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    <p>That's not quite how pipelining works... but to put your mind to ease, here's an excerpt from the <a href="http://docs.python.org/library/subprocess.html#subprocess.Popen" rel="nofollow">subprocess documentation</a>:</p> <blockquote> <p>stdin, stdout and stderr specify the executed programs’ standard input, standard output and standard error file handles, respectively. Valid values are PIPE, an existing file descriptor (a positive integer), an existing file object, and None. PIPE indicates that a <strong>new pipe</strong> to the child should be created. With None, no redirection will occur; the child’s file handles will be inherited from the parent.</p> </blockquote> <p>The likeliest areas at fault would be in the communication with the main process or in your management of the semaphore. Maybe state transitions / synchronization are not proceeding as expected due to a bug? I suggest debugging by adding logging/print statements before &amp; after each blocking call - where you're communicating with the main process and where you acquire/release the semaphore to narrow down where things have gone wrong.</p> <p>Also I'm curious - is the semaphore absolutely necessary?</p>
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    1. POpython multiprocessing each with own subprocess (Kubuntu,Mac)
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    1. COThanks for the reply! So even though I reference /dev/stdin & /dev/stdout multiple times, each process gets their own instance of it, and there's no chance of them confusing one another?? Sweet! Looking further into the errors after killing (^C) the program, it seems the dead-lock arises with a multiprocessing.Queue. I've got a series of them which I picture as having a cascade, or knock-on effect by sending 'endSEQ', and finally 'STOP'. It took long enough to debug last month with one process. Trying to get my head back around it now, :( And I don't think the semaphore is necessary. Gone :)
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    2. COnp! The /dev/stdin & /dev/stdout files map to the special stdin & stdout file descriptors, so they don't represent a central device. --- I don't see use of the Queue in the align_seq child process, is it only used in the main process? If so, then you can just use queue.Queue. Also you say you suspect a deadlock - you're not consuming bidirectionally are you (main & child/ren)?
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    3. COThanks again for clarifying stdin /stdout. Now I think about it, kind of obvious in the way that I use them, but I've never seen it explicitly stated before. You're absolutely right; the Queue's are in a separate part of the program, which is where my deadlocks seem to appear. I'll update the main post because there's a lot more multiprocessing to the program I didn't originally state... Gonna reply to the below posts first though. I've got it now so that sometimes it finishes, and sometimes it breaks right near the end, which I guess is due to latency(??). time.sleep is my temp, dirty fix
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