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I have some problems with my system performance. As I was adviced here, I used sar:

$sar -u 5

and found out that the problems are caused by a low HDD performance, as I supposed (high %iowait).

My disk is Western Digital AV-25, WDC WD5000BUDT-63G8FY0. Vendor specification can be found here.

/etc/fstab:

# <file system>        <dir>         <type>    <options>          <dump> <pass>
devpts                 /dev/pts      devpts    defaults            0      0
shm                    /dev/shm      tmpfs     nodev,nosuid        0      0
/dev/sda2 / ext4 defaults,noatime,data=writeback,barrier=0,nobh,errors=remount-ro 0 1
/dev/sda3 /home ext4 defaults,noatime,data=writeback,barrier=0,nobh,errors=remount-ro 0 1
/dev/sda4 swap swap defaults 0 0

The problem is that from time to time some application (Minecraft game, Chromium browser, Eclipse) hangs up, my processor activity LED turns on, iowait goes to some 50% or more (I have dual core processor) and stays like this for a couple of seconds. Similar things happen when I use applications for the first time after reboot. The worst situation ever was forcing the system to use the swap partition (by some stress tool), the system went unusable.

What can i do now to determine the exact cause of the performance problems? Is it the low hardware performance, some problems with linux io scheduler, application specific problems or something else?

EDIT:

Output of hdparm -t -T /dev/sda under no load:

/dev/sda:
 Timing cached reads:   6244 MB in  2.00 seconds = 3129.13 MB/sec
 Timing buffered disk reads: 230 MB in  3.01 seconds =  76.33 MB/sec
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1  
What is the output of hdparm -t -T /dev/sda? –  David Schwartz Nov 3 '11 at 22:17
    
David Schwartz: I added it as an edit –  Dadam Nov 3 '11 at 22:47
    
Doesn't look slow enough to be a PIO/DMA setting problem. –  ConcernedOfTunbridgeWells Nov 4 '11 at 15:01
    
Are there no related errors in /var/log/messages or does smart report something unusual? –  Nils Nov 7 '11 at 21:12
    
/var/log/log/messages shows nothing, smart output doesn't change –  Dadam Nov 8 '11 at 9:36

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