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RE: Job Processing Was RE: Parallel Merge

From: Nathan Watson-Haigh
Subject: RE: Job Processing Was RE: Parallel Merge
Date: Wed, 24 Aug 2011 11:36:42 +0930


Nathan Watson-Haigh
Senior Bioinformatician | The Australian Wine Research Institute
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-----Original Message-----
> From: [] On Behalf Of
> Tange
> Sent: Tuesday, 23 August 2011 6:06 PM
> To: Nathan Watson-Haigh
> Cc:
> Subject: Re: Job Processing Was RE: Parallel Merge
> On Tue, Aug 23, 2011 at 8:38 AM, Nathan Watson-Haigh
> <> wrote:
> > Hi Ole,
> >
> > I'm in the middle of optimising the processing of such file. While
> I'm at it I have a quick question:
> >
> > I'm processing my input file with -N 2500 as it seems to give me the
> best processing time. My CPU usage and disk IO are well below their
> maximum capacity
> I often face this problem aswell. Starting more processes normally
> solves the problem for me. I believe the issue is that while the disk
> I/O is below maximum capacity on average, there are spikes where it is
> over capacity (e.g. every time it has to seek). During theses spikes
> the CPU is waiting for data to process. By having more processes
> running than processors the "extra" processes can buffer up some input
> which can then be processed when there is idle CPU time.
> So: Try starting twice as many processes (-j 200%).

I'm about to try this out, but you comments raised a couple of questions
for me:

Does this introduces the concept of a queue length vs the number of
processes that can be run at any one time? Are there options for
specifying these separately so I could specify only a subset of
available cores to be used, but still have parallel buffer up the extra
input in the way that you say?

> Low throughput on disks can also be due to disk seeks.  Until recently
> I did not know of a tool that could detect disk seeks, but I have now
> found iostat. The '%util' column is very useful to see how busy the
> disk is:

This could be the issue as my raid array is only running at approx 10%
throughput while parallel is running.

>   iostat -xd 1

This isn't showing anything on my system at the moment, but I'll have a
look into it.

> Using -N indicates that your processing program can take more than one
> argument. If the startup time for the processing program is large, try
> using -X to distribute all the arguments amongst the processes.
> > and wondered how GNU parallel processes/submits new jobs as others
> are completed? I'm thinking that GNU parallel is somehow stalling my
> pipeline. Could you provide some information on this aspect of GNU
> parallel?
> GNU Parallel's main loop (drain_job_queue) is basically one big sleep.
> It gets woken up by a child dying. When a child dies GNU Parallel
> prints out stdout and stderr for that child and a new child is
> spawned. Then GNU Parallel sleeps again.
> /Ole

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