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

examples/from_openmpi3-intel18/submission.sh

@@ -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

examples/gpu/gpu.def

-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

examples/gpu/submission.sh

@@ -7,6 +7,4 @@
 
 source ~/.bashrc
 
-module load compilers/cuda-9.1
-
 singularity run --nv gpu.sif 13000

images/R-4.1.2/R-4.1.2.def

+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

images/cuda11.3/cuda11.3.def

+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

images/cuda11.3/image_create.sh

+#!/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

installation/singularity_install.sh

@@ -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