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[Image] Fix blocking by unattended-upgrade #1347

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Oct 31, 2022
Merged

[Image] Fix blocking by unattended-upgrade #1347

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887f1a7
Fix blocking by unattended-upgrade
Michaelvll Oct 31, 2022
277db7d
adopt to gcp and azure
Michaelvll Oct 31, 2022
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15 changes: 9 additions & 6 deletions sky/templates/aws-ray.yml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,7 @@ initialization_commands: []
# Increment the following for catching performance bugs easier:
# current num items (num SSH connections): 1
setup_commands:
# Disable `unattended-upgrades` to prevent apt-get from hanging. It should be called at the beginning before the process started to avoid being blocked. (This is a temporary fix.)
# Create ~/.ssh/config file in case the file does not exist in the custom image.
# Make sure python3 & pip3 are available on this image.
# We set auto_activate_base to be false for pre-installed conda.
Expand All @@ -97,19 +98,21 @@ setup_commands:
# Line 'sudo grep ..': set the number of threads per process to unlimited to avoid ray job submit stucking issue when the number of running ray jobs increase.
# Line 'mkdir -p ..': disable host key check
# Line 'python3 -c ..': patch the buggy ray files and enable `-o allow_other` option for `goofys`
- mkdir -p ~/.ssh; touch ~/.ssh/config;
- sudo systemctl stop unattended-upgrades || true;
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Q: the user reported that "I was force killing the process with kill -9 ; without it, the systemctl stop also hangs for me". Did we see the same problem (if so, this line will hang)?

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Yes, the line will hang if the unattended-upgrades process is running. We moved it to the front to take best effort to stop it before the process starts. Force killing the process does not work well, as when I manually tried to force killing it on the VM, a new unattended-upgrades will start immediately after killing the previous one.

sudo systemctl disable unattended-upgrades || true;
sudo sed -i 's/Unattended-Upgrade "1"/Unattended-Upgrade "0"/g' /etc/apt/apt.conf.d/20auto-upgrades || true;
sudo kill -9 `sudo lsof /var/lib/dpkg/lock-frontend | awk '{print $2}' | tail -n 1` || true;
sudo pkill -9 apt-get;
sudo pkill -9 dpkg;
sudo dpkg --configure -a;
mkdir -p ~/.ssh; touch ~/.ssh/config;
pip3 --version > /dev/null 2>&1 || (curl -sSL https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3 get-pip.py && echo "PATH=$HOME/.local/bin:$PATH" >> ~/.bashrc);
(type -a python | grep -q python3) || echo 'alias python=python3' >> ~/.bashrc;
(type -a pip | grep -q pip3) || echo 'alias pip=pip3' >> ~/.bashrc;
(which conda > /dev/null 2>&1 && conda init > /dev/null && conda config --set auto_activate_base false) || (wget -nc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash Miniconda3-latest-Linux-x86_64.sh -b && eval "$(~/miniconda3/bin/conda shell.bash hook)" && conda init && conda config --set auto_activate_base true);
source ~/.bashrc;
(pip3 list | grep ray | grep {{ray_version}} 2>&1 > /dev/null || pip3 install -U ray[default]=={{ray_version}}) && mkdir -p ~/sky_workdir && mkdir -p ~/.sky/sky_app;
(pip3 list | grep skypilot && [ "$(cat {{sky_remote_path}}/current_sky_wheel_hash)" == "{{sky_wheel_hash}}" ]) || (pip3 uninstall skypilot -y; pip3 install "$(echo {{sky_remote_path}}/{{sky_wheel_hash}}/skypilot-{{sky_version}}*.whl)[aws]" && echo "{{sky_wheel_hash}}" > {{sky_remote_path}}/current_sky_wheel_hash || exit 1);
sudo systemctl stop unattended-upgrades;
sudo kill -9 `sudo lsof /var/lib/dpkg/lock-frontend | awk '{print $2}' | tail -n 1` || true;
sudo pkill -9 apt-get;
sudo pkill -9 dpkg;
sudo dpkg --configure -a;
sudo bash -c 'rm -rf /etc/security/limits.d; echo "* soft nofile 1048576" >> /etc/security/limits.conf; echo "* hard nofile 1048576" >> /etc/security/limits.conf';
sudo grep -e '^DefaultTasksMax' /etc/systemd/system.conf || (sudo bash -c 'echo "DefaultTasksMax=infinity" >> /etc/systemd/system.conf'); sudo systemctl set-property user-$(id -u $(whoami)).slice TasksMax=infinity; sudo systemctl daemon-reload;
mkdir -p ~/.ssh; (grep -Pzo -q "Host \*\n StrictHostKeyChecking no" ~/.ssh/config) || printf "Host *\n StrictHostKeyChecking no\n" >> ~/.ssh/config;
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15 changes: 9 additions & 6 deletions sky/templates/azure-ray.yml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -88,26 +88,29 @@ initialization_commands: []
# Increment the following for catching performance bugs easier:
# current num items (num SSH connections): 1
setup_commands:
# Disable `unattended-upgrades` to prevent apt-get from hanging. It should be called at the beginning before the process started to avoid being blocked. (This is a temporary fix.)
# Create ~/.ssh/config file in case the file does not exist in the image.
# Make sure python3 & pip3 are available on this image.
# Line 'sudo bash ..': set the ulimit as suggested by ray docs for performance. https://docs.ray.io/en/latest/cluster/vms/user-guides/large-cluster-best-practices.html#system-configuration
# Line 'sudo grep ..': set the number of threads per process to unlimited to avoid ray job submit stucking issue when the number of running ray jobs increase.
# Line 'mkdir -p ..': disable host key check
# Line 'python3 -c ..': patch the buggy ray files and enable `-o allow_other` option for `goofys`
# This also kills the service that is holding the lock on dpkg (problem only exists on aws/azure, not gcp)
- mkdir -p ~/.ssh; touch ~/.ssh/config;
- sudo systemctl stop unattended-upgrades || true;
sudo systemctl disable unattended-upgrades || true;
sudo sed -i 's/Unattended-Upgrade "1"/Unattended-Upgrade "0"/g' /etc/apt/apt.conf.d/20auto-upgrades || true;
sudo kill -9 `sudo lsof /var/lib/dpkg/lock-frontend | awk '{print $2}' | tail -n 1` || true;
sudo pkill -9 apt-get;
sudo pkill -9 dpkg;
sudo dpkg --configure -a;
mkdir -p ~/.ssh; touch ~/.ssh/config;
pip3 --version > /dev/null 2>&1 || (curl -sSL https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3 get-pip.py && echo "PATH=$HOME/.local/bin:$PATH" >> ~/.bashrc);
(type -a python | grep -q python3) || echo 'alias python=python3' >> ~/.bashrc;
(type -a pip | grep -q pip3) || echo 'alias pip=pip3' >> ~/.bashrc;
which conda > /dev/null 2>&1 || (wget -nc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash Miniconda3-latest-Linux-x86_64.sh -b && eval "$(/home/azureuser/miniconda3/bin/conda shell.bash hook)" && conda init && conda config --set auto_activate_base true);
source ~/.bashrc;
(pip3 list | grep ray | grep {{ray_version}} 2>&1 > /dev/null || pip3 install -U ray[default]=={{ray_version}}) && mkdir -p ~/sky_workdir && mkdir -p ~/.sky/sky_app && touch ~/.sudo_as_admin_successful;
(pip3 list | grep skypilot && [ "$(cat {{sky_remote_path}}/current_sky_wheel_hash)" == "{{sky_wheel_hash}}" ]) || (pip3 uninstall skypilot -y; pip3 install "$(echo {{sky_remote_path}}/{{sky_wheel_hash}}/skypilot-{{sky_version}}*.whl)[azure]" && echo "{{sky_wheel_hash}}" > {{sky_remote_path}}/current_sky_wheel_hash || exit 1);
sudo systemctl stop unattended-upgrades;
sudo kill -9 `sudo lsof /var/lib/dpkg/lock-frontend | awk '{print $2}' | tail -n 1` || true;
sudo pkill -9 apt-get;
sudo pkill -9 dpkg;
sudo dpkg --configure -a;
sudo bash -c 'rm -rf /etc/security/limits.d; echo "* soft nofile 1048576" >> /etc/security/limits.conf; echo "* hard nofile 1048576" >> /etc/security/limits.conf';
sudo grep -e '^DefaultTasksMax' /etc/systemd/system.conf || (sudo bash -c 'echo "DefaultTasksMax=infinity" >> /etc/systemd/system.conf'); sudo systemctl set-property user-$(id -u $(whoami)).slice TasksMax=infinity; sudo systemctl daemon-reload;
mkdir -p ~/.ssh; (grep -Pzo -q "Host \*\n StrictHostKeyChecking no" ~/.ssh/config) || printf "Host *\n StrictHostKeyChecking no\n" >> ~/.ssh/config;
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10 changes: 9 additions & 1 deletion sky/templates/gcp-ray.yml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,7 @@ initialization_commands: []
# Increment the following for catching performance bugs easier:
# current num items (num SSH connections): 1 (+1 if tpu_vm)
setup_commands:
# Disable `unattended-upgrades` to prevent apt-get from hanging. It should be called at the beginning before the process started to avoid being blocked. (This is a temporary fix.)
# Line 'mkdir -p ..': Create ~/.ssh/config file in case the file does not exist in the custom image.
# Line 'pip3 --v ..': Make sure python3 & pip3 are available on this image.
# Line 'which conda ..': some images (TPU VM) do not install conda by
Expand All @@ -132,7 +133,14 @@ setup_commands:
# Line 'sudo grep ..': set the number of threads per process to unlimited to avoid ray job submit stucking issue when the number of running ray jobs increase.
# Line 'mkdir -p ..': disable host key check
# Line 'python3 -c ..': patch the buggy ray files and enable `-o allow_other` option for `goofys`
- mkdir -p ~/.ssh; touch ~/.ssh/config;
- sudo systemctl stop unattended-upgrades || true;
sudo systemctl disable unattended-upgrades || true;
sudo sed -i 's/Unattended-Upgrade "1"/Unattended-Upgrade "0"/g' /etc/apt/apt.conf.d/20auto-upgrades || true;
sudo kill -9 `sudo lsof /var/lib/dpkg/lock-frontend | awk '{print $2}' | tail -n 1` || true;
sudo pkill -9 apt-get;
sudo pkill -9 dpkg;
sudo dpkg --configure -a;
mkdir -p ~/.ssh; touch ~/.ssh/config;
pip3 --version > /dev/null 2>&1 || (curl -sSL https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3 get-pip.py && echo "PATH=$HOME/.local/bin:$PATH" >> ~/.bashrc);
(type -a python | grep -q python3) || echo 'alias python=python3' >> ~/.bashrc;
(type -a pip | grep -q pip3) || echo 'alias pip=pip3' >> ~/.bashrc;
Expand Down