Answering my own question here, but for the sake of it... adding:
os.chdir(newpath)
makes it all work... so we have:
def run_cmd(cmd):
"""RUN A BASH CMD"""
import subprocess as sub
p = sub.Popen(['/bin/bash', '-c', cmd],
stdout=sub.PIPE, stderr=sub.STDOUT)
output = urllib.unquote(p.stdout.read())
return output
newpath='/path/to/program/directory'
os.chdir(newpath)
cmd=os.path.join(newpath,'a.out')
output=run_cmd(cmd);
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