AiiDA setup for LSMO members

1. install prerequisites

Install prerequisites from the AiiDA documentation.

2. install conda and create a new environment

If not yet present, install conda:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda
source "$HOME/miniconda/etc/profile.d/conda.sh"
conda init

Create an enviroment aiida1 with python 3.9 and activate this new environment

conda create -n aiida1 python=3.9 -y
conda activate aiida1

Remember to always activate the environment before starting to use AiiDA.

3. create a directory to gather AiiDA related files

mkdir -p $HOME/aiida1
cd $HOME/aiida1
git clone https://github.com/lsmo-epfl/aiida-lsmo-setup.git
export AIIDA_PATH=${HOME}/aiida1

4. install AiiDA and plugins

preferable choice: install from Github in editable mode

This allows you to easily edit the AiiDA plugin packages and contribute back changes upstream:

./aiida-lsmo-setup/install_editable.sh

alternative choice: install from PyPI

This will use packaged versions of all plugins - easier to install:

./aiida-lsmo-setup/install_packages.sh

5. add variables to environment

Conda executes scripts in a special activate.d folder upon activating an environment. Add there any custom commands, e.g., aliases, you want to use with AiiDA (instead of placing them in your .bashrc).

mkdir -p $CONDA_PREFIX/etc/conda/activate.d
cat > $CONDA_PREFIX/etc/conda/activate.d/aiida-init.sh << EOF
export AIIDA_PATH=$HOME/aiida1
eval "\$(_VERDI_COMPLETE=source verdi)"
EOF

Here, we have specified the AIIDA_PATH and enabled tab-autocompletion for the verdi commands.

Now, let's exit and reenter the environment in order for the changes to take effect:

conda deactivate
conda activate aiida1

6. make your AiiDA profile

Run and follow the instructions of

verdi quicksetup

and check that everything is fine with:

verdi status

The only red cross should be for the daemon, that you will start later before submitting a calculation.

7. install computers and codes

Setting up passwordless SSH access

If you haven't done so already

• generate a ssh keypair using ssh-keygen -t rsa
• set up passwordless access using ssh-copy-id username@remote for the clusters you want to use with AiiDA (e.g. fidis, deneb)

See also the AiiDA documentation.

set up AiiDA computers and codes

We have prepared a set of configuration files that allows you to quickly set up computers and codes used in the LSMO:

git clone https://github.com/lsmo-epfl/aiida-lsmo-codes --depth 1
cd aiida-lsmo-codes
./configure.py

This scripts automates three steps: verdi computer setup, verdi computer configure and verdi code setup, which you can use whenever you need to add/modify/delete computers and computers. See the AiiDA documentation for more information.

Note:

• if a computer with the same name exists it won't be set up again. You can verdi computer rename the label the previous computer.
• if a code with the same label exists, it will set up a new code with the same label, so the label is no longer unique (you will need to use the PK to refer to the code). You can remove codes using verdi node delete <PK> (note: all calculations associated to the code will also be removed).

test computers

verdi computer list
verdi computer test fidis
verdi code list

8. try out some examples

You are ready to run your first work chains from the aiida-lsmo repository. For example:

cd aiida-lsmo/examples
verdi run run_IsothermWorkChain_HKUST-1.py raspa@localhost zeopp@localhost

See the documentation of LSMO's work chain and calculation functions.