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Having all the source code in one file
An early, and supposedly influential, analysis of the Coronavirus outbreak was based on results from a model whose 15,000 line C implementation was contained in a single file. There has been lots of tut-tutting from the peanut gallery, about the code all being in one file rather than distributed over many files. The source on Github has been heavily reworked.
Why do programmers work with all the code in one file, rather than split across multiple files? What are the costs and benefits of having the 15K of source in one file, compared to distributing it across multiple files?
There are two kinds of people who work with code all in one file, novices and really capable developers. Richard Stallman is an example of a very capable developer who worked using files containing huge amounts of code, as anybody who looked at the early sources of gcc will be all to familiar.
The benefit of having all the code in one file is that it is easy to find stuff and make global changes. If the source is scattered over multiple files, then working on the code entails knowing which file to look in to find whatever; there is a learning curve (these days screens have lots of pixels, and editors support multiple windows with a different file in each window; I’m sure lots of readers work like this).
Many years ago, when 64K was a lot of memory, I sometimes had to do developer support: people would come to me complaining that the computer was preventing them writing a larger program. What had happened was they had hit the capacity limit of the editor. The source now had to be spread over multiple files to get over this ‘limitation’. In practice people experienced the benefits of using multiple files, e.g., editor loading files faster (because they were a lot smaller) and reduced program build time (because only the code that changed needed to be recompiled).
These days, 15K of source can be loaded or compiled in a blink of an eye (unless a really cheap laptop is being used). Computing power has significantly reduced these benefits that used to exist.
What costs might be associated with keeping all the source in one file?
Monolithic code makes sharing difficult. I don’t know anything about the development environment within which these researched worked. If there were lots of different programs using the same algorithms, or reading/writing the same file formats, then code reuse often provides a benefit that makes it worthwhile splitting off the common functionality. But then the researchers has to learn how to build a program from multiple source files, which a surprising number are unwilling to do (at least it has always been surprising to me).
Within a research group, sharing across researchers might be a possible (assuming they are making some use of the same algorithms and file formats). Involving multiple people in the ongoing evolution of software creates a need for some coordination. At the individual level it may be more cost-efficient for people to have their own private copies of the source, with savings only occurring at the group level. With software development having a low status in academia, I don’t see any of the senior researchers willingly take on a management role, for this code. Perhaps one of the people working on the code is much better than the others (it often happens), but are they going to volunteer themselves as chief dogs body for the code?
In the world of Open Source, where source code is available, cut-and-paste is rampant (along with wholesale copying of files). Working with a copy of somebody else’s source removes a dependency, and if their code works well enough, then go for it.
A cost often claimed by the peanut gallery is that having all the code in a single file is a signal of buggy code. Given that most of the programmers who do this are novices, rather than really capable developers, such code is likely to contain many mistakes. But splitting the code up into multiple files will not reduce the number of mistakes it contains, just distribute them among the files. Correlation is not causation.
For an individual developer, the main benefit of splitting code across multiple files is that it makes developers think about the structure of their code.
For multi-person projects there are the added potential benefits of reusing code, and reducing the time spent reading other people’s code (it’s no fun having to deal with 10K lines when only a few functions are of interest).
I’m not saying that the original code is good, bad, or indifferent. What I am saying is that the having all the source in one file may, or may not, be the most effective way of working. It’s complicated, and I have no problem going with the flow (and limiting the size of the source files I write), but let’s not criticise others for doing what works for them.
Comments on the COVID-19 model source code from Imperial
At the end of March a paper modelling the impact of various scenarios on the spread of COVID-19 infections, by the MRC Centre for Global Infectious Disease Analysis at Imperial College, appears to have influenced the policy of the powers that be. This group recently started publishing their modelling code on GitHub (good for them).
Most of my professional life has been spent analyzing other peoples’ code, for one reason or another (mostly Fortran, then Pascal, and then C). I had heard that the Imperial software was written in C, but the released code is written in R (as of six hours ago, there is the start of a Python version). Ok, I can work with R, but my comments will be general, since I don’t have lots of in depth experience reading R code.
The code comes from a research context, and is evolving, i.e., some amount of messiness is to be expected.
There is not a lot of code to talk about (248 lines setting things up, 111 lines for a Stan model, 371 lines of plotting code, and 85 lines of utility code). The analysis is performed by creating a model using the Stan statistical inference language (in which the high level structure of the problem is specified, compiled to a lower level form and then run; the Stan language is very similar to R). These days, lots of problems are coded using a relatively small number of lines that call fancy libraries to do the heavy lifting. It is becoming rare to have to write tens of thousands of lines of code to solve a problem.
I have two points to make about the code, all designed to reduce the likelihood of mistakes being made by the person working on the source. These points mainly apply to the Stan code, because that is where the important stuff happens, but are equally applicable to all code.
- Numeric literals are embedded in the code, values include:
2.4,1.0,0.5,0.03,1e-5, and1e-9. These values obviously mean something to the person who wrote the code, and they can probably be interpreted by experts in the spread of virus infections. But why are they scattered about the code, rather than appearing together (as a sequence of assignments to variables with meaningful names)? Having all the constants in one place makes it easier to spot when a mistake has been made, e.g., one value has been changed without a corresponding change in another value; it also makes it easier for people new to the code to figure out what is going on, - when commenting out code, make it very obvious, e.g., have
/**********************on its own line, and*****************************/on its own line. Using just/*and*/makes it easy to miss that code has been commented out.
Why have they started a Python implementation? Perhaps somebody on the team is more comfortable working with Python (when deadlines loom, it is always best to go with what you know).
Having both an R and Python version is good, in that coding mistakes are likely to show up as inconsistencies in the results produced. It’s always good to have the output of two independently written programs to compare (apart from the fact it may cost twice as much).
The README mentions performance issues. I imagine that most of the execution time is spent in the Stan code, so R vs. Python is not a performance issue.
Any reader with expertise tuning Stan models for performance might like to check out the code. I’m sure the Imperial folk would be happy to hear about worthwhile speed-ups.
Update
The R source code of the EuroMOMO model, which aims to “… explain number of deaths by a baseline, influenza activity and extreme ambient temperature.”
Coronavirus: a silver lining for evidence-based software engineering?
People rarely measure things in software engineering, and when they do they rarely hang onto the measurements; this might also be true in many other work disciplines.
When I worked on optimizing compilers, I used to spend time comparing code size and performance. It surprised me that many others in the field did not, they seemed to think that if they implemented an optimization, things would get better and that was it. Customers would buy optimizers without knowing how long their programs took to do a task, they seemed to want things to go faster, and they had some money to spend buying stuff to make them feel that things had gotten faster. I quickly learned to stop asking too many questions, like “how fast does your code currently run”, or “how fast would you like it to run”. Sell them something to make them feel better, don’t spoil things by pointing out that their code might already be fast enough.
In one very embarrassing incident, the potential customer was interested in measuring performance, and my optimizer make their important program go slower! As best I could tell, the size of the existing code just fitted in memory, and optimizing for performance made it larger; the system started thrashing and went a lot slower.
What question did potential customers ask? They usually asked whether particular optimizations were implemented (because they had read about them someplace). Now some of these optimizations were likely to make very little difference to performance, but they were easy to understand and short enough to write articles about. And, yes. I always made sure to implement these ‘minor’ optimizations purely to keep customers happy (and increase the chances of making a sale).
Now I work on evidence-based software engineering, and developers rarely measure things, and when they do they rarely hang onto the measurements. So many people have said I could have their data, if they had it!
Will the Coronavirus change things? With everybody working from home, management won’t be able to walk up to developers and ask what they have been doing. Perhaps stuff will start getting recorded more often, and some of it might be kept.
A year from now it might be a lot easier to find information about what developers do. I will let you know next year.
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