Surely the biggest difference is that you guys are mostly testing LLMs on simpler utilities, mostly involving higher-level languages, whereas ProgramBench are all very complex C programs (and much older programs with much more comprehensive test cases).
Eg cal is totally routine. I would expect most sophomores to be able to write a perfectly good cal. In fact the only program you tested which actually has anywhere close to the complexity of SQLite or FFmpeg is is Pkl, and it looks like Opus 4.6 totally failed.
I think your results are consistent. You're just measuring different things. Your benchmarks mostly tests LLMs ability to write technically routine programs of moderate length - yes the bioinformatics package involves specialized domain knowledge, but not specialized Go engineering. ProgramBench is harder.
Eg cal is totally routine. I would expect most sophomores to be able to write a perfectly good cal. In fact the only program you tested which actually has anywhere close to the complexity of SQLite or FFmpeg is is Pkl, and it looks like Opus 4.6 totally failed.
I think your results are consistent. You're just measuring different things. Your benchmarks mostly tests LLMs ability to write technically routine programs of moderate length - yes the bioinformatics package involves specialized domain knowledge, but not specialized Go engineering. ProgramBench is harder.