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Explaining to BBC Newsnight some of the problems with the CRU code

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Re: Explaining to BBC Newsnight some of the problems with the CRU code

#21

Post by pmjordan »

Silhouette wrote: post #18
tome wrote: post #12

Earlier quoted context omitted.

I'm talking from my experience of attending the most highly regarded mathematics undergraduate programme in the UK. There was basic programming training, but the emphasis was on the "basic". There was absolutely no emphasis placed on writing maintainable code. We (in fact "they": I didn't attend the classes) were simply taught some technical details of C. In fact I think the number of hours of teaching time was singl…

> I'm talking from my experience of attending the most highly regarded mathematics undergraduate programme in the UK. That's a bold claim. Which undergraduate programme would that be, and by whom is it the most highly regarded in the UK?

I don't know which university the parent is referring to, but I can confirm that this was also the situation at the University of York, a top-10 UK university, at least at the time. (90%+ were people who hadn't quite made it into the top 2 - hence nicknames of "University of Dork" and "University of Oxford/Cambridge Rejects")

The problem existed not only mathematics, where I ended up giving extra programming classes to friends because the teaching was practically non-existant. Also physics along with the computer simulation and theoretical branches of physics, which I happened to be studying. In fact, we were only taught rudimentary Fortran (!) syntax, and laughably, OpenMP and MPI later on. Nobody who made it through the course alive did so without having either learned to program earlier or investing a large amount of time in self-study and then "winging it" - after all, the final project depended on being able to deliver a simulation of whatever physical system was being investigated.

I started programming when I was 10, so I had no trouble; together with a colleague who had a similar programming history as I, we introduced the rest of our year to basic good programming practices and workflows (split your functionality into stand-alone functions and files; use version control; avoid global variables; the merits of code reviews; etc.). A lot of people had already switched to experimental physics before we started doing this. Obviously, expecting people to understand concurrent programming at that level is pretty dangerous. In my experience, this sort of attitude breeds a view that computer programs are magical things, and once they compile and don't crash or hang, you can trust their results. This exact attitude is what I'm reminded of when I read about this CRU incident.

I don't think any of the staff ever took the issue seriously, though. Even if they weren't prepared to teach it, they should have told everyone to teach themselves over the holidays and provide exercises or whatever. At no point did anyone point out that programming was a difficult craft, and that mastery of it would be expected.

For context to those unfamiliar with the majority of UK science degree programmes: they are typically not as modular or flexible as in other countries. If you failed a module, you had one chance to re-sit the exam a few weeks later. There was no option of re-taking the module including lectures during the next term/semester; each term had a pre-assigned set of modules, there was no flexibility in when they could be taken, so you couldn't defer your concurrency project until you'd taken some more programming classes or so.

Re: Explaining to BBC Newsnight some of the problems with the CRU code

#22

Post by cdavid »

This has to be the stupidest critic I have seen yet on this whole thing. In particular, complaining that the code is not commercial quality is laughable.

Most of the scientific code is awful, in climate science and elsewhere, because the constraints are totally different than commercial code. Maintainability is not so much a concern, and it is only a tool to obtain a result, not an end in itself. People don't care about the code quality most of the time.

There is another concern, which is that you rarely know what you exactly want when programming for research. You don't always have the time to design reasonable API, because the requirements keep changing - and keep in mind that you cannot spend too much time on this because you have to write papers, do some actual research, etc...

Even in my field, which is engineering and where people are expected to be more "programming methods-aware", most of the code is awful. My own code for research is awfully bad compared to what I release as open source for scientific programming: when I release something, I easily spend several times as much work on the thing, because of documentation issues, etc... Doing this for all my code is simply not possible.

If you want to dismiss climate science because of code quality, be ready to throw away the majority of science, from biology to IA through EE. Just look at lapack code: the code is awful, using goto to avoid structured programming, etc... (e.g. http://www.netlib.org/lapack/double/dsgesv.f). And it is used by 99 % of code which does linear algebra, including commercial software.

Re: Explaining to BBC Newsnight some of the problems with the CRU code

#23

Post by AndrewO »

cdavid wrote: post #22

This has to be the stupidest critic I have seen yet on this whole thing. In particular, complaining that the code is not commercial quality is laughable. Most of the scientific code is awful, in climate science and elsewhere, because the constraints are totally different than commercial code. Maintainability is not so much a concern, and it is only a tool to obtain a result, not an end in itself. People don't care ab…

That's a pretty cavalier attitude to have when so much depends on the results (and I mean research programming in general, not just the CRU case). Maintainability may not be a concern, but verifiability certainly should be.

Re: Explaining to BBC Newsnight some of the problems with the CRU code

#24

Post by cdavid »

AndrewO wrote: post #23
cdavid wrote: post #22

This has to be the stupidest critic I have seen yet on this whole thing. In particular, complaining that the code is not commercial quality is laughable. Most of the scientific code is awful, in climate science and elsewhere, because the constraints are totally different than commercial code. Maintainability is not so much a concern, and it is only a tool to obtain a result, not an end in itself. People don't care ab…

That's a pretty cavalier attitude to have when so much depends on the results (and I mean research programming in general, not just the CRU case). Maintainability may not be a concern, but verifiability certainly should be.

Verifiability in science is not a matter of having one program checked by different people. The reality is much more complex than that. This so called climate-gate says more about the perception of research than climate science (although it has certainly became a PR-nightmare for climate science). I think it is just another case of people have an idealistic, out of reality knowledge of how science works. Verifiability is less a concern than most people meant it to be for research. In an ideal world, it should be, but it isn't how science has been done - I would argue it has never been the case.

Scientists are actually very conservative for most parts exactly for this reason: in practice, it is just not possible to rely on consistent repeatability, etc... When you have an established, widely shared view on a topic, it takes great leaps to break it. Most research is not done to break the consensus, but to reenforce it. That's why today, if you want to show that climate is not caused by human activity, you will need to present data which are not as good as the ones one has now, but which are much, much better. So it is most likely true that if you want grants, etc... the easy way, going along the consensus is the right path.

That may not be how people think science should be done, but that's how it is done in practice in my experience. I think that for most researchers, all this affair sounds like a storm in a teapot. The behavior may look shady at times, the experiment is not always great, but that's exactly why for a new consensus to be created, you need to have better proof than the existing consensus. And yes, politics come into play, yes a lot of it is mean and some of it is not ethical. But this does not invalidate science in general - it invalidates how people think science works.

Re: Explaining to BBC Newsnight some of the problems with the CRU code

#25

Post by cdavid »

AndrewO wrote: post #23
cdavid wrote: post #22

This has to be the stupidest critic I have seen yet on this whole thing. In particular, complaining that the code is not commercial quality is laughable. Most of the scientific code is awful, in climate science and elsewhere, because the constraints are totally different than commercial code. Maintainability is not so much a concern, and it is only a tool to obtain a result, not an end in itself. People don't care ab…

That's a pretty cavalier attitude to have when so much depends on the results (and I mean research programming in general, not just the CRU case). Maintainability may not be a concern, but verifiability certainly should be.

Concerning the practical issue of repeatability, that's why most fields require a new fact to be independently repeated by several people. At last year Scientific Python Conference, A. Martelli made an interesting point about verifiable software: the best way to know for sure if your software gives the right answer is to have several, different implementation done by different people. He gave the example of the space shuttle, which has several independent systems with a vote in case they don't agree (wikipedia has some information on it:http://en.wikipedia.org/wiki/Space_Shuttle#Flight_systems).

Re: Explaining to BBC Newsnight some of the problems with the CRU code

#26

Post by jamii »

tome wrote: post #12
Silhouette wrote: post #5

Earlier quoted context omitted.

> Mathematicians and scientists have no formal training in programming (at least in the UK). They're expected just to pick it up and get on with it. That's an unreasonable generalisation. For one thing, many university courses in science and mathematics do seem to incorporate basic programming training these days, either as part of the course, or via other facilities that the university makes available to those takin…

I'm talking from my experience of attending the most highly regarded mathematics undergraduate programme in the UK. There was basic programming training, but the emphasis was on the "basic". There was absolutely no emphasis placed on writing maintainable code. We (in fact "they": I didn't attend the classes) were simply taught some technical details of C. In fact I think the number of hours of teaching time was singl…

During my maths BA I took:

Foundation of computer science

Data structures and algorithms (SML)

Software engineering (Java)

Operating systems (C)

Numerical algorithms (C++)

as well as yearly catam projects: http://www.maths.cam.ac.uk/undergrad/catam/

There were also optional classes in bioinformatics and computational statistics and a number of lecturers encouraged the use of programming in solving weekly problem sheets.

I would estimate at least a third of my year-group were fairly competent programmers come graduation.

Re: Explaining to BBC Newsnight some of the problems with the CRU code

#27

Post by tome »

jamii wrote: post #26
tome wrote: post #12

Earlier quoted context omitted.

I'm talking from my experience of attending the most highly regarded mathematics undergraduate programme in the UK. There was basic programming training, but the emphasis was on the "basic". There was absolutely no emphasis placed on writing maintainable code. We (in fact "they": I didn't attend the classes) were simply taught some technical details of C. In fact I think the number of hours of teaching time was singl…

During my maths BA I took: Foundation of computer science Data structures and algorithms (SML) Software engineering (Java) Operating systems (C) Numerical algorithms (C++) as well as yearly catam projects: http://www.maths.cam.ac.uk/undergrad/catam/ There were also optional classes in bioinformatics and computational statistics and a number of lecturers encouraged the use of programming in solving weekly problem shee…

I don't know when you took it, but that's not possible today unless you do the Mathematics with Computer Science option, which most Maths undergraduates do not, and certainly not the ones who are more into the applied side of things and are likely to end up in climate research.

Re: Explaining to BBC Newsnight some of the problems with the CRU code

#28

Post by tome »

pmjordan wrote: post #21
Silhouette wrote: post #18

Earlier quoted context omitted.

> I'm talking from my experience of attending the most highly regarded mathematics undergraduate programme in the UK. That's a bold claim. Which undergraduate programme would that be, and by whom is it the most highly regarded in the UK?

I don't know which university the parent is referring to, but I can confirm that this was also the situation at the University of York, a top-10 UK university, at least at the time. (90%+ were people who hadn't quite made it into the top 2 - hence nicknames of "University of Dork" and "University of Oxford/Cambridge Rejects") The problem existed not only mathematics, where I ended up giving extra programming classes…

split your functionality into stand-alone functions and files; use version control; avoid global variables; the merits of code reviews

Yes, these are exactly the kinds of things I'm talking about that I have not seen taught in undergraduate mathematics programmes, but they are vital to writing good quality scientific code.

At no point did anyone point out that programming was a difficult craft, and that mastery of it would be expected

Not only difficult, but even experienced programmers introduce serious bugs by accident. Often they find them because they do extensive testing! This is not done to such a degree for scientific code.

Re: Explaining to BBC Newsnight some of the problems with the CRU code

#29

Post by jamii »

tome wrote: post #27
jamii wrote: post #26

Earlier quoted context omitted.

During my maths BA I took: Foundation of computer science Data structures and algorithms (SML) Software engineering (Java) Operating systems (C) Numerical algorithms (C++) as well as yearly catam projects: http://www.maths.cam.ac.uk/undergrad/catam/ There were also optional classes in bioinformatics and computational statistics and a number of lecturers encouraged the use of programming in solving weekly problem shee…

I don't know when you took it, but that's not possible today unless you do the Mathematics with Computer Science option, which most Maths undergraduates do not, and certainly not the ones who are more into the applied side of things and are likely to end up in climate research.

That's unfortunate. Given the nature of modern applied maths it seems like that should be the preferred route.

Re: Explaining to BBC Newsnight some of the problems with the CRU code

#30

Post by tome »

jamii wrote: post #29
tome wrote: post #27

Earlier quoted context omitted.

I don't know when you took it, but that's not possible today unless you do the Mathematics with Computer Science option, which most Maths undergraduates do not, and certainly not the ones who are more into the applied side of things and are likely to end up in climate research.

That's unfortunate. Given the nature of modern applied maths it seems like that should be the preferred route.

Quite right. Understandably the applied maths department wants to give a rigorous theoretical training, but rigorous programming training ought to be given at some point before research starts.
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