Commit c40235d7 authored by David Brusson's avatar David Brusson
Browse files

Mise à jour pour s'accorder à la nouvelle nomenclature des modules + images Cuda et R

parent de91ce7b
......@@ -6,7 +6,12 @@
source ~/.bashrc
module load compilers/intel18
module load mpi/openmpi-3.i18
module load intel/intel18
module load openmpi/openmpi-3.i18
echo "mpirun bandwidth.sif"
mpirun bandwidth.sif
echo ""
echo "mpirun singularity run bandwidth.sif"
mpirun singularity run bandwidth.sif
Bootstrap: docker
From: ubuntu:latest
Bootstrap: localimage
From: /usr/local/images/cuda11.3.sif
%runscript
......@@ -19,16 +19,6 @@ AUTHOR brusson@unistra.fr
%post
echo "Distribution update and infiniband installation"
#Avoid interraction required by tzdata configuration
TZ=Europe/Minsk
ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
apt-get update
apt-get -y install build-essential
apt-get -y install nvidia-cuda-toolkit
echo "sgemm test installation"
cd /sourcefiles
......
......@@ -7,6 +7,4 @@
source ~/.bashrc
module load compilers/cuda-9.1
singularity run --nv gpu.sif 13000
Bootstrap: docker
From: ubuntu:focal
%runscript
R $@
%environment
MAJVER=4
MINVER=1.2
RSTUDIOVER=2021.09.2-382
rootdir=/usr/local/R/R-$MAJVER.$MINVER
rstudiorootdir=/usr/local/R/rstudio-$RSTUDIOVER
export PATH=$rootdir/bin:rstudiorootdir/bin:$PATH
export LD_LIBRARY_PATH=$rootdir/lib64:$rootdir/lib64/R/lib:$rstudiorootdir/lib:$LD_LIBRARY_PATH
export QT_XKB_CONFIG_ROOT=$rstudiorootdir
export R_INSTALL_STAGED=false
export MKL_THREADING_LAYER=gnu
%labels
AUTHOR brusson@unistra.fr
%post
echo "Distribution update and base packages installation"
#Avoid interraction required by tzdata configuration
apt-get update
apt-get -y install apt-utils
apt-get -y install build-essential
DEBIAN_FRONTEND=noninteractive apt-get -y install intel-mkl-full
apt-get -y install python3 python3-pip
apt-get -y install gdal-bin
apt-get -y install libgdal-dev
apt-get -y install dirmngr gnupg apt-transport-https ca-certificates software-properties-common
apt-get -y install libreadline-dev
apt-get -y install xorg-dev
apt-get -y install libbz2-dev
apt-get -y install liblzma-dev
apt-get -y install libpcre2-dev
apt-get -y install libssl-dev
apt-get -y install libcurl4-openssl-dev
apt-get -y install texinfo texlive texlive-fonts-extra
apt-get -y install default-jre default-jdk
apt-get -y install libfreetype-dev
apt-get -y install libjpeg-dev
apt-get -y install libxml2-dev
apt-get -y install libmagick++-dev
apt-get -y install cargo
apt-get -y install libharfbuzz-dev libfribidi-dev
apt-get -y install libproj-dev
apt-get -y install libudunits2-dev
apt-get -y install libjq-dev
apt-get -y install libprotobuf-dev protobuf-compiler
apt-get -y install wget
MAJVER=4
MINVER=1.2
RSTUDIOVER=2021.09.2-382
rootdir=/usr/local/R/R-$MAJVER.$MINVER
rstudiorootdir=/usr/local/R/rstudio-$RSTUDIOVER
rstudiorootdirplus="$(echo ${rstudiorootdir%-*}+${rstudiorootdir##*-})"
mkdir -p $SINGULARITY_ROOTFS/$rootdir
export PATH=$rootdir/bin:rstudiorootdir/bin:$PATH
export LD_LIBRARY_PATH=$rootdir/lib64:$rootdir/lib64/R/lib:$rstudiorootdir/lib:$LD_LIBRARY_PATH
export QT_XKB_CONFIG_ROOT=$rstudiorootdir
export R_INSTALL_STAGED=false
export MKL_THREADING_LAYER=gnu
# R install
cd /tmp
wget -qO- https://cran.r-project.org/src/base/R-$MAJVER/R-$MAJVER.$MINVER.tar.gz | tar xfz -
cd R-$MAJVER.$MINVER
MKL="-Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm"
MAIN_LDFLAGS="$MKL" ./configure --prefix=$rootdir --enable-R-shlib --with-blas="$MKL" --with-lapack --enable-BLAS-shlib
make -j 24 && make -j 24 install && cd /tmp && rm -rf R-$MAJVER.$MINVER
# Rstudio install
cd /usr/local/R
wget -qO- https://download1.rstudio.org/desktop/bionic/amd64/rstudio-$RSTUDIOVER-amd64-debian.tar.gz | tar xfz -
mv $rstudiorootdirplus $rstudiorootdir
# Install packages
R --no-save << EOF
install.packages("rmarkdown", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("knitr", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("rmdformats", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("RCurl", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("osmdata", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("rgdal", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("geojsonR", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("geojson", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("plyr", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("dplyr", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("leaflet", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("readxl", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("rgeos", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("mapview", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("tidyverse", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("units", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("osrm", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("cartography", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("kableExtra", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("concaveman", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("tmap", dependencies = TRUE, repos = "http://cran.rstudio.com/")
install.packages("sfdct", dependencies = TRUE, repos = "http://cran.rstudio.com/")
q()
EOF
Bootstrap: docker
From: ubuntu:focal
%runscript
echo "Please update runscript section"
%setup
echo "#!/bin/bash" >> $SINGULARITY_ROOTFS/usr/local/bin/to_remove.sh
%environment
%labels
AUTHOR brusson@unistra.fr
%post
echo "Distribution update and dependencies installation"
#Avoid interraction required by tzdata configuration
OS=ubuntu2004
TZ=Europe/Minsk
ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
apt-get update
apt-get -y install build-essential
apt-get -y install nvidia-cuda-toolkit
apt-get -y install wget
apt-get -y install cmake
apt-get -y install software-properties-common
apt-get -y install git
wget https://developer.download.nvidia.com/compute/cuda/repos/${OS}/x86_64/cuda-${OS}.pin
mv cuda-${OS}.pin /etc/apt/preferences.d/cuda-repository-pin-600
apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/${OS}/x86_64/7fa2af80.pub
add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/${OS}/x86_64/ /"
apt-get -y install libcudnn8-dev
#!/bin/bash
VER=3.5.3
IMG=cuda11.3
# Remove previous version of the image if still here
rm -f $IMG.sif
# Generate image
/usr/local/singularity/$VER/bin/singularity build $IMG.sif $IMG.def
# Copy image on the singularity VM
scp $IMG.sif hpc-singularity.di.unistra.fr:/usr/local/images
......@@ -17,16 +17,14 @@ yum install -y libuuid-devel
yum install -y libseccomp-devel
# Go
GOVER=1.11.linux-amd64
VER=3.0.3
GOVER=1.17.7.linux-amd64
VER=3.9.5
singularity_dir=/usr/local/singularity/$VER
if [ ! -f /tmp/go$GOVER.tar.gz ]
then
pushd /tmp
wget https://dl.google.com/go/go$GOVER.tar.gz
tar -C /usr/local -xzf go$GOVER.tar.gz
rm -f go$GOVER.tar.gz
pushd /usr/local
wget -qO- https://dl.google.com/go/go$GOVER.tar.gz | tar xfz -
popd
export GOPATH=${HOME}/go
......@@ -39,10 +37,11 @@ then
cd singularity
git checkout tags/v$VER
./mconfig -p $singularity_dir -b buildtree
cd ./buildtree
make
make install
go get -u -v github.com/golang/dep/cmd/dep
./mconfig --prefix=$singularity_dir
make -C builddir
make -C builddir install
ln -sf $singularity_dir/bin/singularity /usr/local/bin/singularity
......
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