HELP! Linux is slowing to a crawl, what's wrong???

My system has a serious underperformance problem lately and I can't nail down what the problem is. I haven't introduced any new hardware into my system and I haven't tickered with my setup very much at all in the past 2-3 months or so. The problem seemed to happen after Thanksgiving and it feels like its getting worse. Sometimes I'll be running nothing but XMMS and the music will actually start skipping and when I look at my system monitor my CPU is peeking out at 100% usage!!! And I can hardly play Enemy Territory at all anymore because its so choppy and so many frames are skipped (I even set the grahpics settings to minimum and saw little benefit) Here's my setup:

Pentium IV 2.8GHz
1024MB RAM
120 GB HD
ATI Radeon 9500 Pro

Debian sarge
Kernel 2.6.8
DE: Gnome

Here's a list of my processes (and my processor is showing really eratic behavior while running these, averaging around 30-40% usage and spiking all the way up to 95% and all the way down to 5% occasionally)

tyler@localhost:~$ ps axu
USER       PID %CPU %MEM   VSZ  RSS TTY      STAT START   TIME COMMAND
root         1  0.0  0.0  1528  524 ?        S    11:18   0:00 init [2]
root         2  0.0  0.0     0    0 ?        SN   11:18   0:00 [ksoftirqd/0]
root         3  0.0  0.0     0    0 ?        S<   11:18   0:00 [events/0]
root         4  0.0  0.0     0    0 ?        S<   11:18   0:00 [khelper]
root        20  0.0  0.0     0    0 ?        S<   11:18   0:04 [kblockd/0]
root        50  0.0  0.0     0    0 ?        S    11:18   0:00 [pdflush]
root        51  0.0  0.0     0    0 ?        S    11:18   0:00 [pdflush]
root        53  0.0  0.0     0    0 ?        S<   11:18   0:00 [aio/0]
root        52  0.0  0.0     0    0 ?        S    11:18   0:00 [kswapd0]
root       189  0.0  0.0     0    0 ?        S    11:18   0:00 [kseriod]
root       210  0.0  0.0     0    0 ?        S<   11:18   0:00 [ata/0]
root       304  0.0  0.0     0    0 ?        S    11:18   0:01 [kjournald]
root       585  0.0  0.0     0    0 ?        S    11:18   0:00 [khubd]
root      2653  0.0  0.0  1708  676 ?        Ss   11:18   0:00 dhclient -e -pf /var/run/dhclient.eth0.pid -lf /var/run/dhclient.eth0.leases eth0
daemon    2657  0.0  0.0  1640  444 ?        Ss   11:18   0:00 /sbin/portmap
root      2822  0.0  0.0  1584  628 ?        Ss   11:18   0:00 /sbin/syslogd
root      2825  0.0  0.1  2428 1444 ?        Ss   11:18   0:00 /sbin/klogd
message   2832  0.0  0.0  2112  988 ?        Ss   11:18   0:00 /usr/bin/dbus-daemon-1 --system
Debian-   2863  0.0  0.1  4240 1488 ?        Ss   11:18   0:00 /usr/sbin/exim4 -bd -q30m
tyler     2868  0.0  0.1  2912 1416 ?        Ss   11:18   0:00 /usr/sbin/famd -T 0
wnn       2872  0.0  0.3  5276 3948 ?        S    11:18   0:00 /usr/bin/Wnn4/jserver
root      2881  0.0  0.0  1564  524 ?        Ss   11:18   0:00 /usr/sbin/inetd
gnunet    2887  2.2  1.2 48212 12848 ?       Ss   11:18   3:13 /usr/bin/gnunetd -c /etc/gnunet.conf
root      2895  0.0  0.1  3496 1524 ?        Ss   11:18   0:00 /usr/sbin/sshd
root      2920  0.0  0.3  4980 3472 ?        Ss   11:18   0:00 /usr/bin/X11/xfs -daemon
root      2992  0.0  0.1  2760 1468 ?        S    11:18   0:00 /bin/bash /etc/rc2.d/S20xprint posix_sh_forced start
root      2993  0.0  0.1  2760 1468 ?        S    11:18   0:00 /bin/bash /etc/rc2.d/S20xprint posix_sh_forced start
root      2994  0.0  0.2  9020 2544 ?        S    11:18   0:00 /usr/bin/Xprt -ac -pn -nolisten tcp -audit 4 -fp /usr/X11R6/lib/X11/fonts/Type1,/usr/X11R6/libroot      2996  0.0  0.1  2760 1472 ?        S    11:18   0:00 /bin/bash /etc/rc2.d/S20xprint posix_sh_forced start
daemon    3003  0.0  0.0  1716  628 ?        Ss   11:18   0:00 /usr/sbin/atd
root      3006  0.0  0.0  1788  736 ?        Ss   11:18   0:00 /usr/sbin/cron
root      3074  0.0  0.2  8912 2340 ?        Ss   11:19   0:00 /usr/bin/gdm
root      3076  0.0  0.2  9256 2720 ?        S    11:19   0:00 /usr/bin/gdm
root      3093  0.0  0.0  1524  476 tty1     Ss+  11:19   0:00 /sbin/getty 38400 tty1
root      3094  0.0  0.0  1524  476 tty2     Ss+  11:19   0:00 /sbin/getty 38400 tty2
root      3095  0.0  0.0  1524  476 tty3     Ss+  11:19   0:00 /sbin/getty 38400 tty3
root      3096  0.0  0.0  1524  476 tty4     Ss+  11:19   0:00 /sbin/getty 38400 tty4
root      3097  0.0  0.0  1524  476 tty5     Ss+  11:19   0:00 /sbin/getty 38400 tty5
root      3098  0.0  0.0  1524  476 tty6     Ss+  11:19   0:00 /sbin/getty 38400 tty6
root      3141  1.7  6.0 77244 62392 ?       S<L  11:19   2:31 /usr/X11R6/bin/X :0 -audit 0 -auth /var/lib/gdm/:0.Xauth -nolisten tcp vt7
root      3178  0.0  0.0     0    0 ?        S    11:19   0:00 [kapmd]
gdm       3217  0.0  0.0  1788  496 ?        S    11:19   0:00 uim-helper-server
tyler     3218  0.0  0.8 18448 8916 ?        Ss   11:19   0:00 /usr/bin/gnome-session
tyler     3268  0.0  0.7 22528 8188 ?        S    11:19   0:01 uim-toolbar-gtk-systray
tyler     3269  0.0  0.0     0    0 ?        Z    11:19   0:00 [uim-xim] <defunct>
tyler     3272  0.0  0.0  1788  496 ?        S    11:19   0:00 uim-helper-server
tyler     3288  0.0  0.7 22528 8188 ?        S    11:19   0:01 uim-toolbar-gtk-systray
tyler     3289  0.0  0.6 16504 7024 ?        S    11:19   0:00 uim-xim
tyler     3290  0.0  0.0  3012  912 ?        Ss   11:19   0:00 /usr/bin/ssh-agent /usr/bin/gnome-session
tyler     3293  0.0  0.6 10092 6860 ?        S    11:19   0:01 /usr/lib/gconf2/gconfd-2 13
tyler     3295  0.0  0.0  2284 1020 ?        S    11:19   0:00 /usr/bin/gnome-keyring-daemon
tyler     3297  0.0  0.2  7120 2832 ?        Ss   11:19   0:00 /usr/lib/bonobo-activation/bonobo-activation-server --ac-activate --ior-output-fd=18
tyler     3299  0.0  0.2  7844 2736 ?        Ss   11:19   0:00 gnome-smproxy --sm-config-prefix /.gnome-smproxy-ENZxck/ --sm-client-id 117f000001000108807860tyler     3301  0.0  0.8 20368 8672 ?        S    11:19   0:00 /usr/lib/control-center/gnome-settings-daemon --oaf-activate-iid=OAFIID:GNOME_SettingsDaemon -tyler     3323  0.0  0.1  3816 1940 ?        S    11:19   0:00 xscreensaver -nosplash
tyler     3347  0.0  0.7 15720 8240 ?        Ss   11:19   0:03 metacity --sm-save-file 1101348598-3170-676145579.ms
tyler     3349  0.0  1.7 27344 18540 ?       Ss   11:19   0:02 gnome-panel --sm-config-prefix /gnome-panel-eRfOVh/ --sm-client-id 117f00000100010880786050000tyler     3351  0.0  1.6 36556 17624 ?       Ss   11:19   0:01 nautilus --sm-config-prefix /nautilus-2xOhci/ --sm-client-id 117f00000100010880786050000007215tyler     3354  0.0  0.3 17372 3660 ?        S    11:19   0:00 /usr/lib/gnome-vfs2/gnome-vfs-daemon --oaf-activate-iid=OAFIID:GNOME_VFS_Daemon_Factory --oaf-tyler     3360  0.0  0.0  2220  764 ?        S    11:19   0:00 /usr/lib/nautilus-cd-burner/mapping-daemon
tyler     3367  0.0  0.9 18944 10204 ?       S    11:20   0:04 /usr/lib/gnome-panel/wnck-applet --oaf-activate-iid=OAFIID:GNOME_Wncklet_Factory --oaf-ior-fd=tyler     3369  0.0  1.4 26972 14740 ?       S    11:20   0:00 /usr/lib/gnome-utils/gdict-applet --oaf-activate-iid=OAFIID:GNOME_GDictApplet_Factory --oaf-iotyler     3371  0.0  1.0 27052 10956 ?       S    11:20   0:01 /usr/lib/uim/uim-toolbar-applet --oaf-activate-iid=OAFIID:GNOME_UimApplet_Factory --oaf-ior-fdtyler     3373  0.0  0.8 19156 9332 ?        S    11:20   0:00 /usr/lib/gnome-applets/gweather-applet-2 --oaf-activate-iid=OAFIID:GNOME_GWeatherApplet_Factortyler     3375  0.0  0.7 17028 8080 ?        S    11:20   0:00 /usr/lib/gnome-panel/clock-applet --oaf-activate-iid=OAFIID:GNOME_ClockApplet_Factory --oaf-iotyler     3464  0.0  0.4 12852 4424 ?        S    11:22   0:00 uim-candwin-gtk
root      4362  0.0  0.2  5500 2248 ?        S    12:07   0:00 /usr/lib/gconf2/gconfd-2 19
tyler     4514  0.0  0.7 45968 7888 ?        S    13:28   0:00 xmms
tyler     4517  3.3  4.1 120024 42724 ?      S    13:28   0:30 /usr/lib/mozilla-firefox/firefox-bin -a firefox
tyler     4543  0.5  1.4 27512 15108 ?       S    13:29   0:05 gnome-system-monitor
tyler     4561  0.0  0.1  4524 1320 ?        S    13:29   0:00 /bin/sh /usr/bin/mozilla-thunderbird
tyler     4588  0.0  0.1  4556 1340 ?        S    13:29   0:00 /bin/sh /usr/lib/mozilla-thunderbird/run-mozilla.sh /usr/lib/mozilla-thunderbird/mozilla-thundtyler     4593  0.2  3.4 113300 35532 ?      S    13:29   0:02 /usr/lib/mozilla-thunderbird/mozilla-thunderbird-bin -contentLocale en-US -UILocale en-US
tyler     4615  0.3  1.8 48008 19372 ?       R    13:37   0:01 gnome-terminal
tyler     4616  0.0  0.0  2236  672 ?        S    13:37   0:00 gnome-pty-helper
tyler     4617  0.0  0.1  4812 1668 pts/2    Ss   13:37   0:00 bash
tyler     4641  0.0  0.0  2528  852 pts/2    R+   13:43   0:00 ps axu

Does anyone have the slightest clue as to why this suddenly happened? It really sucks and its very frusterating. The only thing I can think of (and this is a long-shot) is that around June/July my CPU was damaged by overheating, which caused my machine to freeze up 60% of the time after I booted, but if the machine stayed stable for an hour after booting then it would never freeze up and I could keep it running for days. I don't think I've seen that freezing problem occur since my slow-down problem occured, but I'm not sure since I've only booted 2-3 times since then.

Please, someone lead me in the right direction to get my machine fixed. I don't want to imagine but could it be *gasp* spyware/a virus? (I almost exclusively install things from the Debian package system, so I highly doubt it...)

enable dma on your hard drive with hdparm, look through /var/log/messages for errors or warnings that could indicate hard drive failure. run top in a terminal, sounds like you are having some really high I/O wait times going on, you could have some faulty hardware run memtest on your system to check for bad memory.

Originally posted by anonobomber enable dma on your hard drive with hdparm, look through /var/log/messages for errors or warnings that could indicate hard drive failure. run top in a terminal, sounds like you are having some really high I/O wait times going on, you could have some faulty hardware run memtest on your system to check for bad memory.

I looked thru /var/log/messages, but there were no errors or warnings there. I highly doubt that its a problem with my hard disc, because my CPU usage is at 100% again right now and there is no activity from my hard drive (the access light isn't on). I don't have memtest on my system so I wasn't able to run that, but this system isn't very old at all and I'm not even using half of my available memory most of the time. Oh, now the usage just went from straight 100% back down to a somewhat-normal usage level. *sigh* what on Earth is going on here?

you said your cpu usage is at 100 but i dont see which program is using that much from your list...

i know this may not be of much help but i have had that problem on an XP box, turned out it was windows indexing service... aparently i had too much data for it to handle... i just switched it off and it was fine... i know this cant help you seeing as how it was windows but have you installed some type of program that databases your files?

Madamox is probably on to something, most distros have a cron job that tells them to execute updatedb every X hours/days/weeks/months/minutes/whatever you specify. It probably generated the cron job on it's own, and it usually executes every hour. When it does, it slows the system down a lot. Try poking around in your cron configs.

a couple of things (i don't use gnome)
it is possible something is misconfigured like in /etc/hosts or other network setup files
they discuss this some here
http://www.linuxquestions.org/questi...?postid=829250
also
if gnome saves session when you log out try turn that off and restart gnome
if a process goes rouge in the background it will come back if gnome saves session
also you are running lots of daemons - look for service logs and or daemon logs and look for errors
try cntrl - alt - F1 to look at the controlling tty for errors
once i had performance problem and one error message was scrolling by like crazy in controlling tty (ide-scsi was freeking out)
cntrl alt F7 to get back to X
both for performance in general and diagnosing your problem
i would try (just using the kill thing in the monitor program for starters)
turn off both atd and cron unless you are actually using them
i have also seen famd go all postal and everything will work ok without that as well so turn that off
gnunetd is running are you running some kind of file sharing server that needs that ? try stopping that
do you need sshd server ? try stopping that
check what you have running under inetd and check logs
also look at exim logs though i can't imagine that's the problem

Hmmm I see. Thanks for the help guys, I'll tinker around with things and see if I can't find the problem. And if I can't, you'll hear back from me.