RE: Hyperthreading problem with IRQ handling and scheduling
Thanks for your reply. I will bring this to the attention of the system
administrator (I have root access but I don't think they'll appreciate me
installing a new kernel on my own).
I've just discovered that a similar issue can also occur with pure compute
tasks (no I/O at all). If I run 8 of those in parallel, some of them will
run on logical CPUs of the same physical CPU, and those are slower than the
ones that get a physical CPU to themselves. Since there are enough physical
CPUs available, I don't believe the scheduler should do this. Hopefully
upgrading the kernel will resolve this as well.
From: Stan Hoeppner [mailto:firstname.lastname@example.org]
Sent: vrijdag 4 maart 2011 16:10
Subject: Re: Hyperthreading problem with IRQ handling and scheduling
Sven Groot put forth on 3/3/2011 11:28 PM:
> I am using a cluster of machines running Debian 5.0.4, kernel
> 2.6.26-2-amd64. These machines have dual Intel Xeon E5530 2.4GHz CPUs,
> which are quad-core CPUs with hyperthreading. So that means each
> machine has 8 physical CPUs and a total of 16 logical CPUs.
> I have run into an apparent issue with the kernel scheduler. Under the
> circumstances described below, the scheduler will run two tasks on two
> logical CPUs of the same physical CPU, even if all the remaining
> physical CPUs are idle. This obviously causes a large slowdown for these
First, you're running Debian kernel 2.6.26 which, IIRC, doesn't have all the
scheduler patches required for both mutli-core and HT support, or simply
doesn't have them all enabled, which is the cause of your problem. The
following must all be set. You need a new kernel.
1. Install the latest Debian prepackaged lenny-backport kernel on each
cluster node: linux-image-2.6.32-bpo.5-amd64_2.6.32-30~bpo50+1_i386.deb
If the nodes don't have direct internet access, preventing installation via
apt-get or aptitude, then download the .deb package, copy it to each machine
via scp/ftp/nfs/etc, and install it via dpkg:
I've never installed a backport package directly via dpkg. You may need an
additional switch or two. Others here can answer this.
2. Download the 220.127.116.11 vanilla source from:
Follow the build instructions here:
to create a kernel image with the options and modules you need, and none you
don't, and to create a kernel deb package. Copy the .deb to each cluster
node and perform:
dpkg -i /full/path/to/linux-image-18.104.22.168-custom.1.0_amd64.deb
Second, you may want to ask about this on lkml as well, as far more
expertise in this area of the kernel resides there. Installing a new kernel
will solve the bulk of your problem. To fine tune the performance per
core/thread afterward you'll need assistance from kernel devs on lkml.
Hope this points you in the right direction.
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