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To software engineers criticizing Neil Ferguson’s epidemics simulation code

blog.khinsen.net

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Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#61

Post by moron4hire »

lucideer wrote: post #43
silveraxe93 wrote: post #14

I disagree so strongly with this that I had a visceral reaction while reading it. C++ is a tool, not an end product. If you're not qualified to use a tool correctly it's not the manufacturer's fault, it's yours. Why do so many people believe that good software development is not part of their job? If you write code then you're a developer, no matter your job title. If you write shit software, saying you're a research…

This is such a ridiculous comment I don't know where to start. Are you actually proposing that being a fully experienced & knowledgeable software engineer should be a base requirement for all academic research (in any field)? If you, working as a software engineer, were told tomorrow by your manager that you needed to perform heart surgery, and that that now fell under your responsibilities in your current role, woul…

No, your analogy is definitely the most ridiculous thing here.

Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#62

Post by pjc50 »

klenwell wrote: post #22
flankstaek wrote: post #12

This letter feels as though it is overlooking a large point of contention. >The scientists who wrote this horrible code most probably had no training in software engineering, and no funding to hire software engineers Shouldn't the argument be, that for research that is reliant on coding models, funding be allocated to experts that can assist in creating said models (software engineers)?

The conclusions from the first critical code review cited: All papers based on this code should be retracted immediately. Imperial’s modelling efforts should be reset with a new team that isn’t under Professor Ferguson, and which has a commitment to replicable results with published code from day one. On a personal level, I’d go further and suggest that all academic epidemiology be defunded. This sort of work is best…

That's the most biased opinion imaginable by an astroturf group. There's no information on who they are, but the article currently on their front page is by Toby Young, who is a Spectator/Quillete guy and to be found backing almost all stupid ideas within British politics. https://www.spectator.co.uk/article/This-lockdown-may-kill-m...

Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#63

Post by zaphar »

chasd00 wrote: post #25

they need to defer to the experts of software development. I, as a software engineer, wouldn't try to design an epidemic model, i would defer to experts. Epidemic experts shouldn't be writing the implementation of their model, they should defer to the experts. Also, "It’s you, the software engineering community, that is responsible for tools like C++ that look as if they were designed for shooting yourself in the foo…

The lathe is almost guaranteed to come with a long list of warnings and an entire section of the manual devoted to safe use. Learn C++ resources tend to not come with those sections in the same detail nor are they usually front and center.

Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#64

Post by pbourke »

lucideer wrote: post #43
silveraxe93 wrote: post #14

I disagree so strongly with this that I had a visceral reaction while reading it. C++ is a tool, not an end product. If you're not qualified to use a tool correctly it's not the manufacturer's fault, it's yours. Why do so many people believe that good software development is not part of their job? If you write code then you're a developer, no matter your job title. If you write shit software, saying you're a research…

This is such a ridiculous comment I don't know where to start. Are you actually proposing that being a fully experienced & knowledgeable software engineer should be a base requirement for all academic research (in any field)? If you, working as a software engineer, were told tomorrow by your manager that you needed to perform heart surgery, and that that now fell under your responsibilities in your current role, woul…

> Funding dictates this is impossible, so they make do.

Put another way: software quality is not valued in academia. Let’s say the code in question was in great shape. Would it have mattered at all in the trajectory of anyone’s career? No. This is probably the one academic code base in a million that has received any negative reputational hit due to its quality.

Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#65

Post by zozbot234 »

silveraxe93 wrote: post #14

I disagree so strongly with this that I had a visceral reaction while reading it. C++ is a tool, not an end product. If you're not qualified to use a tool correctly it's not the manufacturer's fault, it's yours. Why do so many people believe that good software development is not part of their job? If you write code then you're a developer, no matter your job title. If you write shit software, saying you're a research…

Some tools are inherently safer than others. The whole difference between C++ and Rust is that it's a bit harder to shoot yourself in the foot while using Rust, the way you can with C++. It's not that you can't do it, but generally it involves purposely bypassing its safety mechanisms. You're still supposed to know what you're doing, but you know where you need to pay attention.

Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#66

Post by w0utert »

llarsson wrote: post #6

Not a comment on the specific repo in question, but I just want to note that I have seen utter monstrosities of academic code written in Python, MATLAB, and R - languages that are ostensibly "easier" than C++. I so not think that poor code quality is due to the many footguns C++ admittedly gives you. I am sure that the main research is not in the implemented code. But with unclear code, it is exceedingly hard to know…

Exactly. The C++ code in the GitHub repo is absolutely frightening, but I'm 100% sure if would be pretty much the same in e.g. Python, probaly even worse. From my own experience code quality is inversely related to barrier of entry, which means I see a lot more terrible MATLAB and Python code than terrible C++ code.

The only conclusion you can draw from a repo like this, is the conclusion I've drawn countless times when the next piece of modeling code developed by some math or physics expert lands on my desk: these kinds of things can not be developed by domain experts alone, you always need to include skilled software engineers to translate the prototypes they develop (preferably in something like MATLAB) into production code.

Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#67

Post by Joeboy »

lern_too_spel wrote: post #37
klenwell wrote: post #22

Earlier quoted context omitted.

The conclusions from the first critical code review cited: All papers based on this code should be retracted immediately. Imperial’s modelling efforts should be reset with a new team that isn’t under Professor Ferguson, and which has a commitment to replicable results with published code from day one. On a personal level, I’d go further and suggest that all academic epidemiology be defunded. This sort of work is best…

That was a shitty code review. Seeding issues like the ones cited don't affect the results of a Monte Carlo simulation, and there are tests in the repo, just not automated ones. The section you quoted shows the reason for the review's sloppiness. The reviewer set out to find a way to justify their own beliefs instead of to actually read the code.

> That was a shitty code review

Damn straight. The only sense in which it was not a shitty code review, is that it didn't actually review any code. Looking into the linked tickets is a time consuming faff, but people should actually do it before taking the blog post at face value.

Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#68

Post by jstewartmobile »

With all due respect, Konrad can go f himself. Plenty of performant, non-foot-gun, alternatives to C++ these days. The choice of that language, and any abuses of it fall entirely upon Ferguson and his team.

And for this nugget:

“It’s also you, the software engineering community, that has made no effort to warn the non-expert public of the dangers of these tools.”

I say he deserves it without lube. Hardly a day goes by on Lobsters or HN where we (including many C++ devs) don’t complain at great length on what a reeking dumpster fire C++ is.

Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#69

Post by silveraxe93 »

lucideer wrote: post #43
silveraxe93 wrote: post #14

I disagree so strongly with this that I had a visceral reaction while reading it. C++ is a tool, not an end product. If you're not qualified to use a tool correctly it's not the manufacturer's fault, it's yours. Why do so many people believe that good software development is not part of their job? If you write code then you're a developer, no matter your job title. If you write shit software, saying you're a research…

This is such a ridiculous comment I don't know where to start. Are you actually proposing that being a fully experienced & knowledgeable software engineer should be a base requirement for all academic research (in any field)? If you, working as a software engineer, were told tomorrow by your manager that you needed to perform heart surgery, and that that now fell under your responsibilities in your current role, woul…

Where in my comment did you see me proposing that "being a fully experienced & knowledgeable software engineer should be a base requirement for all academic research (in any field)"

Go back and re-read it please. I'm saying you need to be capable of using the tools for your job.

If I was working as a software engineer, I'd not be asked to perform heart surgery. A more realistic example would be a software engineer being tasked to develop software in the medical industry, where I would expect them to understand the subject matter enough to ascertain their software is not crap.

Re: To software engineers criticizing Neil Ferguson’s epidemics simulation code

#70

Post by scarmig »

ptheywood wrote: post #5
htk wrote: post #3

I get what he’s saying, but the “non-experts” using code to represent their models should also let outside help come when the need arises. When your model predicts an apocalyptical scenario and government is taking drastic measures based on it, it’s a good time to expose your “non-expert code” to the software engineering communities (and all other associated fields) to take a look.

This is starting to happen through Research Software Engineers, although as it is still a (relatively) new movement within academia. https://society-rse.org/ https://www.software.ac.uk/

I looked at the job vacancies posted on the Society for Research Software Engineering. Those with salaries listed:

Senior RSE, London: £35,965 to £52,701

Web Application Developer, London: £35,965 to £43,470

Research Software Engineer, Hannover: Salary Scale 13 TV-L (AFAICT this is €41259 to €59545)

I'm the type to be happy to take a pay cut, especially if there are work-life advantages involved. But a 80%-90% cut is asking a bit much. It's not like London's a particularly cheap place to live, either.

Not sure how to fix it.

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