Python memory allocation error using subprocess.Popen

Question

I am doing some bioinformatics work. I have a python script that at one point calls a program to do an expensive process (sequence alignment..uses a lot of computational pow

Answer 1

This doesn't have anything to do with Python or the subprocess module. subprocess.Popen is merely reporting to you the error that it is receiving from the operating system. (What operating system are you using, by the way?) From man 2 fork on Linux:

ENOMEM    fork()  failed  to  allocate  the  necessary  kernel  structures
          because memory is tight.

Are you calling subprocess.Popen multiple times? If so then I think the best you can do is make sure that the previous invocation of your process is terminated and reaped before the next invocation.