Why am I seeing an error message about my CPU and SSE 4.1?:
RuntimeError: This CPU does not support the required instruction set (SSE4.1)
Some functions in MDTraj require specific CPU features (and compiler support for them) to enable faster performance.
Let me guess – you’re using a Linux cluster running CentOS 5? Your system compiler is gcc 4.1?
It’s likely your machine actually DOES support SSE4.1 instructions, but your compiler is too old (e.g. gcc 4.1, released over 8 years ago) to emit them. Try installing MDTraj from the prebuilt conda packages, or getting a more modern compiler. (When building MDTraj from source, you can set the CC environment variable to point to a different compiler.)
For Pande lab members on vsp-compute, set the environment variable CC to gcc44, and then recompile from source
$ cd path-to-mdtraj/
$ export CC=gcc44
$ python setup.py install