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rocket_rmpi_install2.sh
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rocket_rmpi_install2.sh
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#!/bin/bash
# A script to install OpenMPI on Rocket
# and then also install Parallel R
cd $HOME
module purge
module load gcc-5.2.0
# Give installation directory a name
export MPIDIR=ROpenMPI31
# Make installation directory
rm -r $MPIDIR
mkdir $MPIDIR
# Go into installation directory
cd $MPIDIR
# Get OpenMPI
wget https://www.open-mpi.org/software/ompi/v3.1/downloads/openmpi-3.1.0.tar.gz
# Decompress OpenMPI
tar -xvf openmpi-3.1.0.tar.gz
# Go into OpenMPI directory
cd openmpi-3.1.0
./configure --prefix=$HOME/$MPIDIR/install --with-slurm \
FC=/storage/software/gcc-5.2.0/bin/gfortran \
CXX=/storage/software/gcc-5.2.0/bin/g++ \
--disable-dlopen \
CPPFLAGS="-I/storage/software/zlib-1.2.8/include"
# Build library
make all
# Install the library
make all install
cd $HOME
export RDIR=R_directory
rm -r $RDIR
mkdir $RDIR
cd $RDIR
# Get Curses (https://www.gnu.org/software/ncurses/)
wget https://invisible-mirror.net/archives/ncurses/ncurses-6.1.tar.gz
tar -xvf ncurses-6.1.tar.gz
cd ncurses-6.1
./configure --prefix=$HOME/$RDIR/extrasinstall --with-shared \
CC=$HOME/$MPIDIR/install/bin/mpicc
make
make install
export LD_LIBRARY_PATH=$HOME/$RDIR/extrasinstall/lib:$LD_LIBRARY_PATH
cd ..
# Get Readline (http://tiswww.case.edu/php/chet/readline/rltop.html)
wget ftp://ftp.gnu.org/gnu/readline/readline-7.0.tar.gz
tar -xvf readline-7.0.tar.gz
cd readline-7.0
./configure --with-curses --prefix=$HOME/$RDIR/extrasinstall \
--enable-shared --enable-static CC=$HOME/$MPIDIR/install/bin/mpicc
make
make install
cd ..
# Get zlib
wget https://sourceforge.net/projects/libpng/files/zlib/1.2.8/zlib-1.2.8.tar.gz
tar -xvf zlib-1.2.8.tar.gz
cd zlib-1.2.8
make distclean
./configure --prefix=$HOME/$RDIR/extrasinstall
make
make install
cd ..
# Get openssl
wget https://www.openssl.org/source/openssl-1.0.2o.tar.gz
tar -xvf openssl-1.0.2o.tar.gz
cd openssl-1.0.2o
./config shared --prefix=$HOME/$RDIR/extrasinstall
make
make install
cd ..
# Get xz
wget https://sourceforge.net/projects/lzmautils/files/xz-5.2.4.tar.gz/download
mv download xz-5.2.4.tar.gz
tar -xvf xz-5.2.4.tar.gz
cd xz-5.2.4
./configure --prefix=$HOME/$RDIR/extrasinstall \
--enable-shared --enable-static CC=$HOME/$MPIDIR/install/bin/mpicc
make
make install
cd ..
# Get curl
wget https://github.com/curl/curl/releases/download/curl-7_59_0/curl-7.59.0.tar.gz
tar -xvf curl-7.59.0.tar.gz
cd curl-7.59.0
./configure --prefix=$HOME/$RDIR/extrasinstall \
--enable-shared --enable-static CC=$HOME/$MPIDIR/install/bin/mpicc \
--with-ssl=$HOME/$RDIR/extrasinstall/
make
make install
cd ..
# Get R version 3.5.0
# https://cran.r-project.org/doc/manuals/R-admin.html#Getting-and-unpacking-the-sources
wget http://ftp.eenet.ee/pub/cran/src/base/R-3/R-3.5.0.tar.gz
tar -xvf R-3.5.0.tar.gz
export PKG_CONFIG_PATH=$OME/$RDIR/extrasinstall/lib/pkgconfig:$PKG_CONFIG_PATH
cd R-3.5.0
./configure --prefix=$HOME/$RDIR/R350install \
CC=$HOME/$MPIDIR/install/bin/mpicc \
CXX=$HOME/$MPIDIR/install/bin/mpicxx \
F77=$HOME/$MPIDIR/install/bin/mpif90 \
FC=$HOME/$MPIDIR/install/bin/mpif90 \
--with-recommended-packages \
--enable-static --enable-shared\
LDFLAGS="-L$HOME/$RDIR/extrasinstall/lib -lcurl" \
CPPFLAGS="-I$HOME/$RDIR/extrasinstall/include" \
--with-x=no
make
make install
cd ..
mkdir -p ~/R/x86_64-unknown-linux-gnu-library/3.5
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/$RDIR/R350install/lib64/R/lib:$HOME/$RDIR/R350install/lib64/R/library
export MPIINCLUDE=$HOME/$MPIDIR/install/include
export MPILIB=$HOME/$MPIDIR/install/lib
# Get RMPI http://www.stats.uwo.ca/faculty/yu/Rmpi/
wget https://cran.r-project.org/src/contrib/Rmpi_0.6-7.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library Rmpi_0.6-7.tar.gz
# Get Rmethods https://cran.r-project.org/web/packages/R.methodsS3/index.html
wget https://cran.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I/$MPIINCLUDE LDFLAGS=' -L/$MPILIB'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library R.methodsS3_1.7.1.tar.gz
# Get R.oo https://cran.r-project.org/web/packages/R.oo/index.html
wget https://cran.r-project.org/src/contrib/R.oo_1.22.0.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I/$MPIINCLUDE LDFLAGS=' -L/$MPILIB'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library R.oo_1.22.0.tar.gz
# Get doMC https://cran.r-project.org/web/packages/doMC/index.html
wget https://cran.r-project.org/src/contrib/doMC_1.3.5.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I/$MPIINCLUDE LDFLAGS=' -L$HOME/$MPIDIR/install//lib'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library doMC_1.3.5.tar.gz
# Get utils https://cran.r-project.org/web/packages/R.utils/index.html
wget https://cran.r-project.org/src/contrib/R.utils_2.6.0.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$HOME/$MPIDIR/install//lib'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library R.utils_2.6.0.tar.gz
# Get SNOW https://cran.r-project.org/web/packages/snow/index.html
wget https://cran.r-project.org/src/contrib/snow_0.4-2.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$HOME/$MPIDIR/install//lib'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library snow_0.4-2.tar.gz
# Get iterators https://cran.r-project.org/web/packages/iterators/index.html
wget https://cran.r-project.org/src/contrib/iterators_1.0.9.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$HOME/$MPIDIR/install//lib'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library iterators_1.0.9.tar.gz
# Get codetools https://cran.r-project.org/web/packages/codetools/index.html
wget https://cran.r-project.org/src/contrib/codetools_0.2-15.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library codetools_0.2-15.tar.gz
# Get foreach https://cran.r-project.org/web/packages/foreach/index.html
wget https://cran.r-project.org/src/contrib/foreach_1.4.4.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$HOME/$MPIDIR/install//lib'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library foreach_1.4.4.tar.gz
# Get doparallel https://cran.r-project.org/web/packages/doParallel/index.html
wget https://cran.r-project.org/src/contrib/doParallel_1.0.11.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library doParallel_1.0.11.tar.gz
# Get doMPI https://cran.r-project.org/web/packages/doMPI/index.html
wget https://cran.r-project.org/src/contrib/doMPI_0.2.2.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library doMPI_0.2.2.tar.gz
# Get doSNOW https://cran.r-project.org/web/packages/doSNOW/
wget https://cran.r-project.org/src/contrib/doSNOW_1.0.16.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library doSNOW_1.0.16.tar.gz
# Get snowfall https://cran.r-project.org/web/packages/snowfall/index.html
wget https://cran.r-project.org/src/contrib/snowfall_1.84-6.1.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library snowfall_1.84-6.1.tar.gz
# Get rlecuyer https://cran.r-project.org/web/packages/rlecuyer/index.html
wget https://cran.r-project.org/src/contrib/rlecuyer_0.3-4.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-Rmpi-include=$MPIINCLUDE \
--with-Rmpi-libpath=$MPILIB \
--with-Rmpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library rlecuyer_0.3-4.tar.gz
# Get pdbMPI https://cran.r-project.org/web/packages/pbdMPI/index.html
wget https://cran.r-project.org/src/contrib/pbdMPI_0.3-6.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library pbdMPI_0.3-6.tar.gz
#get https://cran.r-project.org/web/packages/rlecuyer/index.html
wget https://cran.r-project.org/src/contrib/rlecuyer_0.3-4.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library rlecuyer_0.3-4.tar.gz
#get https://cran.r-project.org/web/packages/pbdSLAP/index.html
wget https://cran.r-project.org/src/contrib/pbdSLAP_0.2-4.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library pbdSLAP_0.2-4.tar.gz
# get https://cran.r-project.org/web/packages/pbdBASE/index.html
wget https://cran.r-project.org/src/contrib/pbdBASE_0.4-5.1.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library pbdBASE_0.4-5.1.tar.gz
# Get pdbMAT https://cran.r-project.org/web/packages/pbDMAT/index.html
wget https://cran.r-project.org/src/contrib/pbdDMAT_0.4-2.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library pbdDMAT_0.4-2.tar.gz
# Get and install the HDF5 Parallel IO library
wget www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.10.1.tar.gz
tar -xvf hdf5-1.10.1.tar.gz
cd hdf5-1.10.1
export HDF5DIR=hdf5
./configure \
--prefix=$HOME/$RDIR/$HDF5DIR/HDF5install/ \
--enable-parallel \
--enable-shared \
CC=$HOME/$MPIDIR/install/bin/mpicc \
CFLAGS="-fPIC -I$MPIINCLUDE" \
CPPFLAGS="-fPIC -I$MPIINCLUDE" \
LDFLAGS="-L$MPILIB"
make
make install
cd ..
# Get and install netcdf, information at:
# https://www.unidata.ucar.edu/software/netcdf/docs/index.html
wget https://github.com/Unidata/netcdf-c/archive/v4.6.1.tar.gz
tar -xvf v4.6.1.tar.gz
export NETCDF4DIR=netcdf4
cd netcdf-c-4.6.1
./configure \
--prefix=$HOME/$RDIR/$NETCDF4DIR/netcdf4install/ \
--enable-netcdf4 \
--enable-shared \
CC="$HOME/$MPIDIR/install/bin/mpicc -g" \
CFLAGS="-fPIC -I$MPIINCLUDE -I$HOME/$RDIR/$HDF5DIR/HDF5install/include" \
CPPFLAGS="-fPIC -I$MPIINCLUDE -I$HOME/$RDIR/$HDF5DIR/HDF5install/include" \
LDFLAGS="-L$MPILIB -L$HOME/$HDF5DIR/HDF5install/lib -lhdf5"
make
make install
cd ..
# Get pdbNETCDF4 https://cran.r-project.org/web//packages/pbdNCDF4/index.html
wget https://cran.r-project.org/src/contrib/pbdNCDF4_0.1-4.tar.gz
tar -zxvf pbdNCDF4_0.1-4.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-nc-config=$HOME/$RDIR/$NETCDF4DIR/netcdf4install/bin \
--enable-parallel \
--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library pbdNCDF4
# Get chron which is needed for data.table https://cran.r-project.org/web/packages/chro
n/index.html
wget https://cran.r-project.org/src/contrib/chron_2.3-52.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library chron_2.3-52.tar.gz
# Get data.table https://cran.r-project.org/web/packages/data.table/index.html
wget https://cran.r-project.org/src/contrib/data.table_1.11.4.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library data.table_1.11.4.tar.gz
# Get PM cluster https://cran.r-project.org/web/packages/pmclust/index.html
wget https://cran.r-project.org/src/contrib/pmclust_0.2-0.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library pmclust_0.2-0.tar.gz
#Coda dependency for the cubfit https://cran.r-project.org/web/packages/coda/index.html
wget https://cran.r-project.org/src/contrib/coda_0.19-1.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library coda_0.19-1.tar.gz
# VGAM https://cran.r-project.org/web/packages/VGAM/index.html
wget https://cran.r-project.org/src/contrib/VGAM_1.0-5.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library VGAM_1.0-5.tar.gz
# Cubfit demo https://cran.r-project.org/web/packages/cubfits/index.html
wget https://cran.r-project.org/src/contrib/cubfits_0.1-3.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library cubfits_0.1-3.tar.gz
# Get pdbDEMO https://cran.r-project.org/web//packages/pbdDEMO/index.html
#wget https://github.com/wrathematics/pbdDEMO/archive/v0.2-0.tar.gz
wget https://cran.r-project.org/src/contrib/pbdDEMO_0.3-1.tar.gz
$HOME/$RDIR/R350install/bin/R CMD INSTALL \
--configure-vars="CPPFLAGS=-I$MPIINCLUDE LDFLAGS=' -L$MPILIB'" \
--configure-args="--with-mpi-include=$MPIINCLUDE \
--with-mpi-libpath=$MPILIB \
--with-mpi-type=OPENMPI" \
-l $HOME/$RDIR/R350install/lib64/R/library pbdDEMO_0.3-1.tar.gz