Archive for the ‘Scientific Software’ Category

March 29th, 2017

UK to launch 6 major HPC centres

Tomorrow, I’ll be attending the launch event for the UK’s new HPC centres and have been asked to deliver a short talk as part of the program. As someone who paddles in the shallow-end of the HPC pool I find this both flattering and more than a little terrifying. What can little-ole-me say to the national HPC glitterati that might be useful?

This blog post is an attempt at gathering my thoughts together for that talk.

The technology gap in research computing

Broadly speaking, my role in academia is to hang out with researchers, compute providers (cloud and HPC) and software vendors in an attempt to be vaguely useful in the area of research software. I’m a Research Software Engineer with a focus on Long Tail Science: The large number of very small research groups who do a huge amount of modern research.

Time and again, what I see can be summarized in this quote by Greg Wilsongwilson

This is very true in the world of High Performance Computing.

Geek Top Gear

I love technology and I love HPC in particular. I love to geek out on Flops, Ghz, SIMD instructions, GPUs, FPGAs…..all that stuff. I help support The University of Sheffield’s local HPC service and worked in Research IT at The University of Manchester for around a decade before moving to Sheffield.

I’ve given and seen many a HPC-related talk in my time and have certainly been guilty of delivering what I now refer to as the ‘Geek Top Gear’ speech.  For maximum effect, you need to do it in a Jeremy Clarkson voice and, if you’re feeling really macho, kiss your bicep at the point where you tell the audience how many Petaflops your system can do in Linpack.

*Begin Jeremy Clarkson Impression*

Our new HPC system has got 100,000 of the latest Intel Kaby Lake cores...which is a lot!

Usually running at 2.6Ghz, these cores can turbo-boost to 3.2Ghz for those moments when we need that extra boost of power. Obviously, being Kaby Lake, these cores have all the instruction extensions you’d expect with AVX2, FMA, SSE, ABM and many many other TLAs for all your SIMD needs. Of course every HPC system needs accelerators…..and we have the best of them: Xeon Phis with 68 cores each and NVIDIA GPUs with thousands of tiny little cores will handle every massively parallel job you can throw at them….Easily. We connect these many many cores together with high-speed interconnect fashioned from threads of pure unicorn hair and cool the whole thing with the tears of virigin nerds.

YEEEEEES! Our new HPC system is the best one since the last one and, achieving over a Gajillion Petaflops in the Linpack test (kiss bicep), it will change your life forever.

more_power

Any questions?

Audience member 1: What’s a core?
Audience member 2: Why does it run my R script slower than my laptop?
Audience member 3: Do you have Excel installed on it?

There is a huge gap between what many HPC providers like to focus on and what the typical long-tail researcher wants or needs. I propose that the best bridge for this gap is the Research Software Engineer (RSE).

Research Software Engineer as Alpine guide

In my fellowship proposal, I compared the role of a Research Software Engineer to that of an alpine guide:

Technological development in software is more like a cliff-face than a ladder – there are many routes to the top, to a solution. Further, the cliff face is dynamic – constantly and quickly changing as new technologies emerge and decline. Determining which technologies to deploy and how best to deploy them is in itself a specialist domain, with many features of traditional research.

Researchers need empowerment and training to give them confidence with the available equipment and the challenges they face. This role, akin to that of an Alpine guide, involves support, guidance, and load carrying. When optimally performed it results in a researcher who knows what challenges they can attack alone, and where they need appropriate support. Guides can help decide whether to exploit well-trodden paths or explore new possibilities as they navigate through this dynamic environment.

At Sheffield, we have built a pool of these Research Software Engineers to provide exactly this kind of support and it’s working extremely well so far. Not only are we helping individual research groups but we are also using our experiences in the field to help shape the University HPC environment in collaboration with the IT department.

Supercomputing: Irrelevant to many?

“Never bring an anecdote to a data-fight” so the saying goes and all I have from my own experiences are a bucket load of anecdotes, case studies and cursory log-mining experiments that indicate that even those who DO use HPC are not doing so effectively. Fortunately, others have stepped up to the plate and we have survey and interview data on how researchers are using compute resources.

How Do Scientists Develop and Use Scientific Software? is a report on a 2009 survey of 1972 researchers from around the world. They found that “79.9% of the scientists never use scientific software on a supercomputer

When I first learned of this number, I found it faintly depressing. This technology that I love so much and for which University IT departments dedicate special days to seems to be pretty much irrelevant to the majority of researchers. Could it be that even in an era of big data, machine learning and research software engineering that most people only need a laptop?

Only ever needing a laptop certainly doesn’t fit with what I’ve seen while working in the trenches. Almost every researcher I’ve met who does computational research wishes it was faster or that they had more memory to allow them to do larger problems. Speed is the easiest thing to sell to researchers in the world of RSE. They come for faster execution and leave with a side-order of version control, testing and documentation. A combination of software development and migration to even a small HPC system can easily result in 100x or even 1000x speed-ups for many researchers.

In my experience, it’s not that researchers don’t need HPC, it’s that the jump from their laptop-based workflow to one that makes good use of a HPC system is too large for them to bridge without a little help. Providing that help can result in some great partnerships such as the recent one between the Sheffield RSE group and the Sheffield Faculty of Arts and Humanities.

language

Want to know how that partnership started? I compiled an experimental R/Rcpp package that they were struggling with and then took them for coffee and said ‘That code took a while to run. Here’s how we can make it go faster….Now…what exactly are you doing because it looks cool?’ Fast forward a year or so and we are on the cusp of starting a great new project that will include traditional HPC and cloud computing as part of their R-based workflow.

My experiences seem to be reflected in the data. In  their 2011 article, A Survey of the Practice of Computational Science, Prabhu et al interviewed 114 randomly selected researchers from Princeton University. Princeton have a very strong, well supported HPC centre which provides both resources and the expertise to use them. Even at such a well equipped institution, the authors write that  ‘Despite enormous wait times, many scientists run their programs only on desktops’ although they did report much higher HPC usage compared to the Hanny et al survey.

Other salient quotes from the Prabhu interviews include

“only 18% of researchers who optimize code leveraged profiling tools to inform their optimization plans”

“only 7% of researchers leveraged any form of thread based shared memory CPU parallelism”

“Only 11% of researchers utilized loop based parallelism”

“Currently, many researchers fit their scientific models to only a subset of available parameters for faster program runs.”

“Across disciplines, an order of magnitude performance improvement was cited as a requirement for significant changes in research quality”

HPC: There’s plenty of room at the bottom

Potential users of HPC look different to those of 20 years ago. The popularity explosion of languages such as MATLAB, Python and R have democratized programming and the world is awash with inefficient research software. Most of the time, this lack of efficiency is not a problem (see ‘In defense of inefficient scientific code‘) but if a researcher needs to scale up what they are doing, it can become limiting. Researchers might wait for days for the results to come in and limit the scope of their investigations to fit the hardware they have access to — their laptop usually.

The paper of Prabu et al said that an order of magnitude (10x) speed up was cited by researchers as a requirement for significant changes in research quality. For an experienced Research Software Engineer with access to cloud or HPC facilities, a 10x speed-up is usually pretty easy to achieve for this new audience. 100x or even 1000x can be achieved fairly frequently if you employ multiple hardware and software techniques. Compared to squeezing out a few percent more performance from HPC-centric code such as LAPACK or CASTEP, it’s not even all that difficult. I recently sped up one researcher’s MATLAB code by a factor of 800x in a couple of days and I’m a fairly middling developer if I’m brutally honest.

The whole point of High Performance Computing is to accelerate science and right now there is more computational science around than there has ever been before. Furthermore, it’s easier than ever to accelerate! There’s plenty of room at the bottom.

Closing the computational gap with people, training and compute power

The UK’s 6 new HPC centers represent the cutting edge of hardware technology. They provide a crucial component of our national hardware infrastructure, will contribute to research in HPC itself and will doubtless be of huge benefit to computational science. Furthermore, all of the funded proposals include significant engagement with the national Research Software Engineering community – the vital bridge between many researchers and HPC.

Co-development of research software with effort from both RSEs and researchers can be an extremely powerful model. Combine this with further collaboration between RSEs and compute providers and we have an environment that I think is both very exciting and capable of helping to close the rich/poor compute divide.

As an RSE who works with both researchers and University-level HPC providers, I ask for 3 things to be considered by these new regional centres.

  • Enjoy your new compute-ferraris. I look forward to seeing how hard you can push them.
  • You will be learning new good practice in how to provide HPC services. Disseminate this to those of us running smaller services.
  • There’s plenty of room at the bottom! Help us to support the new wave of computational researchers.

Thanks to languages such as MATLAB, Python and R, general purpose programming has been fully democratized. I look forward to working with these new centres to help democratize high performance computing.

 

January 12th, 2017

If you are a researcher and are currently writing scripts or developing code then I have a suggestion for you. If you haven’t done it already, get yourself a willing volunteer and send them your code/analysis/simulation/voodoo and ask them to run it on their machine to see what happens. Bonus points are awarded for choosing someone who uses a different operating system from you!

This simple act is one of the things I recommend in my talk Is Your Research Software Correct and it can often help improve both code and workflow.

It quickly exposes patterns that are not good practice. For example, scattered references to ‘/home/walkingrandomly/mydata.dat’ suddenly don’t seem like a great idea when your code buddy is running windows. The ‘minimal tweaking’ required to move your analysis from your machine to theirs starts to feel a lot less minimal as you get to the bottom of the second page of instructions.

Crashy McCrashFace

When I start working with someone new, the first thing I ask them to do is to provide access to their code and simple script called runme or similar that will build and run their code and spit out an answer that we agree is OK. Many projects stumble at this hurdle! Perhaps my compiler is different to theirs and objects to their abuse (or otherwise) of the standards or maybe they’ve forgotten to include vital dependencies or input data.

Email ping-pong ensues as we attempt to get the latest version…zip files with names like PhD_code_ver1b_ForMike_withdata_fixed.zip get thrown about while everyone wonders where Bob is because he totally got it working on Windows back in 2009.

git clone

‘Hey Mike, just clone the git repo and run the test suite. It should be fine because the latest continuous integration run didn’t throw up any issues. The benchmark code and data we’d like you to optimise is in the benchmarks folder along with the timings and results from our most recent tests. Ignore the papers folder, that just reproduces all of the results from our recent papers and links to Zenodo DOIs’

‘…………’

‘Are you OK Mike?’

‘I’m…..fine. Just have something in my eye’

 

January 10th, 2017

I work at The University of Sheffield where I am one of the leaders of the new Research Software Engineering function. One of the things that my group does is help people make use of Sheffield’s High Performance Computing cluster, Iceberg.

Iceberg is a heterogenous system with around 3440 CPU cores and a sprinkling of GPUs. It’s been in use for several years and has been upgraded a few times over that period. It’s a very traditional HPC system that makes use of Linux and a variant of  Sun Grid Engine as the scheduler and had served us well.

iceberg

A while ago, the sysadmin pointed me to a goldmine of a resource — Iceberg’s accounting log. This 15 Gigabyte file contains information on every job submitted since July 2009. That’s more than 7 years of the HPC usage of 3249 users — over 46 million individual jobs.

The file format is very straightforward. There’s one line per job and each line consists of a set of colon separated fields.  The first few fields look like something like this:

long.q:node54.iceberg.shef.ac.uk:el:abc07de:

The username is field 4 and the number of slots used by the job is field 35. On our system, slots correspond to CPU cores. If you want to run a 16 core job, you ask for 16 slots.

With one line of awk, we can determine the maximum number of slots ever requested by each user.

gawk -F: '$35>=slots[$4] {slots[$4]=$35};END{for(n in slots){print n, slots[n]}}' accounting > ./users_max_slots.csv

As a quick check, I grepped the output file for my username and saw that the maximum number of cores I’d ever requested was 20. I ran a 32 core MPI ‘Hello World’ job, reran the line of awk and confirmed that my new maximum was 32 cores.

There are several ways I could have filtered the number of users but I was having awk lessons from David Jones so let’s create a new file containing the users who have only ever requested 1 slot.

gawk -F: '$35>=slots[$4] {slots[$4]=$35};END{for(n in slots){if(slots[n]==1){print n, slots[n]}}}' accounting > users_where_max_is_one_slot.csv

Running wc on these files allows us to determine how many users are in each group

wc users_max_slots.csv 

3250  6498 32706 users_max_slots.csv

One of those users turned out to be a blank line so 3249 usernames have been used on Iceberg over the last 7 years.

wc users_where_max_is_one_slot.csv 
2393  4786 23837 users_where_max_is_one_slot.csv

That is, 2393 of our 3249 users (just over 73%) over the last 7 years have only ever run 1 slot, and therefore 1 core, jobs.

High Performance?

So 73% of all users have only ever submitted single core jobs. This does not necessarily mean that they have not been making use of parallelism. For example, they might have been running job arrays – hundreds or thousands of single core jobs performing parameter sweeps or monte carlo simulations.

Maybe they were running parallel codes but only asked the scheduler for one core. In the early days this would have led to oversubscribed nodes, possibly up to 16 jobs, each trying to run 16 cores.These days, our sysadmin does some voodoo to ensure that jobs can only use the number of cores that have been requested, no matter how many threads their code is spawning. Either way, making this mistake is not great for performance.

Whatever is going on, this figure of 73% is surprising to me!

Thanks to David Jones for the awk lessons although if I’ve made a mistake, it’s all my fault!

Update (11th Jan 2017)

UCL’s Ian Kirker took a look at the usage of their general purpose cluster and found that 71.8% of their users have only ever run 1 core jobs. https://twitter.com/ikirker/status/819133966292807680

 

 

December 12th, 2016

I was in Stockholm last week to give an invited talk at the Workshop on Nordic Big Biomedical Data for Action. I was representing the Software Sustainability Institute and delivered the latest version of my talk Is Your Research Software Correct? screen-shot-2016-12-11-at-12-47-14

It was a great event which introduced me to some nice initiatives going on waaaay up north. Initiatives such as Code Refinery who’s aims align well with those of the UK’s software sustainability Institute. Code refinery was introduced by Radovan Bast — Slide deck at http://cicero.xyz/v2/remark/github/coderefinery/talk-intro/niasc-2016/talk.md/#1

coderefinery

Other talks included the introduction of a scalable, parallel version of BLAST, Big Data Processing for Genomics and Delivering Bioinformatics Software as Virtual Machine images. I also got chance to geek out with some High Performance Computing and Bioinformatics people over interesting Swedish food.

Slides from most of the talks are available at http://www.nordicehealth.se/2016/12/04/workshop-on-nordic-big-biomedical-data-for-action/

October 13th, 2016

I was recently invited to give a talk at the Sheffield R Users Group and decided to give a brief overview of how R relates to other technologies. Subjects included Mathematica’s integration of R, Intel’s compilers, Math Kernel Library and how they can make R faster and a range of Microsoft technologies including R Tools for Visual Studio, Microsoft R Open and the MRAN for reproducibility. I also touched upon the NAG Library, Maple’s code generation for R, GPUs and Spark.

Did I miss anything? If you were to give a similar talk, what might you have included?

September 5th, 2016

One of the great things about being a Research Software Engineer is the diversity of work you can get involved with. I specialise in smaller interventions which means that I can be working with physicists on Monday, engineers on Tuesday, geneticists on Wednesday….you get the idea.

Last month, I got to work with some Ecologists along with Anna Krystalli. We undertook the arduous journey from Sheffield down to Exeter to deliver talks and workshops at a post-conference symposium on reproducibility in science, organised by Malika Ihle and Isabel Winney, at the International Symposium on Behavioural Ecology.

I gave my talk, Is your research software correct?, and also delivered a workshop on using projects and version control using R and RStudio in the Code Cafe style. For the full write up of the day, see the excellent blog post by Anna over at the Mozilla Science Lab blog.

Updates : More resources

April 18th, 2016

The Engineering and Physical Sciences Research Council (EPSRC) is the UK’s main agency for funding research in engineering and the physical sciences. In 2015, they made a very unusual type of fellowship call – one that was targeted specifically at Research Software Engineers. This was the first fellowship of its kind in the world  and I believe it represents a strong commitment by EPSRC to the improvement of research software.

Research Software Engineers are the people behind research software. They make a huge contribution to science but often lack reward and recognition for the work that they do. This fellowship is a huge step in the right direction to providing some of that recognition. Quoting from the call document:

This call will support Research Software Engineer (RSE) Fellowships for a period of up to five years. The RSE Fellowship describes exceptional individuals with combined expertise in programming and a solid knowledge of the research environment. The Research Software Engineer works with researchers to gain an understanding of the problems they face, and then develops, maintains and extends software to provide the answers.

201 people responded to the call with an ‘Intent to submit’ outline application. Of these, 7 were successful. As part of my work with the EPSRC funded Research Software Engineering Network (RSE-N), I got in touch with the new cohort of RSE fellows and interviewed them about their projects and careers.

Follow the links below to see what they had to say.

April 18th, 2016

This interview with The University of Bristol’s Chrys Woods is part of my series of interviews on the new cohort of EPSRC Research Software Engineering Fellows.

Could you tell us a little about yourself and how you became a Research Software Engineer?

I have been coding since preschool when my Dad bought me a Texas Instruments TI-99/4A. This had a simple BASIC, but no tape or disk storage, meaning that all of the code was lost when the computer was switched off. After that, I had an Amiga as a teenager, and had fun coding little games in my spare time. I grew up in a seaside town on the East Coast, and the industry there was just fishing and making frozen food, so it didn’t occur to me that I could do programming as a job. It was just for fun. It was only when I went to University (Southampton) that I saw that programming could be useful for science. I undertook a 3rd-year computational chemistry research project with Jon Essex at Southampton, and from there I was hooked and wanted to become a computational chemist. In Jon’s group in the late 1990’s I helped to build Beowulf compute clusters from scratch (assembling shelves, doing all the cabling, building the cluster installer disks, job schedulers etc.), as well as developing lots of software in first Fortran 77 and then C++ and Python. From there, I moved to Bristol, and wrote lots of grant applications and managed to work for about 10 years on a series of EPSRC and BBSRC funded software development projects (sincere thanks to both funders for the grants). These all culminated in a framework for molecular simulation, called Sire (http://siremol.org), around which a reasonable community has formed (about 20+ people have developed the code over the years).

The experience of working with this community made me realise that software engineering was about helping other people develop and play with code. It showed me the importance of leading by example, e.g. adding in tests, using clean designs and APIs, and writing clear documentation (although I readily admit that I am a really bad documenter).

About 2 years ago I was offered a job in BrisSynBio (a BBSRC/EPSRC Synthetic Biology Research Centre), as a technical lead, systems administrator and RSE. I have really enjoyed this position, as it made me step back from my research and really work in “services” to support other researchers. This gave me a completely new perspective on research, as I saw the world from the view of e.g. administrators, finance, procurement and technical services. This showed me that successful research depends on a whole team of energised, committed and dedicated people, and that research software engineers can play an important role as part of the research development team.

What do you think is the role of a Research Software Engineer? Is it different from a ‘normal’ researcher?

For me, research software engineering is about helping junior researchers develop their code right the first time. Helping them to structure their code so that it is easier for them to write flexible, trustably correct and performance portable software without them having to be overburdened with learning a lot of computer science. Following this, good RSE work is helping researchers build flexible frameworks that allow researchers to play with their scientific ideas. The code should allow them to prototype and play with new ideas, to get them running quickly and efficiently first time without having to have people come and re-engineer everything later.

You’ve recently won an EPSRC RSE Fellowship – congratulations! Can you give a brief overview of your project?

My project is about providing a new member of a research team – the research software engineer. This will enable a new way of doing research. Research is team based, and I want to help change the culture so that RSEs are seen as a member of the research team and not a service. The EPSRC RSE project provides funding for me as an RSE to be embedded within research groups to work with them to develop new research. Twenty projects will initially be supported; 10 in the first wave that have been allocated, and then 10 that will be allocated in response to a call. The projects cover everything from modelling chemical reactions, designing new optical machines, creating great visualisations in an interactive 3D planetarium, modelling bacterial factories and engineering new scaffolds for future vaccines.

cwoods

How long did it take you to write your Fellowship application (Any other thoughts/advice on the application process?)

I found out about the call when on holiday in Switzerland from a friend. That got me started thinking about a model for how RSEs could be added to a research team. Once I’d worked out the model, I found the proposal to be very easy to write. Indeed, it was the opportunity to write the proposal that I had always wanted to write – to put software development and good software engineering front and centre in the proposal itself. When I got back from from holiday I alerted HPC users at Bristol about what I was planning, and then met up with researchers from across the University in 10 minute quick flash talks set out my proposal for RSE projects. People contributed projects quickly, and I was soon oversubscribed. Then, writing the proposal was just about putting it all down on paper.

The strangest part was that I had consciously left an academic role when I moved into BrisSynBio, and had accepted that I was never going to become “an academic”. The hardest part was talking with my wife and persuading her that I should go back into that world.

Where do you want to be in 5 years?

I want to be running a large and successful RSE group and contributing to the development of computational science/engineering as a complete discipline, i.e. being on the path to having departments with faculty, teaching of undergraduates in good software engineering best practice, researchers in software engineering, collaborating with scientists as parts of teams to develop the next generation of well-engineered code to support 21st century science. I also want to help inspire the next generation of potential RSEs and help (1) raise awareness that programming a computer can help you leave a seaside town and travel the world, and (2) maths, physics and programming are useful skills, that there is stable career pathway for scientific software developers and RSEs, that this is an exciting and dynamic career choice, it does let you work with intelligent and energetic people, and most importantly, it puts you in a position to shape how the technology of the future will be designed and developed.

Who are your project partners?

Cresset, a company that writes software for the pharmaceutical industry, and the Software Sustainability Institute. Also, all of the researchers who will be supported by the RSE projects.

Tell me about your RSE group.

We are now building the RSE group at Bristol. Currently it is me, a new junior RSE to be appointed, and some graduates on our new Graduate Accelerator Programme (GAP) who will be appointed later this year. We anticipate growing further over the next few years.

Which programming languages and technologies do you regularly use?

C++ is my favourite, especially the functional coding support in C++11/14, closely followed by Python. I find the combination of C++ and Python is extremely powerful. It allows easy writing of fast, performant parallel code in the C++ layer, yet retains flexibility in the scripting layer which treats C++ as a library of building blocks. All unit testing can be via Python scripts that stress these building blocks.

I teach a lot of python and strongly recommend it to newcomers, e.g. see http://chryswoods.com/main/courses.html

Are there any languages/technologies that you used to use a lot but have now moved away from? Why?

Fortran. I have a soft spot for F77, but it is very 20th century. It is missing modern containers, generics, templates, virtual functions, task based parallelism, easy wrapping with scripting languages, integration with unit testing suites, etc. etc. It is also missing easy handling of low-level memory, while also providing a high level memory interface.

Perl. I loved Perl. I teach Perl, but no-one comes any more. Python is better, and it is difficult to argue against. And then the Perl community turned in on itself in going from Perl 5 to Perl 6.

Is there anything on your ‘to-learn’ list?

Management. How to Teach. Any new programming paradigm. LLVM and stuff that bridges the gap between scripted and compiled languages. Anything else in the programming world that is cool.

And, MATLAB, R, etc., as I need to learn how to interface with the communities that use those tools.

Humility. We don’t always know what is best (even if we do think we are right).

Do you have any advice for anyone who wants to become a Research Software Engineer?

My advice applies to anyone who wants to work in a university as an academic. Never forget that each grant and each award is a gift from the public. You are not given this gift so that you are employed there forever. It is given so that, in some way, you can make a difference to society. Be in research because you want to make a difference. The counter to this, is that there is a life outside academia, and it is not a failure to move on to other roles. Sometimes, like my BrisSynBio position, they can make you stronger

For research software engineering, I would say learn to communicate with people. Being able to talk with people is just as important as being able to talk with the computer. Also, learn the paradigms of programming (structural, object, functional etc.), as once you get these, different computer languages are just different syntax. Finally, learn some maths and science. They may be harder to learn, but they are fundamental, and without understanding these, it is very hard to really appreciate the complexities of research code, or to see the potential optimisations or approximations that may be available.

April 18th, 2016

This interview with the University of Sheffield’s Paul Richmond is part of my series of interviews on the new cohort of EPSRC Research Software Engineering Fellows.

Could you tell us a little about yourself and how you became a Research Software Engineer?

I have been working as a Research Associate (early career research) since I completed my PhD in 2010. During this time I have been working on the fringe of both novel computer science research and the application of emerging parallel computing architectures to various areas of science and engineering. Whilst carving a reasonably successful career as an early career researcher it became clear that in order to progress within the academic environment it would require me to become more specialised in novel research than to participate in applying my skills of parallel computing to broader research domains. The role of the research software engineer is one that means different things to different people. For me it is the role of applying my specialist skills of parallel computing to a wide range of domains. It is a position which encourages the development of my novel research software (FLAME GPU) giving me the flexibility to embed it as broadly as possible.

What do you think is the role of a Research Software Engineer? Is it different from a ‘normal’ researcher?

To me the role of RSE is one which is about facilitating research. This can be through hands on help or the provision of software, skills or a community which provides a specific researching computing need. Having worked both as a researcher and in my new role as a self recognised RSE my view is that it is important that people are able to transcend the boundary between the two. Many RSEs come from support backgrounds rather than research however there are countless researchers who work on providing research software or multi-disciplinary research computing skills. I feel that researchers should be encouraged to move into the roles of RSEs where appropriate but also that this shouldn’t be seen as a career limiting move. RSEs should be free to transition back into academia as a when the research requests it. I hope to demonstrate throughout my position as a RSE Fellow that it is possible to exist alongside this boundary delivering typical academic outputs whilst working collaboratively in a facilitation role.

You’ve recently won an EPSRC RSE Fellowship – congratulations! Can you give a brief overview of your project?

My RSE Fellowship is all about changing the way people think about coding and the way in which they use workstation and HPC computing. In the future computers will be highly parallel with hugh numbers of cores, we are already seeing this pattern emerge today through accelerated computing in the form of GPUs. The traditional “serial” was of thinking needs to change and parallelism needs to be incorporated into computational research from the ground up to enable researchers to target future computing systems. To ensure that this happens my fellowship proposed 1) a combination of software and tools targeting many core architectures, 2) upskilling of researchers on a national scale and embedding of parallel programming techniques within the undergraduate, and postgraduate curriculums and 3) a local and national community in which researchers can receive software consultancy and work collaboratively to embed accelerated computing into their research. As a result of this fellowship researchers will gain access to unprecedented levels of compute performance enabling them utilise scalable computational approaches to solve scientific chand challenges.

prichmond

How long did it take you to write your Fellowship application (Any other thoughts/advice on the application process?)

The turnaround for the fellowship application was actually very quick. From consultation with colleagues it is normally expected that an EPSRC fellowship application should take about 6 months to complete, undergoing many rounds of internal review before submission. Following notification to continue to full submission (after expressions of interest) there was only just over a month and I had a weeks holiday booked the week before the final deadline… Trying to pick-up internet on holiday in Ireland, actually on Craggy Island (where Father Ted was filmed) was somewhat of a challenge. Fortunately every other applicant was in the same boat and I already had a good amount of material prepared on my ambitions for accelerated computing. Once through to the interview stage having a number of mock interviews helped tremendously in calming my nerves and polishing my pitch.

Who are your project partners?

NVIDIA, ARCHER, EPCC, OCR, ACRC, Oxford e-Science, WRG and N8, TRansport Systems Catapult, DNV.GL.

Bradford University, EPCC (Edinbugh), UCL, Oxford University

Tell me about your RSE group.

Sheffield has two EPSRC RSE fellows and we’ve teamed up to form the Sheffield Research Software Engineering group. We’ve only existed for a month! At the moment its just us but we have funds to recruit a few more people so watch this space.

Which programming languages and technologies do you regularly use?

It’s probably easier to list those that I don’t regularly use! My GOTO: languages are (get it? but seriously I don’t program with GOTO’s);

  • C
  • C++ (note not the same as above and should not be referred to as C/C++ #endrant)
  • CUDA
  • OpenMP/OpenACC/OpenGL
  • Assembly (ARM and PTX)
  • C++ extensions: e.g. Qt (for UI dev), Boost and C++11.

Other languages I use slightly less regularly are;

  • Python,
  • Java (if I have to, which I do especially for Eclipse plugins)
  • Fortran,
  • Javascript

Are there any languages/technologies that you used to use a lot but have now moved away from? Why?

I use java less and less now. It was taught on my undergraduate curriculum very heavily and at one point was the future for OpenGL on the web. There is just no need for java applets any more….

Is there anything on your ‘to-learn’ list?

Ohh yes. Vulkan is at the top of my list. As the successor to OpenGL for graphics with multi core support I look forward to integrating it with accelerated simulation models.

Do you have any advice for anyone who wants to become a Research Software Engineer?

Software underpins everything and is embedded within almost every research domain. Don’t let anyone tell you that there is no career progression for RSEs in academia. They (the research community) need us just as much as we need them and it’s up to you (and the collective us) to show the world how vital RSEs are in the academic environment.

April 18th, 2016

This interview with the University of Cambridges’s Chris Richardson is part of my series of interviews on the new cohort of EPSRC Research Software Engineering Fellows.

Could you tell us a little about yourself and how you became a Research Software Engineer?

I did a PhD in GeoPhysics, followed by a PostDoc in Japan, over 15 years ago. Although it was a numerical project (on transport of magma), it was rather frustrating to code in Fortran.

I might joke now, that I could solve some of my PhD problems in 5 minutes using some of the more modern tools that we are developing! Partly, that is because of the higher level of abstraction, and the offloading of more routine tasks to libraries.

When I finished my PostDoc, I decided to apply for a Computer Officer role, which I knew would involve some dull, standard IT support but it also came with interesting stuff… code, numerics etc., without the pressure of teaching, publishing and raising grants.

I have been involved with many different computational projects over the years, including calculating neutron diffraction of adsorbed monolayers (Chemistry), and dynamic geomorphology – how a landscape changes over time as a response to tectonics (Geophysics).

More recently, I started working with the FEniCS team, first via an EPSRC dCSE grant, administered by NAG. The idea of dCSE was to improve code for running on HPC systems – we needed to get better parallel I/O into FEniCS, so it was a perfect match. It was an opportunity for me to learn C++ and really get involved in some of the internal issues in parallel coding.

After the end of the project, I continued to work on FEniCS from time to time, and I gradually got accepted as a member of the core developer team. We applied for a (now rebranded) ECSE project and also some projects with commercial partners.

What do you think is the role of a Research Software Engineer? Is it different from a ‘normal’ researcher?

I suppose it depends what you mean by “normal”. Mostly, I would expect an RSE to work collaboratively with other scientists and engineers, and not to lead scientific projects themselves. So, whilst not being a PI on a project, they need to communicate effectively with the scientific team they are working with, provide the technical expertise to realise the computational aspects of the project, and have some scientific understanding too.

Ultimately, it is important to have something invested in a collaboration, so it is not just a service, but a personal involvement, which might result in a joint publication or another form of recognition. And that is not so different from many “normal” researchers below the PI level.

You’ve recently won an EPSRC RSE Fellowship – congratulations! Can you give a brief overview of your project?

I am part of a team, writing a finite element analysis library. Finite element analysis (FEA) goes way back to the early days of computing, and has been used by engineers for decades, because it is very good at modelling physics in arbitrary shaped objects. One of the problems of FEA is that it is tricky to program, so our library FEniCS takes care of some of the more difficult aspects, whilst allowing the user a great deal of flexibility in describing the equations or meshes to solve on.

I am extending FEniCS to use: (a) complex numbers – useful for wave-like phenomena, (b) powerful non-linear solvers, which can solve difficult problems more quickly, (c) curved boundaries – needed for interface problems, e.g. surface tension, and (d) dynamic meshes, which can change in geometry and topology over time.

As well as “just doing programming”, I want to engage with the scientific community to apply these techniques to actual physical problems, and form collaborations with domain scientists in their specialist areas. Ultimately, I want to build up a small RSE team who can help scientists across diverse fields to solve their computational problems, using FEniCS, or other relevant packages.

I also hope to be involved in teaching and training more sustainable practices in the scientific community, helping people to use revision control, and write more reusable code.

gear

How long did it take you to write your Fellowship application?

The EPSRC call was very widely advertised, and I received multiple emails about it. Since the first hurdle was small – only an A4 sheet – I decided to give it a go.

I guess it was a standard EPSRC call template, and things like – ‘Early career stage researcher’ seemed like a possible blocker, but the A4 sheet was accepted, so I made a full application, and the feedback from reviewers was very positive. Writing the full application was very stressful, and really a full-time occupation for a few weeks. I felt like someone who had an exam but hadn’t revised for it. Some friends said to me: “make it easy for the reviewers” – which is good advice. By closely reading the call documents, I tried to tick off as many points as possible, and make my application match the criteria as well as I could.

I was quite nervous for the interview, and I’m sure I said a few stupid things, but I don’t think that’s particularly unusual. Everyone at EPSRC was very friendly.

Who are your project partners?

I’ve got academic project partners at Southampton and Oxford Universities in the UK, as well as at Simula Research in Norway, and Rice University in the US. Industrial partners are BP and Melior Innovations.

Who are the users of FEniCS?

FEniCS has got a lot of users across the world, but in many ways, it is difficult to know who they are. We have many different distribution channels, so we can’t really monitor downloads. One estimate is the number of questions we get on the user forum. These have come from 50+ countries around the world, and average about two questions per day.

How long have you been involved?

I have been involved for about the last 5 years, gradually building up from being a user, to a part-time contributor, to core developer.

Do you find it it difficult to get recognition/ full time employment for your work?

I’m not sure if I get recognition, I suppose becoming an EPSRC fellow is recognition, and I usually do get included as an author on scientific papers. Recently we started issuing release FEniCS notes in Arch. Num. Soft., which is a way to get recognition for pure library development.

How many Fenics developers and which version control system do you use?

There are about half a dozen core contributors, mostly Europe-based, and we use “git” on bitbucket.org.

Tell me about your group.

I am in a small institute, with researchers from Earth Sciences, Chemistry, Chemical Engineering, Engineering and Applied Maths. I am the only RSE in the building, but we are on the West Cambridge campus, which includes the University High Performance Computing Service (HPCS), just across the road. I am working with Filippo Spiga from HPCS and his team. I also spend quite a lot of time at the Engineering Department, where one of the other FEniCS developers (Dr Garth Wells) is based.

What’s your plan for the future?

The head of the BP Institute is a professor in Earth Sciences, and he has always been very supportive. He sees my RSE fellowship as an opportunity to expand our RSE activities in the future. I want to help researchers write RSE time into their grant proposals, so we can collaborate on a wide range of projects, continuing after the period of the fellowship.

Which programming languages and technologies do you regularly use?

For serious coding, almost everything is in C++11 now. Some people complain that it is not good for scientific computing, but there are some excellent libraries, such as Eigen3 and boost::multi_array which provide highly optimised matrix algebra, and access to multi-dimensional arrays, in much the same way as Fortran or C.

  • Python is very useful for doing things quickly, and has really taken over almost entirely from shell scripting.
  • SWIG – a bit esoteric, but essential for wrapping C++ to Python.
  • Google tests. Atlassian Bamboo CI. Run tests inside docker inside Bamboo.
  • ParaView – really useful for visualisation.

What would we like? We have a user forum, based on q2a, but it would be much nicer if it had a “Stack Exchange” like interface. Maybe we should investigate using Area51.

Are there any languages/technologies that you used to use a lot but have now moved away from? Why?

  • Fortran. I know it’s still widely used, and there are modern versions, but I’m not going back.
  • Shell scripting. I mostly use Python instead now – it’s easier to understand.

Is there anything on your ‘to-learn’ list?

  • How to use Python in ParaView
  • How to write threaded code that is efficient for Finite Element
  • Using hybrid OpenMP/MPI
  • Intel Xeon Phi

Do you have any advice for anyone who wants to become a Research Software Engineer?

I think you need to be multi-skilled. You need to understand people – psychology and culture; programming – obviously; and have some basic understanding of the science itself, even if you don’t know all the details.