Here’s the Python code to run an arbitrary command returning its stdout data, or raise an exception on non-zero exit codes:
proc = subprocess.Popen(
    cmd,
    stderr=subprocess.STDOUT,  # Merge stdout and stderr
    stdout=subprocess.PIPE,
    shell=True)
communicate is used to wait for the process to exit:
stdoutdata, stderrdata = proc.communicate()
The subprocess module does not support timeout–ability to kill a process running for more than X number of seconds–therefore, communicate may take forever to run.
What is the simplest way to implement timeouts in a Python program meant to run on Windows and Linux?
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Answer
In Python 3.3+:
from subprocess import STDOUT, check_output output = check_output(cmd, stderr=STDOUT, timeout=seconds)
output is a byte string that contains command’s merged stdout, stderr data. 
check_output raises CalledProcessError on non-zero exit status as specified in the question’s text unlike proc.communicate() method.
I’ve removed shell=True because it is often used unnecessarily. You can  always add it back if cmd indeed requires it. If you add shell=True i.e., if the child process spawns its own descendants; check_output() can return much later than the timeout indicates, see Subprocess timeout failure.
The timeout feature is available on Python 2.x via the subprocess32 backport of the 3.2+ subprocess module.