CPU Spiking on 12.2 by Nepomuk(?)

seanthor · September 10, 2012, 1:23am

Hi all,

After clean install of 12.2 (on ext4), I’ve noticed that several cores on my i7 have been spiking. There are a few programs that seem responsible, and I think they are related to nepomuk and virtuoso. I’ve tried to kill and restart the programs, but each time the cores start spiking again once restarted between 10-100%. After killing them with htop in konsole, I tried

akonadictl restart

but alas it did not solve itself.

I don’t remember this activity with 12.1, should I be concerned? Did a clean install of both / and /home, then copied my backup from external HDD to the new /home:

cp -r -vvv seanthor /home

Also had to use chown to reset permissions for new /home/seanthor.

The main culprits seem to be:
/usr/bin/virtuoso-t +foreground +configfile /tmp/virtuoso_ik2795.ini +wait
nepomukservicestub
nepomukserver

Please let me know if I should be concerned, and/or if you need more information.

htop screenshot:
SUSE Paste

seanthor · September 10, 2012, 3:05am

Here is some text from htop in case this helps:

<pre style='color:#1f1c1b;background-color:#ffffff;'>

  1  |                                                   0.7%]     5  ||                                                  1.3%]
  2  ||                                                  1.3%]     6  ||                                                  1.3%]
  3                                                      0.0%]     7                                                      0.0%]
  4  ||||||||||||||||||||||||||||||||||||||||||||||||||100.0%]     8                                                      0.0%]
  Mem|||||||||||||||||||||||||||||||||||||||||||||1258/3955MB]     Tasks: 171, 361 thr; 2 running
  Swp|                                               9/2053MB]     Load average: 1.92 2.52 2.60 
                                                                    Uptime: 02:48:46

  PID USER      PRI  NI  VIRT   RES   SHR S CPU% MEM%   TIME+  Command
11217 seanthor   39  19  134M 28544  4256 R 99.0  0.7  4:40.38 /usr/bin/virtuoso-t +foreground +configfile /tmp/virtuoso_X11212.ini +
11255 seanthor   20   0 24168  3328  1416 R  1.0  0.1  0:00.90 htop
 9433 seanthor   20   0 1192M  110M 30508 S  0.0  2.8  0:37.80 kdeinit4: plasma-desktop [kdeinit]
 9251 root       20   0  224M 62436 28776 S  0.0  1.5  1:18.98 /usr/bin/Xorg -br :0 vt7 -nolisten tcp -auth /var/lib/xdm/authdir/auth
11111 seanthor   20   0  652M 47124 30960 S  0.0  1.2  0:04.60 kdeinit4: konsole [kdeinit]
 9417 seanthor   20   0  620M 42416 17020 S  0.0  1.0  0:36.18 kwin -session 1014b110daef000134719962700000148970000_1347221293_89531
 4284 root       20   0  188M  2672  1708 S  0.0  0.1  0:04.06 /usr/lib/udisks/udisks-daemon
11257 seanthor   20   0  388M 11224  5372 S  0.0  0.3  0:00.02 kdeinit4: kio_trash [kdeinit] trash local:/tmp/ksocket-seantho
  743 messagebu  20   0 29100  2076   792 S  0.0  0.1  0:02.56 /bin/dbus-daemon --system --address=systemd: --nofork --nopidfile --sy
10733 seanthor   20   0  419M 31604 10732 S  0.0  0.8  0:05.20 /usr/lib64/firefox/plugin-container /usr/lib64/browser-plugins/libflas
    1 root       20   0 43692  1992  1020 S  0.0  0.0  0:01.02 /sbin/init showopts
  324 root       20   0 34160   892   604 S  0.0  0.0  0:00.07 /lib/udev/udevd
  333 root       20   0 41172  1036   892 S  0.0  0.0  0:00.20 /lib/systemd/systemd-journald
  509 root       20   0 33892  1040   664 S  0.0  0.0  0:00.00 /lib/udev/udevd
  510 root       20   0 34156   616   324 S  0.0  0.0  0:00.00 /lib/udev/udevd
  638 root       20   0 10824   452   336 S  0.0  0.0  0:00.45 /sbin/mount.ntfs-3g /dev/sda2 /windows/D -o rw,noexec,nosuid,nodev,gid
  639 root       20   0 10824   452   336 S  0.0  0.0  0:00.37 /sbin/mount.ntfs-3g /dev/sda1 /windows/C -o rw,noexec,nosuid,nodev,gid
  657 root       20   0  8520  2332   252 S  0.0  0.1  0:01.76 /usr/sbin/haveged -F 1 -w 1024 -v 0
  659 avahi      20   0 30128   944   680 S  0.0  0.0  0:00.02 avahi-daemon: running [linux-lzgz.local]
  679 root       20   0 34504  1024   768 S  0.0  0.0  0:00.01 /lib/systemd/systemd-logind
  703 root       20   0 12628   420   360 S  0.0  0.0  0:00.00 /sbin/agetty tty1 38400
  725 root       20   0  317M   700   216 S  0.0  0.0  0:00.05 /sbin/rsyslogd -c 5 -f /etc/rsyslog.conf
  728 root       20   0  317M   700   216 S  0.0  0.0  0:00.00 /sbin/rsyslogd -c 5 -f /etc/rsyslog.conf
  729 root       20   0  317M   700   216 S  0.0  0.0  0:00.02 /sbin/rsyslogd -c 5 -f /etc/rsyslog.conf
  730 root       20   0  317M   700   216 S  0.0  0.0  0:00.00 /sbin/rsyslogd -c 5 -f /etc/rsyslog.conf
  722 root       20   0  317M   700   216 S  0.0  0.0  0:00.09 /sbin/rsyslogd -c 5 -f /etc/rsyslog.conf
  744 root       20   0  4220   344   216 S  0.0  0.0  0:00.00 /usr/sbin/acpid
  977 root       20   0 28928   480   312 S  0.0  0.0  0:00.00 /usr/bin/kdm
 1944 root       20   0 10072   728   572 S  0.0  0.0  0:00.00 /sbin/dhclient6 -6 -cf /var/lib/dhcp6/dhclient6.eth1.conf -lf /var/lib
 2455 root       20   0 16868    12     0 S  0.0  0.0  0:00.00 /sbin/dhcpcd --netconfig -L -E -HHH -c /etc/sysconfig/network/scripts/
 3222 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3223 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3224 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3225 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3226 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3227 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3228 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3229 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3230 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3231 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3232 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3233 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3234 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3235 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3236 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3237 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3238 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3239 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3240 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3241 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3242 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3243 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3244 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3245 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3246 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3247 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3248 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
 3249 root       20   0 4090M  1940  1100 S  0.0  0.0  0:00.00 /usr/sbin/console-kit-daemon --no-daemon
F1Help  F2Setup F3SearchF4FilterF5Tree  F6SortByF7Nice -F8Nice +F9Kill  F10Quit</pre>

Sorry for the line wrapping, not sure how to work around…

londy · September 11, 2012, 9:22am

It’s probably just creating its database. It takes awhile the first time it runs. It’s normal. If you click on the system tray’s expand arrow button, you’ll see Desktop Search File Indexer. Right click on it and you can configure it: disable it completely, choose which folders to index, etc.

seanthor · September 12, 2012, 3:14am

I’ve tried ignoring the spiking jumping around the cores, but today it was occuring on most of the cores rather than just a couple–ie 6-8 cores near 100% simultanesouly. I also noted some odd behavior, such as extreme sluggishness, freezing of the GUI and programs taking 20 secs to several mins to open (or fail to open) over the past 20 mins. When I tried to download a PDF file, I noticed that my HDD is now FULL. When I did the install on Sunday, there was about 166 GB on a roughly 570 GB partition. Now there is an additional 400 GB of data, and I have no clue where it came from.

Is this related, or do I nee to start a new thread? Also, is there a log file I can check to see what the hell is going on?

seanthor · September 12, 2012, 3:44am

I just noticed that in my home folder there is a file “.xsession-errors” that is 86.6 GB! So far I have not been able to open it.

Also the directory .kde4 contains 329 GB.

I think I is the bulk of it, but I still have not narrowed done the culprit.

seanthor · September 12, 2012, 4:05am

UPDATE: I have confirmed the location as a log file currently 329.2 GiB. It’s labeled “soprano-virtuoso” and is located at:

/home/seanthor/.kde4/share/apps/nepomuk/repository/main/data/virtuosobackend/soprano-virtuoso.log

I am not sure what is going wrong, and would appreciate guidance on how to proceed.

(On a side note, I’m sorry if the chain of posts is annoying, but this problem is quite confusing and very frustrating to me. I was not expecting to be able to find 2 files containing 400+ GiB.)

malcolmlewis · September 12, 2012, 5:09am

Hi
Have you seen this thread?
http://forums.opensuse.org/english/get-technical-help-here/applications/457333-nepomuk-problem.html
Some bugs;
https://bugzilla.redhat.com/show_bug.cgi?id=746499
https://bugs.launchpad.net/ubuntu/+source/virtuoso-opensource/+bug/883222
https://bugs.kde.org/show_bug.cgi?id=280750

–
Cheers Malcolm °¿° (Linux Counter #276890)
openSUSE 12.2 (x86_64) Kernel 3.4.6-2.10-desktop
up 1 day 7:14, 4 users, load average: 0.44, 0.25, 0.14
CPU Intel i5 CPU M520@2.40GHz | Intel Arrandale GPU

londy · September 12, 2012, 6:42am

Well, I would just delete that folder and start over.

Q. My Nepomuk database has been corrupted. How do I clean it?
A. In the extreme case your database is really corrupted and all other attempts have failed, you can delete the$KDEHOME/share/apps/nepomuk directory (where $KDEHOME is usually .kde or .kde4) while Nepomuk is not running. The database will be cleared, but you will also lose existing information such as tags, ratings and comments.

Nepomuk - KDE UserBase Wiki

Just for reference, my database is 75mb (only 5,000 files indexed) and the log file is 80 bytes. It’s working fine for me.

londy · September 12, 2012, 7:14am

seanthor:

I don’t remember this activity with 12.1, should I be concerned? Did a clean install of both / and /home, then copied my backup from external HDD to the new /home:
cp -r -vvv seanthor /home 

Did you do this while logged into kde and with nepomuk running? If yes, then that might have corrupted the database.

seanthor · September 13, 2012, 12:08am

Thank you, I must have missed that forum post, and I did check out the bugs. I’ve deleted the log and db file, and will see if that helps.

seanthor · September 13, 2012, 12:13am

I’ve deleted the giant files, should I delete the entire nepomuk directory just to be safe? I was planning to wait and see. Although I think you’re right, I botched the copying. Whoops. :shame:

seanthor · February 3, 2013, 4:09am

Update: since taking the above actions, the problem has not recurred.

Also I have received no news of a bugfix for this problem at this time.

Cheers!