Use e4defrag to defrag your files

If your ext4 file system is created with the extent option (it's default in recent distros), you can use the e4defrag utility to check and defragment it online i.e. without umounting.

Just check fragmentation level with something like this (you need to be root to see details):

sudo e4defrag -c /path/to/myfiles

Here's an example of the output you can get:

$ sudo e4defrag -c iso/

<Fragmented files>                             now/best       size/ext

1. /home/gerlos/iso/debian-live-7.5.0-i386-rescue.iso

                                                 7/1         111177 KB

2. /home/gerlos/iso/systemrescuecd-x86-4.4.1.iso

                                                 4/1         100897 KB

3. /home/gerlos/iso/debian-live-7.5.0-amd64-rescue.iso

                                                 6/1         116053 KB

4. /home/gerlos/iso/ubuntu-14.04.2-server-amd64.iso

                                                 8/1          76160 KB

5. /home/gerlos/iso/ubuntu-14.10-desktop-amd64.iso

                                                15/1          75712 KB



 Total/best extents             40/5

 Average size per extent            90577 KB

 Fragmentation score                0

 [0-30 no problem: 31-55 a little bit fragmented: 56- needs defrag]

 This directory (iso/) does not need defragmentation.

 Done.

As in this example, most of the time it will tell you that no defragmentation is needed, but if you want to do it anyway you can use (you don't need to use sudo to defrag your own files):

e4defrag /path/to/myfiles

Your users can even run it on their own files, there's no need to be root unless you want to work on other user's or system files.

e4defrag is in the e2fsprogs package, and I guess it's already installed on your Ubuntu system.