AiiDA
Automated Interactive Infrastructure and Database for Computational Science

AiiDA is a flexible and scalable informatics' infrastructure to manage, preserve, and disseminate the simulations, data, and workflows of modern-day computational science. Able to store the full provenance of each object, and based on a tailored database built for efficient data mining of heterogeneous results, AiiDA gives the user the ability to interact seamlessly with any number of remote HPC resources and codes, thanks to its flexible plugin interface and workflow engine for the automation of complex sequences of simulations.

Journal ref: G. Pizzi, A. Cepellotti, R. Sabatini, N. Marzari, and B. Kozinsky, AiiDA: automated interactive infrastructure and database for computational science, Comp. Mat. Sci. 111, 218-230 (2016)

Open access link: arXiv:1504.0116

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Tutorial on writing reproducible workflows for computational materials science

👤 🕔 January 19, 2019 Comments Off on Tutorial on writing reproducible workflows for computational materials science

Coordinates

When May 21st, 2019 (9:00) until May 24th, 2019 (13:00)

Where EPFL, Lausanne, Switzerland

Registration Registration link (closing March 24th, 2019)

About

This 3.5-day tutorial is designed to get Master students, PhD students and Postdocs from the field of computational materials science started with writing reproducible workflows. Participants will be introduced to the state of the art in workflow management and high-throughput computations by experts in the field, and gain in-depth hands-on experience using a tool that they can directly apply to their own research.

Our tool of choice is the AiiDA framework for workflow management and provenance tracking, which is backed by a significant community of users and developers, and has interfaces to more than 20 materials science codes (see plugin registry), including to the ab initio codes Quantum ESPRESSO, VASP, cp2k, Castep, Siesta, Fleur, Crystal, NWChem, Wannier90, and Yambo. AiiDA’s permissive open source license (MIT) enables participants to use it both in academic and commercial settings. By virtue of its general design and flexible plugin system, AiiDA is easily extended to new codes and new use cases.

  • The first day will serve as an introduction to AiiDA for novices,  and is designed to be skipped by participants with previous AiiDA experience (as determined by an online questionnaire during registration).
    In order to avoid losing time on installation issues, participants will have the option to connect to virtual machines preconfigured with AiiDA (or to come with AiiDA already installed on their laptop).
  • The remaining 2.5 days will include the highlight talks by the invited speakers as well as in-depth tutorials on writing AiiDA workflows, given by the organizers and six core developers of AiiDA. An online questionnaire will determine the ab initio codes used by participants, and we aim to cover 3 popular codes with explicit examples.
    On the third day, participants will have the choice to either explore advanced aspects of workflow management or to focus on designing a new AiiDA plugin.
  • Discussion sessions, as well as a poster session and an open-mic session are scheduled to foster interaction between the participants, to discuss and answer questions.

While this tutorial is deliberately open to computational materials scientists at many levels, we do require the following  for participation:

  • familiarity with a Unix operating system and the bash shell (or equivalent)
  • familiarity with python
  • familiarity with a job scheduler (e.g. slurm, torque, sge, …)
  • full participation for (at least) the last 2.5 days

Speakers & organisers

The following invited speakers will illustrate the use workflows in their research using a recent example, highlighting both the challenges encountered and possible solutions.

  • Stefaan Cottenier (UGent, BE)
  • Marco Govoni (ANL, US)
  • Fawzi Mohamed (FHI, GE)
  • Guido Petretto (UC Louvain, BE)

Tutorial lectures and assistance during hands-on session will be provided by a team of core AiiDA developers and active plugin developers:

  • Espen Flage-Larsen (SINTEF, No)
  • Andrea Ferretti (CNR, Istituto Nanoscienze, IT)
  • Alberto Garcia (ICMAB-CSIC, ES)
  • Sebastiaan Huber (EPFL, CH)
  • Leopold Talirz (EPFL, CH)
  • Giovanni Pizzi (EPFL, CH)
  • Spyros Zoupanos (EPFL, CH)
  • Aliaksandr Yakutovich (EPFL, CH)
  • Snehal Kumbhar (EPFL, CH)

The tutorial is organised by Leopold Talirz (EPFL, CH), Sebastiaan Huber (EPFL, CH), Espen Flage-Larsen (SINTEF, NO), Alberto García (ICMAB, ES) and Andrea Ferretti (CNR, IT) who bring expertise in a diverse set of ab initio codes and their applications in different work environments (universities, research institutes and companies).

For generic information concerning the tutorial, contact aiida.workflows2019@gmail.com .

Preliminary Programme

Please note that this programme is preliminary and subject to change.

In the following, morning sessions are 9h-13h, and afternoon sessions 14h30-18h30, each with one coffee break.

Day 1, Tuesday (optional, introduction to AiiDA)

Morning:

  • Introduction by the organizers (15 min)
  • Introduction to AiiDA (1 h)
  • Hands-on: Understanding and browsing the provenance graph
  • Hands-on: The verdi command line and the AiiDA python API
  • Hands-on: Submit, monitor and debug calculations

Afternoon:

  • Hands-on: Querying the results of calculations
  • Hands-on: Running a small screening study

Day 2, Wednesday

Morning

  • Introduction by the organizers (15 min)
  • Highlight talk by Stefaan Cottenier (via video) (45 min + 15 min for questions)
  • Highlight talk by Marco Govoni (45 min + 15 min for questions)
  • Introduction: From single calculations to workflows (30 min)
  • Hands-on: Writing your first workflow – equation of state

Afternoon:

  • Hands-on: Writing your first workflow – equation of state – Continued
  • Real-life workflows: phonons, DFT+U, …
  • Hands-on: How to deal with crashes? Making your workflow more robust
  • Discussion session: Problems encountered during hands-on (30min)

Evening: Standing buffet dinner & poster session

Day 3, Thursday

Morning

  • Highlight talk by Fawzi Mohamed (45 minutes + 15 minutes for questions)
  • Making AiiDA work with your code – the AiiDA plugin system (30 min)
  • Wrapping your workflow in a web application – the AiiDA Lab ecosystem (30 min)
  • Open-mic session: participants discuss their own use cases (30min)
  • Splitting up in groups (30 min)
    • Group A: Developing a new workflow for your code
    • Group B: Wrapping a workflow in a web application
    • Group C: Writing a plugin for a new code

Afternoon

  • Hands-on:
    • Group A: Developing a new workflow for your code
    • Group B: Wrapping a workflow in a web application
    • Group C: Writing a plugin for a new code
  • (on demand) AiiDA workflow engine under the hood

Evening: Social dinner

Day 4, Friday

Morning

  • Highlight talk by Guido Petretto (45 minutes + 15 minutes for questions)
  • Data management plans made easy – AiiDA & the Materials Cloud (30 minutes)
  • Hands-on: continued from Thursday
  • Closing remarks by the organizers, feedback forms (15min)

Departure starting from 13:00

Funding

The tutorial will be offered free of charge, with roughly 40 participants. By default, participants are expected to cover their costs for travel and lodging, but we aim to reimburse the cost of lodging for participants who require financial assistance (which they need to motivate during registration).

We are very grateful to our sponsors for helping to make this event possible: