[Beowulf] Re: Tracing down 250ms open/chdir calls

Trond Myklebust trond.myklebust at fys.uio.no
Mon Feb 16 07:56:38 EST 2009


On Mon, 2009-02-16 at 08:55 +0100, Carsten Aulbert wrote:
> Hi all,
> 
> sorry in advance for this vague subject and also the vague email, I'm
> trying my best to summarize the problem:
> 
> On our large cluster we sometimes encounter the problem that our main
> scheduling processes are often in state D and in the end not capable
> anymore of pushing work to the cluster.
> 
> The head nodes are 8 core boxes with Xeon CPUs and equipped with 16 GB
> of memory, when certain types of jobs are running we see system loads of
> about 20-30 which might go up to 80-100 from time to time. Looking at
> the individual cores they are mostly busy with system tasks (e.g. htop
> shows 'red' bars).
> 
> stat -tt -c showed that several system calls of the scheduler take a
> long time to complete, most notably open and chdir which took between
> 180 and 230ms to complete (during our testing). Since most of these open
> and chdir are via NFSv3 I'm including that list as well. The NFS servers
> are Sun Fire X4500 boxes running Solaris 10u5 right now.
> 
> A standard output line looks like:
> 93.37   38.997264     230753      169    78      open
> 
> i.e. 93.37% of the system-related time was spend in 169 successful open
> calls which took 230753us/call, thus 39 wall clock seconds were spend in
> a minute just doing open.
> 
> We tried several things to understand the problem, but apart from moving
> more files (mostly log files of currently running jobs) off NFS we did
> not move far ahead so far. On
> https://n0.aei.uni-hannover.de/twiki/bin/view/ATLAS/H2Problems
> we have summarized some things.
> 
> With the help of 'stress' and a tiny program just doing open/putc/close
> into a single file, I've tried to get a feeling how good or bad things
> are when compared to other head nodes with different tasks/loads:
> 
> https://n0.aei.uni-hannover.de/twiki/bin/view/ATLAS/OpenCloseIotest
> 
> (this test may or may not help in the long run, I'm just poking into the
> dark).
> 
> Now my questions:
> 
> * Do you have any suggestions how to continue debugging this problem?
> * Does anyone know how to improve the situation? Next on my agenda would
> be to try different IO algorithms, any hints which ones should be good
> for such boxes?
> * I guess I missed vital information. please let me know if you need
> more information of the system
> 
> Please Cc me from linux-kernel, I'm only on the other two addressed lists.
> 
> Cheers and a lot of TIA
> 
> Carsten

2.6.27.7 has a known NFS client performance bug due to a change in the
authentication code. The fix was merged in 2.6.27.9: see the commit
http://git.kernel.org/?p=linux/kernel/git/stable/linux-2.6.27.y.git&a=commitdiff&h=a0f04d0096bd7edb543576c55f7a0993628f924a

Cheers
  Trond

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