Why am I seeing weird “symbol not found” errors while trying to import mdtraj?
Let me guess – you’re using a Linux cluster running CentOS 5? Your system compiler is gcc 4.1?
You need a more recent version of gcc (>= 4.4). You can set the CC and CXX environment variables to point to a different compiler.
Unfortunately, installing from conda will not help you here. You must compile from source on CentOS 5 (or similar).
For Pande lab members on vsp-compute, set the following environment variables and compile from source
$ export CC=gcc44 $ export CXX=g++44 $ python setup.py install