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HPC ReproHack - Collaborative Hackpad

tags: Reprohack hackpad
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    Remote
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    2022-03-21 to 2022-03-31
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    Start at 10:00 UTC
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    Slides: https://bit.ly/hpc-reprohack-slides
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    Closing Event Slides: https://bit.ly/hpc-reprohack-closing-slides
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    Paper List:
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    Participant Guidelines: https://reprohack.org/participant_guidelines
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    Code of Conduct: https://reprohack.org/code-of-conduct
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    Chat to us on Slack: https://reprohack-autoinvite.herokuapp.com/
  • :Bird: Twitter: #HPCReproHack @ReproHack
  • hackmd docs: https://hackmd.io/s/features

Participants:

Please review our Code of Conduct

Please sign in below:

  • Jane Doe (pronouns/ Affiliation / twitter / etc)
  • Anna Krystalli, (she/her), University of Sheffield, @annakrystalli
  • Omar Adesida, (he/him), University of Warwick
  • Radu Cimpeanu, (he/him), University of Warwick, @rcimpeanu
  • Joe Gilkes, (he/him), University of Warwick
  • Colm Connaughton, (he/him), University of Warwick
  • Kat Blow, (she/her), University of Warwick
  • David Quigley, (he/him), University of Warwick
  • Albert Bartok-Partay (he/him), University of Warwick, @albapa
  • Connor Allen (he/him), University of Warwick
  • Aravinthen Rajkumar (he/him), University of Warwick
  • Andrew Angus (he/him), University of Warwick
  • Tanmoy Chakraborty (he/him), University of Warwick
  • Benedict Saunders (he/him), University of Warwick
  • Peter Lewin-Jones (he/him), University of Warwick
  • Arkadiy Davydov (he/him), University of Warwick
  • Adam Smith (he/him), University of Warwick
  • Harvey Devereux (he/him), University of Warwick
  • Claudia Viaro (she/her), University of Warwick
  • Tom Goffrey (he/him), University of Warwick
  • Alex Beeson, University of Warwick

Mentors:

Prof. David Quigley

  • Computational Statistical Physics
  • Density Functional Theory
  • Molecular and atomistic simulation
  • High Performance Computing
  • Computing: C/Fortran/Python and parallel computing in multiple languages.

Dr. Radu Cimpeanu

  • Computational fluid dynamics
  • Computational acoustics
  • Industrial mathematics
  • Reduced-order modelling (asymptotic analysis, differential equations)
  • Scientific computing
  • C/C++ and open-source platforms employing them (e.g. Gerris, Basilisk, oomph-lib), Matlab

Prof. Colm Connaughton

  • Non-equilibrium statistical physics
  • Complex systems
  • Applications of data science
  • Computational jack-of-all-trades

Dr Albert Bartok-Partay

  • Ab initio modelling
  • Machine learning interatomic potentials
  • High Performance Computing
  • Fortran, python

Prof. Giovanni Montana

  • Statistical modelling of high-dimensional data
  • Reinforcement learning
  • Data science applications in bioinformatics and digital healthcare
  • Computing: Python, C, Rust

Dr. Tom Goffrey

  • Plasma Physics
  • Astrophysics
  • High Performance Computing
  • Fortran, python

Dr. Marya Bazzi

  • Network Science
  • Applications of data science
  • Python/Matlab

Agenda

Date Time Event
21st March 10:00 - 10:15 Anna Krystalli: Welcome, Introduction to event.
10:15 - 10:40 Martin Callaghan: HPC in the age of Data Science
10:40 - 11:30 Twin Karmakharm: Reproducibility on HPC
11:30 - 11:45
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11:45 - 12:10 Heather Ratcliffe: Introduction to Sulis
12:10 - 12:35 Mike Croucher: Reproducible MATLAB on HPC
12:35 - 12:55 Mozhgan Kabiri Chimeh: NVIDIA AI & HPC Containers
13:00 - 14:00 LUNCH
14:00 - 14:20 Anna Krystalli: Introduction to ReproHacking
14:20 - 17:00 Initial ReproHack Session
22nd March 14:00 - 16:00 Drop In support session
24th March 14:00 - 16:00 Drop In support session
28th March 14:00 - 16:00 Drop In support session
30th March 14:00 - 16:00 Drop In support session
31st March 10:00 - 13:00 Closing Event: Space 30 of the Radcliffe Conference Centre

Questions for Speaker(s)

Questions for Martin Callaghan

  • How will research software engineering adapt to environmental issues? Are current methodologies sustainable in the light of increasing computational demands?
  • .

Questions for Twin Karmakharm

Questions for Heather Ratcliffe

  • .
  • .

Questions for Mike Croucher

  • .
  • .

Questions for Mozhgan Kabiri Chimeh

  • .
  • .

Plan of Action

Welcome and Introduction

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Form teams

Feel free to tackle papers individually or as teams.

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Select papers

  • Choose paper from list of proposed papers

  • Register the paper selected and the participants reproducing below. You can copy, paste and edit the following template:

### **Paper:** <Title of the paper reproduced>
**Mentor:**  Mentor Name
**Reviewers:** Reviewer 1, Reviewer 2 etc.

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Reproduce

  • Attempt to reproduce papers from available materials and documentation on the Sulis HPC System
  • Make notes about your experiences, in particular with respect to how easy it is to:
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    navigate the materials
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    reproduce the analysis
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    reuse the materials

We will have all afternoon on the first day to begin ReproHacking with support from all mentors and organisers. You will expected to carry on working on your project in your own time over the next 10 days.

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Need help? Join a Drop-in session

There will four 2hr drop in sessions throughout the event (see agenda for details) where mentors will be available to provide support if you are stuck with anything. Most will be online, accessible throuh the event MS Team. The session on the 22nd March will also be hosted in person in the Complexity/MathSys common room (D1.07)

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Feedback to authors

By the end of the event, please ensure your group has completed the feedback form for authors. You might want to make a note of the questions in the form at the beginning, compile notes as a group somewhere else (feel free to use the event hackpad) and then submit your repsonses at the end.

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Feedback to the group

During the closing session on the 31st March, we will regroup to hear from each group about their experiences. Each group will be expected to give a short presentation (5-10 mins) summarising their experiences and lessons learnt. Feel free to create slides if you wish.

There will be plenty of time for discussion and Q&As on the day.


The Closing Event will be held at Radcliffe Conference Centre, Space 30
From the main entrance follow the corridor to the left and follow signs for space 30.

Folk are welcome to arrive early and help themselves to coffee and nibbles in the main lounge, but we’ll also have our own coffee area immediately adjacent to the conference room.

http://campus-cms.warwick.ac.uk/share/6952aec0dce6fb924fc2ccfdae2acefd (space 30 shows up as MR9 on that map)

Paper Registration

Use the following template (also provided in "Plan of Action") and register your review below.

Paper: [Title of the paper reproduced]

Mentor: Mentor Name
Reviewers: Reviewer 1, Reviewer 2 etc.

Paper: PlanGAN: Model-based Planning With Sparse Rewards and Multiple Goals

Mentor: Giovanni Montana
Reviewers: Adam Smith, Claudia Viaro, David Ireland, Alex Beeson, Mianchu Wang

Paper: Encapsulated nanowires: Boosting electronic transport in carbon nanotubes

Mentor: Albert Bartok-Partay
Reviewers: Connor Allen, Joe Gilkes, Arkadiy Davydov

Paper: Beyond the ponderomotive limit: Direct laser acceleration of relativistic electrons in sub-critical plasmas

Mentor: Tom Goffrey
Reviewers: Andrew Angus

Paper: Comminucation: Thermodynamics of stacking disorder in ice nuclei

Mentor: Colm Connaughton
Reviewers: Omar Adesida, Kat Blow, Aravinthen Rajkumar

Paper: Accelerating the prediction of large carbon clusters via structure search: Evaluation of machine-learning and classical potentials

Mentor: David Quigley
Reviewers: Benedict Saunders, Tanmoy Chakraborty

Paper: Droplet impact onto a spring-supported plate: analysis and simulations

Mentor: Radu Cimpeanu
Reviewers: Harvey Devereux, Peter Lewin-Jones

Discussion topics

Regroup notes

Feedback

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One thing you enjoyed:

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One thing that could be improved:

  • Maybe a short period of time on the first day could be set aside for some/all groups to "go in blind" without any help, from authors or HPC engineers. Perhaps for an hour then informally feedback if they managed to get anything installed or running. This would also highlight if some papers needed more engineering or author input to get going.
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