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Best Practices for Scientific Computing

20 points| punchagan | 13 years ago |arxiv.org | reply

10 comments

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[+] johnx123-up|13 years ago|reply
Recent version is v2 http://arxiv.org/abs/1210.0530v2

Summary:

  1. Write programs for people, not computers.
  2. Automate repetitive tasks.
  3. Use the computer to record history.
  4. Make incremental changes.
  5. Use version control.
  6. Don’t repeat yourself (or others).
  7. Plan for mistakes.
  8. Optimize software only after it works correctly.
  9. Document design and purpose, not mechanics.
  10. Conduct code reviews.
[+] akashshah|13 years ago|reply
This sounds like best plans for computing in general, not just scientific computing
[+] simgidacav|13 years ago|reply
Very good points (indeed, I totally agree on each and every of them!), but there's the risk that someone writing a software just for sake of the task will just argue «I'm not interested in doing this, but in the task».

This is exactly what happens for many users when you suggest them to install GNU/Linux and enjoy freedom. They say: «I don't want to learn another OS. I just use the computer to get things done». Then they'll keep using Excel.

[+] pif|13 years ago|reply
> there's the risk that someone writing a software just for sake of the task will just argue ...

It's not a risk, it's a certainty! That's why the the last point is about conducting reviews.

[+] zerostar07|13 years ago|reply
In practice, scientific software is always work-in-progress in general, people who write it are in many cases novices and software remains unattended after the results have been published. Although scientists should learn to write good programs, we shouldn't expect them to write the best software; a lot of science is not engineering.
[+] pfortuny|13 years ago|reply
Honestly,

I shall never understand why a work like this (useful and to the point) needs a 'Conclusion' section. There are no conclusions, just a list of practices.

I know this is an absurd rant but can we stop this nonsense?

Conclusion: please stop concluding something which is not an argumentation.

[+] merijnv|13 years ago|reply
Because scientists are aggressively selective in what they read (you have to be, given the volume of text produced) and skip large parts of the paper to see if they're interesting. A very common paper reading approach is:

  1. Read abstract. Interesting? Go to 2, else stop reading.
  2. Read introduction. Still interesting? Go to 3, else stop reading.
  3. Read conclusion. Still interesting? Read the rest of the paper, else stop reading.
The conclusion is there to summarise everything and let people decide whether they want to bother reading the entire thing.