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Re: parallel sort strangeness

From: Pádraig Brady
Subject: Re: parallel sort strangeness
Date: Thu, 28 Jul 2011 14:46:52 +0100
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:5.0) Gecko/20110707 Thunderbird/5.0

On 07/28/2011 01:16 PM, Jim Meyering wrote:
> For some reason, sort is now very slow here (Fedora 15, x86_64, with
> little free RAM), even for tiny inputs, but only some of the time,
> and not when I set OMP_NUM_THREADS=1.
> (I noticed because ./bootstrap was taking *forever*, traced it,
> which showed gnulib-tool taking all the time, then traced gnulib-tool,
> which showed slow sort -- it runs thousands of small ones.)
> time sh -c "printf 'a\nb\n'|LC_ALL=C sort | uniq -d"
> sh -c "printf 'a\nb\n'|LC_ALL=C sort | uniq -d"  0.00s user 3.18s system 98% 
> cpu 3.218 total
> $ time sh -c "printf 'a\nb\n'|LC_ALL=C sort | uniq -d"
> sh -c "printf 'a\nb\n'|LC_ALL=C sort | uniq -d"  0.01s user 39.90s system 99% 
> cpu 40.077 total
> $ time sh -c "printf 'a\nb\n'|LC_ALL=C sort | uniq -d"
> sh -c "printf 'a\nb\n'|LC_ALL=C sort | uniq -d"  0.00s user 5.65s system 99% 
> cpu 5.679 total
> $ time sh -c "printf 'a\nb\n'|LC_ALL=C sort | uniq -d"
> sh -c "printf 'a\nb\n'|LC_ALL=C sort | uniq -d"  0.00s user 34.16s system 13% 
> cpu 4:12.40 total
> Then I can run the very same command 40 times in a row, with it
> terminating in less than .3s total.
> Then once more and it takes 5 seconds.

Testing here (2 core, 4 threads) does show a large jump in time,
but only the first time I specified a large number of threads.

$ time sh -c "printf 'a\nb\n'|LC_ALL=C sort | uniq -d"

real    0m0.031s
user    0m0.015s
sys     0m0.012s

$ time sh -c "printf 'a\nb\n'|LC_ALL=C sort --parallel=100 | uniq -d"

real    0m2.095s
user    0m0.042s
sys     0m2.042s

$ time sh -c "printf 'a\nb\n'|LC_ALL=C sort --parallel=100 | uniq -d"

real    0m0.207s
user    0m0.050s
sys     0m0.157s

My first thought was memory usage which seems more likely as
more memory is used for the multithreaded case.  Also when
doing any perf testing with sort I now disable MALLOC_PERTURB_
considering what large buffers it allocates, otherwise that
would disable any lazy allocation that could be done.
I was half considering unsetting MALLOC_PERTURB_ for the
large buffer allocation internally in sort.

A wild guess on your 5s delay is, maybe that run caused
something to be swaped out. Maybe your swap is on a
mechanical disk which needed to be spun up?
It's unlikely related, but I've had particular issues with
kswapd0 spinning on F15, and I'm running a patched kernel
to fix the issue.

Could you repeat tests with a small -S or try the bootstrap
with MALLOC_PERTURB_ unset?


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