WORKING VERSION

Vagrantfile

@@ -12,6 +12,14 @@ launch_gui     = ENV.has_key?('VAGRANT_NO_GUI') ? false : true
 # Currently on GitHub Actions it fails if accelerate3d activated
 on_ci          = ENV.has_key?('VAGRANT_ON_GH') ? true : false
 
+$script = <<-SCRIPT
+echo "I am provisioningi aiidalab folder creating..."
+AIIDALAB_VOL=/var/aiidalab_volume
+mkdir -p ${AIIDALAB_VOL}
+chown 1000:100 ${AIIDALAB_VOL}
+chmod 0775 ${AIIDALAB_VOL}
+SCRIPT
+
 Vagrant.configure(2) do |config|
 
   ## VIRTUALBOX provider
@@ -79,7 +87,7 @@ Vagrant.configure(2) do |config|
   # Disable the default shared folder of vagrant
   config.vm.synced_folder ".", "/vagrant", disabled: true
 
-  # provisioner: set up VM via ansible. To (re-)run this step:
+  # provisioner: set up VM with ansible. To (re-)run this step:
   #   vagrant provision --provision-with ansible
   # Note we use a static inventory, see: https://www.vagrantup.com/docs/provisioning/ansible_intro#static-inventory
   config.vm.network :private_network, ip: gconfig["ansible_host"]
@@ -95,4 +103,15 @@ Vagrant.configure(2) do |config|
     # Ensure that public key auth is not disabled by the user's config
     ansible.raw_ssh_args = ['-o PubKeyAuthentication=yes -o DSAAuthentication=yes']
   end
+  # Create a folder for AiiDAlab volume mount. To (re-)run this step:
+  #  vagrant provision --provision-with shell
+  config.vm.provision "shell", inline: $script
+  # provisioner: set up VM with docker. To (re-)run this step:
+  #   vagrant provision --provision-with docker
+  config.vm.provision "docker" do |d|
+    d.run "ghcr.io/aiidalab/qe:pr-381",
+      daemonize: true,
+      restart: "always",
+      args: "-e JUPYTER_TOKEN='easy' -p 8888:8888 -v /var/aiidalab_volume:/home/jovyan"
+  end
 end

inventory.yml

@@ -26,7 +26,7 @@ all:
     vm_cpus: 2
     vm_vram: 128
     vm_headless: false
-    vm_browser: chromium-browser  # 'chromium-browser' or 'firefox'
+    vm_browser: firefox  # 'chromium-browser' or 'firefox'
     vm_data_folder: "/usr/local/share"  # this is used to put shared data files in
     # vm_shared_folder: "/shared"  # this is currently inactive in Vagrant config
     vm_timezone: "Europe/Zurich"

playbook-qe.yml

@@ -0,0 +1,317 @@
+- name: Prepare for VM build
+
+  hosts: "{{ build_hosts | default('vagrant-ssh') }}"
+  gather_facts: false
+
+  pre_tasks:
+
+  - name: test configuration
+    tags: [init]
+    debug:
+      msg: RUNNING PLAYBOOK FOR '{{ vm_name }}' VERSION '{{ vm_version }}'
+
+  - name: testing ansible environment
+    tags: [init]
+    debug:
+      msg: Connecting to host '{{ inventory_hostname }}' as user '{{ ansible_user }}'
+
+  - name: Install linux-headers-generic for guest-additions
+    tags: [init]
+    when: "inventory_hostname.startswith('vagrant')"
+    become: true
+    apt:
+      cache_valid_time: 86400  # One day
+      name:
+      - linux-headers-generic
+
+  - name: Make local dist folder
+    tags: [init]
+    local_action:
+      module: file
+      state: directory
+      path: "{{ local_dist_folder }}/"
+    when: release_notes_locally is defined and release_notes_locally
+
+- name: Build VM
+  hosts: "{{ build_hosts | default('vagrant-ssh') }}"
+
+  tasks:
+
+  # Generic Tasks
+  # These tasks are run for any VM build, regardless of the software installed
+  # They setup the VM user, commandline interface, and (optionally) desktop GUI
+
+  - name: Update system package managers (apt, pip)
+    tags: [init]
+    include_tasks: local/tasks/ensure-apt-pip.yml
+
+  - name: "Add QM user '{{ vm_user }}'"
+    tags: [add_user, ci_test]
+    import_tasks: local/tasks/add-qm-user.yml
+
+  - name: "Add release notes section for the operating system"
+    tags: [release_notes]
+    import_tasks: local/tasks/release-notes-system.yml
+
+  - name: Customise bash terminal for QM
+    tags: [customise-bash]
+    become: true
+    become_user: "{{ vm_user }}"
+    import_tasks: local/tasks/customise-bash.yml
+
+  - name: Install common text editors
+    tags: [editors]
+    import_role:
+      name: marvel-nccr.editors
+    vars:
+      editors_vm_user: "{{ vm_user }}"
+
+  - name: Add desktop GUI
+    tags: [ubuntu_desktop]
+    when: not vm_headless
+    import_role:
+      name: marvel-nccr.ubuntu_desktop
+    vars:
+      ubuntu_desktop_vm_user: "{{ vm_user }}"
+      ubuntu_desktop_browser: "{{ vm_browser }}"
+
+  - name: Customise GUI for QM
+    tags: [customise-gui]
+    when: not vm_headless
+    become: true
+    become_user: "{{ vm_user }}"
+    import_tasks: local/tasks/customise-gui.yml
+
+  - name: Setup QM to run simulations
+    tags: [simsetup]
+    import_tasks: local/tasks/simulation-setup.yml
+
+  # Build Specific Tasks
+  # These tasks can be customised for specific VM builds,
+  # depending on the software one requires to be installed
+
+  # - name: "Add user README"
+  #   tags: [add_readme]
+  #   become: true
+  #   become_user: "{{ vm_user }}"
+  #   template:
+  #     src: local/tasks/files/README.md.j2
+  #     dest: "{{ readme_vm_path }}"
+  #   vars:
+  #     software_urls:
+  #       Quantum ESPRESSO: http://www.quantum-espresso.org/
+
+  # - name: Install plotting tools (via apt)
+  #   # TODO we may want to eventually install these with conda
+  #   # (jmol and gnuplot are already installed via conda-forge)
+  #   tags: [plotting]
+  #   import_tasks: local/tasks/plotting-tools.yml
+  #   vars:
+  #     packages: [grace, xcrysden, default-jre]
+
+  # - name: install SLURM service
+  #   tags: [slurm]
+  #   import_role:
+  #     name: marvel-nccr.slurm
+
+  # # TODO control version
+  # # could install with conda, but how to set up the systemd service?
+  # - name: install RabbitMQ server service
+  #   tags: [rabbitmq]
+  #   become: true
+  #   become_user: "{{ root_user }}"
+  #   import_tasks: local/tasks/rabbitmq.yml
+
+  # # TODO control version
+  # # could install with conda, but how to set up the systemd service?
+  # - name: install PostrgeSQL server service
+  #   tags: [postgresql]
+  #   become: true
+  #   become_user: "{{ root_user }}"
+  #   import_tasks: local/tasks/postgresql.yml
+
+  # - name: install conda+mamba
+  #   tags: [conda]
+  #   import_role:
+  #     name: chrisjsewell.conda.user_install
+  #   become: true
+  #   become_user: "{{ vm_user }}"
+  #   vars:
+  #     conda_folder: "~/.conda"
+  #     conda_installer_url: https://github.com/conda-forge/miniforge/releases/download/22.11.1-4/Mambaforge-22.11.1-4-Linux-x86_64.sh
+  #     conda_installer_checksum: sha256:16c7d256de783ceeb39970e675efa4a8eb830dcbb83187f1197abfea0bf07d30
+  #     conda_activate_alias: workon
+
+  # - name: Install code environment
+  #   tags: [code-envs]
+  #   # TODO ideally this would be import_tasks, but then we can't use loop
+  #   include_tasks: local/tasks/conda-env-install.yml
+  #   vars:
+  #     conda_env: "{{ item.name }}"
+  #     code_packages: "{{ item.pkgs }}"
+  #     # TODO allow for `conda env config vars set` to be used,
+  #     # e.g. for export OMP_NUM_THREADS=1
+  #   loop:
+  #   # note here we specify exact versions of libxc/openmpi/mpich
+  #   # this is because we want conda to re-use as many packages as possible
+  #   # since re-used packages do not incur more disk memory usage
+  #   - {name: qespresso, pkgs: [qe=7.2, libxc=5.2.3, openmpi=4.1.2]}
+  #   - {name: visualise, pkgs: [jmol, gnuplot, cif2cell, python=3.9]}
+  #   loop_control:
+  #     label: "{{ item.name }}"
+
+  # - name: Install AiiDA environment
+  #   tags: [aiida-env]
+  #   become: true
+  #   become_user: "{{ vm_user }}"
+  #   import_tasks: local/tasks/aiida-conda-env.yml
+  #   vars:
+  #     conda_env: "{{ aiida_conda_env }}"
+  #     aiida_packages:
+  #     - python=3.9
+  #     - pip
+  #     - aiida-core=2
+  #     - aiida-core.notebook
+  #     - aiida-quantumespresso=4
+  #     - aiida-pseudo=1
+  #     - ipykernel
+  #     - jupyterlab
+  #     - jupyterlab-tour
+  #     - jupyterlab-spellchecker
+  #     - mamba_gator  # Provides Conda/Mamba management as a standalone application or as extension for JupyterLab.
+
+  # - name: Create an aiida-profile
+  #   tags: [aiida-profile]
+  #   become: true
+  #   become_user: "{{ vm_user }}"
+  #   import_tasks: local/tasks/aiida-profile.yml
+  #   vars:
+  #     name: "{{ aiida_profile }}"
+  #     aiida_run_verdi: "~/.conda/bin/conda run -n {{ aiida_conda_env }} verdi"
+  #     postgres_user: postgres
+  #     parameters:
+  #       first_name: Max
+  #       last_name: Scientist
+  #       email: aiida@localhost
+  #       institution: Quantum Mobile
+  #       db_host: localhost
+  #       db_port: 5432
+  #       db_name: aiidadb
+  #       db_username: aiida
+  #       db_password: "ne9N_LDK-*JSS"
+  #     daemon_service: true
+
+  # - name: Create AiiDA Jupyter service
+  #   tags: [aiida-jupyter]
+  #   become: true
+  #   become_user: "{{ vm_user }}"
+  #   import_tasks: local/tasks/aiida-jupyter.yml
+
+  # - name: "Create AiiDA computers"
+  #   tags: [aiida-computers]
+  #   become: true
+  #   become_user: "{{ vm_user }}"
+  #   verdi_computer:
+  #     verdi: "~/.conda/bin/conda run -n {{ aiida_conda_env }} verdi"
+  #     profile: "{{ aiida_profile }}"
+  #     label: "{{ item.l }}"
+  #     scheduler: "{{ item.s }}"
+  #     transport: core.local
+  #     hostname: localhost
+  #     work_dir: "~/.aiida_run"
+  #     mpirun_command: "mpirun -np {tot_num_mpiprocs}"
+  #     mpiprocs_per_machine: 2
+  #     configure: "--safe-interval=0"
+  #   loop:
+  #   - {l: local_direct, s: core.direct}
+  #   - {l: local_slurm, s: core.slurm}
+  #   loop_control:
+  #     label: "{{ item.l }}"
+
+  # - name: "Add AiiDA Codes"
+  #   tags: [aiida-codes]
+  #   become: true
+  #   become_user: "{{ vm_user }}"
+  #   verdi_code:
+  #     verdi: ~/.conda/bin/conda run -n {{ aiida_conda_env }} verdi
+  #     profile: "{{ aiida_profile }}"
+  #     label: "{{ item.label }}"
+  #     description: "Local code for '{{ item.exec }}' in Conda env '{{ item.env }}'"
+  #     computer: local_slurm
+  #     input_plugin: "{{ item.plugin }}"
+  #     remote_abs_path: "/home/max/.conda/envs/{{ item.env }}/bin/{{ item.exec }}"
+  #     prepend_text: |
+  #       ulimit -s unlimited
+  #       eval "$(conda shell.bash hook)"
+  #       conda activate {{ item.env }}
+  #       {{ item.prepend | default('') }}
+  #   loop_control:
+  #     label: "{{ item.label }}"
+  #   loop:
+  #   - {label: qe.pw, plugin: quantumespresso.pw, env: qespresso, exec: pw.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.cp, plugin: quantumespresso.cp, env: qespresso, exec: cp.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.pp, plugin: quantumespresso.pp, env: qespresso, exec: pp.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.ph, plugin: quantumespresso.ph, env: qespresso, exec: ph.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.neb, plugin: quantumespresso.neb, env: qespresso, exec: neb.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.epw, plugin: quantumespresso.epw, env: qespresso, exec: epw.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.projwfc, plugin: quantumespresso.projwfc, env: qespresso, exec: projwfc.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.pw2wannier90, plugin: quantumespresso.pw2wannier90, env: qespresso, exec: pw2wannier90.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.dos, plugin: quantumespresso.dos, env: qespresso, exec: dos.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.q2r, plugin: quantumespresso.q2r, env: qespresso, exec: q2r.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: qe.matdyn, plugin: quantumespresso.matdyn, env: qespresso, exec: matdyn.x, prepend: export OMP_NUM_THREADS=1}
+  #   - {label: nwchem.main, plugin: nwchem.nwchem, env: nwchem, exec: nwchem}
+  #   - {label: siesta.main, plugin: siesta.siesta, env: siesta, exec: siesta}
+  #   - {label: cp2k.main, plugin: cp2k, env: cp2k, exec: cp2k.psmp}
+  #   - {label: abinit.main, plugin: abinit, env: abinit, exec: abinit}
+
+  # TODO release notes for aiida computers/codes
+
+  # - name: Download and install SSSP potentials
+  #   tags: [aiida-pseudo]
+  #   import_tasks: local/tasks/aiida-pseudo-sssp.yml
+  #   vars:
+  #     # for quantum mobile
+  #     aiida_pseudo_cmd: "~/.conda/bin/conda run -n {{ aiida_conda_env }} aiida-pseudo"
+  #     aiida_pseudo_base_folder: "{{ vm_data_folder }}"
+  #     aiida_pseudo_functional: PBE
+  #     aiida_pseudo_protocol: efficiency
+  #     aiida_pseudo_version: "1.1"
+  #     aiida_pseudo_profile: "{{ aiida_profile }}"
+
+  # - name: Download and install DOJO potentials
+  #   tags: [aiida-pseudo]
+  #   import_tasks: local/tasks/aiida-pseudo-dojo.yml
+  #   vars:
+  #     # for sisesta
+  #     aiida_pseudo_cmd: "~/.conda/bin/conda run -n {{ aiida_conda_env }} aiida-pseudo"
+  #     aiida_pseudo_base_folder: "{{ vm_data_folder }}"
+  #     aiida_pseudo_functional: PBE
+  #     aiida_pseudo_relativistic: FR
+  #     aiida_pseudo_protocol: standard
+  #     aiida_pseudo_format: psml
+  #     aiida_pseudo_version: "0.4"
+  #     aiida_pseudo_profile: "{{ aiida_profile }}"
+
+  # - name: aiida-example scripts
+  #   tags: [aiida-examples]
+  #   become: true
+  #   become_user: "{{ vm_user }}"
+  #   import_tasks: local/tasks/aiida-examples.yml
+  #   vars:
+  #     aiida_examples_folder: "~/Desktop/aiida-examples"
+  #     aiida_verdi_cmd: "~/.conda/bin/conda run -n {{ aiida_conda_env }} verdi"
+
+
+  post_tasks:
+
+  # These break idempotency,
+  # so only run once all other tasks have completed
+
+  - name: "Clean caches"
+    tags: [never, cleanup]
+    import_tasks: local/tasks/clean-caches.yml
+
+  - name: "Remove {{ build_dir }} content"
+    tags: [never, cleanup]
+    become: true
+    command: rm -rf {{ build_dir }}/*