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INSTALLATION_GUIDE.md

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AiiDAlab Aurora installation on Windows PC

1. Basic software

2. AiiDAlab

  • Open a terminal and install aiidalab-launch

    pip install aiidalab-launch

    User manual: https://aiidalab.readthedocs.io/en/latest/usage/index.html#aiidalab-launch

  • Change the default docker image (Note: Docker should be running)

    aiidalab-launch profiles edit default

    and modify the file into this:

    port = 8888
default_apps = [ "aiidalab-widgets-base",]
system_user = "aiida"
image = "aiidalab/aiidalab-docker-stack:22.8.1"
home_mount = "aiidalab_default_home"
extra_mount = []

  • If you get an error saying it cannot connect to Docker, it might be due to a Windows bug. Run this:

    python <path-to-python-end>\Scripts\pywin32_postinstall.py -install

    where <path-to-python-end> might be C:\Users\USERNAME\Miniconda3 and USERNAME it is your Windows terminal username.

  • From the terminal run:

    aiidalab-launch start

  • If it works well, you will get an URL like https://localhost:8888/...
    Open it in a browser.

  • If you get an error, it might be due to a bug of aiidalab-launch. No worries. Run this

    docker ps -a

    and find the ID of the container and check if it is up and running.
    Then run

    docker exec -it CONTAINERID /bin/bash

    where CONTAINERID is the ID that you just found. This will connect to a shell within the Docker container. Then:

    su aiida
jupyter notebook list

    You will get a long URL, with a token (token=...).

    Go to https://localhost:8888 and enter token and a new password. Remember this password, it may be asked to you in the future if you restart the container.

    AiiDAlab should finally open! :-)

3. AiiDA configuration

  • Open a Terminal within AiiDAlab (or run docker exec -it CONTAINERID /bin/bash in a shell). Everything that follow is executed in this terminal, unless otherwise stated. You must make sure you are login as aiida user, by doing:

    su aiida

  • Set up SSH passwordless login to the LAB pc:

    ssh-keygen
cd
cat ~/.ssh/id_rsa.pub

    Copy the key that was just printed (contained in the ~/.ssh/id_rsa.pub file) to the LAB pc into this file (create it if it is not there):

    C:\Users\USERNAME\.ssh\authorized_keys

    or if you are an admin:

    C:\ProgramData\ssh\administrator_authorized_keys

    (a way to edit this file might be to open a PowerShell as administrator (right click-administrator) and run Notepad C:\ProgramData\ssh\administrator_authorized_keys).

  • install all the git repos of the plugins:

    pip install dgbowl-schemas

mkdir ~/src

cd ~/src
git clone https://github.com/lorisercole/aiida-core.git
cd aiida-core
git checkout windows
pip install -e .

cd ~/src
git clone https://github.com/ramirezfranciscof/aiida-calcmonitor.git
cd aiida-calcmonitor
git checkout tom_mon_bug_fixes
pip install -e .

cd ~/src
git clone https://github.com/epfl-theos/aiida-aurora.git
cd aiida-aurora
pip install -e .

cd
mkdir ~/aiida_run
reentry scan
verdi daemon restart --reset

    NOTE: in some computers python still uses the aiida-core installed in the root directory, so you will get an error about the transport (shell_type). To fix this, log into the Docker container and install aiida-core by hand:

    docker exec -it CONTAINERID /bin/bash
# the user will be root
cd /home/aiida/src/aiida-core
pip install .

    Then restart the daemon from an AiiDAlab Terminal.

  • If everything went well

    verdi plugin list aiida.schedulers

    should list the tomato scheduler;

    verdi plugin list aiida.calculations

    should list the aurora and calcmonitor calculations plugins.

  • Now, for example from the AiiDAlab Explorer, navigate to aiida-aurora/examples/config_files and modify the files to match your installation:

    • the username and key_filename in computer_ddm07162_config.yml
    • the remote_abs_path in code_ketchup-0.2rc2.yml. This will probably be 
      remote_abs_path: "/Users/USERNAME/Miniconda3/envs/tomato/Scripts/ketchup.exe"
      Find where the ketchup.exe code is located in the LAB pc. NOTE that here we write the path without C: and using / instead of \.

  • In the LAB pc, open the file (create the folder and file, if they are not present)

    C:\Users\USERNAME\Documents\WindowsPowerShell\profile.ps1

    and add this line

    Set-Alias -Name ketchup -value C:\Users\svfe\Miniconda3\envs\tomato-0.2rc2\Scripts\ketchup.exe

    (where you insert the correct path to ketchup.exe).
    This will allow one to call ketchup without loading the virtual environment (which is essential for the AiiDA scheduler). You can check that this works from the LAB pc, by opening a new terminal and entering ketchup --version. If it runs, it works!

  • Back to the AiiDAlab terminal, let's run

    cd ~/src/aiida-aurora/examples/config_files
./setup.sh

    This should configure all the computers and codes needed by Aurora.

  • You can test the connection to the LAB computer and localhost with

    verdi computer test ddm07162
verdi computer test localhost-verdi

    (NOTE: the first test will return one error about echo. This is normal).

  • Create the necessary AiiDA groups:

    verdi group create BatterySamples
verdi group create CyclingSpecs
verdi group create WorkChains

4. Aurora app installation

  • Setup custom app store (if Aurora not available in the official app store) https://aiidalab.readthedocs.io/en/latest/admin/index.html

    # apps.yaml
aurora:
releases:
  - url: 'git+https://github.com/epfl-theos/aiidalab-aurora@develop'
    metadata:
      categories:
      - utilities
      logo: https://raw.githubusercontent.com/aiidalab/aiidalab-widgets-base/master/miscellaneous/logos/aiidalab.png
      title: Aurora BIG-MAP app
      description: An AiiDAlab application for the Aurora BIG-MAP Stakeholder initiative.
      authors: Loris Ercole
      external_url: https://github.com/epfl-theos/aiidalab-aurora
      documentation_url: https://github.com/epfl-theos/aiidalab-aurora#readme

  • Install Aurora app If the version is not correct, or it does not update. You can update by hand in this way:

    cd ~/apps/aurora
git checkout develop
git pull

    Then reload AiiDAlab page.

  • The Tasks button shows all the open windows/notebooks/terminals. Shut them down if you do not use them anymore.

  • To update the list of available samples, edit the JSON file ~/apps/aurora/available_samples.json.