Imperial RSE Community - Events

Imperial Research Software Engineering Community Session - Thursday 8th March 2018, 16:00-17:30

ROOM 217/218, HUXLEY BUILDING, SOUTH KENSINGTON CAMPUS

The next meeting of the Imperial College Research Software Engineering (RSE) Community will take place on Thursday 8th March with two talks:

16:00: What do we know about Research Software Engineers?
  Simon Hettrick, Deputy Director, Software Sustainability Institute - University of Southampton
16:20: Smart Forming: A Python web application for running Matlab simulation models on HPC infrastructure
  Chris Knight, Department of Physics, Imperial College London
17:00: Discussion  (refreshments available)

Smart Forming: A Python web application for running Matlab simulation models on HPC infrastructure
Speaker: Chris Knight

Developed by the RSE service at Imperial for the Metal Forming Technologies group in Mechanical Engineering, the Smart Forming Python web app allows users to upload and run Matlab simulation models on the college HPC facilities from the comfort of an easy to use web interface. After uploading a model users can configure model parameters and input data before submitting jobs to CX1. On completion, the user receives an email containing download links for their log file and output data. Chris Knight, the main developer on the project, will discuss the exciting tech stack which powers the app (Python, Django, Celery, Paramiko, SQLite, Docker and more) and will give a live demo of the app in action.

Speaker bios:

Simon Hettrick is Deputy Director of the Software Sustainability Institute, and co-Director of the Southampton Research Software Group.

At the Software Sustainability Institute, Simon is responsible for the policy research and campaigning. He works with stakeholders from across the research community to develop policies that support research software, the people who develop that software and the researchers who rely on it. Simon's research focusses on the use of software in the research community with the aim of understanding practices and demographics.

Simon is a passionate advocate for Research Software Engineers. He was the founding chair of the UK's community of Research Software Engineers and has been a member of the Association ever since. He is the Principal Investigator of the RSE Network.

Before working at the Institute, Simon worked in patent law. His PhD focussed on the development of a new type of efficient waveguide laser.

Chris Knight is currently completing his PhD in Computational Physics: applying a large parallel fluid solver written in C with MPI to investigate the relationship between sand grain size distributions and fluid-grain interaction forces in dense sand packings. Chris has also worked as a software engineer developing cloud based containerised Python apps and tooling for Big Data analysis with Apache Spark.


Past Events

Imperial Research Software Engineering Community Session @ HPC Summer School 2017 - 20th September 2017, 10:00-12:00

WEDNESDAY 20TH SEPTEMBER 2017 - 10:00-12:00 - ROOM 121, SAF BUILDING, SOUTH KENSINGTON CAMPUS

The next meeting of the Imperial College Research Software Engineering (RSE) Community will take place on Wednesday 20th September as part of the Imperial College HPC Summer School 2017. The draft agenda for the session is shown below.

More details on the Summer School, which runs from Monday 18th - Friday 22nd September can be found at http://www.imperial.ac.uk/computational-methods/news-and-events/hpc-2017/.

Session schedule:

10:00 Welcome and introduction - Jeremy Cohen, Department of Computing
10:05 An introduction to RSE at Imperial and the Research Computing Service
  - Spencer Sherwin, Director, Research Computing Service
  - Mark Woodbridge, Research Software Engineering Team Lead, Research Computing Service
  - Jeremy Cohen, Founder, Imperial Research Software Engineering Community
10:30 Docker without Docker: How to run containers on HPC environments without any prerequisites!
Jonathan Passerat-Palmbach, Department of Computing
 

Containers have seen a growing adoption in the academic world over the last few years. They allow researchers to make their experimental pipelines available to the community, therefore increasing the reproducibility of their results.

In order to integrate these packaged applications in large-scale experiments, they have to be run on HPC/HTC infrastructures. However, the native Docker service requires administrator--like privileges on the machine that end-users rarely have for security reasons.

In this talk, we explore the recent developments in the OpenMOLE project (https://next.openmole.org) to circumvent these restrictions and enable the execution of scientific pipelines based on Docker images on HPC clusters. Our solution does not involve any remote third-party entity and can also be used with any container image supporting the Open Container Initiative format via an external loader (https://github.com/vincenthage/proot-oci-loader).

The solution is already integrated in the OpenMOLE platform and you can read more about the work leading to this feature in this paper http://journal.frontiersin.org/article/10.3389/fninf.2017.00021/full

11:00 Scientific Python and Continuous Integration for HPC
Ed Smith, Department of Civil and Environmental Engineering
  In this talk I give an overview of my year as an RSE, including teaching Python and coupling a fluid dynamics continuum simulation to a particle solver. In particular, I will describe the process of ensuring software is correct using software engineering best practice including verification using unit testing and coupled validation driven by Python. I'll finish by outlining plans for Continuous Integration on high performance platforms such as cx1.
11:20 Research Software Engineering Discussion Breakouts
 

Attendees split into small groups to discuss different aspects of RSE. (~20 mins)
Groups report back on their discussions and key findings (~ 15mins)

Refreshments available.


Imperial Research Software Engineering Community Meeting - 31st May 2017 - Data Engineering for Vaccine Development, Mark Woodbridge, IAVI

 

WEDNESDAY 31ST MAY 2017 - 16:00-17:30 - SOUTH KENSINGTON CAMPUS - ROOM TBC

The next meeting of the Imperial College Research Software Engineering (RSE) Community will take place on Wednesday 31st May, 16:00 – 17:30, room TBC. We are pleased to welcome Mark Woodbridge from IAVI who will be speaking on data engineering for vaccine development.

The agenda is as follows:

Data Engineering for Vaccine Development17:00 Networking; Drinks and snacks availableFree registration for this event will be available via Eventbrite soon.

Abstract: Data Engineering for Vaccine Development

Biomedical research organisations have traditionally leveraged laboratory assays to validate hypotheses. However, the development of high-throughput experiments and the availability of large public datasets demands the capability to handle data at scale and conduct data driven (“dry lab”) research. This talk will describe IAVI’s first steps towards developing and deploying infrastructure and tools for data science.

Speaker biography: Mark Woodbridge studied Computer Science and Computational Linguistics before working as a Research Software Engineer at the University of Cambridge and Imperial College London. He is now responsible for facilitating a programme of data-driven research for vaccine development at the International AIDS Vaccine Initiative (IAVI). 


Imperial Research Software Engineering Community Meeting - 22nd March 2017 - Modern Fortran for Computational Science, Dr Wadud Miah, Numerical Algorithms Group 

 

WEDNESDAY 22ND MARCH 2017 - 16:30-18:00 - SOUTH KENSINGTON CAMPUS - HUXLEY BUILDING LECTURE THEATRE 311

The March 2017 meeting of the Imperial College Research Software Engineering (RSE) Community will take place on Wednesday 22nd March, 16:30 – 18:00 in the Huxley Building, LT311, on the South Kensington Campus. We are pleased to welcome Dr Wadud Miah from Numerical Algorithms Group who will be speaking on modern Fortran.

The agenda is as follows:

16:30 Welcome and Introduction

16:35 Modern Fortran for Computational Science - Dr Wadud Miah, Numerical Algorithms Group

17:30 Networking; Drinks and snacks availableFree registration for this event is available at: http://imperialrse-mar17.eventbrite.co.uk

Abstract: Modern Fortran for Computational ScienceFortran is the dominant programming language of computational science. Codes written in Fortran account for over 80% of CPU cycles on the Archer UK supercomputer service and around 70% of CPU cycles on the top 500 supercomputers in the world. Surveys have shown that a large percentage of the computational community are still using the Fortran 77 standard and uptake on the more modern standards (e.g. 95, 2003 and 2008) are still lagging behind. Anecdotal evidence has shown that scientists are using non-standard compiler specific features which reduces the portability of their codes. This presentation will give an update on the latest Fortran standards to increase the portability and performance of computational codes.Speaker biography: Wadud Miah completed his PhD at the Aeronautics department at Imperial College and used modern Fortran extensively for his research. He has worked as a computational scientist at various institutions where he used modern Fortran to advance computational science. He now works for the Numerical Algorithms Group as a HPC specialist and is running the Fortran Modernisation Workshop (http://www.nag.co.uk/content/fortran-modernization-workshop).


Imperial Research Software Engineering Community Meeting - Friday 30th September 2016

FRIDAY 30TH SEPTEMBER 2016 - 10:00-12:00 - SOUTH KENSINGTON CAMPUS - HUXLEY BUILDING LECTURE THEATRE 311

This event is part of the Imperial's HPC Service Summer School week.

This session will include four talks and a panel discussion. The schedule is as follows:

09:45 Coffee and pastries available
10:00 Session introduction and RSE update
  (Jeremy Cohen, Department of Computing, Imperial College)
10:15 Parallel Programming for the 21st Century
  (Victor Eijkhout, Texas Advanced Computing Centre)
10:55 Spectral/hp element computation on HPC infrastructure
  (Chris Cantwell, Department of Aeronautics, Imperial College London)
11:15 Why do Italians hand gesture? Improving communication in scientific computing
  (Anna Freni-Sterrantino, Small Area Health Statistics Unit)
11:35 Panel discussion: The challenges and importance of good research software development practices for HPC
Panel members:  
  Simon Burbidge, Imperial HPC Service
  Victor Eijkhout, Texas Advanced Computing Centre
  Spencer Sherwin, Department of Aeronautics
  David Colling, Department of Physics
  Stephen McGough, University of Durham


Imperial Research Software Engineering Community Meeting - 26th May 2016 

THURSDAY 26TH MAY - 16:00-18:00 - SOUTH KENSINGTON CAMPUS - HUXLEY BUILDING LECTURE THEATRE 144

The May 2016 meeting of the Imperial College Research Software Engineering (RSE) Community will take place on Thursday 26th May, 16:00 – 18:00 in the Huxley Building, LT144, on the South Kensington Campus. 

We will have a main talk from Dr Peter Vincent, Department of Aeronautics and lead of the PyFR project (http://www.pyfr.org), followed by a set of 3-minute lightning talks* and an RSE discussion.

Please register for this event at: https://imperial-rse-may16.eventbrite.co.uk

The agenda is as follows:

16:00 PyFR: Next-Generation High-Order Computational Fluid Dynamics on Modern Hardware Platforms
Peter Vincent, Department of Aeronautics
16:30 3-minute lightning talks*
  Ghislain Vaillant - A methodology for library design - introducing Armin Ronacher's beautiful native libraries approach
  Ally Donaldson - Metamorphic testing
  Jonathan Passerat-Palmbach - Scala in 2016 - Welcome to the Future [Today]
  Maxime Noel - Research Software Engineering with Python
  Francois Piat - The ArrayFire GPU programming library
  Sarah Stewart - Software management plans
  Torsten Reimer - Software version control and GitHub Enterprise
17:00 RSE discussion
17:30 Networking; Drinks and snacks available

Main talk:

PyFR: Next-Generation High-Order Computational Fluid Dynamics on Modern Hardware Platforms

High-order numerical methods for unstructured grids combine the superior accuracy of high-order spectral or finite difference methods with the geometrical flexibility of low-order finite volume or finite element schemes. The Flux Reconstruction (FR) approach unifies various high-order schemes for unstructured grids within a single framework. Additionally, the FR approach exhibits a significant degree of element locality, and is thus able to run efficiently on modern many-core hardware platforms, such as Graphical Processing Units (GPUs). The aforementioned properties of FR mean it offers a promising route to performing affordable, and hence industrially relevant, scale-resolving simulations of hitherto intractable unsteady flows within the vicinity of real-world engineering geometries. In this talk I will present PyFR (www.pyfr.org), an open-source Python based framework for solving advection-diffusion type problems using the FR approach. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of a custom Mako-derived domain specific language. The latest release of PyFR is able to solve the compressible Euler and Navier-Stokes equations on grids of quadrilateral and triangular elements in two dimensions, and hexahedral, tetrahedral, prismatic, and pyramidal elements in three dimensions, targeting clusters of multi-core CPUs, NVIDIA GPUs, AMD GPUs, Intel Xeon Phis, and heterogeneous mixtures thereof. Results will be presented for various benchmark and `real-world' flow problems, and scalability of PyFR will be demonstrated on clusters with 1000s of NVIDIA GPUs. Throughout the talk the importance of algorithm-software-hardware co-design, in the context of next-generation computational fluid dynamics, will be highlighted.

Project page: http://www.pyfr.org

* Lightning talks: The lightning talks are intended to provide an opportunity for you to give a brief, informal overview of a topic that you think may be of interest to other community members. You may want to introduce an application or tool you've been working on or a library that you think may be of interest to other developers. Perhaps you've recently read a great blog post that you'd like to highlight, or you have an RSE-related idea you'd like to present and get some feedback on in the susequent discussion session.

  • Lightning talks will have a limit of 3 minutes each.
  • Presenters may provide 1 slide to use as a background for their presentation.

Imperial Research Software Engineering Community Meeting - February 2016

WEDNESDAY 17TH FEBRUARY - 16:15-18:00 - SOUTH KENSINGTON CAMPUS - HUXLEY BUILDING LECTURE THEATRE 311

Continuing the programme of RSE community meetings, this session will focus on computational and research data support software with an introduction from the College's Research Data Management team followed by talks on two tools OpenMOLE (http://www.openmole.org) and FGLab (https://kaixhin.github.io/FGLab/). 

Tea/coffee will be available from 15:45 and there will be an opportunity to network with other attendees following the talks.

SESSION INTRODUCTION: RESEARCH DATA MANAGEMENT - Sarah Stewart, Research Data Support, Central Library

THE OPENMOLE WORKFLOW ENGINE: EXPLORATION OF SCIENTIFIC APPLICATIONS AT SCALE USING DISTRIBUTED COMPUTING.
Speaker: Jonathan Passerat-Palmbach, Department of Computing

OpenMOLE (Open MOdeL Experiment) is a scientific workflow management system with a strong emphasis on workload distribution. The OpenMOLE platform is formed of a combination of 1) reusable cutting edge methods and exploratory algorithms, 2) expressed using a high level workflow formalism and 3) exploiting distributed computing (clusters, grids, clouds) to scale up to the needs of real world scientific experiments.

OpenMOLE makes it simple to execute existing applications on distributed computing environments. If you want to execute the same program for many different inputs (parameters or datasets), OpenMOLE is the tool you need.

The typical usages of OpenMOLE are high performance model calibration, model exploration, machine learning, optimization, data processing.

FGLAB: EXPERIMENTAL DASHBOARD
Speaker: Kai Arulkumaran, Department of Bioengineering

FGLab is an electronic lab notebook that is designed to make prototyping experiments easier. Experiment details and results are sent to a database, which allows analytics to be performed after their completion. FGLab is designed to be used with existing code in a way that is independent of either programming language or operating system, and can scale up from a single machine to a small group of machines. In this talk I will introduce how FGLab enables a more systematic approach in the exploratory stages of research, and finish with a live demo.
Project page: https://kaixhin.github.io/FGLab/


Imperial Research Software Engineering Community Meeting - January 2016

WEDNESDAY 20TH JANUARY - 16:00-18:00 - SOUTH KENSINGTON CAMPUS - HUXLEY BUILDING ROOM 217/218

Continuing the programme of RSE community meetings, this event will include two talks followed by drinks and an opportunity to network with colleagues from across Imperial. Join us in Huxley 217/218 from 4.00pm on Wednesday 20th Jan.

OPEN SOURCE SOFTWARE PACKAGING, DISTRIBUTION AND MAINTENANCE
Speaker: Dr Ghislain Vaillant, Department of Computing

This talk will look at distribution and maintenance of open source software from the perspective of Ghislain's experience working with the Debian Linux community.

HPC AND COMPUTATIONAL METHODS TRAINING
Speaker: Dr Katerina Michalickova, Imperial College HPC Service

I will introduce the HPC service group and describe the resources available to the College community. The second part of the talk will focus on training in HPC and computational methods in general.  Here, I will present the Computational Methods Hub that is dedicated to training of doctoral students. 


Imperial Research Software Engineering Community - Tech Talk & Networking Kick-off Event

WEDNESDAY 2nd December - 16:30-18:30 - SOUTH KENSINGTON CAMPUS - HUXLEY BUILDING ROOM 217/218

This will be the first in a series of regular tech talk & networking community events within Imperial. Join us at 4.30pm for two short talks followed by drinks and an opportunity to network with colleagues from across Imperial.To help give an idea of the number of attendees and to plan catering, please register for this event via EventBrite.

Draft Agenda:

16:30: Welcome and introduction to the RSE community - Jeremy Cohen, Department of Computing

16:45: Research data management for developers and scientists - Torsten Reimer, Scholarly Communications Officer, Research Office

17:05: Python for MATLAB users: An introduction to Python for scientific computation - Ed Smith, Department of Chemical Engineering

17:30: Drinks reception and networking

Research data management for developers and scientists - Dr Torsten Reimer
I will discuss the policy landscape relating to research data and software and the emerging College infrastructure in this area, present preliminary results from a survey on College support for distributed version control and start a discussion on how the College could support research software development and developers.

Speaker Bio: Dr Torsten Reimer is Scholarly Communications Officer at Imperial College London, where he manages the cross-College Open Access and Research Data Management activities. Torsten is working with sector bodies, funders and vendors to improve the scholarly communications system and is involved in initiatives such as ORCID. He is also a fellow of the UK's Software Sustainability Institute. Before joining Imperial College, Torsten worked at the digital infrastructure service provider Jisc, King's College London, the University of Munich, the Bavarian State Library and a software company.

Python for MATLAB users: An introduction to Python for scientific computation - Dr Edward Smith
In many departments at Imperial, programming in MATLAB is the only experience students get of writing code. While MATLAB is excellent for numerical work, it is a commercial program, focused on numerical tasks & obscures important concepts in programming. In this talk, the open source language Python is introduced as an alternative to MATLAB. The pros and cons are discussed along with a few minimal examples of Python code. Python constructs such as lists, objects & iterators are introduced. The key libraries are discussed which allow Python to be used for scientific applications. The talk will finish with a few example projects by the speaker which have used Python.The talk is aimed at existing users of MATLAB but should be of interest to people wanting a very brief introduction to Python for use in scientific computing.

Speaker Bio: I am a research associate in chemical engineering at Imperial. My research aims to develop software which couples discrete particle based methods to continuum grid based techniques on high performance computers. I first learnt MATLAB as an undergrad and over the last 7 years have taught and applied it extensivly to scientific simulation & post processing. My PhD work started with emphasis on low level programming in Fortran to maximise efficiency but over time has shifted to improving reusability for collaborative projects with version control. The shift to Python happened gradually (and somewhat grudgingly) over the last 4 years. Python is now completely established as a replacement for MATLAB in my work.


External Events

The following external events may be of interest to community members:

3rd CONFERENCE OF RESEARCH SOFTWARE ENGINEERS (RSE2018) - 3rd-4th SEPTEMBER 2018, BIRMINGHAM, UK
See http://rse.ac.uk/conf2018/ for more information.

COLLABORATIONS WORKSHOP 2018 (CW18) - 26th-28th MARCH 2018, CARDIFF, UK
See https://www.software.ac.uk/cw18 for more information.

2nd CONFERENCE OF RESEARCH SOFTWARE ENGINEERS (RSE2017) - 7th-8th SEPTEMBER 2017, MANCHESTER, UK
See http://rse.ac.uk/conf2017/ for more information.

SOFTWARE SUSTAINABILITY INSTITUTE COLLABORATIONS WORKSHOP 2017 - 27-29 MARCH 2017, LEEDS, UK
See https://www.software.ac.uk/cw17 for more information.