Part of a series addressing the challenges of a mutual first contact. Previous question here
Humans meet some distant alien species. They are mutual first contacts. After learning the languages of each other, they begin to share scientific and engineering knowledge with one another, but here's the problem: given our separate lines of evolution and scientific development, we have different systems of units, computer architectures, character encodings, names for the same mathematical concepts, mathematical notation (including default numeric base), etc...
x86 has arisen as the de-facto standard of computer architecture. It's complicated. Really complicated. Yet many architectures support emulating at least a subset of x86. Outside of that, we've settled on binary, 8 bits per byte, IEEE floating point numbers, two's complement integers, big-endian network transmission, UTF-8 strings, and a ton of network protocols, file formats, and programming languages.
Add on top of that having to coordinate character encodings between the two civilizations (assuming both have something as unwieldy and complicated as Unicode due to a broad diversity of cultures)
These are very real challenges that we would face if we wanted to connect our internets, for instance.
Computer architecture is not particularly daunting with compilers targeting the alien machines, though some difficulties arise from the different assumptions made about computer architecture. What is fast on a human computer might be painfully slow on an alien computer and vice-versa. What produces an accurate result on a human computer might be off by a small but deadly amount if run on an alien computer because of differences in sub-integral implementations. What runs without errors might crash an alien computer. This ultimately isn't a problem we haven't faced before. Given enough time, one race's architecture will likely win out over the other.
Networks and encodings are a much bigger struggle. We either need to create translation layers between two protocols or create new protocols that both civilizations understand and use. Do we use two different encodings or do we combine them into a super unicode? Should we make room for future races?
How do two interstellar civilizations come to unify their computer technology?