Software

This is a short story about performance, profiling and optimization. First, some backstory. For my current job I’m doing quantum chemical calculations on proteins. If this doesn’t mean anything to you, don’t worry, it’s not important for this article. However, this means that I’m working with data files that contain the structure of proteins a lot. The most popular file format is called PDB and the part of it that is interesting to me is the information about atoms, atom names, atom types, atom positions and so on....

Nowadays, I get the impression that most people realize how dependent we all are on the tech giants. Those few companies that are worth more than some countries and which shaped the internet of today to the point that, without them, most of it would simply break down. Most people also seem to know, at least to some degree, that companies like Google, Amazon and especially Facebook are not totally benign and do some pretty shady stuff with people’s data (to put it mildly)....

A while ago I decided to learn a new programming language. I don’t exactly remember why but I felt like I wanted to. There were two candidates I was interested in, Rust and Julia. A colleague of mine really loves Julia and I’ve read a bit about it so I was interested enough to give it a try. Also, it is heavily geared towards scientists and scientific computing including data science so it seemed like a natural thing for me to try....

I’m currently experiencing the pleasure of collaborating on an open source project with someone else on GitHub and I love doing it. There was an issue with runtime performance and we looked into it, discussed ideas and coded up several prototypic solutions (I admit mine were rather dirty). At one point I reviewed someone else’s pull request and wanted to add something to it. Sure, I can use the online editing features of GitHub but that doesn’t really tie in well with my code-writing workflow, not to mention that all the autocompletion, linting and inline compiler errors won’t be present....

I’ve recently realized something. My use of the Linux operating system and all it offers has been evolving in something of a wave-like pattern. When I started out, the first thing I tried was Linux Mint which is something a former Windows user might do as it works in a fairly familiar way. I quickly realized that I wanted to dive deeper and do more things than what Mint let me do easily....