corelab2/software.yaml at master · coregenomics/corelab2 · GitHub

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---
- name: 'Install Ubuntu packages'
  hosts: 'all'
  vars:
    zfs_max: 4187689984

  tasks:

  - name: 'Install key for R packages'
    become: yes
    apt_key:
      keyserver: 'keyserver.ubuntu.com'
      id: 'E298A3A825C0D65DFD57CBB651716619E084DAB9'

  - name: 'Install repository for R packages'
    become: yes
    apt_repository:
      repo: 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'
      filename: 'r'

  # Instructions to install distribution specific nvidia cuda:
  # https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch=x86_64&target_distro=Ubuntu&target_version=1804&target_type=debnetwork
  - name: 'Pin nvidia cuda versions'
    become: yes
    get_url:
      url: 'https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin'
      dest: '/etc/apt/preferences.d/cuda-repository-pin-600'
    tags: 'cuda'

  - name: 'Install key for nvidia cuda packages'
    become: yes
    apt_key:
      url: 'https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub'
    tags: 'cuda'

  - name: 'Install repository for nvidia cuda packages'
    become: yes
    apt_repository:
      repo: 'deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /'
      filename: 'cuda'
    tags: 'cuda'

  - name: 'Install key for syncthing packages'
    become: yes
    apt_key:
      url: 'https://syncthing.net/release-key.txt'

  - name: 'Install repository for syncthing packages'
    apt_repository:
      repo: 'deb https://apt.syncthing.net/ syncthing release'
      filename: 'syncthing'

  - name: 'Install key for google cloud sdk'
    become: yes
    apt_key:
      url: 'https://packages.cloud.google.com/apt/doc/apt-key.gpg'
      keyring: '/usr/share/keyrings/cloud.google.gpg'

  - name: 'Install repository for google cloud sdk distribution'
    become: yes
    apt_repository:
      repo: 'deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main'
      filename: 'google-cloud-sdk'

  - name: 'Install packages'
    become: yes
    apt:
      name:
        - 'ubuntu-desktop'
        # Scientific software.
        - 'r-base-dev'
        - 'linux-headers-generic' # Required for nvidia driver
        - 'cuda'
        # R package dependencies.
        - 'libcairo2-dev'
        - 'libcurl4-openssl-dev'
        - 'libssl-dev'
        - 'libxml2-dev'
        # Monitoring.
        - 'collectd'
        # Utilities.
        - 'emacs-nox'
        - 'google-cloud-sdk'
        - 'htop'
        - 'iperf3'
        - 'ncdu'
        - 'time'
        - 'tmux'
        - 'tree'
        - 'syncthing'

  - name: 'Unignore collectd tmpfs and zfs_arc'
    become: yes
    replace:
      path: '/etc/collectd/collectd.conf'
      regexp: '{{ item.regexp }}'
      replace: '{{ item.replace }}'
    loop:
      - regexp: '(	)(FSType tmpfs)'
        replace: '\1# \2'
      - regexp: '#(LoadPlugin zfs_arc)'
        replace: '\1'
    tags: 'collectd'

  - name: 'Ignore collectd filesystems and mountpoints'
    become: yes
    lineinfile:
      path: '/etc/collectd/collectd.conf'
      insertafter: '<Plugin df>'
      line: '	{{ line }}'
    loop:
      - 'FSType pstore'
      - 'FSType debugfs'
      - 'FSType configfs'
      - 'FSType tracefs'
      - 'FSType binfmt_misc'
      - 'MountPoint "/run"'
      - 'MountPoint "/run/lock"'
      - 'MountPoint "/run/user"'
      - 'MountPoint "/run/user/0"'
      - 'MountPoint "/dev"'
      - 'MountPoint "/dev/shm"'
      - 'MountPoint "/sys/fs/cgroup"'
      # /root conflicts with / because both are read as "df-root".
      - 'MountPoint "/root"'
    loop_control:
      loop_var: 'line'
    tags: 'collectd'

  - name: 'Gather logrotate files'
    find:
      path: '/etc/logrotate.d'
    register: logrotate
    tags: 'zfs'

  - name: 'Disable compression because ZFS compresses logs'
    become: yes
    replace:
      path: '{{ path }}'
      regexp: '([^#y])compress'
      replace: '\1#compress'
    loop: '{{ logrotate.files | map(attribute="path") | list }}'
    loop_control:
      loop_var: 'path'
    tags: 'zfs'

  - name: 'Detect ZFS c_max'
    shell:
      cmd: sed -nr 's/^c_max .* ([[:digit:]]+)$/\1/p' /proc/spl/kstat/zfs/arcstats
      warn: false
    changed_when: false
    register: c_max
    tags: 'zfs'

  - name: 'ZFS set current c_max'
    become: yes
    shell:
      cmd: 'echo {{ zfs_max }} > /sys/module/zfs/parameters/zfs_arc_max'
    when: 'c_max.stdout | int != zfs_max'
    tags: 'zfs'

  - name: 'ZFS set persistent c_max'
    become: yes
    copy:
      dest: /etc/modprobe.d/zfs.conf
      content: |
        options zfs zfs_arc_max={{ zfs_max }}
    register: zfs_conf
    tags: 'zfs'

  - name: 'Apply zfs.conf to initramfs'
    become: yes
    command: /usr/sbin/update-initramfs -u
    when: 'zfs_conf.changed'
    tags: 'zfs'