES_DIR}/module_maker_inc.sh
+source ${INCLUDES_DIR}/require_inc.sh
+
+require rcps-core/1.0.0
+require compilers/intel
+require mpi/intel
+
+if [ ! -f $SRC_ARCHIVE_LOCATION/$SRC_ARCHIVE_CPMD ]
+then
+    echo ""
+    echo "***** ERROR: Cannot find CPMD archive"
+    echo ""
+    echo "You need to download the CPMD source archive from the CPMD download portal"
+    echo "(http://cpmd.org/download) using your license login. Note: both Latest"
+    echo "Distribution and pathes are needed. Also the additional packages: "
+    echo "cpmd2cube.tar.gz."
+    echo "Place them somewhere in your file-system and set the SRC_ARCHIVE_*"
+    echo "variables appropriately."
+    echo ""
+    exit 1
+fi
+
+
+temp_dir=`mktemp -d -p /dev/shm`
+cd $temp_dir
+
+# Firstly CPMD
+
+echo "***** Building CPMD ..."
+
+# Unpack source archive, apply patches and configure for building in install location.
+
+tar xvzf $SRC_ARCHIVE_LOCATION/$SRC_ARCHIVE_CPMD
+cd CPMD
+
+for p in $PATCHES
+do
+    echo "Applying patch $p ..."
+    patch -p0 < $SRC_ARCHIVE_LOCATION/$p
+done
+
+INSTALL_LOC=$INSTALL_PREFIX
+mkdir -p $INSTALL_LOC
+./configure.sh -DEST=$INSTALL_LOC LINUX-X86_64-INTEL-MPI
+
+cd $INSTALL_LOC
+
+# Need to fix Makefile before building on Legion/Grace/Thomas
+
+cp Makefile Makefile_orig
+sed -e '/CPP =/s/-C//' -e '/FC = /s/mpif90/mpiifort/' -e '/LD =/s/mpif90/mpiifort/' Makefile_orig > Makefile
+
+# Build in install location.
+
+echo "Compiling ..."
+make 2>&1 | tee $LOG_LOCATION/CPMD_build.log_`date +%d.%m.%Y-%H.%M`
+
+echo ""
+echo "***** Building cpmd2cube ..."
+
+# Unpack source archive, and configure for building in install location.
+
+cd $temp_dir
+tar xvzf $SRC_ARCHIVE_LOCATION/$SRC_ARCHIVE_CPMD2CUBE
+cd cpmd2cube
+mkdir -p $INSTALL_LOC/cpmd2cube
+
+./Configure -DEST=$INSTALL_LOC/cpmd2cube -m Linux-PC-IFORT
+
+cd  $INSTALL_LOC/cpmd2cube
+
+# Need to fix Makefile before building on Legion/Grace/Thomas
+
+cp Makefile Makefile_orig
+sed -e '/^LFLAGS/s/-i-static/-static-intel/' Makefile_orig > Makefile
+
+# Build in install location
+
+echo "Compiling cpmd2cube ..."
+make 2>&1 | tee $LOG_LOCATION/cpmd2cube_build.log_`date +%d.%m.%Y-%H.%M`
+mv cpmd2cube.x cutcube.x trimcube.x ../bin
+
+echo "Finished."

Cuba-4.2_install

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+#!/usr/bin/env bash
+
+###############################################
+# Installing Cuba 4.2
+#
+# by Brian Alston, 2018
+#
+# Numerical integration library for Mathematica 11.0.1
+#
+# Updated July 2018 to downgrade version of Mathematica
+#
+# Note: 11.1 is the most recent version of Mathematica
+# that Cuba will work with. It is NOT compatible with
+# 11.2 or 11.3 see IN03009733
+#
+# Will need modules: gcc-libs/4.9.2, compilers/gnu/4.9.2
+# qt/5.4.2/gnu-4.9.2, xorg-utils/X11R7.7, mathematica/11.0.1
+
+VERSION=${VERSION:-4.2}
+VER=`echo $VERSION | sed 's/\.//'`
+INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/Cuba/${VERSION}_gnu-4.9.2_Math-11.0.1}
+MD5=${MD5:-a3eb0751d4872a3f86401694bc5bedae}
+SRC_ARCHIVE=${SRC_ARCHIVE:-http://www.feynarts.de/cuba/Cuba-${VERSION}.tar.gz}
+
+export PATH=$INSTALL_PREFIX/bin:$PATH
+
+dirname=$(dirname $0 2>/dev/null || pwd)
+INCLUDES_DIR=${INCLUDES_DIR:-${dirname}/includes}
+source ${INCLUDES_DIR}/module_maker_inc.sh
+source ${INCLUDES_DIR}/require_inc.sh
+
+require gcc-libs/4.9.2
+require compilers/gnu/4.9.2
+require bison/3.0.4/gnu-4.9.2
+require gperf/3.0.4/gnu-4.9.2
+require qt/5.4.2/gnu-4.9.2
+require xorg-utils/X11R7.7
+require mathematica/11.0.1
+
+temp_dir=`mktemp -d -p /dev/shm`
+
+cd $temp_dir
+
+wget $SRC_ARCHIVE
+
+CHECKSUM=`md5sum Cuba-${VERSION}.tar.gz | awk '{print $1}'`
+
+if [[ "$MD5" == "$CHECKSUM" ]]
+then
+   tar xvzf Cuba-${VERSION}.tar.gz
+   cd Cuba-${VERSION}
+   ./configure --prefix=${INSTALL_PREFIX} 
+   make
+   make check
+   make install
+
+else
+   echo "***** Hash mismatch,"
+   echo "	Expected: $MD5"
+   echo "	Got:      $CHECKSUM"
+fi

EPACTS-3.3.0_install

@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+
+###############################################
+# Installing EPACTS 3.3.0
+#
+# by Brian Alston, June 2018
+#
+# Using Ian's require function to load modules
+#
+# 
+
+VERSION=${VERSION:-3.3.0}
+INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/EPACTS/${VERSION}}
+SRC_ARCHIVE=${SRC_ARCHIVE:- https://github.com/statgen/EPACTS.git}
+
+export PATH=$INSTALL_PREFIX/bin:$PATH
+
+dirname=$(dirname $0 2>/dev/null || pwd)
+INCLUDES_DIR=${INCLUDES_DIR:-${dirname}/includes}
+source ${INCLUDES_DIR}/module_maker_inc.sh
+source ${INCLUDES_DIR}/require_inc.sh
+
+require gcc-libs/4.9.2
+require compilers/gnu/4.9.2
+require r/recommended
+require gnuplot/5.0.1
+require groff/1.22.3/gnu-4.9.2
+require autoconf/2.69
+require automake/1.16.1
+
+temp_dir=`mktemp -d -p /dev/shm`
+# temp_dir='/home/ccspapp/Software/EPACTS'
+echo "Building in $temp_dir ..."
+cd $temp_dir
+module list
+read -p "Press [Enter] key to start ..."
+
+cd $temp_dir
+
+git clone $SRC_ARCHIVE
+
+cd EPACTS
+aclocal
+autoconf
+automake --add-missing
+./configure --prefix=$INSTALL_PREFIX
+make
+
+# No make check provided.
+
+make install

Gurobi-7.5.1_install

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+# This script installs Gurobi Optimizer 7.5.1
+# Brian Alston October 2017
+
+VERSION=${VERSION:-7.5.1}
+INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/Gurobi}
+SRC_ARCHIVE=${SRC_ARCHIVE:-http://packages.gurobi.com/7.5/gurobi${VERSION}_linux64.tar.gz}
+MD5=${MD5:-4ec7147562cc5d63b1790019064cd723}
+
+set -e
+startDir=`pwd`
+mkdir -p /dev/shm/Gurobi
+temp_dir=`mktemp -d -p /dev/shm/Gurobi`
+
+cd $temp_dir
+wget $SRC_ARCHIVE
+ARCHIVE=`basename $SRC_ARCHIVE`
+CHECKSUM=`md5sum ${ARCHIVE}| awk '{print $1}'`
+
+if [ "$MD5" == "$CHECKSUM" ]
+then
+
+    # Unpack the archive in the correct location.
+
+    mkdir -p $INSTALL_PREFIX
+    cd $INSTALL_PREFIX
+    tar xvzf $temp_dir/$ARCHIVE
+
+    # Set up client license file for UCL.
+
+    echo "TOKENSERVER=lic-gurobi.ucl.ac.uk" > gurobi.lic
+
+else
+  echo "Hash mismatch."
+  echo "Expected: $MD5"
+  echo "Got: $CHECKSUM"
+fi
+

Lynx-2.8.9_install

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+###############################################
+# Installing Lynx 2.8.9
+#
+# by Brian Alston,  March 2018
+# Udated 4th May for 2.8.9dev.17
+#
+# Will need modules: rcps-core/1.0.0
+
+VERSION=${VERSION:-2.8.9dev.17}
+VER=`echo $VERSION | sed 's/\.//'`
+INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/Lynx/$VERSION}
+MD5=${MD5:-8a8f442138c17bb5ce225218e45eb8f2}
+SRC_ARCHIVE=${SRC_ARCHIVE:-http://invisible-island.net/datafiles/release/lynx-cur.tar.gz}
+LOCAL_ARCHIVE=${LOCAL_ARCHIVE:-lynx-cur.tar.gz}
+export PATH=$INSTALL_PREFIX/bin:$PATH
+
+temp_dir=`mktemp -d -p /dev/shm`
+
+cd $temp_dir
+
+wget $SRC_ARCHIVE
+
+CHECKSUM=`md5sum $LOCAL_ARCHIVE | awk '{print $1}'`
+
+if [[ "$MD5" == "$CHECKSUM" ]]
+then
+   tar xvzf $LOCAL_ARCHIVE
+   cd lynx$VERSION
+   ./configure --prefix=/shared/ucl/apps/Lynx/$VERSION --with-ssl 2>&1 | tee configure-log
+   make 2>&1 | tee make-log
+   make install 2>&1 | tee make_install-log
+   make install-help 2>&1 | tee -a make_install-log
+   make install-doc  2>&1 | tee -a make_install-log
+
+else
+   echo "***** Hash mismatch,"
+   echo "	Expected: $MD5"
+   echo "	Got:      $CHECKSUM"
+fi

Nektar++_OpenMPI_GNU_install

@@ -0,0 +1,52 @@
+#!/usr/bin/env bash
+
+###############################################
+# Installing Nektar++: OpenMPI with GNU compilers
+#
+# by Brian Alston, March 2017 
+#
+# Using Ian's require function to load modules
+#
+# Will need modules: see list of modules below.
+
+VERSION=${VERSION:-4.3.5}
+INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/Nektar++/$VERSION/GNU_OpenMPI}
+SRC_ARCHIVE=${SRC_ARCHIVE:-nektar++-$VERSION.tar.gz}
+SRC_ARCHIVE_LOCATION=${SRC_ARCHIVE_LOCATION:-http://www.nektar.info/downloads/file/nektar-source-tar-gz/}
+
+export PATH=$INSTALL_PREFIX/bin:$PATH
+
+dirname=$(dirname $0 2>/dev/null || pwd)
+INCLUDES_DIR=${INCLUDES_DIR:-${dirname}/includes}
+source ${INCLUDES_DIR}/module_maker_inc.sh
+source ${INCLUDES_DIR}/require_inc.sh
+
+require rcps-core/1.0.0
+require compilers/gnu
+require mpi/openmpi/1.10.1/gnu-4.9.2
+require python3/recommended
+require openblas/0.2.14/gnu-4.9.2
+require boost/1_54_0/mpi/gnu-4.9.2-ompi-1.10.1
+require fftw/3.3.4-ompi-1.10.1/gnu-4.9.2
+require ghostscript/9.19/gnu-4.9.2
+require texlive/2015
+
+# May be able to use graphicsmagik: gm convert
+require libtool/2.4.6
+require perl/5.22.0
+require graphicsmagick/1.3.21
+
+# temp_dir=`mktemp -d -p /dev/shm`
+temp_dir=`mktemp -d -p ~/Software/Nektar++`
+cd $temp_dir
+
+wget $SRC_ARCHIVE_LOCATION -O $SRC_ARCHIVE
+tar xvzf $SRC_ARCHIVE
+cd nektar++-$VERSION
+mkdir build
+cd build
+cmake -DNEKTAR_USE_MPI:BOOL=ON -DNEKTAR_BUILD_TIMINGS:BOOL=ON -DNEKTAR_USE_FFTW:BOOL=ON \
+      -DNEKTAR_USE_OPENBLAS:BOOL=ON -DNEKTAR_USE_PETSC:BOOL=OFF -DNEKTAR_USE_SCOTCH:BOOL=ON \
+      -DNEKTAR_USE_SYSTEM_BLAS_LAPACK:BOOL=OFF -DCONVERT:STRING="gm convert" \
+      -DCMAKE_INSTALL_PREFIX:STRING="$INSTALL_PREFIX"  ../ 
+make install