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Imperial College London have released their Covid-19 epidemic simulation

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Re: Imperial College London have released their Covid-19 epidemic simulation

#31

Post by cataphract »

abainbridge wrote: post #7

This code is great fun. Start here to explore the horror: https://github.com/mrc-ide/covid-sim/blob/master/src/CovidSi... I like the way InitModel() crashes (I think) if a global pointer called bmh (short for bitmap header) isn't first initialized by calling InitBMHead() from Bitmap.cpp. I guess it's obvious to academics with giant brains that InitModel() depends on a bitmap existing. But it gets worse - the pointer…

I've seen a lot of code coming out of academia that exhibits a similar complete lack of structure and completely ignores the most basic software development best practices (such as having tests). There are exceptions, and research software engineers are a thing, but unsurprisingly most academics focus their careers on the science rather than the code.

Re: Imperial College London have released their Covid-19 epidemic simulation

#33

Post by Johnjonjoan »

devit wrote: post #27

Is this thing actually being used for policy decisions? Given the complexity, poor language/framework choice (should have used either Rust or Tensorflow), bad code design, and unclear determination of the parameters (especially the fact they don't seem to be estimated from real data with Bayesian inference, or if they are they didn't release that), as well as the ludicrous CPU and RAM usage making it impossible for m…

Metawards is also being used.

https://github.com/ldanon/MetaWards

Re: Imperial College London have released their Covid-19 epidemic simulation

#34

Post by mytailorisrich »

cataphract wrote: post #31
abainbridge wrote: post #7

This code is great fun. Start here to explore the horror: https://github.com/mrc-ide/covid-sim/blob/master/src/CovidSi... I like the way InitModel() crashes (I think) if a global pointer called bmh (short for bitmap header) isn't first initialized by calling InitBMHead() from Bitmap.cpp. I guess it's obvious to academics with giant brains that InitModel() depends on a bitmap existing. But it gets worse - the pointer…

I've seen a lot of code coming out of academia that exhibits a similar complete lack of structure and completely ignores the most basic software development best practices (such as having tests). There are exceptions, and research software engineers are a thing, but unsurprisingly most academics focus their careers on the science rather than the code.

Sometimes those people found a startup company, come up with a 'prototype', and are lucky enough to be acquired.

Then, you end up having to turn this 'style' of code into a product and to maintain it...

Re: Imperial College London have released their Covid-19 epidemic simulation

#35

Post by renewiltord »

te_chris wrote: post #16
lbeltrame wrote: post #10

Some people have raised issues with the model[1][2], or rather, the software implementation of it. There's also a (flagged) submission on HN discussing this[3] referencing [1]. [1] (warning: possibly partisan link) https://lockdownsceptics.org/code-review-of-fergusons-model/ [2] https://github.com/mrc-ide/covid-sim/issues/165 [3] https://news.ycombinator.com/item?id=23099212

That issue is unhelpful. Yes, no good tests, but how about suggesting ways it can actually be improved? Why are devs such bores when it comes to things like this? They have released the model, review it and suggest improvements! Don't grandstand "We, the undersigned etc etc" as if that's going to help improve the codebase in the slightest. Carmack is OK with it, he's put his name to reviewing it. That's not to excuse…

Carmack has different motivations. He has nothing to prove and simplistically looks to make things better. You can tell in his appearance on Joe Rogan.

Most HN users are just publicly preening. It's like a Mechanical Turk GPT2. I actually doubt they can write code.

Re: Imperial College London have released their Covid-19 epidemic simulation

#36

Post by mshook »

tasogare wrote: post #21
mshook wrote: post #14

Earlier quoted context omitted.

Just argument parsing makes my eyes bleed... https://github.com/mrc-ide/covid-sim/blob/master/src/CovidSi... That stuff is priceless: else if (argv[i][1] == 'C' && argv[i][2] == 'L' && argv[i][3] == 'P' && argv[i][4] == '1' && argv[i][5] == ':') I guess string comparisons are complicated. I also fail to see why they used ':' as the separator and why they didn't use a proper library to parse argv...

Because when you have only a very limited number of arguments it’s easier to do it that way than selecting a lib, adding it to the project, reading the doc, trying it and integrating it for real. I add the issue in C#, and after trying 2 or 3 libs (including one by Microsoft) I just gave up.

I hear you but in their case they have more than 130 LOC to parse ARGV. Doing all that manually hurts both code readability and maintainability.

Re: Imperial College London have released their Covid-19 epidemic simulation

#37

Post by heisenzombie »

cataphract wrote: post #31
abainbridge wrote: post #7

This code is great fun. Start here to explore the horror: https://github.com/mrc-ide/covid-sim/blob/master/src/CovidSi... I like the way InitModel() crashes (I think) if a global pointer called bmh (short for bitmap header) isn't first initialized by calling InitBMHead() from Bitmap.cpp. I guess it's obvious to academics with giant brains that InitModel() depends on a bitmap existing. But it gets worse - the pointer…

I've seen a lot of code coming out of academia that exhibits a similar complete lack of structure and completely ignores the most basic software development best practices (such as having tests). There are exceptions, and research software engineers are a thing, but unsurprisingly most academics focus their careers on the science rather than the code.

It’s the same reason that if you go into a working Physics laboratory, most things will seem to be wrapped in kitchen aluminium foil. There’s better ways of making thermal insulation, EMF shielding, grounding, dust protection... but the foil is /right there/ and the experiment only really needs to work /once/

Re: Imperial College London have released their Covid-19 epidemic simulation

#38

Post by lbeltrame »

cataphract wrote: post #31
abainbridge wrote: post #7

This code is great fun. Start here to explore the horror: https://github.com/mrc-ide/covid-sim/blob/master/src/CovidSi... I like the way InitModel() crashes (I think) if a global pointer called bmh (short for bitmap header) isn't first initialized by calling InitBMHead() from Bitmap.cpp. I guess it's obvious to academics with giant brains that InitModel() depends on a bitmap existing. But it gets worse - the pointer…

I've seen a lot of code coming out of academia that exhibits a similar complete lack of structure and completely ignores the most basic software development best practices (such as having tests). There are exceptions, and research software engineers are a thing, but unsurprisingly most academics focus their careers on the science rather than the code.

I once had to debug a crash in a very popular program used in genomics (for those in the know, it was an early version of "samtools" IIRC) and I found it really hard to read.

(In the end the crash was due to corrupted input data, so I fixed the data and stopped debugging)

Re: Imperial College London have released their Covid-19 epidemic simulation

#39

Post by OJFord »

howd00 wrote: post #12
asplake wrote: post #2

Alumnus here, it’s Imperial College, London. It is a university (in its own right), but always goes by that name.

Only since 2007. Uni of London before that for 100 years. Used to play them at sports as part of the ULU league.

No, Imperial's royal charter (what's needed to be 'a university' and award degrees in your own right) dates to 1907. I believe that's true of most of UoL's constituents, just not the smaller ones perhaps like SOAS or other field-focused colleges.

Re: Imperial College London have released their Covid-19 epidemic simulation

#40

Post by Gibbon1 »

heisenzombie wrote: post #37
cataphract wrote: post #31

Earlier quoted context omitted.

I've seen a lot of code coming out of academia that exhibits a similar complete lack of structure and completely ignores the most basic software development best practices (such as having tests). There are exceptions, and research software engineers are a thing, but unsurprisingly most academics focus their careers on the science rather than the code.

It’s the same reason that if you go into a working Physics laboratory, most things will seem to be wrapped in kitchen aluminium foil. There’s better ways of making thermal insulation, EMF shielding, grounding, dust protection... but the foil is /right there/ and the experiment only really needs to work /once/

In physics labs everything is wrapped in foil because they use heat tape to bake the shit of it.
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