I have seen this on a few different cpanel servers. Mainly seems an issue with some kernels but I have a server at softlayer and it seems it does it after a server has been up a few days.
At first I thought this was just an issue with grsecurity kernels but seems its an issue with any kernel on it after it been up a few days. On other servers though I have been able to change kernel versions and fix it. I suppose this may be related to disk space used as well.
Problem with my softlayer server is that teh tech didnt follow my partitong directions and installed everything in one slab / so I guess when you edit or add quota it has to scan the entire disk.
I had recently rebooted that server into a 2.6.29-grsecurity kernel and it fixed the issue but tonight I was messing around and it started all over. Not as bad as before but still around 305 minutes of totally lagging the server.
My mount options are
LABEL=/ / ext3 defaults,noatime,usrquota 1 1
Seems to do the same with or without noatime.
Has anyone ran into this issue or know any solution?
os is centos5 64 bit