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I have a system that is a few years old that is running Fedora 7 (I know, it's old too). Now I have PS3 Media Server running (and some other things, like Vmware and Plone) and I noticed that I was getting unexpected interruptions in the streamed movies.

Normally this system reads and writes at speeds in the 25-30 MiB/sec. I found out (see below) that at some moments everything stops for 15-30 seconds. I looked over the other questions and answers here but I was unable to find any hints what could be wrong (software wise). What I did here was open a movie and seek to a later point. My PS3 uses the media server to get thumbnails for every minute to allow me to seek to the desired scene.

What I see below is that this simple operation grinds the entire system to a halt. The whole system halts waiting for IO. Also the number of context switches drops dramatically to about 650. I checked to see if the system was swapping or otherwise reporting any errors or warnings in the logfiles. I have not been able to spot anything that seems related.

I used iotop to get more info and I just disccovered that all the running applications that were doing a handfull of KiB/sec of IO were suddenly 99% IOWAIT instead of the 0.01% that they were doing normally.

At this moment my best guess is failing hardware (harddisk).

My question to you guys: How do I find out what the real problem is?

System info: Intel Pentium D CPU 2.80GHz Linux storage 2.6.22.1-27.fc7 #1 SMP Tue Jul 17 17:13:26 EDT 2007 i686 i686 i386 GNU/Linux

Sample of the output from dstat -f on my system.

-------cpu0-usage--------------cpu1-usage------ --dsk/sda-----dsk/sdb-----dsk/sdc-----dsk/sdd-- ---paging-- ---system-->
usr sys idl wai hiq siq:usr sys idl wai hiq siq| read  writ: read  writ: read  writ: read  writ|  in   out | int   csw >
  3  12  84   1   0   0:  2  14  83   1   0   0|4096B   68k:  32k    0 :   0     0 :   0     0 |   0     0 | 125  4903 >
  0   6  94   0   0   0:  1   8  91   0   0   0|   0  8192B:  16k    0 :   0     0 :   0     0 |   0     0 | 109  3734 >
  0   2  96   2   0   0:  0   1  96   0   1   2|4096B   28k:1040k    0 :   0     0 :   0     0 |   0     0 | 998  3969 >
  0   2  98   0   0   0:  1   0  97   2   0   0|   0     0 :  32k    0 :   0     0 :   0     0 |   0     0 | 115  3805 >
  1   1  98   0   0   0:  0   4  96   0   0   0|   0     0 :  32k    0 :   0     0 :   0     0 |   0     0 | 121  3850 >
  1   3  96   0   0   0:  2   4  80   0   2  12|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |8110  5076 >
  1   3  40  55   0   1:  1   2  32  57   1   7|   0   716k:2656k    0 :   0     0 :   0     0 |   0     0 |4213  4562 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0    56k:   0     0 :   0     0 :   0     0 |   0     0 |  78   833 >
  0   0  85  15   0   0:  0   0   0 100   0   0|   0    16k:   0     0 :   0     0 :   0     0 |   0     0 |  74   623 >
  0   0 100   0   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  65   572 >
  0   0  14  86   0   0:  0   0   0 100   0   0|   0    56k:   0     0 :   0     0 :   0     0 |   0     0 |  82   717 >
  1   0   0  99   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  69   583 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  69   576 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  73   586 >
  1   0   0  99   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  70   587 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  70   593 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  70   578 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  64   586 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  66   586 >
  1   0  11  88   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  63   575 >
  0   1  99   0   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  64   568 >
  0   0  79  21   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  65   571 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  64   574 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  65   581 >
  1   0   0  99   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  65   579 >
  0   0   0 100   0   0:  0   1   0  99   0   0|   0   228k:   0     0 :   0     0 :   0     0 |   0     0 | 115  1230 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  66   579 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  65   574 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  65   583 >
  1   0   0  99   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  64   581 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0    16k:   0     0 :   0     0 :   0     0 |   0     0 |  67   595 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  64   583 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  65   584 >
  0   0   0 100   0   0:  0   0   0 100   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 |  65   584 >
 10  17   8  66   0   0:  0   0   0 100   0   0|   0  4096B:   0     0 :   0     0 :   0     0 |   0     0 |  67   595 >
  1   3  17  76   1   2:  1   3  19  72   1   4|   0  3336k:3488k    0 :   0     0 :   0     0 |   0     0 |3386  4124 >
  2   3  86   9   0   0:  1   4  72   7   1  15|   0     0 :  11M    0 :   0     0 :   0     0 |   0     0 |8925  5683 >
  0   3  94   3   0   0:  1   3  80   4   2  10|   0     0 :6624k    0 :   0     0 :   0     0 |   0     0 |5744  4896 >
  1   4  92   3   0   0:  0   7  81   6   1   5|8192B  412k: 448k    0 :   0     0 :   0     0 |   0     0 |2927  4535 >
  1   1  97   1   0   0:  1   3  96   0   0   0|8192B   72k:  32k    0 :   0     0 :   0     0 |   0     0 | 131  3931 >
  1   2  97   0   0   0:  0   2  98   0   0   0|   0    24k:   0     0 :   0     0 :   0     0 |   0     0 | 112  3889 >
  1  16  83   0   0   0:  2  21  74   2   0   1|  12k   32k:  32k    0 :   0     0 :   0     0 |   0     0 | 130  4828 >
  1   2  97   0   0   0:  0   2  98   0   0   0|   0     0 :  48k    0 :   0     0 :   0     0 |   0     0 | 127  3838 >
  0   1  99   0   0   0:  1   2  97   0   0   0|4096B   44k:   0     0 :   0     0 :   0     0 |   0     0 | 113  3925 >
  0   3  95   2   0   0:  0   1  99   0   0   0|8192B   44k:  16k    0 :   0     0 :   0     0 |   0     0 | 136  3973 >
  1   1  96   1   0   1:  0   1  99   0   0   0|4096B   40k:  32k    0 :   0     0 :   0     0 |   0     0 | 124  3926 >
  0   2  98   0   0   0:  1   1  98   0   0   0|   0     0 :   0     0 :   0     0 :   0     0 |   0     0 | 107  3792 >

Additional info: iotop normally shows this:

Total DISK READ: 3.82 K/s | Total DISK WRITE: 26.72 K/s
  TID  PRIO  USER     DISK READ  DISK WRITE  SWAPIN     IO>    COMMAND
13516 be/2 root        3.82 K/s   11.45 K/s  0.00 %  1.44 % vmware-vmx -C /personal/VMWare
13514 be/2 root        0.00 B/s    7.63 K/s  0.00 %  0.01 % vmware-vmx -C /personal/VMWare
13517 be/2 root        0.00 B/s    7.63 K/s  0.00 %  0.01 % vmware-vmx -C /personal/VMWare
13519 be/4 root        0.00 B/s   26.72 K/s  0.00 %  0.00 % vmware-vmx -C /personal/VMWare
    1 be/4 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % init [5]
    2 be/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [kthreadd]
    3 rt/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [migration/0]
    4 be/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [ksoftirqd/0]
    5 rt/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [watchdog/0]
    6 rt/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [migration/1]
    7 be/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [ksoftirqd/1]
    8 rt/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [watchdog/1]
    9 be/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [events/0]

When blocked it shows this:

Total DISK READ: 0.00 B/s | Total DISK WRITE: 0.00 B/s
  TID  PRIO  USER     DISK READ  DISK WRITE  SWAPIN     IO>    COMMAND
 3013 be/4 nobody      0.00 B/s    0.00 B/s  0.00 % 99.99 % httpd.vmware -DSSL -DSSL_ONLY 
 9828 be/4 root        0.00 B/s    0.00 B/s  0.00 % 99.99 % vmware-vmx -C /personal/VMWare/
16464 be/4 niels       0.00 B/s    0.00 B/s  0.00 % 99.99 % java -Xmx768M -Djava.encoding=UT~e/niels/pms-linux-1.10.5/pms.jar
14013 be/4 niels       0.00 B/s    0.00 B/s  0.00 % 99.99 % java -Xmx768M -Djava.encoding=UT~e/niels/pms-linux-1.10.5/pms.jar
13516 be/2 root        0.00 B/s    0.00 B/s  0.00 % 99.99 % vmware-vmx -C /personal/VMWare/
13555 be/2 root        0.00 B/s    0.00 B/s  0.00 % 99.99 % vmware-vmx -C /personal/VMWare/
    1 be/4 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % init [5]
    2 be/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [kthreadd]
    3 rt/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [migration/0]
    4 be/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [ksoftirqd/0]
    5 rt/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [watchdog/0]
    6 rt/3 root        0.00 B/s    0.00 B/s  0.00 %  0.00 % [migration/1]

So there is no actual IO to wait for and still everything is waiting for their IO.

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1  
Are there any errors in any logs or dmesg? Are these IO operations local or over the network? If over the network have you ruled out networking issues? –  3dinfluence Nov 11 '09 at 21:25
    
Nope, no relevant errors. There is only one 'error' in the logs: "kernel: /dev/vmmon[13566]: /dev/rtc enable interrupt failed: -22". To my knowledge this causes timing issues in VMware but nothing like this IO problem. –  Niels Basjes Nov 12 '09 at 11:14
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2 Answers

up vote 4 down vote accepted

Have you tried iotop? It lists processes trying to do io.

Also try smartctl -a /dev/sd* to see if there are any S.M.A.R.T. errors.

share|improve this answer
    
I've added the output I got from iotop. Given the rather old kernel I cannot extract SMART info from my SATA disks. –  Niels Basjes Nov 12 '09 at 11:11
1  
If having an old kernel is blocking you, try booting to a current livecd and trying from there. –  faultyserver Nov 12 '09 at 21:29
1  
After some tests I rebooted the system and till now the problem hasn't occurred. I'm crediting you for giving the most useful answer in fixing this issue. Thanks. –  Niels Basjes Feb 12 '10 at 19:48
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maybe this kernel bug is the cause. i have the same problem on 20G RAM/2 spindles hosting nodes running 8-9 vmware server 2.0.1 vms. You might have to upgrade to 2.6.32 or downgrade to 2.6.18 .
My ugly patch , vmware server specific, was to shift memory mapped (.vmem) files to a tmpfs mounted directory.

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