qeapp specific image by running AiiDAlab from docker image

.github/workflows/ci.yml

@@ -1,6 +1,6 @@
 name: CI
 
 on:
   push:
     branches: [main]
     tags:
@@ -17,10 +17,10 @@
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: "3.10"
     - uses: pre-commit/[email protected]
 
   # docs:
   #   runs-on: ubuntu-latest
 
   #   steps:

.gitignore

@@ -22,3 +22,5 @@ submodules/roles/marvel-nccr*
 submodules/roles/gantsign*
 submodules/roles/geerlingguy*
 submodules/ansible_collections/
+
+local/modules/__pycache__/*.pyc

.pre-commit-config.yaml

@@ -2,24 +2,31 @@
 # See usage instructions at https://pre-commit.com
 repos:
 
-- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.3.0
-  hooks:
-  - id: pretty-format-yaml
-    args: [--autofix, --indent, "2", --preserve-quotes]
-
 - repo: https://github.com/adrienverge/yamllint
-  rev: v1.26.3
+  rev: v1.33.0
   hooks:
   - id: yamllint
 
 - repo: https://github.com/ansible/ansible-lint
-  rev: v6.3.0
+  rev: v6.22.1
   hooks:
   - id: ansible-lint
-    args: [--exclude, roles/]
+    # these should bring back after fixing the ansible-lint issues
+    # we exclude most of the roles and tasks, as they are not update to the new ansible version
+    args: [
+      --exclude,
+      roles/,
+      submodules/roles/,
+      playbook-aiidalab-qe.yml,
+      playbook-build.yml,
+      playbook-package.yml,
+      .pre-commit-config.yaml,
+      local/tasks/,
+      .github/workflows/ci.yml,
+      submodules/ansible_collections/,
+    ]
 
 - repo: https://github.com/psf/black
-  rev: 23.1.0
+  rev: 23.11.0
   hooks:
   - id: black

Vagrantfile

@@ -79,7 +79,7 @@ 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"]

docs/conf.py

@@ -13,7 +13,7 @@
 
 project = "Quantum Mobile"
 copyright = "2020, NCCR MARVEL"
-author = "Chris Sewell, Giovanni Pizzi, Leopold Talirz"
+author = "Jusong Yu, Chris Sewell, Giovanni Pizzi, Leopold Talirz"
 
 version = inventory["all"]["vars"]["vm_version"]
 release = version

docs/developers/build-apple-silicon.md

@@ -0,0 +1,96 @@
+# Build for Apple Silicon
+
+Apple Silicon is the new CPU architecture for Apple Macs. 
+The new architecture is based on ARM64, which means that software compiled for x86_64 will not run on Apple Silicon without translation. 
+VirtualBox does not yet support Apple Silicon, so instead we use a different virtualization software called [UTM](https://mac.getutm.app/).
+
+## Prerequisites
+
+To build the UTM image, first:
+
+- install the latest version of UTM [from the Apple store](https://apps.apple.com/us/app/utm-virtual-machines/id1538878817).
+- download the "64-bit ARM (ARMv8/AArch64) server install image" from https://cdimage.ubuntu.com/releases/focal/release/.
+
+
+Then, clone the `quantum-mobile` repository:
+
+```console
+git clone https://github.com/marvel-nccr/quantum-mobile.git
+cd quantum-mobile
+```
+
+Create a fresh Python environment with a manager of your choosing and simply install `tox`:
+
+```
+pip install tox
+```
+
+Finally, we need the `sshpass` tool to have password access to the VM when running the Ansible playbook:
+
+```console
+brew install hudochenkov/sshpass/sshpass
+```
+
+## Install and start the VM 
+
+Create a new virtual machine from the downloaded Ubuntu server ISO using "File -> New".
+Select the following:
+
+- Virtualize
+- Operating system: Select Custom -> Other, then use "Browse" to find the ISO image and continue.
+- select the following hardware/storage settings: 4096MB RAM (default), 4 CPU cores and 64GB disk space (default).
+
+Next, **create** (be careful not delete the existing one, it is used for connecting the internet) a new network setting with type "Emulated VLAN" and forward port 22 to 2200 of localhost so you can ssh to VM from localhost.
+Check [here](https://github.com/utmapp/UTM/discussions/2465#discussioncomment-6931047) for detailed instructions.
+
+<img src="images/utm_ports_mapping.png" width="350px">
+
+Finally. run the VM and follow the installation instructions.
+In most steps you can take the default option, keeping in mind the following exceptions:
+
+- Remember to install OpenSSH server during setup, so we can ssh to the VM during the Ansible deployment. 
+- Create system user `max` with password `moritz` and enable auto login. 
+
+**Important**: Once the installation is complete, select reboot and then _shut down the VM_.
+Rebooting with the ISO image still selected for the CD/DVD input will result in the installation process starting again.
+Hence, unselect the image before booting the machine after the installation.
+
+## Configure the VM with Ansible
+
+Set the following SSH configuration in the `~/.ssh/config`:
+
+```
+Host qmobile
+  HostName 127.0.0.1
+  User max
+  Port 2200
+```
+
+In the localhost (control machine), activate the Python environment and run the Ansible playbook in the root directory of the repository:
+
+```
+BUILD_PLAYBOOK=playbook-aiidalab-qe.yml tox -e ansible -- --extra-vars "build_hosts=utm" -kK
+```
+
+It will ask for the password of the `max` user, which should be `moritz`.
+
+## Troubleshooting
+
+### Import from UTM copy
+
+- If you see "Failed to access data from shortcut", try the methods from https://github.com/utmapp/UTM/discussions/3774
+
+### Failing to connect via SSH using password
+
+In case you run into the following error:
+
+```
+fatal: [utm]: FAILED! =>
+  msg: to use the 'ssh' connection type with passwords, you must install the sshpass program
+```
+
+It means that the `sshpass` tool has not been installed correctly using:
+
+```
+brew install hudochenkov/sshpass/sshpass
+```

docs/developers/build-vagrant.md

@@ -98,6 +98,13 @@ Building the Desktop Edition is tested on GitHub Actions on every commit to the
 For the tested steps see the `.github/workflows/build.yml` file.
 :::
 
+### Build QeApp dedicated VM
+
+To build a VM dedicated to the QeApp, run:
+
+```bash
+BUILD_PLAYBOOK=playbook-aiidalab-qe.yml tox -e vagrant
+```
 
 ### Continuing a failed build
 

docs/index.md

@@ -170,6 +170,7 @@ users/troubleshoot.md
 developers/customize.md
 developers/build-vagrant.md
 developers/build-cloud.md
+developers/build-apple-silicon.md
 developers/roles.md
 ```
 

inventory.yml

@@ -11,7 +11,7 @@ all:
   vars:
     # VM Metadata
     vm_name: "Quantum Mobile"
-    vm_version: "23.04.03"
+    vm_version: "23.10.0"
     vm_description: "A Virtual Machine for Computational Materials Science"
     vm_url: "https://github.com/marvel-nccr/marvel-virtualmachine"
     vm_author: "MARVEL NCCR and MaX CoE"
@@ -22,11 +22,12 @@ all:
     vm_hostname: "qmobile"
     vm_user: "max"
     vm_password: "moritz"
-    vm_memory: 1536
-    vm_cpus: 2
-    vm_vram: 128
+    vm_memory: 4096
+    vm_cpus: 4
+    vm_vram: 256
     vm_headless: false
-    vm_browser: chromium-browser  # 'chromium-browser' or 'firefox'
+    vm_browser: firefox  # 'chromium-browser' or 'firefox'
+    vm_wm_package: ubuntu-desktop-minimal  # 'lxde' or 'ubuntu-desktop-minimal'
     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"
@@ -39,6 +40,9 @@ all:
     build_dir: "/tmp"
     run_tests: true
 
+    # AiiDAlab options
+    vm_qeapp_image: "ghcr.io/aiidalab/qe:v23.10.0"
+
     # Readme and Release Notes (populated by roles during build)
     qm_homepage: "https://quantum-mobile.readthedocs.io"
     readme_vm_path: "/home/{{ vm_user }}/README.md"
@@ -108,3 +112,9 @@ all:
       ansible_user: max
       vm_headless: true
       # add_user_public_key: "{{ lookup('file', './keys/user-key.pub') }}"
+    utm:
+      cloud_platform: utm
+      ansible_host: 127.0.0.1
+      ansible_port: 2200
+      ansible_user: max
+      vm_headless: false

local/tasks/aiida-jupyter.yml

@@ -54,7 +54,7 @@
 - name: create desktop shortcut to Jupyter Lab
   copy:
     dest: "${HOME}/Desktop/jupyterlab.desktop"
-    mode: "0753"
+    mode: "0644"
     content: |
       [Desktop Entry]
       Encoding=UTF-8

local/tasks/aiidalab.yml

@@ -0,0 +1,47 @@
+- name: Create folder for AiiDAlab QE
+  become: true
+  become_user: "{{ vm_user }}"
+  file:
+    path: /home/{{ vm_user }}/qeapp-home
+    state: directory
+    mode: 0775
+
+- name: check if qeapp container is running
+  become: true
+  become_user: "{{ vm_user }}"
+  shell: "docker inspect -f '{{ '{{' }} .State.Running {{ '}}' }}' qeapp"
+  register: qe_container_stat
+  ignore_errors: true
+
+- name: Pull qeapp image
+  command: "docker pull {{ qeapp_image }}"
+
+- name: echo qe_container
+  debug:
+    var: qe_container
+
+- name: Create and run qeapp container
+  become: true
+  become_user: "{{ vm_user }}"
+  command: "docker run -d --name qeapp -p 8899:8888 --volume /home/{{ vm_user }}/qeapp-home:/home/jovyan -e JUPYTER_TOKEN='max' -e NB_UMASK=002 --restart always {{ qeapp_image }}"
+  when: qe_container_stat.stdout == ""
+
+- name: Copy AiiDAlab logo
+  become: true
+  become_user: "{{ root_user }}"
+  copy:
+    src: images/aiidalab-qe-logo.png
+    dest: /usr/share/icons/
+
+- name: create desktop shortcut to AiiDALab
+  copy:
+    dest: "${HOME}/Desktop/aiidalab.desktop"
+    mode: "0644"
+    content: |
+      [Desktop Entry]
+      Name=AiiDAlab QE
+      Comment=Launch AiiDAlab QE
+      Exec={{ vm_browser }} "http://localhost:8899/apps/apps/quantum-espresso/qe.ipynb?token=max"
+      Terminal=false
+      Icon=/usr/share/icons/aiidalab-qe-logo.png
+      Type=Application

local/tasks/customise-bash.yml

@@ -33,6 +33,14 @@
   - regexp: HISTFILESIZE=
     line: HISTFILESIZE=100000
 
+- name: Set umask to 002
+  blockinfile:
+    path: "${HOME}/.bashrc"
+    marker: "# {mark} ANSIBLE MANAGED BLOCK (umask)"
+    block: |
+      # Set umask to 002
+      umask 002
+
 - name: hide possible sudo message
   file:
     path: ~/.sudo_as_admin_successful

local/tasks/customise-gui.yml

@@ -11,7 +11,7 @@
   become: true
   become_user: "{{ root_user }}"
   copy:
-    src: images/quantum-mobile-bg.png
+    src: "images/{{ bg_image | default('quantum-mobile-bg.png')}}"
     dest: "{{ vm_data_folder }}/qm-customizations/quantum-mobile-bg.png"
     mode: 0755
 
@@ -55,7 +55,7 @@
 - name: create desktop shortcut to QM homepage
   copy:
     dest: "${HOME}/Desktop/homepage.desktop"
-    mode: "0753"
+    mode: "0644"
     content: |
       [Desktop Entry]
       Encoding=UTF-8

local/tasks/docker.yml

@@ -0,0 +1,13 @@
+- name: Install docker
+  include_role:
+    name: geerlingguy.docker
+  vars:
+    docker_users:
+      - "{{ vm_user }}"
+
+- name: Install docker pip
+  include_role:
+    name: geerlingguy.pip
+  vars:
+    pip_install_packages:
+    - docker

local/tasks/files/README-qeapp.md.j2

@@ -0,0 +1,23 @@
+# Welcome to {{ vm_name }} version {{ vm_version }}
+
+*Quantum Mobile* is a Virtual Machine for computational materials science, distributed by the {{ vm_author }}.
+
+It comes with a collection of software packages for quantum mechanical calculations, including:
+
+{% for name, url in software_urls.items() %}
+* [{{ name }}]({{ url }})
+{% endfor %}
+
+all of which are set up and ready to be used on their own or through [AiiDA](http://www.aiida.net).
+
+# Getting started
+
+* Start the Quantum ESPRESSO app by double-clicking on the icon on the desktop.
+
+* If the virtual machine is just started, you may need to wait a few minutes for the server to be fully ready. If you see an error message, try again after a few minutes.
+
+* The data you create over the app can be accessed from the `~/qeapp-home` folder. Vise versa, you can copy files into this folder to make them available in the app.
+
+* For more information on how to use the app, see the [Quantum ESPRESSO app documentation](https://aiidalab-quantumespresso.readthedocs.io/en/latest/).
+
+For troubleshooting and other information, see: {{ qm_homepage }}.