[R-sig-hpc] foreach + doMC not fully parallel?
scionforbai at gmail.com
Tue Aug 31 13:16:01 CEST 2010
> I did a reboot and %dopar% started working fully again. I then did
> suspend/resume and the problem came back.
> Linux 2.6.32-24-generic #38 SMP Mon Jul 26 15:08:51 EDT 2010 x86_64 GNU/Linux
Yes, looks like the scheduler is confused after resume. In the
not-fully-loaded-cores scenario, do you see maybe a high CPU usage by
process like 'ksoftirqd' or 'kthreadd' (high can be also just 4-5%)?
If this is true, this is hardly a kernel problem (you are using the
most uptodate LongTimeSupport kernel, which is actually overtested).
The origin of this problem can be a daemon or some other
hardware-dealing software (audio? video - like ati-nvidia-compiz?
bluetooth? ethernet/wifi?) that doesn't get restarted properly after
suspend and clog the scheduler with a lot of soft-irq. I observed such
behavior for example with the license managers for matlab or eclipse,
and this with a more recent kernel. Try to use powertop and see if you
have a big difference in interrupts between both scenarios, and take a
note in your logs for error messages after resume and the list of
processes actually running after a fresh boot and after a resume. It
should point out (maybe) which resource blocks your scheduler.
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