#
# SPDX-License-Identifier: Apache-2.0
+set -eu -o pipefail
+
SUDO=sudo
wait_for_apt_locks() {
done
}
+# $DIST should not have a dot if there is one in /etc/os-release (e.g. 18.04)
+DIST=$(. /etc/os-release; echo $ID$VERSION_ID | tr -d '.')
+
# Run apt-get update
$SUDO DEBIAN_FRONTEND=noninteractive apt-get --yes update
TMP_LSB=`/usr/bin/lsb_release -c -s`
LSB_RELEASE_CODENAME=${TMP_LSB//[$'\t\r\n ']}
+SET_RESOLVER=
+if [ -n "$RESOLVER" ]; then
+ SET_RESOLVER="--dns ${RESOLVER}"
+fi
+
# Add the arvados apt repository
echo "# apt.arvados.org" |$SUDO tee --append /etc/apt/sources.list.d/apt.arvados.org.list
echo "deb http://apt.arvados.org/$LSB_RELEASE_CODENAME $LSB_RELEASE_CODENAME${REPOSUFFIX} main" |$SUDO tee --append /etc/apt/sources.list.d/apt.arvados.org.list
# Add the arvados signing key
cat /tmp/1078ECD7.asc | $SUDO apt-key add -
-# Add the debian keys
-wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get install --yes debian-keyring debian-archive-keyring
+# Add the debian keys (but don't abort if we can't find them, e.g. on Ubuntu where we don't need them)
+wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get install --yes debian-keyring debian-archive-keyring 2>/dev/null || true
# Fix locale
$SUDO /bin/sed -ri 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
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
- wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install python3-distutils
-fi
+ xfsprogs \
+ squashfs-tools
# Install the Arvados packages we need
wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
- python-arvados-fuse \
- crunch-run \
- arvados-docker-cleaner \
- docker.io
+ python3-arvados-fuse \
+ arvados-docker-cleaner
+
+# We want Docker 20.10 or later so that we support glibc 2.33 and up in the container, cf.
+# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1005906
+dockerversion=5:20.10.13~3-0
+if [[ "$DIST" =~ ^debian ]]; then
+ family="debian"
+ if [ "$DIST" == "debian10" ]; then
+ distro="buster"
+ elif [ "$DIST" == "debian11" ]; then
+ distro="bullseye"
+ fi
+elif [[ "$DIST" =~ ^ubuntu ]]; then
+ family="ubuntu"
+ if [ "$DIST" == "ubuntu1804" ]; then
+ distro="bionic"
+ elif [ "$DIST" == "ubuntu2004" ]; then
+ distro="focal"
+ fi
+else
+ echo "Unsupported distribution $DIST"
+ exit 1
+fi
+curl -fsSL https://download.docker.com/linux/$family/gpg | $SUDO gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
+echo deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/$family/ $distro stable | \
+ $SUDO tee /etc/apt/sources.list.d/docker.list
+$SUDO apt-get update
+$SUDO apt-get -yq --no-install-recommends install docker-ce=${dockerversion}~${family}-${distro}
+
+# Set a higher ulimit and the resolver (if set) for docker
+$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"
+$SUDO systemctl disable docker
+
+# Get Go and build singularity
+mkdir -p /var/lib/arvados
+rm -rf /var/lib/arvados/go/
+curl -s https://storage.googleapis.com/golang/go${GOVERSION}.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
+ln -sf /var/lib/arvados/go/bin/* /usr/local/bin/
+
+singularityversion=3.9.9
+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
wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes remove unattended-upgrades --purge
$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 ${RESOLVER}/g" /lib/systemd/system/docker.service
-$SUDO systemctl daemon-reload
-
# 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 ${RESOLVER};/" /etc/dhcp/dhclient.conf
+fi
+
+# AWS_EBS_AUTOSCALE is not always set, work around unset variable check
+EBS_AUTOSCALE=${AWS_EBS_AUTOSCALE:-}
+
+if [ "$EBS_AUTOSCALE" != "1" ]; then
+ # 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
+else
+ wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install jq unzip
+
+ curl -s "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "/tmp/awscliv2.zip"
+ unzip -q /tmp/awscliv2.zip -d /tmp && $SUDO /tmp/aws/install
+ # Pinned to v2.4.5 because we apply a patch below
+ #export EBS_AUTOSCALE_VERSION=$(curl --silent "https://api.github.com/repos/awslabs/amazon-ebs-autoscale/releases/latest" | jq -r .tag_name)
+ export EBS_AUTOSCALE_VERSION="v2.4.5"
+ cd /opt && $SUDO git clone https://github.com/awslabs/amazon-ebs-autoscale.git
+ cd /opt/amazon-ebs-autoscale && $SUDO git checkout $EBS_AUTOSCALE_VERSION
+ $SUDO patch -p1 < /tmp/create-ebs-volume-nvme.patch
+
+ # This script really requires bash and the shebang line is wrong
+ $SUDO sed -i 's|^#!/bin/sh|#!/bin/bash|' /opt/amazon-ebs-autoscale/bin/ebs-autoscale
+
+ # Set up the cloud-init script that makes use of the AWS EBS autoscaler
+ $SUDO mv /tmp/usr-local-bin-ensure-encrypted-partitions-aws-ebs-autoscale.sh /usr/local/bin/ensure-encrypted-partitions.sh
+fi
-# Set up the cloud-init script that will ensure encrypted disks
-$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
+ # 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/ /"
+ # Ubuntu 18.04's add-apt-repository does not understand 'contrib'
+ $SUDO add-apt-repository contrib || true
+ $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
+
+ $SUDO apt-get update
+ $SUDO apt-get -y install libnvidia-container1 libnvidia-container-tools nvidia-container-toolkit
+ # This service fails to start when the image is booted without Nvidia GPUs present, which makes
+ # `systemctl is-system-running` respond with "degraded" and since that command is our default
+ # BootProbeCommand, compute nodes never finish booting from Arvados' perspective.
+ # Disable the service to avoid this. This should be fine because crunch-run does its own basic
+ # CUDA initialization.
+ $SUDO systemctl disable nvidia-persistenced.service
+fi
+
+$SUDO apt-get clean
projects / arvados.git / blobdiff