First of all thanks for your attention. My question is how to reduce the execution time of my code.

Here is the relevant code. The below code is called in iteration from the main.

def call_prism(prism_input_file,random_length):
   prism_output_file = "path.txt"
   cmd = "prism %s -simpath %d %s" % (prism_input_file,random_length,prism_output_file)
   p = os.popen(cmd)
   p.close()
   return prism_output_file


def main(prism_input_file, number_of_strings):
...
  for n in range(number_of_strings):
        prism_output_file = call_prism(prism_input_file,z[n])
        ...

  return

I used statistics from the "profile statistics browser" when I profiled my code. The "file close" system command took the maximum time (14.546 seconds). The call_prism routine is called 10 times. But the number_of_strings is usually in thousands, so, my program takes lot of time to complete.

Let me know if you need more information. By the way I tried with subprocess, too. Thanks.