Especially in HPC there are lots of workloads that do not benefit from SMT. Such workloads are almost always bottlenecked on either memory bandwidth or vector execution ports. These are exactly the resources that are shared between the sibling threads.

So now you have a choice of either disabling SMT in the bios, or make sure the application correctly interprets the CPU topology and only spawns one thread per physical core. The former is often the easier option, both from software development and system administration perspective.