Set timeout for GPMC in Python

Currently we use call gpmc in python by subprocess and use communicate to set TIMEOUT
p = popen("GPMC/bin/gpmc")
try:
    p.communicate(timeout = TIMEOUT)
except subprocess.TimeoutExpired:
    p.terminate()

But it does not always succeed because of some bugs in subprocess.

We should use the parameter in gpmc:  -cpu-lim 

