SUDO=sudo
+wait_for_apt_locks() {
+ while $SUDO fuser /var/{lib/{dpkg,apt/lists},cache/apt/archives}/lock >/dev/null 2>&1; do
+ echo "APT: Waiting for apt/dpkg locks to be released..."
+ sleep 1
+ done
+}
+
# Run apt-get update
$SUDO DEBIAN_FRONTEND=noninteractive apt-get --yes update
# Install gnupg and dirmgr or gpg key checks will fail
-$SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
gnupg \
dirmngr \
lsb-release
# For good measure, apt-get upgrade
-$SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes upgrade
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes upgrade
# Make sure cloud-init is installed
-$SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install cloud-init
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install cloud-init
if [[ ! -d /var/lib/cloud/scripts/per-boot ]]; then
mkdir -p /var/lib/cloud/scripts/per-boot
fi
# Add the arvados signing key
cat /tmp/1078ECD7.asc | $SUDO apt-key add -
# Add the debian keys
-$SUDO DEBIAN_FRONTEND=noninteractive apt-get install --yes debian-keyring debian-archive-keyring
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get install --yes debian-keyring debian-archive-keyring
# Fix locale
$SUDO /bin/sed -ri 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
$SUDO /usr/sbin/locale-gen
# Install some packages we always need
-$SUDO DEBIAN_FRONTEND=noninteractive apt-get --yes update
-$SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get --yes update
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
openssh-server \
apt-utils \
git \
libcurl4-openssl-dev \
lvm2 \
cryptsetup \
- xfsprogs
-
-# See if python3-distutils is installable, and if so install it. This is a
-# temporary workaround for an Arvados packaging bug and should be removed once
-# Arvados 2.0.4 or 2.1.0 is released, whichever comes first.
-# See https://dev.arvados.org/issues/16611 for more information
-if apt-cache -qq show python3-distutils >/dev/null 2>&1; then
- $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install python3-distutils
-fi
+ xfsprogs \
+ squashfs-tools
# Install the Arvados packages we need
-$SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
- python-arvados-fuse \
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
+ python3-arvados-fuse \
crunch-run \
arvados-docker-cleaner \
docker.io
+# Get Go and build singularity
+goversion=1.17.1
+mkdir -p /var/lib/arvados
+rm -rf /var/lib/arvados/go/
+curl -s https://storage.googleapis.com/golang/go${goversion}.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
+ln -sf /var/lib/arvados/go/bin/* /usr/local/bin/
+
+singularityversion=3.7.4
+curl -Ls https://github.com/sylabs/singularity/archive/refs/tags/v${singularityversion}.tar.gz | tar -C /var/lib/arvados -xzf -
+cd /var/lib/arvados/singularity-${singularityversion}
+
+# build dependencies for singularity
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
+ make build-essential libssl-dev uuid-dev cryptsetup
+
+echo $singularityversion > VERSION
+./mconfig --prefix=/var/lib/arvados
+make -C ./builddir
+make -C ./builddir install
+ln -sf /var/lib/arvados/bin/* /usr/local/bin/
+
+# set `mksquashfs mem` in the singularity config file if it is configured
+if [ "$MKSQUASHFS_MEM" != "" ]; then
+ echo "mksquashfs mem = ${MKSQUASHFS_MEM}" >> /var/lib/arvados/etc/singularity/singularity.conf
+fi
+
+# Print singularity version installed
+singularity --version
+
# Remove unattended-upgrades if it is installed
-$SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes remove unattended-upgrades --purge
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes remove unattended-upgrades --purge
# Configure arvados-docker-cleaner
$SUDO mkdir -p /etc/arvados/docker-cleaner
$SUDO sed -i 's/GRUB_CMDLINE_LINUX=""/GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"/g' /etc/default/grub
$SUDO update-grub
-# Set a higher ulimit for docker
-$SUDO sed -i "s/ExecStart=\(.*\)/ExecStart=\1 --default-ulimit nofile=10000:10000 --dns ${RESOLVER}/g" /lib/systemd/system/docker.service
+# Set a higher ulimit and the resolver (if set) for docker
+if [ "x$RESOLVER" != "x" ]; then
+ SET_RESOLVER="--dns ${RESOLVER}"
+fi
+
+$SUDO sed "s/ExecStart=\(.*\)/ExecStart=\1 --default-ulimit nofile=10000:10000 ${SET_RESOLVER}/g" \
+ /lib/systemd/system/docker.service \
+ > /etc/systemd/system/docker.service
+
$SUDO systemctl daemon-reload
+# docker should not start on boot: we restart it inside /usr/local/bin/ensure-encrypted-partitions.sh,
+# and the BootProbeCommand might be "docker ps -q"
+$SUDO systemctl disable docker
+
# Make sure user_allow_other is set in fuse.conf
$SUDO sed -i 's/#user_allow_other/user_allow_other/g' /etc/fuse.conf
$SUDO chmod 600 /home/crunch/.ssh/authorized_keys
$SUDO chmod 700 /home/crunch/.ssh/
-# Make sure we resolve via the provided resolver IP. Prepending is good enough because
+# Make sure we resolve via the provided resolver IP if set. Prepending is good enough because
# unless 'rotate' is set, the nameservers are queried in order (cf. man resolv.conf)
-$SUDO sed -i "s/#prepend domain-name-servers 127.0.0.1;/prepend domain-name-servers ${RESOLVER};/" /etc/dhcp/dhclient.conf
-
+if [ "x$RESOLVER" != "x" ]; then
+ $SUDO sed -i "s/#prepend domain-name-servers 127.0.0.1;/prepend domain-name-servers ${RESOLVER};/" /etc/dhcp/dhclient.conf
+fi
# Set up the cloud-init script that will ensure encrypted disks
$SUDO mv /tmp/usr-local-bin-ensure-encrypted-partitions.sh /usr/local/bin/ensure-encrypted-partitions.sh
$SUDO chmod 755 /usr/local/bin/ensure-encrypted-partitions.sh
$SUDO chown root:root /usr/local/bin/ensure-encrypted-partitions.sh
$SUDO mv /tmp/etc-cloud-cloud.cfg.d-07_compute_arvados_dispatch_cloud.cfg /etc/cloud/cloud.cfg.d/07_compute_arvados_dispatch_cloud.cfg
$SUDO chown root:root /etc/cloud/cloud.cfg.d/07_compute_arvados_dispatch_cloud.cfg
+
+if [ "$NVIDIA_GPU_SUPPORT" == "1" ]; then
+ # $DIST should not have a dot if there is one in /etc/os-release (e.g. 18.04)
+ DIST=$(. /etc/os-release; echo $ID$VERSION_ID | tr -d '.')
+ # We need a kernel and matching headers
+ if [[ "$DIST" =~ ^debian ]]; then
+ $SUDO apt-get -y install linux-image-cloud-amd64 linux-headers-cloud-amd64
+ elif [ "$CLOUD" == "azure" ]; then
+ $SUDO apt-get -y install linux-image-azure linux-headers-azure
+ elif [ "$CLOUD" == "aws" ]; then
+ $SUDO apt-get -y install linux-image-aws linux-headers-aws
+ fi
+
+ # Install CUDA
+ $SUDO apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/$DIST/x86_64/7fa2af80.pub
+ $SUDO apt-get -y install software-properties-common
+ $SUDO add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/$DIST/x86_64/ /"
+ $SUDO add-apt-repository contrib
+ $SUDO apt-get update
+ $SUDO apt-get -y install cuda
+
+ # Install libnvidia-container, the tooling for Docker/Singularity
+ curl -s -L https://nvidia.github.io/libnvidia-container/gpgkey | \
+ $SUDO apt-key add -
+ if [ "$DIST" == "debian11" ]; then
+ # As of 2021-12-16 libnvidia-container and friends are only available for
+ # Debian 10, not yet Debian 11. Install experimental rc1 package as per this
+ # workaround:
+ # https://github.com/NVIDIA/nvidia-docker/issues/1549#issuecomment-989670662
+ curl -s -L https://nvidia.github.io/libnvidia-container/debian10/libnvidia-container.list | \
+ $SUDO tee /etc/apt/sources.list.d/libnvidia-container.list
+ $SUDO sed -i -e '/experimental/ s/^#//g' /etc/apt/sources.list.d/libnvidia-container.list
+ else
+ # here, $DIST should have a dot if there is one in /etc/os-release (e.g. 18.04)...
+ DIST=$(. /etc/os-release; echo $ID$VERSION_ID)
+ curl -s -L https://nvidia.github.io/libnvidia-container/$DIST/libnvidia-container.list | \
+ $SUDO tee /etc/apt/sources.list.d/libnvidia-container.list
+ fi
+
+ if [ "$DIST" == "debian10" ]; then
+ # Debian 10 comes with Docker 18.xx, we need 19.03 or later
+ curl -fsSL https://download.docker.com/linux/debian/gpg | $SUDO gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
+ echo deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/debian/ buster stable | \
+ $SUDO tee /etc/apt/sources.list.d/docker.list
+ $SUDO apt-get update
+ $SUDO apt-get -yq --no-install-recommends install docker-ce=5:19.03.15~3-0~debian-buster
+
+ $SUDO sed "s/ExecStart=\(.*\)/ExecStart=\1 --default-ulimit nofile=10000:10000 ${SET_RESOLVER}/g" \
+ /lib/systemd/system/docker.service \
+ > /etc/systemd/system/docker.service
+
+ $SUDO systemctl daemon-reload
+
+ # docker should not start on boot: we restart it inside /usr/local/bin/ensure-encrypted-partitions.sh,
+ # and the BootProbeCommand might be "docker ps -q"
+ $SUDO systemctl disable docker
+ fi
+ $SUDO apt-get update
+ $SUDO apt-get -y install libnvidia-container1 libnvidia-container-tools nvidia-container-toolkit
+fi
+
+$SUDO apt-get clean