HPC ReproHack - Collaborative Hackpad
===

###### tags: `Reprohack` `hackpad`

:::info
- :earth_africa: **Remote**
- :calendar: **2022-03-21 to 2022-03-31**
- :watch: Start at **10:00 UTC**
- :arrow_forward: **Slides:** https://bit.ly/hpc-reprohack-slides
- :arrow_forward: **Closing Event Slides:** https://bit.ly/hpc-reprohack-closing-slides
- :page_with_curl: **Paper List:**
- Event List: https://reprohack.org/event/14/
- Central List: https://reprohack.org/paper/
- :scroll: **Participant Guidelines:** https://reprohack.org/participant_guidelines
- :purple_heart: **Code of Conduct:** https://reprohack.org/code-of-conduct
- :left_speech_bubble: **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](https://reprohack.org/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](https://twitter.com/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](https://twitter.com/apbartok)
- 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
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---

## 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 | :coffee: |
| | 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**](http://campus-cms.warwick.ac.uk/share/6952aec0dce6fb924fc2ccfdae2acefd ) |

:::

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# Questions for Speaker(s)
<!-- Please add any questions for our speaker below -->

## Questions for Martin Callaghan

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

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## Questions for Twin Karmakharm

- Maybe not just for Twin, but does anyone know of a good tool to make Git play nicely with Jupyter notebooks?
A https://nbdime.readthedocs.io/en/latest/
A Also binder

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## Questions for Heather Ratcliffe

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## Questions for Mike Croucher

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## Questions for Mozhgan Kabiri Chimeh

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# Plan of Action
## Welcome and Introduction

- Into Slides (https://bit.ly/hpc-reprohack-slides)

:computer: Form teams
---
Feel free to tackle papers individually or as teams.

:dart: Select papers
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- 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.

:books: Reproduce
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- 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:
- :earth_africa: navigate the materials
- :repeat: reproduce the analysis
- :recycle: 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.

:question: 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](http://campus-cms.warwick.ac.uk/share/27e6d654232f82d0db957b2b403e680a))**

:memo: 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.

:arrow_forward: 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.

<br>

> **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

<!-- Please register your paper in the space below using the template provided -->

### **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

<!-- Feel free to use this space to add topics for discussion and make notes on those discussions. You can remove if you don't plan to have any guided discussion sessions -->

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# Regroup notes
<!-- Any other notes you'd like to add. -->

***

# Feedback

## :green_book: One thing you enjoyed:

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## :red_circle: 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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