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R-4.0.2_MPI_install
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#!/usr/bin/env bash
###############################################
# Installing R and Bioconductor MPI support
# packages.
#
# This replaces the old ~ccaabaa/Software/R/extra-pkgs-order.txt file from
# previous version of R on Legion etc. It will need to be updated each time
# an extra package is added to the current R installation.
#
# For R 4.0.2 and later Note: R-<version>_packages_install should be run first.
#
# This is needed on Grace for the Rmpi package to install correctly:
#
# export OMPI_MCA_mtl=^psm
#
# by Brian Alston, June 2016
# Updated Nov 2016 for R 3.3.2
# Updated May 2017 for R 3.4.0
# Updated December 2017 for R 3.4.2
# Updated June 2018 for R 3.5.0
# Updated June 2018 (19th) to fix MPI support - now using mpi/openmpi/3.0.0/gnu-4.9.2
# Updated September 2018 for R 3.5.1
# Also for udunits 2.2.26.
# Updated April 2019 for R 3.5.3
# Updated July 2019 for R 3.6.0
# Updated April 2020 for R 3.6.3
# Updated June 2020 for R 4.0.2
#
# Using Ian's require function to load modules
#
# Will need modules: see list of modules below.
VERSION=${VERSION:-4.0.2}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/R/R-${VERSION}-OpenBLAS}
export RLIB_MAIN=${RLIB_MAIN:-${INSTALL_PREFIX}/lib64/R/library}
export RLIB_DB=${RLIB_DB:-/home/ccspapp/Scratch/R/R-${VERSION}-OpenBLAS/library}
export REPROS=${REPROS:-https://cloud.r-project.org/}
LOCALDIR=${LOCALDIR:-/shared/ucl/apps/build_scripts/files/R_UCL}
export PATH=$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 beta-modules
require gcc-libs/9.2.0
require compilers/gnu/9.2.0
require openblas/0.3.7-serial/gnu-9.2.0
require java/1.8.0_92
require fftw/3.3.8/gnu-9.2.0
require ghostscript/9.19/gnu-4.9.2
require texinfo/6.6/gnu-4.9.2
require texlive/2019
require gsl/2.6/gnu-9.2.0
require hdf/5-1.10.5/gnu-9.2.0
require udunits/2.2.26/gnu-9.2.0
require netcdf/4.7.4/gnu-9.2.0
require mpi/openmpi/3.1.5/gnu-9.2.0
require pcre2/10.35/gnu-9.2.0
# Not currently installed - 15/4/2020
# require jags/4.2.0/gnu.4.9.2-openblas
# require root/5.34.36/gnu-4.9.2-fftw-3.3.6-gsl-2.4
# require glpk/4.60/gnu-4.9.2
require perl/5.22.0
require libtool/2.4.6
require freetype/2.8.1/gnu-4.9.2
require graphicsmagick/1.3.21
require python/2.7.12
require sqlite/3.31.1/gnu-9.2.0
require proj.4/7.0.0/gnu-9.2.0
require sqlite/3.31.1/gnu-9.2.0
require proj.4/7.0.0/gnu-9.2.0
require gdal/3.0.4/gnu-9.2.0
require geos/3.8.1/gnu-9.2.0
require gmt/6.0.0/gnu-9.2.0
require v8/3.15
# Not currently installed - 15/4/2020
# module load protobuf/12-2017/gnu-4.9.2
# module load jq/1.5/gnu-4.9.2
require r/4.0.2-openblas/gnu-9.2.0
temp_dir=`mktemp -d -p /dev/shm`
# temp_dir='/home/ccspapp/Software/R'
echo "Building in $temp_dir ..."
cd $temp_dir
module list
read -p "Press [Enter] key to start ..."
cd $temp_dir
mkdir -p $RLIB_DB
export OMPI_MCA_btl=vader,self
# Note: some old packages need to be installed from local files that have had minor updates applied eg:
#
# adapt fails to install on R > 3.0.1 with: ERROR: a 'NAMESPACE' file is required
#
# tar xvzf adapt_1.0-4.tar.gz
# cd adapt
# Create NAMESPACE with contents:
#
# exportPattern("^[^\\.]")
#
# cd ..
# tar cvzf adapt_1.0-4-ucl.tar.gz adapt
#
# Do this for all packages that fail with abover error.
R_input=${LOCALDIR}/R_packages_MPI_1_3.6.3.R
R --no-save < $R_input