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 && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
+ python3-arvados-fuse \
crunch-run \
arvados-docker-cleaner \
docker.io
+# Get Go and build singularity
+goversion=1.16.3
+mkdir -p /var/lib/arvados
+rm -rf /var/lib/arvados/go/
+curl -s https://storage.googleapis.com/golang/go${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 $singularityversion > VERSION
+./mconfig --prefix=/var/lib/arvados
+make -C ./builddir
+make -C ./builddir install
+ln -sf /var/lib/arvados/bin/* /usr/local/bin/
+
+# Print singularity version installed
+singularity --version
+
# Remove unattended-upgrades if it is installed
-$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
+
$SUDO systemctl daemon-reload
+# docker should not start on boot: we restart it inside /usr/local/bin/ensure-encrypted-partitions.sh,
+# and the BootProbeCommand defaults to "docker ps -q"
+$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
projects / arvados.git / blobdiff