1 #!/bin/bash -euxo pipefail
3 # Copyright (C) The Arvados Authors. All rights reserved.
5 # SPDX-License-Identifier: Apache-2.0
11 wait_for_apt_locks() {
12 while $SUDO fuser /var/{lib/{dpkg,apt/lists},cache/apt/archives}/lock >/dev/null 2>&1; do
13 echo "APT: Waiting for apt/dpkg locks to be released..."
19 $SUDO DEBIAN_FRONTEND=noninteractive apt-get --yes update
21 # Install gnupg and dirmgr or gpg key checks will fail
22 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
27 # For good measure, apt-get upgrade
28 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes upgrade
30 # Make sure cloud-init is installed
31 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install cloud-init
32 if [[ ! -d /var/lib/cloud/scripts/per-boot ]]; then
33 mkdir -p /var/lib/cloud/scripts/per-boot
36 TMP_LSB=`/usr/bin/lsb_release -c -s`
37 LSB_RELEASE_CODENAME=${TMP_LSB//[$'\t\r\n ']}
39 # Add the arvados apt repository
40 echo "# apt.arvados.org" |$SUDO tee --append /etc/apt/sources.list.d/apt.arvados.org.list
41 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
43 # Add the arvados signing key
44 cat /tmp/1078ECD7.asc | $SUDO apt-key add -
46 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get install --yes debian-keyring debian-archive-keyring
49 $SUDO /bin/sed -ri 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
50 $SUDO /usr/sbin/locale-gen
52 # Install some packages we always need
53 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get --yes update
54 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
60 libcurl4-openssl-dev \
66 # Install the Arvados packages we need
67 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
68 python3-arvados-fuse \
69 arvados-docker-cleaner \
72 # Get Go and build singularity
74 mkdir -p /var/lib/arvados
75 rm -rf /var/lib/arvados/go/
76 curl -s https://storage.googleapis.com/golang/go${goversion}.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
77 ln -sf /var/lib/arvados/go/bin/* /usr/local/bin/
79 singularityversion=3.7.4
80 curl -Ls https://github.com/sylabs/singularity/archive/refs/tags/v${singularityversion}.tar.gz | tar -C /var/lib/arvados -xzf -
81 cd /var/lib/arvados/singularity-${singularityversion}
83 # build dependencies for singularity
84 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
85 make build-essential libssl-dev uuid-dev cryptsetup
87 echo $singularityversion > VERSION
88 ./mconfig --prefix=/var/lib/arvados
90 make -C ./builddir install
91 ln -sf /var/lib/arvados/bin/* /usr/local/bin/
93 # set `mksquashfs mem` in the singularity config file if it is configured
94 if [ "$MKSQUASHFS_MEM" != "" ]; then
95 echo "mksquashfs mem = ${MKSQUASHFS_MEM}" >> /var/lib/arvados/etc/singularity/singularity.conf
98 # Print singularity version installed
101 # Remove unattended-upgrades if it is installed
102 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes remove unattended-upgrades --purge
104 # Configure arvados-docker-cleaner
105 $SUDO mkdir -p /etc/arvados/docker-cleaner
106 $SUDO echo -e "{\n \"Quota\": \"10G\",\n \"RemoveStoppedContainers\": \"always\"\n}" > /etc/arvados/docker-cleaner/docker-cleaner.json
108 # Enable cgroup accounting
109 $SUDO sed -i 's/GRUB_CMDLINE_LINUX=""/GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"/g' /etc/default/grub
112 # Set a higher ulimit and the resolver (if set) for docker
113 if [ "x$RESOLVER" != "x" ]; then
114 SET_RESOLVER="--dns ${RESOLVER}"
117 $SUDO sed "s/ExecStart=\(.*\)/ExecStart=\1 --default-ulimit nofile=10000:10000 ${SET_RESOLVER}/g" \
118 /lib/systemd/system/docker.service \
119 > /etc/systemd/system/docker.service
121 $SUDO systemctl daemon-reload
123 # docker should not start on boot: we restart it inside /usr/local/bin/ensure-encrypted-partitions.sh,
124 # and the BootProbeCommand might be "docker ps -q"
125 $SUDO systemctl disable docker
127 # Make sure user_allow_other is set in fuse.conf
128 $SUDO sed -i 's/#user_allow_other/user_allow_other/g' /etc/fuse.conf
130 # Add crunch user with sudo powers
131 $SUDO adduser --disabled-password --gecos "Crunch user,,,," crunch
132 # Do not require a password to sudo
133 echo -e "# for the crunch user\ncrunch ALL=(ALL) NOPASSWD:ALL" | $SUDO tee /etc/sudoers.d/91-crunch
135 # Set up the ssh public key for the crunch user
136 $SUDO mkdir /home/crunch/.ssh
137 $SUDO mv /tmp/crunch-authorized_keys /home/crunch/.ssh/authorized_keys
138 $SUDO chown -R crunch:crunch /home/crunch/.ssh
139 $SUDO chmod 600 /home/crunch/.ssh/authorized_keys
140 $SUDO chmod 700 /home/crunch/.ssh/
142 # Make sure we resolve via the provided resolver IP if set. Prepending is good enough because
143 # unless 'rotate' is set, the nameservers are queried in order (cf. man resolv.conf)
144 if [ "x$RESOLVER" != "x" ]; then
145 $SUDO sed -i "s/#prepend domain-name-servers 127.0.0.1;/prepend domain-name-servers ${RESOLVER};/" /etc/dhcp/dhclient.conf
148 if [ "$AWS_EBS_AUTOSCALE" != "1" ]; then
149 # Set up the cloud-init script that will ensure encrypted disks
150 $SUDO mv /tmp/usr-local-bin-ensure-encrypted-partitions.sh /usr/local/bin/ensure-encrypted-partitions.sh
152 wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install jq unzip
154 curl -s "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "/tmp/awscliv2.zip"
155 unzip -q /tmp/awscliv2.zip -d /tmp && $SUDO /tmp/aws/install
156 # Pinned to v2.4.5 because we apply a patch below
157 #export EBS_AUTOSCALE_VERSION=$(curl --silent "https://api.github.com/repos/awslabs/amazon-ebs-autoscale/releases/latest" | jq -r .tag_name)
158 export EBS_AUTOSCALE_VERSION="v2.4.5"
159 cd /opt && $SUDO git clone https://github.com/awslabs/amazon-ebs-autoscale.git
160 cd /opt/amazon-ebs-autoscale && $SUDO git checkout $EBS_AUTOSCALE_VERSION
161 $SUDO patch -p1 < /tmp/create-ebs-volume-nvme.patch
163 # This script really requires bash and the shebang line is wrong
164 $SUDO sed -i 's|^#!/bin/sh|#!/bin/bash|' /opt/amazon-ebs-autoscale/bin/ebs-autoscale
166 # Set up the cloud-init script that makes use of the AWS EBS autoscaler
167 $SUDO mv /tmp/usr-local-bin-ensure-encrypted-partitions-aws-ebs-autoscale.sh /usr/local/bin/ensure-encrypted-partitions.sh
170 $SUDO chmod 755 /usr/local/bin/ensure-encrypted-partitions.sh
171 $SUDO chown root:root /usr/local/bin/ensure-encrypted-partitions.sh
172 $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
173 $SUDO chown root:root /etc/cloud/cloud.cfg.d/07_compute_arvados_dispatch_cloud.cfg
175 if [ "$NVIDIA_GPU_SUPPORT" == "1" ]; then
176 # $DIST should not have a dot if there is one in /etc/os-release (e.g. 18.04)
177 DIST=$(. /etc/os-release; echo $ID$VERSION_ID | tr -d '.')
178 # We need a kernel and matching headers
179 if [[ "$DIST" =~ ^debian ]]; then
180 $SUDO apt-get -y install linux-image-cloud-amd64 linux-headers-cloud-amd64
181 elif [ "$CLOUD" == "azure" ]; then
182 $SUDO apt-get -y install linux-image-azure linux-headers-azure
183 elif [ "$CLOUD" == "aws" ]; then
184 $SUDO apt-get -y install linux-image-aws linux-headers-aws
188 $SUDO apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/$DIST/x86_64/7fa2af80.pub
189 $SUDO apt-get -y install software-properties-common
190 $SUDO add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/$DIST/x86_64/ /"
191 $SUDO add-apt-repository contrib
193 $SUDO apt-get -y install cuda
195 # Install libnvidia-container, the tooling for Docker/Singularity
196 curl -s -L https://nvidia.github.io/libnvidia-container/gpgkey | \
198 if [ "$DIST" == "debian11" ]; then
199 # As of 2021-12-16 libnvidia-container and friends are only available for
200 # Debian 10, not yet Debian 11. Install experimental rc1 package as per this
202 # https://github.com/NVIDIA/nvidia-docker/issues/1549#issuecomment-989670662
203 curl -s -L https://nvidia.github.io/libnvidia-container/debian10/libnvidia-container.list | \
204 $SUDO tee /etc/apt/sources.list.d/libnvidia-container.list
205 $SUDO sed -i -e '/experimental/ s/^#//g' /etc/apt/sources.list.d/libnvidia-container.list
207 # here, $DIST should have a dot if there is one in /etc/os-release (e.g. 18.04)...
208 DIST=$(. /etc/os-release; echo $ID$VERSION_ID)
209 curl -s -L https://nvidia.github.io/libnvidia-container/$DIST/libnvidia-container.list | \
210 $SUDO tee /etc/apt/sources.list.d/libnvidia-container.list
213 if [ "$DIST" == "debian10" ]; then
214 # Debian 10 comes with Docker 18.xx, we need 19.03 or later
215 curl -fsSL https://download.docker.com/linux/debian/gpg | $SUDO gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
216 echo deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/debian/ buster stable | \
217 $SUDO tee /etc/apt/sources.list.d/docker.list
219 $SUDO apt-get -yq --no-install-recommends install docker-ce=5:19.03.15~3-0~debian-buster
221 $SUDO sed "s/ExecStart=\(.*\)/ExecStart=\1 --default-ulimit nofile=10000:10000 ${SET_RESOLVER}/g" \
222 /lib/systemd/system/docker.service \
223 > /etc/systemd/system/docker.service
225 $SUDO systemctl daemon-reload
227 # docker should not start on boot: we restart it inside /usr/local/bin/ensure-encrypted-partitions.sh,
228 # and the BootProbeCommand might be "docker ps -q"
229 $SUDO systemctl disable docker
232 $SUDO apt-get -y install libnvidia-container1 libnvidia-container-tools nvidia-container-toolkit
233 # This service fails to start when the image is booted without Nvidia GPUs present, which makes
234 # `systemctl is-system-running` respond with "degraded" and since that command is our default
235 # BootProbeCommand, compute nodes never finish booting from Arvados' perspective.
236 # Disable the service to avoid this. This should be fine because crunch-run does its own basic
237 # CUDA initialization.
238 $SUDO systemctl disable nvidia-persistenced.service