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Old 10-09-2012, 11:26 AM   #1
yaximik
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help needed...


Hello,

Recently my RHEL58 box slowed down significantly. Log in as root ot user, opening new terminal or a 1 kb text file take >30 sec. Nothing seem hogging the processor:

code:

[root@G5NNJN1 ~]# top

top - 11:19:26 up 58 min, 2 users, load average: 0.07, 0.11, 0.04
Tasks: 359 total, 1 running, 357 sleeping, 0 stopped, 1 zombie
Cpu(s): 0.6%us, 0.1%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Mem: 98992148k total, 1091372k used, 97900776k free, 47344k buffers
Swap: 1048568k total, 0k used, 1048568k free, 621692k cached

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
6352 root 15 0 120m 23m 7120 S 9.0 0.0 0:24.65 Xorg
6861 root 15 0 279m 16m 9812 S 1.7 0.0 0:00.13 gnome-terminal
6882 root 15 0 12888 1308 820 R 0.7 0.0 0:00.04 top
6774 root 15 0 723m 102m 26m S 0.3 0.1 0:36.23 firefox
1 root 15 0 10364 688 572 S 0.0 0.0 0:02.26 init
2 root RT -5 0 0 0 S 0.0 0.0 0:00.00 migration/0
3 root 34 19 0 0 0 S 0.0 0.0 0:00.00 ksoftirqd/0
4 root RT -5 0 0 0 S 0.0 0.0 0:00.00 watchdog/0
5 root RT -5 0 0 0 S 0.0 0.0 0:00.00 migration/1
6 root 34 19 0 0 0 S 0.0 0.0 0:00.00 ksoftirqd/1
7 root RT -5 0 0 0 S 0.0 0.0 0:00.00 watchdog/1
8 root RT -5 0 0 0 S 0.0 0.0 0:00.00 migration/2
9 root 34 19 0 0 0 S 0.0 0.0 0:00.00 ksoftirqd/2
10 root RT -5 0 0 0 S 0.0 0.0 0:00.00 watchdog/2
11 root RT -5 0 0 0 S 0.0 0.0 0:00.00 migration/3
12 root 34 19 0 0 0 S 0.0 0.0 0:00.00 ksoftirqd/3
13 root RT -5 0 0 0 S 0.0 0.0 0:00.00 watchdog/3

The most recent updates from RHN were xorg-x11-server and kernel updates. I already tried rolling back to pre-update versions of both xorg and kernel - no change. Tech service at Dell couldnot suggest anything other than what I tried. RedHat sends me back to Dell. Here are processes - something unusual?

code:

[root@G5NNJN1 ~]# ps -A
PID TTY TIME CMD
1 ? 00:00:02 init
2 ? 00:00:00 migration/0
3 ? 00:00:00 ksoftirqd/0
4 ? 00:00:00 watchdog/0
5 ? 00:00:00 migration/1
6 ? 00:00:00 ksoftirqd/1
7 ? 00:00:00 watchdog/1
8 ? 00:00:00 migration/2
9 ? 00:00:00 ksoftirqd/2
10 ? 00:00:00 watchdog/2
11 ? 00:00:00 migration/3
12 ? 00:00:00 ksoftirqd/3
13 ? 00:00:00 watchdog/3
14 ? 00:00:00 migration/4
15 ? 00:00:00 ksoftirqd/4
16 ? 00:00:00 watchdog/4
17 ? 00:00:00 migration/5
18 ? 00:00:00 ksoftirqd/5
19 ? 00:00:00 watchdog/5
20 ? 00:00:00 migration/6
21 ? 00:00:00 ksoftirqd/6
22 ? 00:00:00 watchdog/6
23 ? 00:00:00 migration/7
24 ? 00:00:00 ksoftirqd/7
25 ? 00:00:00 watchdog/7
26 ? 00:00:00 migration/8
27 ? 00:00:00 ksoftirqd/8
28 ? 00:00:00 watchdog/8
29 ? 00:00:00 migration/9
30 ? 00:00:00 ksoftirqd/9
31 ? 00:00:00 watchdog/9
32 ? 00:00:00 migration/10
33 ? 00:00:00 ksoftirqd/10
34 ? 00:00:00 watchdog/10
35 ? 00:00:00 migration/11
36 ? 00:00:00 ksoftirqd/11
37 ? 00:00:00 watchdog/11
38 ? 00:00:00 migration/12
39 ? 00:00:00 ksoftirqd/12
40 ? 00:00:00 watchdog/12
41 ? 00:00:00 migration/13
42 ? 00:00:00 ksoftirqd/13
43 ? 00:00:00 watchdog/13
44 ? 00:00:00 migration/14
45 ? 00:00:00 ksoftirqd/14
46 ? 00:00:00 watchdog/14
47 ? 00:00:00 migration/15
48 ? 00:00:00 ksoftirqd/15
49 ? 00:00:00 watchdog/15
50 ? 00:00:00 events/0
51 ? 00:00:00 events/1
52 ? 00:00:00 events/2
53 ? 00:00:00 events/3
54 ? 00:00:00 events/4
55 ? 00:00:00 events/5
56 ? 00:00:00 events/6
57 ? 00:00:00 events/7
58 ? 00:00:00 events/8
59 ? 00:00:00 events/9
60 ? 00:00:00 events/10
61 ? 00:00:00 events/11
62 ? 00:00:00 events/12
63 ? 00:00:00 events/13
64 ? 00:00:00 events/14
65 ? 00:00:00 events/15
66 ? 00:00:00 khelper
843 ? 00:00:00 kthread
863 ? 00:00:00 kblockd/0
864 ? 00:00:00 kblockd/1
865 ? 00:00:00 kblockd/2
866 ? 00:00:00 kblockd/3
867 ? 00:00:00 kblockd/4
868 ? 00:00:00 kblockd/5
869 ? 00:00:00 kblockd/6
870 ? 00:00:00 kblockd/7
871 ? 00:00:00 kblockd/8
872 ? 00:00:00 kblockd/9
873 ? 00:00:00 kblockd/10
874 ? 00:00:00 kblockd/11
875 ? 00:00:00 kblockd/12
876 ? 00:00:00 kblockd/13
877 ? 00:00:00 kblockd/14
878 ? 00:00:00 kblockd/15
879 ? 00:00:00 kacpid
993 ? 00:00:00 cqueue/0
994 ? 00:00:00 cqueue/1
995 ? 00:00:00 cqueue/2
996 ? 00:00:00 cqueue/3
997 ? 00:00:00 cqueue/4
998 ? 00:00:00 cqueue/5
999 ? 00:00:00 cqueue/6
1000 ? 00:00:00 cqueue/7
1001 ? 00:00:00 cqueue/8
1002 ? 00:00:00 cqueue/9
1003 ? 00:00:00 cqueue/10
1004 ? 00:00:00 cqueue/11
1005 ? 00:00:00 cqueue/12
1006 ? 00:00:00 cqueue/13
1007 ? 00:00:00 cqueue/14
1008 ? 00:00:00 cqueue/15
1011 ? 00:00:00 khubd
1013 ? 00:00:00 kseriod
1202 ? 00:00:00 khungtaskd
1203 ? 00:00:00 pdflush
1204 ? 00:00:00 pdflush
1205 ? 00:00:00 kswapd0
1206 ? 00:00:00 kswapd1
1207 ? 00:00:00 aio/0
1208 ? 00:00:00 aio/1
1209 ? 00:00:00 aio/2
1210 ? 00:00:00 aio/3
1211 ? 00:00:00 aio/4
1212 ? 00:00:00 aio/5
1213 ? 00:00:00 aio/6
1214 ? 00:00:00 aio/7
1215 ? 00:00:00 aio/8
1216 ? 00:00:00 aio/9
1217 ? 00:00:00 aio/10
1218 ? 00:00:00 aio/11
1219 ? 00:00:00 aio/12
1220 ? 00:00:00 aio/13
1221 ? 00:00:00 aio/14
1222 ? 00:00:00 aio/15
1378 ? 00:00:00 kpsmoused
1523 ? 00:00:00 scsi_eh_0
1524 ? 00:00:00 megasas_ocr/0
1525 ? 00:00:00 megasas_ocr/1
1526 ? 00:00:00 megasas_ocr/2
1527 ? 00:00:00 megasas_ocr/3
1528 ? 00:00:00 megasas_ocr/4
1529 ? 00:00:00 megasas_ocr/5
1530 ? 00:00:00 megasas_ocr/6
1531 ? 00:00:00 megasas_ocr/7
1532 ? 00:00:00 megasas_ocr/8
1533 ? 00:00:00 megasas_ocr/9
1534 ? 00:00:00 megasas_ocr/10
1535 ? 00:00:00 megasas_ocr/11
1536 ? 00:00:00 megasas_ocr/12
1537 ? 00:00:00 megasas_ocr/13
1538 ? 00:00:00 megasas_ocr/14
1539 ? 00:00:00 megasas_ocr/15
1574 ? 00:00:00 ata/0
1575 ? 00:00:00 ata/1
1576 ? 00:00:00 ata/2
1577 ? 00:00:00 ata/3
1578 ? 00:00:00 ata/4
1579 ? 00:00:00 ata/5
1580 ? 00:00:00 ata/6
1581 ? 00:00:00 ata/7
1582 ? 00:00:00 ata/8
1583 ? 00:00:00 ata/9
1584 ? 00:00:00 ata/10
1585 ? 00:00:00 ata/11
1586 ? 00:00:00 ata/12
1587 ? 00:00:00 ata/13
1588 ? 00:00:00 ata/14
1589 ? 00:00:00 ata/15
1590 ? 00:00:00 ata_aux
1608 ? 00:00:01 scsi_eh_1
1609 ? 00:00:00 scsi_eh_2
1627 ? 00:00:00 kstriped
1696 ? 00:00:00 ksnapd
1767 ? 00:00:00 kjournald
1797 ? 00:00:00 kauditd
1834 ? 00:00:00 udevd
2676 ? 00:00:00 kedac
2719 ? 00:00:00 scsi_eh_3
2720 ? 00:00:00 usb-storage
3821 ? 00:00:00 kmpathd/0
3822 ? 00:00:00 kmpathd/1
3823 ? 00:00:00 kmpathd/2
3824 ? 00:00:00 kmpathd/3
3825 ? 00:00:00 kmpathd/4
3826 ? 00:00:00 kmpathd/5
3827 ? 00:00:00 kmpathd/6
3828 ? 00:00:00 kmpathd/7
3829 ? 00:00:00 kmpathd/8
3830 ? 00:00:00 kmpathd/9
3831 ? 00:00:00 kmpathd/10
3832 ? 00:00:00 kmpathd/11
3833 ? 00:00:00 kmpathd/12
3834 ? 00:00:00 kmpathd/13
3835 ? 00:00:00 kmpathd/14
3836 ? 00:00:00 kmpathd/15
3837 ? 00:00:00 kmpath_handlerd
3862 ? 00:00:00 kjournald
3864 ? 00:00:00 kjournald
3870 ? 00:00:00 kjournald
3875 ? 00:00:00 kjournald
3880 ? 00:00:00 kjournald
4166 ? 00:00:00 iscsi_eh
4307 ? 00:00:00 cnic_wq
4326 ? 00:00:00 bnx2i_thread/0
4327 ? 00:00:00 bnx2i_thread/1
4328 ? 00:00:00 bnx2i_thread/2
4329 ? 00:00:00 bnx2i_thread/3
4330 ? 00:00:00 bnx2i_thread/4
4331 ? 00:00:00 bnx2i_thread/5
4332 ? 00:00:00 bnx2i_thread/6
4333 ? 00:00:00 bnx2i_thread/7
4334 ? 00:00:00 bnx2i_thread/8
4335 ? 00:00:00 bnx2i_thread/9
4336 ? 00:00:00 bnx2i_thread/10
4337 ? 00:00:00 bnx2i_thread/11
4339 ? 00:00:00 bnx2i_thread/12
4340 ? 00:00:00 bnx2i_thread/13
4341 ? 00:00:00 bnx2i_thread/14
4342 ? 00:00:00 bnx2i_thread/15
4382 ? 00:00:00 ib_addr
4436 ? 00:00:00 ib_mcast
4437 ? 00:00:00 ib_inform
4438 ? 00:00:00 local_sa
4456 ? 00:00:00 iw_cm_wq
4474 ? 00:00:00 ib_cm/0
4475 ? 00:00:00 ib_cm/1
4476 ? 00:00:00 ib_cm/2
4477 ? 00:00:00 ib_cm/3
4478 ? 00:00:00 ib_cm/4
4479 ? 00:00:00 ib_cm/5
4480 ? 00:00:00 ib_cm/6
4481 ? 00:00:00 ib_cm/7
4482 ? 00:00:00 ib_cm/8
4483 ? 00:00:00 ib_cm/9
4484 ? 00:00:00 ib_cm/10
4485 ? 00:00:00 ib_cm/11
4486 ? 00:00:00 ib_cm/12
4487 ? 00:00:00 ib_cm/13
4488 ? 00:00:00 ib_cm/14
4489 ? 00:00:00 ib_cm/15
4507 ? 00:00:00 rdma_cm
4550 ? 00:00:00 iscsiuio
4556 ? 00:00:00 iscsid
4557 ? 00:00:00 iscsid
4591 ? 00:00:00 mcstransd
4746 ? 00:00:00 auditd
4748 ? 00:00:00 audispd
4765 ? 00:00:00 restorecond
4774 ? 00:00:00 syslogd
4778 ? 00:00:00 klogd
4903 ? 00:00:00 kondemand/0
4904 ? 00:00:00 kondemand/1
4905 ? 00:00:00 kondemand/2
4906 ? 00:00:00 kondemand/3
4907 ? 00:00:00 kondemand/4
4908 ? 00:00:00 kondemand/5
4909 ? 00:00:00 kondemand/6
4910 ? 00:00:00 kondemand/7
4911 ? 00:00:00 kondemand/8
4912 ? 00:00:00 kondemand/9
4913 ? 00:00:00 kondemand/10
4914 ? 00:00:00 kondemand/11
4915 ? 00:00:00 kondemand/12
4916 ? 00:00:00 kondemand/13
4917 ? 00:00:00 kondemand/14
4918 ? 00:00:00 kondemand/15
4947 ? 00:00:00 irqbalance
4965 ? 00:00:00 portmap
5010 ? 00:00:00 rpciod/0
5011 ? 00:00:00 rpciod/1
5012 ? 00:00:00 rpciod/2
5013 ? 00:00:00 rpciod/3
5014 ? 00:00:00 rpciod/4
5015 ? 00:00:00 rpciod/5
5016 ? 00:00:00 rpciod/6
5017 ? 00:00:00 rpciod/7
5018 ? 00:00:00 rpciod/8
5019 ? 00:00:00 rpciod/9
5020 ? 00:00:00 rpciod/10
5021 ? 00:00:00 rpciod/11
5022 ? 00:00:00 rpciod/12
5023 ? 00:00:00 rpciod/13
5024 ? 00:00:00 rpciod/14
5025 ? 00:00:00 rpciod/15
5046 ? 00:00:00 rpc.statd
5074 ? 00:00:00 rpc.idmapd
5096 ? 00:00:00 dbus-daemon
5108 ? 00:00:00 setroubleshootd
5117 ? 00:00:00 hcid
5123 ? 00:00:00 sdpd
5189 ? 00:00:00 krfcommd
5226 ? 00:00:00 pcscd
5236 ? 00:00:00 acpid
5447 ? 00:00:01 hald
5448 ? 00:00:00 hald-runner
5455 ? 00:00:00 hald-addon-acpi
5460 ? 00:00:00 hald-addon-keyb
5473 ? 00:00:01 hald-addon-stor
5508 ? 00:00:00 hidd
5556 ? 00:00:00 automount
5576 ? 00:00:00 sshd
5585 ? 00:00:00 cupsd
5598 ? 00:00:00 xinetd
5617 ? 00:00:00 ntpd
5683 ? 00:00:00 sendmail
5694 ? 00:00:00 sendmail
5704 ? 00:00:00 gpm
5713 ? 00:00:00 crond
5748 ? 00:00:00 xfs
5757 ? 00:00:00 winbindd
5774 ? 00:00:00 atd
5786 ? 00:00:00 winbindd
5807 ? 00:00:00 rhnsd
5825 ? 00:00:00 avahi-daemon
5826 ? 00:00:00 avahi-daemon
5887 ? 00:00:00 smartd
5892 tty1 00:00:00 mingetty
5893 tty2 00:00:00 mingetty
5894 tty3 00:00:00 mingetty
5895 tty4 00:00:00 mingetty
5896 tty5 00:00:00 mingetty
5898 ? 00:00:00 gdm-binary
5939 ? 00:00:00 gdm-binary
5941 ? 00:00:00 gdm-rh-security
5947 ? 00:00:00 yum-updatesd
5949 ? 00:00:00 gam_server
5961 ? 00:00:00 winbindd
5962 ? 00:00:00 winbindd
6151 ? 00:00:00 nm-system-setti
6178 ? 00:00:00 mount.ntfs-3g
6352 tty7 00:00:41 Xorg
6365 ? 00:00:00 gnome-session
6397 ? 00:00:00 Xsession <defunct>
6400 ? 00:00:00 ssh-agent
6428 ? 00:00:00 scim-launcher
6431 ? 00:00:00 dbus-launch
6432 ? 00:00:00 dbus-daemon
6439 ? 00:00:00 gconfd-2
6443 ? 00:00:00 scim-helper-man
6444 ? 00:00:00 scim-panel-gtk
6446 ? 00:00:00 scim-launcher
6449 ? 00:00:00 gnome-keyring-d
6451 ? 00:00:00 gnome-settings-
6471 ? 00:00:00 metacity
6476 ? 00:00:00 gnome-panel
6478 ? 00:00:00 nautilus
6484 ? 00:00:00 gnome-screensav
6486 ? 00:00:00 bonobo-activati
6492 ? 00:00:00 gnome-vfs-daemo
6496 ? 00:00:00 wnck-applet
6500 ? 00:00:00 notification-ar
6502 ? 00:00:00 mixer_applet2
6504 ? 00:00:00 clock-applet
6519 ? 00:00:00 mapping-daemon
6522 ? 00:00:00 eggcups
6525 ? 00:00:00 gnome-volume-ma
6527 ? 00:00:00 bt-applet
6535 ? 00:00:00 nm-applet
6537 ? 00:00:00 puplet
6541 ? 00:00:00 /usr/bin/sealer
6543 ? 00:00:00 gnome-power-man
6545 ? 00:00:00 pam-panel-icon
6549 ? 00:00:00 pam_timestamp_c
6554 ? 00:00:00 notification-da
6717 tty6 00:00:00 mingetty
6774 ? 00:00:43 firefox
6861 ? 00:00:00 gnome-terminal
6864 ? 00:00:00 gnome-pty-helpe
6865 pts/1 00:00:00 bash
6891 pts/1 00:00:00 ps


Anywhere else to look what may be causing the problem?
 
Old 10-09-2012, 11:31 AM   #2
Basher52
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Normally there should be 3 versions that you can boot into (if my mind is in the right place), have you tried the 2 previous and having the same problem?
 
Old 10-09-2012, 01:48 PM   #3
yaximik
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Yes, I went down three versions to the kernel the box came with, still no diff.
 
Old 10-09-2012, 05:25 PM   #4
flshope
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Have you tried starting the gnome-system-monitor to see if the processors are maxed out? Of course, opening this appl could take a while if just opening a terminal takes 30 sec.
 
Old 10-09-2012, 06:00 PM   #5
jlinkels
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98 GB of RAM?? Did you really put that into the machine?

jlinkels
 
Old 10-09-2012, 08:18 PM   #6
yaximik
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yes, 96GB of RAM, perhaps I could get away with 48GB, but I need a lot of it for bioinformatics. This is not the reason for slowing down, as it was working just fine until recently.
I wonder, in the above output for ps -A why I have as many as 15 instances of several processes? On my SciLInux55 box at home I do not have anything like that, most are single or double processes. Could this be a reason, and if so where such spawning is coming from?
 
Old 10-10-2012, 08:37 AM   #7
jlinkels
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Quote:
Originally Posted by yaximik View Post
yes, 96GB of RAM, perhaps I could get away with 48GB, but I need a lot of it for bioinformatics. This is not the reason for slowing down
No, I understand that. But the amount was so high that I thought it was reported incorrectly. Once that is incorrect, you wouldn't know how that would influence the system.

But if your memory requirements are so high, why is only 1 GB being used. Did you not start up the memory consuming programs yet?

I also see that the CPU load is low, very low << 1. That remains like that all the time?

Monitor the % of "wa" in the line CPU(s). If it increases, there is an I/O problem somewhere.

Press '1' in the top program to see all CPU loads individually.

I can't answer on the number of duplicate processes. When do they appear? Right after booting?

Please surround logs etc with [ CODE][ /CODE] tags. It makes them more readable.

jlinkels
 
Old 10-10-2012, 08:11 PM   #8
yaximik
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I cannot use any programs as the system is slow, it is just idling in either user or root mode as I am trying to figure out what is wrong. It is slow right after login, which itself is slow (after entering password). On average it is somewhat between 30 sec to 60 sec delay in response.

After pressing 1 in to all %wa for all 16 CPU (0 to 15) stays at 0.0%. The average %CPU stays at less than 1% with two-four processes running or popping up.

When I googled processes that are present at 16 instances, I got some very bad indications. For example:

ksoftirqd is a per-cpu kernel thread that runs when the machine is under heavy soft-interrupt load. Soft interrupts are normally serviced on return from a hard interrupt, but it's possible for soft interrupts to be triggered more quickly than they can be serviced. If a soft interrupt is triggered for a second time while soft interrupts are being handled, the ksoftirq daemon is triggered to handle the soft interrupts in process context. If ksoftirqd is taking more than a tiny percentage of CPU time, this indicates the machine is under heavy soft interrupt load.

I have 16 instances of those running all the time, even right after reboot.

In a general, the kblockd kernel threads are responsible for performing low-level disk operations. A high utilization of these could indicate that the server IO queue is backed up and the server is not managing to perform its disk writes quick enough

I have 16 instances of these, but they are not chewing up memory or hogging processor.

For the uninitiated, kondemand is a kernel thread that belongs to the ondemand governor of cpufreq subsystem, which changes the p-states of the system, based on the utilization statistics. Thus it’s something that helps in power management.

Again I have 16 of this - why? And 16 rpciod - something to do with NFS I/O. I do not even use NFS, where it comes from?

I probably could kill instances 3-15 of each, buit they will show up again upon restart, do not they?
 
Old 10-10-2012, 08:57 PM   #9
yaximik
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Well, I connot even kill them with kill -9 or even kill -11...
 
Old 10-10-2012, 10:50 PM   #10
nigelc
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What does cat /proc/interrupts show?

Have you tried a memory test?
 
Old 10-11-2012, 11:18 AM   #11
yaximik
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The box just fixed itself this morning, no reboot, just got back in its normal (apparently) state. ps -A shows the same processes, that is multiple instances are all the same. I am totally puzzled...
 
  


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