From 412c9db54cb65772655c9c4d3b9e407b126ee771 Mon Sep 17 00:00:00 2001
From: Wouter Deconinck <wdconinc@gmail.com>
Date: Sun, 27 Mar 2022 21:20:25 +0000
Subject: [PATCH] Intel oneAPI 2022.1.2 HPC kit and CUDA build containers
---
.gitlab-ci.yml | 24 ++
containers.yaml | 18 ++
containers/cuda/Dockerfile | 72 ++++++
containers/cuda/bashrc | 452 +++++++++++++++++++++++++++++++++++
containers/debian/Dockerfile | 2 +
containers/oneapi/Dockerfile | 72 ++++++
containers/oneapi/bashrc | 452 +++++++++++++++++++++++++++++++++++
7 files changed, 1092 insertions(+)
create mode 100644 containers.yaml
create mode 100644 containers/cuda/Dockerfile
create mode 100644 containers/cuda/bashrc
create mode 100644 containers/oneapi/Dockerfile
create mode 100644 containers/oneapi/bashrc
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4c431bae5..d3c51ecec 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -184,6 +184,30 @@ debian_base:default:
containers/debian
- !reference [.build, script]
+oneapi_base:default:
+ extends: .build
+ stage: build:base
+ needs:
+ - version
+ variables:
+ BUILD_IMAGE: "oneapi_base"
+ script:
+ - docker build -t ${CI_REGISTRY_IMAGE}/${BUILD_IMAGE}:${INTERNAL_TAG}
+ containers/oneapi
+ - !reference [.build, script]
+
+cuda_base:default:
+ extends: .build
+ stage: build:base
+ needs:
+ - version
+ variables:
+ BUILD_IMAGE: "cuda_base"
+ script:
+ - docker build -t ${CI_REGISTRY_IMAGE}/${BUILD_IMAGE}:${INTERNAL_TAG}
+ containers/oneapi
+ - !reference [.build, script]
+
jug_dev:default:
extends: .build
stage: build:jug
diff --git a/containers.yaml b/containers.yaml
new file mode 100644
index 000000000..c9a6da725
--- /dev/null
+++ b/containers.yaml
@@ -0,0 +1,18 @@
+base:
+ debian:
+ develop: amd64/debian:testing-20211220-slim
+ runtime: amd64/debian:testing-20211220-slim
+ Dockerfile: containers/base/Dockerfile.in
+ oneapi:
+ develop: intel/oneapi-hpckit:2022.1.2-devel-ubuntu18.04
+ runtime: intel/oneapi-runtime:2022.1.2-devel-ubuntu18.04
+ Dockerfile: containers/base/Dockerfile.in
+ cuda:
+ develop: nvidia/cuda:11.6.0-devel-ubuntu18.04
+ runtime: nvidia/cuda:11.6.0-runtime-ubuntu18.04
+ Dockerfile: containers/base/Dockerfile.in
+jug:
+ jug_dev:
+ Dockerfile: containers/jug/dev.Dockerfile
+ jug_xl:
+ Dockerfile: containers/jug/xl.Dockerfile
diff --git a/containers/cuda/Dockerfile b/containers/cuda/Dockerfile
new file mode 100644
index 000000000..947cd8aaf
--- /dev/null
+++ b/containers/cuda/Dockerfile
@@ -0,0 +1,72 @@
+#syntax=docker/dockerfile:1.2
+
+# Minimal container based on Intel oneAPI for up-to-date packages.
+# Very lightweight container with a minimal build environment (LOL)
+
+FROM nvidia/cuda:11.6.0-devel-ubuntu18.04
+LABEL maintainer="Wouter Deconinck <wouter.deconinck@umanitoba.ca" \
+ name="cuda_base" \
+ march="amd64"
+
+COPY bashrc /root/.bashrc
+
+ENV CLICOLOR_FORCE=1 \
+ LANGUAGE=en_US.UTF-8 \
+ LANG=en_US.UTF-8 \
+ LC_ALL=en_US.UTF-8
+
+## Install additional packages. Remove the auto-cleanup functionality
+## for docker, as we're using the new buildkit cache instead.
+## We also install gitlab-runner, from the buster package (as bullseye is not available atm)
+## TODO: libyaml-cpp-dev is a dependency for afterburner. We can probably remove
+## this once afterburner is added to spack
+RUN --mount=type=cache,target=/var/cache/apt \
+ rm -f /etc/apt/apt.conf.d/docker-clean \
+ && ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime \
+ && echo "US/Eastern" > /etc/timezone \
+ && apt-get -yqq update \
+ && apt-get -yqq upgrade \
+ && apt-get -yqq install --no-install-recommends \
+ bc \
+ ca-certificates \
+ clang-format \
+ clang-tidy \
+ curl \
+ file \
+ build-essential \
+ gdb \
+ ghostscript \
+ git \
+ gnupg2 \
+ gv \
+ iproute2 \
+ iputils-ping \
+ iputils-tracepath \
+ less \
+ libcbor-xs-perl \
+ libjson-xs-perl \
+ libyaml-cpp-dev \
+ locales \
+ lua-posix \
+ make \
+ nano \
+ openssh-client \
+ parallel \
+ poppler-utils \
+ time \
+ unzip \
+ valgrind \
+ vim-nox \
+ wget \
+ && localedef -i en_US -f UTF-8 en_US.UTF-8 \
+ && gcc --version \
+ && curl -L \
+ "https://packages.gitlab.com/install/repositories/runner/gitlab-runner/script.deb.sh" \
+ | bash \
+ && sed -i "s/bookworm/buster/" \
+ /etc/apt/sources.list.d/runner_gitlab-runner.list \
+ && apt-get -yqq update \
+ && apt-get -yqq install --no-install-recommends \
+ gitlab-runner \
+ && apt-get -yqq autoremove \
+ && rm -rf /var/lib/apt/lists/*
diff --git a/containers/cuda/bashrc b/containers/cuda/bashrc
new file mode 100644
index 000000000..4d1c1f348
--- /dev/null
+++ b/containers/cuda/bashrc
@@ -0,0 +1,452 @@
+#!/bin/bash
+iatest=$(expr index "$-" i)
+
+#######################################################
+# SOURCED ALIAS'S AND SCRIPTS BY zachbrowne.me
+#######################################################
+
+# Source global definitions
+if [ -f /etc/bashrc ]; then
+ . /etc/bashrc
+fi
+
+# Enable bash programmable completion features in interactive shells
+if [ -f /usr/share/bash-completion/bash_completion ]; then
+ . /usr/share/bash-completion/bash_completion
+elif [ -f /etc/bash_completion ]; then
+ . /etc/bash_completion
+fi
+
+#######################################################
+# EXPORTS
+#######################################################
+
+# Disable the bell
+if [[ $iatest > 0 ]]; then bind "set bell-style visible"; fi
+
+# Expand the history size
+export HISTFILESIZE=10000
+export HISTSIZE=500
+
+# Don't put duplicate lines in the history and do not add lines that start with a space
+export HISTCONTROL=erasedups:ignoredups:ignorespace
+
+# Check the window size after each command and, if necessary, update the values of LINES and COLUMNS
+shopt -s checkwinsize
+
+# Causes bash to append to history instead of overwriting it so if you start a new terminal, you have old session history
+shopt -s histappend
+PROMPT_COMMAND='history -a'
+
+# Allow ctrl-S for history navigation (with ctrl-R)
+stty -ixon
+
+# Ignore case on auto-completion
+# Note: bind used instead of sticking these in .inputrc
+if [[ $iatest > 0 ]]; then bind "set completion-ignore-case on"; fi
+
+# Show auto-completion list automatically, without double tab
+if [[ $iatest > 0 ]]; then bind "set show-all-if-ambiguous On"; fi
+
+# Set the default editor
+export EDITOR=vim
+export VISUAL=vim
+alias pico='edit'
+alias spico='sedit'
+alias nano='edit'
+alias snano='sedit'
+
+# To have colors for ls and all grep commands such as grep, egrep and zgrep
+export CLICOLOR=1
+export LS_COLORS='no=00:fi=00:di=00;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.avi=01;35:*.fli=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.ogg=01;35:*.mp3=01;35:*.wav=01;35:*.xml=00;31:'
+#export GREP_OPTIONS='--color=auto' #deprecated
+#alias grep="/usr/bin/grep $GREP_OPTIONS"
+#unset GREP_OPTIONS
+
+# Color for manpages in less makes manpages a little easier to read
+export LESS_TERMCAP_mb=$'\E[01;31m'
+export LESS_TERMCAP_md=$'\E[01;31m'
+export LESS_TERMCAP_me=$'\E[0m'
+export LESS_TERMCAP_se=$'\E[0m'
+export LESS_TERMCAP_so=$'\E[01;44;33m'
+export LESS_TERMCAP_ue=$'\E[0m'
+export LESS_TERMCAP_us=$'\E[01;32m'
+
+#######################################################
+# GENERAL ALIAS'S
+#######################################################
+
+# Alias's to modified commands
+alias cp='cp -i'
+alias mv='mv -i'
+alias rm='rm -iv'
+alias mkdir='mkdir -p'
+alias ps='ps auxf'
+alias ping='ping -c 10'
+alias less='less -R'
+alias cls='clear'
+alias apt-get='apt-get'
+alias multitail='multitail --no-repeat -c'
+alias freshclam='freshclam'
+alias vi='vim'
+alias vis='vim "+set si"'
+
+# Change directory aliases
+alias home='cd ~'
+alias cd..='cd ..'
+alias ..='cd ..'
+alias ...='cd ../..'
+alias ....='cd ../../..'
+alias .....='cd ../../../..'
+
+# cd into the old directory
+alias bd='cd "$OLDPWD"'
+
+# Remove a directory and all files
+alias rmd='/bin/rm --recursive --force --verbose '
+
+# Alias's for multiple directory listing commands
+alias la='ls -Alh' # show hidden files
+alias ls='ls -aFh --color=always' # add colors and file type extensions
+alias lx='ls -lXBh' # sort by extension
+alias lk='ls -lSrh' # sort by size
+alias lc='ls -lcrh' # sort by change time
+alias lu='ls -lurh' # sort by access time
+alias lr='ls -lRh' # recursive ls
+alias lt='ls -ltrh' # sort by date
+alias lm='ls -alh |more' # pipe through 'more'
+alias lw='ls -xAh' # wide listing format
+alias ll='ls -Fls' # long listing format
+alias labc='ls -lap' #alphabetical sort
+alias lf="ls -l | egrep -v '^d'" # files only
+alias ldir="ls -l | egrep '^d'" # directories only
+
+# alias chmod commands
+alias mx='chmod a+x'
+alias 000='chmod -R 000'
+alias 644='chmod -R 644'
+alias 666='chmod -R 666'
+alias 755='chmod -R 755'
+alias 777='chmod -R 777'
+
+# Search command line history
+alias h="history | grep "
+
+# Search running processes
+alias p="ps aux | grep "
+alias topcpu="/bin/ps -eo pcpu,pid,user,args | sort -k 1 -r | head -10"
+
+# Search files in the current folder
+alias f="find . | grep "
+
+# Count all files (recursively) in the current folder
+alias countfiles="for t in files links directories; do echo \`find . -type \${t:0:1} | wc -l\` \$t; done 2> /dev/null"
+
+# To see if a command is aliased, a file, or a built-in command
+alias checkcommand="type -t"
+
+# Show all logs in /var/log
+alias logs="sudo find /var/log -type f -exec file {} \; | grep 'text' | cut -d' ' -f1 | sed -e's/:$//g' | grep -v '[0-9]$' | xargs tail -f"
+
+# SHA1
+alias sha1='openssl sha1'
+
+#######################################################
+# SPECIAL FUNCTIONS
+#######################################################
+
+# Extracts any archive(s) (if unp isn't installed)
+extract () {
+ for archive in $*; do
+ if [ -f $archive ] ; then
+ case $archive in
+ *.tar.bz2) tar xvjf $archive ;;
+ *.tar.gz) tar xvzf $archive ;;
+ *.bz2) bunzip2 $archive ;;
+ *.rar) rar x $archive ;;
+ *.gz) gunzip $archive ;;
+ *.tar) tar xvf $archive ;;
+ *.tbz2) tar xvjf $archive ;;
+ *.tgz) tar xvzf $archive ;;
+ *.zip) unzip $archive ;;
+ *.Z) uncompress $archive ;;
+ *.7z) 7z x $archive ;;
+ *) echo "don't know how to extract '$archive'..." ;;
+ esac
+ else
+ echo "'$archive' is not a valid file!"
+ fi
+ done
+}
+
+# Searches for text in all files in the current folder
+ftext ()
+{
+ # -i case-insensitive
+ # -I ignore binary files
+ # -H causes filename to be printed
+ # -r recursive search
+ # -n causes line number to be printed
+ # optional: -F treat search term as a literal, not a regular expression
+ # optional: -l only print filenames and not the matching lines ex. grep -irl "$1" *
+ grep -iIHrn --color=always "$1" . | less -r
+}
+
+# Copy file with a progress bar
+cpp()
+{
+ set -e
+ strace -q -ewrite cp -- "${1}" "${2}" 2>&1 \
+ | awk '{
+ count += $NF
+ if (count % 10 == 0) {
+ percent = count / total_size * 100
+ printf "%3d%% [", percent
+ for (i=0;i<=percent;i++)
+ printf "="
+ printf ">"
+ for (i=percent;i<100;i++)
+ printf " "
+ printf "]\r"
+ }
+ }
+ END { print "" }' total_size=$(stat -c '%s' "${1}") count=0
+}
+
+# Copy and go to the directory
+cpg ()
+{
+ if [ -d "$2" ];then
+ cp $1 $2 && cd $2
+ else
+ cp $1 $2
+ fi
+}
+
+# Move and go to the directory
+mvg ()
+{
+ if [ -d "$2" ];then
+ mv $1 $2 && cd $2
+ else
+ mv $1 $2
+ fi
+}
+
+# Create and go to the directory
+mkdirg ()
+{
+ mkdir -p $1
+ cd $1
+}
+
+# Goes up a specified number of directories (i.e. up 4)
+up ()
+{
+ local d=""
+ limit=$1
+ for ((i=1 ; i <= limit ; i++))
+ do
+ d=$d/..
+ done
+ d=$(echo $d | sed 's/^\///')
+ if [ -z "$d" ]; then
+ d=..
+ fi
+ cd $d
+}
+
+#Automatically do an ls after each cd
+# cd ()
+# {
+# if [ -n "$1" ]; then
+# builtin cd "$@" && ls
+# else
+# builtin cd ~ && ls
+# fi
+# }
+
+# Returns the last 2 fields of the working directory
+pwdtail ()
+{
+ pwd|awk -F/ '{nlast = NF -1;print $nlast"/"$NF}'
+}
+
+# Show the current version of the operating system
+ver ()
+{
+ local dtype
+ dtype=$(distribution)
+
+ if [ $dtype == "redhat" ]; then
+ if [ -s /etc/redhat-release ]; then
+ cat /etc/redhat-release && uname -a
+ else
+ cat /etc/issue && uname -a
+ fi
+ elif [ $dtype == "suse" ]; then
+ cat /etc/SuSE-release
+ elif [ $dtype == "debian" ]; then
+ lsb_release -a
+ # sudo cat /etc/issue && sudo cat /etc/issue.net && sudo cat /etc/lsb_release && sudo cat /etc/os-release # Linux Mint option 2
+ elif [ $dtype == "gentoo" ]; then
+ cat /etc/gentoo-release
+ elif [ $dtype == "mandriva" ]; then
+ cat /etc/mandriva-release
+ elif [ $dtype == "slackware" ]; then
+ cat /etc/slackware-version
+ else
+ if [ -s /etc/issue ]; then
+ cat /etc/issue
+ else
+ echo "Error: Unknown distribution"
+ exit 1
+ fi
+ fi
+}
+
+# For some reason, rot13 pops up everywhere
+rot13 () {
+ if [ $# -eq 0 ]; then
+ tr '[a-m][n-z][A-M][N-Z]' '[n-z][a-m][N-Z][A-M]'
+ else
+ echo $* | tr '[a-m][n-z][A-M][N-Z]' '[n-z][a-m][N-Z][A-M]'
+ fi
+}
+
+# Trim leading and trailing spaces (for scripts)
+trim()
+{
+ local var=$@
+ var="${var#"${var%%[![:space:]]*}"}" # remove leading whitespace characters
+ var="${var%"${var##*[![:space:]]}"}" # remove trailing whitespace characters
+ echo -n "$var"
+}
+
+#######################################################
+# Set the ultimate amazing command prompt
+#######################################################
+
+alias cpu="grep 'cpu ' /proc/stat | awk '{usage=(\$2+\$4)*100/(\$2+\$4+\$5)} END {print usage}' | awk '{printf(\"%.1f\n\", \$1)}'"
+function __setprompt
+{
+ local LAST_COMMAND=$? # Must come first!
+
+ # Define colors
+ local LIGHTGRAY="\033[0;37m"
+ local WHITE="\033[1;37m"
+ local BLACK="\033[0;30m"
+ local DARKGRAY="\033[1;30m"
+ local RED="\033[0;31m"
+ local LIGHTRED="\033[1;31m"
+ local GREEN="\033[0;32m"
+ local LIGHTGREEN="\033[1;32m"
+ local BROWN="\033[0;33m"
+ local YELLOW="\033[1;33m"
+ local BLUE="\033[0;34m"
+ local LIGHTBLUE="\033[1;34m"
+ local MAGENTA="\033[0;35m"
+ local LIGHTMAGENTA="\033[1;35m"
+ local CYAN="\033[0;36m"
+ local LIGHTCYAN="\033[1;36m"
+ local NOCOLOR="\033[0m"
+
+ # Show error exit code if there is one
+ if [[ $LAST_COMMAND != 0 ]]; then
+ # PS1="\[${RED}\](\[${LIGHTRED}\]ERROR\[${RED}\])-(\[${LIGHTRED}\]Exit Code \[${WHITE}\]${LAST_COMMAND}\[${RED}\])-(\[${LIGHTRED}\]"
+ PS1="\[${DARKGRAY}\](\[${LIGHTRED}\]ERROR\[${DARKGRAY}\])-(\[${RED}\]Exit Code \[${LIGHTRED}\]${LAST_COMMAND}\[${DARKGRAY}\])-(\[${RED}\]"
+ if [[ $LAST_COMMAND == 1 ]]; then
+ PS1+="General error"
+ elif [ $LAST_COMMAND == 2 ]; then
+ PS1+="Missing keyword, command, or permission problem"
+ elif [ $LAST_COMMAND == 126 ]; then
+ PS1+="Permission problem or command is not an executable"
+ elif [ $LAST_COMMAND == 127 ]; then
+ PS1+="Command not found"
+ elif [ $LAST_COMMAND == 128 ]; then
+ PS1+="Invalid argument to exit"
+ elif [ $LAST_COMMAND == 129 ]; then
+ PS1+="Fatal error signal 1"
+ elif [ $LAST_COMMAND == 130 ]; then
+ PS1+="Script terminated by Control-C"
+ elif [ $LAST_COMMAND == 131 ]; then
+ PS1+="Fatal error signal 3"
+ elif [ $LAST_COMMAND == 132 ]; then
+ PS1+="Fatal error signal 4"
+ elif [ $LAST_COMMAND == 133 ]; then
+ PS1+="Fatal error signal 5"
+ elif [ $LAST_COMMAND == 134 ]; then
+ PS1+="Fatal error signal 6"
+ elif [ $LAST_COMMAND == 135 ]; then
+ PS1+="Fatal error signal 7"
+ elif [ $LAST_COMMAND == 136 ]; then
+ PS1+="Fatal error signal 8"
+ elif [ $LAST_COMMAND == 137 ]; then
+ PS1+="Fatal error signal 9"
+ elif [ $LAST_COMMAND -gt 255 ]; then
+ PS1+="Exit status out of range"
+ else
+ PS1+="Unknown error code"
+ fi
+ PS1+="\[${DARKGRAY}\])\[${NOCOLOR}\]\n"
+ else
+ PS1=""
+ fi
+
+ # Date
+ PS1+="\[${DARKGRAY}\](\[${CYAN}\]\$(date +%a) $(date +%b-'%-m')" # Date
+ PS1+="${BLUE} $(date +'%-I':%M:%S%P)\[${DARKGRAY}\])-" # Time
+
+ # CPU
+ PS1+="(\[${MAGENTA}\]CPU $(cpu)%"
+
+ # Jobs
+ PS1+="\[${DARKGRAY}\]:\[${MAGENTA}\]\j"
+
+ # Network Connections (for a server - comment out for non-server)
+ PS1+="\[${DARKGRAY}\]:\[${MAGENTA}\]Net $(awk 'END {print NR}' /proc/net/tcp)"
+
+ PS1+="\[${DARKGRAY}\])-"
+
+ # User and server
+ local SSH_IP=`echo $SSH_CLIENT | awk '{ print $1 }'`
+ local SSH2_IP=`echo $SSH2_CLIENT | awk '{ print $1 }'`
+ if [ $SSH2_IP ] || [ $SSH_IP ] ; then
+ PS1+="(\[${RED}\]\u@\h"
+ else
+ PS1+="(\[${RED}\]\u"
+ fi
+
+ # Current directory
+ PS1+="\[${DARKGRAY}\]:\[${BROWN}\]\w\[${DARKGRAY}\])-"
+
+ # Total size of files in current directory
+ PS1+="(\[${GREEN}\]$(/bin/ls -lah | /bin/grep -m 1 total | /bin/sed 's/total //')\[${DARKGRAY}\]:"
+
+ # Number of files
+ PS1+="\[${GREEN}\]\$(/bin/ls -A -1 | /usr/bin/wc -l)\[${DARKGRAY}\])"
+
+ # Skip to the next line
+ PS1+="\n"
+
+ # singularity?
+ if [ -e /environment ] ; then
+ PS1+="singularity"
+ fi
+
+ if [[ $EUID -ne 0 ]]; then
+ PS1+="\[${GREEN}\]>\[${NOCOLOR}\] " # Normal user
+ else
+ PS1+="\[${RED}\]>\[${NOCOLOR}\] " # Root user
+ fi
+
+ # PS2 is used to continue a command using the \ character
+ PS2="\[${DARKGRAY}\]>\[${NOCOLOR}\] "
+
+ # PS3 is used to enter a number choice in a script
+ PS3='Please enter a number from above list: '
+
+ # PS4 is used for tracing a script in debug mode
+ PS4='\[${DARKGRAY}\]+\[${NOCOLOR}\] '
+}
+PROMPT_COMMAND='__setprompt'
diff --git a/containers/debian/Dockerfile b/containers/debian/Dockerfile
index 1c71071fa..d0caed73b 100644
--- a/containers/debian/Dockerfile
+++ b/containers/debian/Dockerfile
@@ -22,6 +22,8 @@ ENV CLICOLOR_FORCE=1 \
## this once afterburner is added to spack
RUN --mount=type=cache,target=/var/cache/apt \
rm -f /etc/apt/apt.conf.d/docker-clean \
+ && ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime \
+ && echo "US/Eastern" > /etc/timezone \
&& apt-get -yqq update \
&& apt-get -yqq upgrade \
&& apt-get -yqq install --no-install-recommends \
diff --git a/containers/oneapi/Dockerfile b/containers/oneapi/Dockerfile
new file mode 100644
index 000000000..b30c36975
--- /dev/null
+++ b/containers/oneapi/Dockerfile
@@ -0,0 +1,72 @@
+#syntax=docker/dockerfile:1.2
+
+# Minimal container based on Intel oneAPI for up-to-date packages.
+# Very lightweight container with a minimal build environment (LOL)
+
+FROM intel/oneapi-hpckit:2022.1.2-devel-ubuntu18.04
+LABEL maintainer="Wouter Deconinck <wouter.deconinck@umanitoba.ca" \
+ name="oneapi_base" \
+ march="amd64"
+
+COPY bashrc /root/.bashrc
+
+ENV CLICOLOR_FORCE=1 \
+ LANGUAGE=en_US.UTF-8 \
+ LANG=en_US.UTF-8 \
+ LC_ALL=en_US.UTF-8
+
+## Install additional packages. Remove the auto-cleanup functionality
+## for docker, as we're using the new buildkit cache instead.
+## We also install gitlab-runner, from the buster package (as bullseye is not available atm)
+## TODO: libyaml-cpp-dev is a dependency for afterburner. We can probably remove
+## this once afterburner is added to spack
+RUN --mount=type=cache,target=/var/cache/apt \
+ rm -f /etc/apt/apt.conf.d/docker-clean \
+ && ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime \
+ && echo "US/Eastern" > /etc/timezone \
+ && apt-get -yqq update \
+ && apt-get -yqq upgrade \
+ && apt-get -yqq install --no-install-recommends \
+ bc \
+ ca-certificates \
+ clang-format \
+ clang-tidy \
+ curl \
+ file \
+ build-essential \
+ gdb \
+ ghostscript \
+ git \
+ gnupg2 \
+ gv \
+ iproute2 \
+ iputils-ping \
+ iputils-tracepath \
+ less \
+ libcbor-xs-perl \
+ libjson-xs-perl \
+ libyaml-cpp-dev \
+ locales \
+ lua-posix \
+ make \
+ nano \
+ openssh-client \
+ parallel \
+ poppler-utils \
+ time \
+ unzip \
+ valgrind \
+ vim-nox \
+ wget \
+ && localedef -i en_US -f UTF-8 en_US.UTF-8 \
+ && gcc --version \
+ && curl -L \
+ "https://packages.gitlab.com/install/repositories/runner/gitlab-runner/script.deb.sh" \
+ | bash \
+ && sed -i "s/bookworm/buster/" \
+ /etc/apt/sources.list.d/runner_gitlab-runner.list \
+ && apt-get -yqq update \
+ && apt-get -yqq install --no-install-recommends \
+ gitlab-runner \
+ && apt-get -yqq autoremove \
+ && rm -rf /var/lib/apt/lists/*
diff --git a/containers/oneapi/bashrc b/containers/oneapi/bashrc
new file mode 100644
index 000000000..4d1c1f348
--- /dev/null
+++ b/containers/oneapi/bashrc
@@ -0,0 +1,452 @@
+#!/bin/bash
+iatest=$(expr index "$-" i)
+
+#######################################################
+# SOURCED ALIAS'S AND SCRIPTS BY zachbrowne.me
+#######################################################
+
+# Source global definitions
+if [ -f /etc/bashrc ]; then
+ . /etc/bashrc
+fi
+
+# Enable bash programmable completion features in interactive shells
+if [ -f /usr/share/bash-completion/bash_completion ]; then
+ . /usr/share/bash-completion/bash_completion
+elif [ -f /etc/bash_completion ]; then
+ . /etc/bash_completion
+fi
+
+#######################################################
+# EXPORTS
+#######################################################
+
+# Disable the bell
+if [[ $iatest > 0 ]]; then bind "set bell-style visible"; fi
+
+# Expand the history size
+export HISTFILESIZE=10000
+export HISTSIZE=500
+
+# Don't put duplicate lines in the history and do not add lines that start with a space
+export HISTCONTROL=erasedups:ignoredups:ignorespace
+
+# Check the window size after each command and, if necessary, update the values of LINES and COLUMNS
+shopt -s checkwinsize
+
+# Causes bash to append to history instead of overwriting it so if you start a new terminal, you have old session history
+shopt -s histappend
+PROMPT_COMMAND='history -a'
+
+# Allow ctrl-S for history navigation (with ctrl-R)
+stty -ixon
+
+# Ignore case on auto-completion
+# Note: bind used instead of sticking these in .inputrc
+if [[ $iatest > 0 ]]; then bind "set completion-ignore-case on"; fi
+
+# Show auto-completion list automatically, without double tab
+if [[ $iatest > 0 ]]; then bind "set show-all-if-ambiguous On"; fi
+
+# Set the default editor
+export EDITOR=vim
+export VISUAL=vim
+alias pico='edit'
+alias spico='sedit'
+alias nano='edit'
+alias snano='sedit'
+
+# To have colors for ls and all grep commands such as grep, egrep and zgrep
+export CLICOLOR=1
+export LS_COLORS='no=00:fi=00:di=00;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.avi=01;35:*.fli=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.ogg=01;35:*.mp3=01;35:*.wav=01;35:*.xml=00;31:'
+#export GREP_OPTIONS='--color=auto' #deprecated
+#alias grep="/usr/bin/grep $GREP_OPTIONS"
+#unset GREP_OPTIONS
+
+# Color for manpages in less makes manpages a little easier to read
+export LESS_TERMCAP_mb=$'\E[01;31m'
+export LESS_TERMCAP_md=$'\E[01;31m'
+export LESS_TERMCAP_me=$'\E[0m'
+export LESS_TERMCAP_se=$'\E[0m'
+export LESS_TERMCAP_so=$'\E[01;44;33m'
+export LESS_TERMCAP_ue=$'\E[0m'
+export LESS_TERMCAP_us=$'\E[01;32m'
+
+#######################################################
+# GENERAL ALIAS'S
+#######################################################
+
+# Alias's to modified commands
+alias cp='cp -i'
+alias mv='mv -i'
+alias rm='rm -iv'
+alias mkdir='mkdir -p'
+alias ps='ps auxf'
+alias ping='ping -c 10'
+alias less='less -R'
+alias cls='clear'
+alias apt-get='apt-get'
+alias multitail='multitail --no-repeat -c'
+alias freshclam='freshclam'
+alias vi='vim'
+alias vis='vim "+set si"'
+
+# Change directory aliases
+alias home='cd ~'
+alias cd..='cd ..'
+alias ..='cd ..'
+alias ...='cd ../..'
+alias ....='cd ../../..'
+alias .....='cd ../../../..'
+
+# cd into the old directory
+alias bd='cd "$OLDPWD"'
+
+# Remove a directory and all files
+alias rmd='/bin/rm --recursive --force --verbose '
+
+# Alias's for multiple directory listing commands
+alias la='ls -Alh' # show hidden files
+alias ls='ls -aFh --color=always' # add colors and file type extensions
+alias lx='ls -lXBh' # sort by extension
+alias lk='ls -lSrh' # sort by size
+alias lc='ls -lcrh' # sort by change time
+alias lu='ls -lurh' # sort by access time
+alias lr='ls -lRh' # recursive ls
+alias lt='ls -ltrh' # sort by date
+alias lm='ls -alh |more' # pipe through 'more'
+alias lw='ls -xAh' # wide listing format
+alias ll='ls -Fls' # long listing format
+alias labc='ls -lap' #alphabetical sort
+alias lf="ls -l | egrep -v '^d'" # files only
+alias ldir="ls -l | egrep '^d'" # directories only
+
+# alias chmod commands
+alias mx='chmod a+x'
+alias 000='chmod -R 000'
+alias 644='chmod -R 644'
+alias 666='chmod -R 666'
+alias 755='chmod -R 755'
+alias 777='chmod -R 777'
+
+# Search command line history
+alias h="history | grep "
+
+# Search running processes
+alias p="ps aux | grep "
+alias topcpu="/bin/ps -eo pcpu,pid,user,args | sort -k 1 -r | head -10"
+
+# Search files in the current folder
+alias f="find . | grep "
+
+# Count all files (recursively) in the current folder
+alias countfiles="for t in files links directories; do echo \`find . -type \${t:0:1} | wc -l\` \$t; done 2> /dev/null"
+
+# To see if a command is aliased, a file, or a built-in command
+alias checkcommand="type -t"
+
+# Show all logs in /var/log
+alias logs="sudo find /var/log -type f -exec file {} \; | grep 'text' | cut -d' ' -f1 | sed -e's/:$//g' | grep -v '[0-9]$' | xargs tail -f"
+
+# SHA1
+alias sha1='openssl sha1'
+
+#######################################################
+# SPECIAL FUNCTIONS
+#######################################################
+
+# Extracts any archive(s) (if unp isn't installed)
+extract () {
+ for archive in $*; do
+ if [ -f $archive ] ; then
+ case $archive in
+ *.tar.bz2) tar xvjf $archive ;;
+ *.tar.gz) tar xvzf $archive ;;
+ *.bz2) bunzip2 $archive ;;
+ *.rar) rar x $archive ;;
+ *.gz) gunzip $archive ;;
+ *.tar) tar xvf $archive ;;
+ *.tbz2) tar xvjf $archive ;;
+ *.tgz) tar xvzf $archive ;;
+ *.zip) unzip $archive ;;
+ *.Z) uncompress $archive ;;
+ *.7z) 7z x $archive ;;
+ *) echo "don't know how to extract '$archive'..." ;;
+ esac
+ else
+ echo "'$archive' is not a valid file!"
+ fi
+ done
+}
+
+# Searches for text in all files in the current folder
+ftext ()
+{
+ # -i case-insensitive
+ # -I ignore binary files
+ # -H causes filename to be printed
+ # -r recursive search
+ # -n causes line number to be printed
+ # optional: -F treat search term as a literal, not a regular expression
+ # optional: -l only print filenames and not the matching lines ex. grep -irl "$1" *
+ grep -iIHrn --color=always "$1" . | less -r
+}
+
+# Copy file with a progress bar
+cpp()
+{
+ set -e
+ strace -q -ewrite cp -- "${1}" "${2}" 2>&1 \
+ | awk '{
+ count += $NF
+ if (count % 10 == 0) {
+ percent = count / total_size * 100
+ printf "%3d%% [", percent
+ for (i=0;i<=percent;i++)
+ printf "="
+ printf ">"
+ for (i=percent;i<100;i++)
+ printf " "
+ printf "]\r"
+ }
+ }
+ END { print "" }' total_size=$(stat -c '%s' "${1}") count=0
+}
+
+# Copy and go to the directory
+cpg ()
+{
+ if [ -d "$2" ];then
+ cp $1 $2 && cd $2
+ else
+ cp $1 $2
+ fi
+}
+
+# Move and go to the directory
+mvg ()
+{
+ if [ -d "$2" ];then
+ mv $1 $2 && cd $2
+ else
+ mv $1 $2
+ fi
+}
+
+# Create and go to the directory
+mkdirg ()
+{
+ mkdir -p $1
+ cd $1
+}
+
+# Goes up a specified number of directories (i.e. up 4)
+up ()
+{
+ local d=""
+ limit=$1
+ for ((i=1 ; i <= limit ; i++))
+ do
+ d=$d/..
+ done
+ d=$(echo $d | sed 's/^\///')
+ if [ -z "$d" ]; then
+ d=..
+ fi
+ cd $d
+}
+
+#Automatically do an ls after each cd
+# cd ()
+# {
+# if [ -n "$1" ]; then
+# builtin cd "$@" && ls
+# else
+# builtin cd ~ && ls
+# fi
+# }
+
+# Returns the last 2 fields of the working directory
+pwdtail ()
+{
+ pwd|awk -F/ '{nlast = NF -1;print $nlast"/"$NF}'
+}
+
+# Show the current version of the operating system
+ver ()
+{
+ local dtype
+ dtype=$(distribution)
+
+ if [ $dtype == "redhat" ]; then
+ if [ -s /etc/redhat-release ]; then
+ cat /etc/redhat-release && uname -a
+ else
+ cat /etc/issue && uname -a
+ fi
+ elif [ $dtype == "suse" ]; then
+ cat /etc/SuSE-release
+ elif [ $dtype == "debian" ]; then
+ lsb_release -a
+ # sudo cat /etc/issue && sudo cat /etc/issue.net && sudo cat /etc/lsb_release && sudo cat /etc/os-release # Linux Mint option 2
+ elif [ $dtype == "gentoo" ]; then
+ cat /etc/gentoo-release
+ elif [ $dtype == "mandriva" ]; then
+ cat /etc/mandriva-release
+ elif [ $dtype == "slackware" ]; then
+ cat /etc/slackware-version
+ else
+ if [ -s /etc/issue ]; then
+ cat /etc/issue
+ else
+ echo "Error: Unknown distribution"
+ exit 1
+ fi
+ fi
+}
+
+# For some reason, rot13 pops up everywhere
+rot13 () {
+ if [ $# -eq 0 ]; then
+ tr '[a-m][n-z][A-M][N-Z]' '[n-z][a-m][N-Z][A-M]'
+ else
+ echo $* | tr '[a-m][n-z][A-M][N-Z]' '[n-z][a-m][N-Z][A-M]'
+ fi
+}
+
+# Trim leading and trailing spaces (for scripts)
+trim()
+{
+ local var=$@
+ var="${var#"${var%%[![:space:]]*}"}" # remove leading whitespace characters
+ var="${var%"${var##*[![:space:]]}"}" # remove trailing whitespace characters
+ echo -n "$var"
+}
+
+#######################################################
+# Set the ultimate amazing command prompt
+#######################################################
+
+alias cpu="grep 'cpu ' /proc/stat | awk '{usage=(\$2+\$4)*100/(\$2+\$4+\$5)} END {print usage}' | awk '{printf(\"%.1f\n\", \$1)}'"
+function __setprompt
+{
+ local LAST_COMMAND=$? # Must come first!
+
+ # Define colors
+ local LIGHTGRAY="\033[0;37m"
+ local WHITE="\033[1;37m"
+ local BLACK="\033[0;30m"
+ local DARKGRAY="\033[1;30m"
+ local RED="\033[0;31m"
+ local LIGHTRED="\033[1;31m"
+ local GREEN="\033[0;32m"
+ local LIGHTGREEN="\033[1;32m"
+ local BROWN="\033[0;33m"
+ local YELLOW="\033[1;33m"
+ local BLUE="\033[0;34m"
+ local LIGHTBLUE="\033[1;34m"
+ local MAGENTA="\033[0;35m"
+ local LIGHTMAGENTA="\033[1;35m"
+ local CYAN="\033[0;36m"
+ local LIGHTCYAN="\033[1;36m"
+ local NOCOLOR="\033[0m"
+
+ # Show error exit code if there is one
+ if [[ $LAST_COMMAND != 0 ]]; then
+ # PS1="\[${RED}\](\[${LIGHTRED}\]ERROR\[${RED}\])-(\[${LIGHTRED}\]Exit Code \[${WHITE}\]${LAST_COMMAND}\[${RED}\])-(\[${LIGHTRED}\]"
+ PS1="\[${DARKGRAY}\](\[${LIGHTRED}\]ERROR\[${DARKGRAY}\])-(\[${RED}\]Exit Code \[${LIGHTRED}\]${LAST_COMMAND}\[${DARKGRAY}\])-(\[${RED}\]"
+ if [[ $LAST_COMMAND == 1 ]]; then
+ PS1+="General error"
+ elif [ $LAST_COMMAND == 2 ]; then
+ PS1+="Missing keyword, command, or permission problem"
+ elif [ $LAST_COMMAND == 126 ]; then
+ PS1+="Permission problem or command is not an executable"
+ elif [ $LAST_COMMAND == 127 ]; then
+ PS1+="Command not found"
+ elif [ $LAST_COMMAND == 128 ]; then
+ PS1+="Invalid argument to exit"
+ elif [ $LAST_COMMAND == 129 ]; then
+ PS1+="Fatal error signal 1"
+ elif [ $LAST_COMMAND == 130 ]; then
+ PS1+="Script terminated by Control-C"
+ elif [ $LAST_COMMAND == 131 ]; then
+ PS1+="Fatal error signal 3"
+ elif [ $LAST_COMMAND == 132 ]; then
+ PS1+="Fatal error signal 4"
+ elif [ $LAST_COMMAND == 133 ]; then
+ PS1+="Fatal error signal 5"
+ elif [ $LAST_COMMAND == 134 ]; then
+ PS1+="Fatal error signal 6"
+ elif [ $LAST_COMMAND == 135 ]; then
+ PS1+="Fatal error signal 7"
+ elif [ $LAST_COMMAND == 136 ]; then
+ PS1+="Fatal error signal 8"
+ elif [ $LAST_COMMAND == 137 ]; then
+ PS1+="Fatal error signal 9"
+ elif [ $LAST_COMMAND -gt 255 ]; then
+ PS1+="Exit status out of range"
+ else
+ PS1+="Unknown error code"
+ fi
+ PS1+="\[${DARKGRAY}\])\[${NOCOLOR}\]\n"
+ else
+ PS1=""
+ fi
+
+ # Date
+ PS1+="\[${DARKGRAY}\](\[${CYAN}\]\$(date +%a) $(date +%b-'%-m')" # Date
+ PS1+="${BLUE} $(date +'%-I':%M:%S%P)\[${DARKGRAY}\])-" # Time
+
+ # CPU
+ PS1+="(\[${MAGENTA}\]CPU $(cpu)%"
+
+ # Jobs
+ PS1+="\[${DARKGRAY}\]:\[${MAGENTA}\]\j"
+
+ # Network Connections (for a server - comment out for non-server)
+ PS1+="\[${DARKGRAY}\]:\[${MAGENTA}\]Net $(awk 'END {print NR}' /proc/net/tcp)"
+
+ PS1+="\[${DARKGRAY}\])-"
+
+ # User and server
+ local SSH_IP=`echo $SSH_CLIENT | awk '{ print $1 }'`
+ local SSH2_IP=`echo $SSH2_CLIENT | awk '{ print $1 }'`
+ if [ $SSH2_IP ] || [ $SSH_IP ] ; then
+ PS1+="(\[${RED}\]\u@\h"
+ else
+ PS1+="(\[${RED}\]\u"
+ fi
+
+ # Current directory
+ PS1+="\[${DARKGRAY}\]:\[${BROWN}\]\w\[${DARKGRAY}\])-"
+
+ # Total size of files in current directory
+ PS1+="(\[${GREEN}\]$(/bin/ls -lah | /bin/grep -m 1 total | /bin/sed 's/total //')\[${DARKGRAY}\]:"
+
+ # Number of files
+ PS1+="\[${GREEN}\]\$(/bin/ls -A -1 | /usr/bin/wc -l)\[${DARKGRAY}\])"
+
+ # Skip to the next line
+ PS1+="\n"
+
+ # singularity?
+ if [ -e /environment ] ; then
+ PS1+="singularity"
+ fi
+
+ if [[ $EUID -ne 0 ]]; then
+ PS1+="\[${GREEN}\]>\[${NOCOLOR}\] " # Normal user
+ else
+ PS1+="\[${RED}\]>\[${NOCOLOR}\] " # Root user
+ fi
+
+ # PS2 is used to continue a command using the \ character
+ PS2="\[${DARKGRAY}\]>\[${NOCOLOR}\] "
+
+ # PS3 is used to enter a number choice in a script
+ PS3='Please enter a number from above list: '
+
+ # PS4 is used for tracing a script in debug mode
+ PS4='\[${DARKGRAY}\]+\[${NOCOLOR}\] '
+}
+PROMPT_COMMAND='__setprompt'
--
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