I installed ubuntu 14.04 about 2 months ago and about 1 month ago this issue began to occur:

Whenever HDD is used (saving a file, file download, opening a file..even small ones) there is about 60% chance that computer freezes for about 20 seconds. I can move mouse, but nothing reacts. When I turn on mySQL server and apache and browse hosted web, it freezes really often.

I don't recall installing anything special that month ago, which could cause this. Before that, I had ubuntu 12.04 and everything was fine. My RAM is only half full and the application for testing a system didn't show anything.

I am on a Lenovo Z570 notebook, i5 dual core CPU, 4 GB RAM. One physical 750GB disk, three NTFS partitions (I have dualboot with windows) and the linux filesystem.

Any idea, what might cause this? Thank you very much for any help!

EDIT: few new things: It seems that this bug applies only to the Home folder and subfolders. Whenever I create, copy or delete file or folder, everything is fine for 3 seconds and then the HDD starts spinning and everything freezes for 20-30 seconds. I remembered, that maybe that month ago a friend changed some config files so that my three partitions would attach during the boot. Maybe that could have caused this issue, but can't tell for sure.

Screenshot of System monitor: http://i.stack.imgur.com/CEuFf.png

  • The thing you call 'my RAM' is actually quite a bit more then 'half full', and there is also some swapping, as 'my swap' gets used. I'd say you probably run out of my RAM. – mikewhatever Mar 28 '15 at 22:55
  • Yes, I didn't write it properly, screenshot shows 3/4 full ram, but I've been watchin the monitor for many days and the freezes doesn't seem to depend on ram usage. As you can see, the swap and ram graph doesn't change. I'm almost sure it depends on disc usage. – Martin Čejka Mar 28 '15 at 23:05
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    Then, one of the partitions may be too full, or you might want to experiment with the i/o scheduler. In 12.04 it was CFQ, and in 14.04 it's deadline. phoronix.com/… – mikewhatever Mar 28 '15 at 23:21
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    I/O errors maybe ? Try running dmesg when it happens (or look at /var/log/dmesg). – MoonSweep Mar 28 '15 at 23:50
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    I'd suggest installing gsmartcontrol and run short and extended self-tests (or, if you're comfortable with command line, install only smartmontools and use smartctl). – MoonSweep Mar 29 '15 at 14:18

Finally I solved it by uninstalling applications and deleting folders in my home folder. I had 4 bitnami stacks (which is apache, mysql server and application each) installed at one time at home folder, each with about 10 000 files inside. I uninstalled 2 of them and the freeze time dropped from 30 seconds to 2 seconds and then I unistalled all of them and it's perfectly quick as it should be now.

  • Just out of curiosity: what type of file system do you have on the partition with the home directory? How much space did it have left? How many free inodes did/does it have? Is it highly fragmented? All common Linux file systems (ext4, btrfs, xfs) should have no problem dealing with ±100,000 inodes with the default creation/tuning parameters. You'd need to throw tens of millions of files at them to make them hiccup. – David Foerster Feb 15 '16 at 9:45
  • Sorry, I already reinstalled my linux and there is no way to get these information now. But I had the ext4 filesystem. – Martin Čejka Apr 7 '16 at 5:47

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