As far as I understand, the warning "Partition 1 does not end on cylinder boundary" can be ignored since most hard drives after 1996 use Logical Block Addressing (LBA) and so the physical sector characteristics of a drive are no longer a relevant concern when aligning disk partitions.
Below is the output of fdisk from default installations of Oracle Linux 6.3 and Oracle Linux 5.8. Both were created under Virtualbox so they have the same "virtual" disk characteristics.
Oracle Linux 6.3
<pre>
# fdisk -lu /dev/sda
Disk /dev/sda: 21.5 GB, 21474836480 bytes
255 heads, 63 sectors/track, 2610 cylinders, total 41943040 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x000a2ccf
Device Boot Start End Blocks Id System
/dev/sda1 * 2048 1026047 512000 83 Linux
Partition 1 does not end on cylinder boundary.
/dev/sda2 1026048 41943039 20458496 8e Linux LVM
fdisk -v
fdisk (util-linux-ng 2.17.2)
</pre>
Oracle Linux 5.8
<pre>
# fdisk -lu /dev/sda
Disk /dev/sda: 21.4 GB, 21474836480 bytes
255 heads, 63 sectors/track, 2610 cylinders, total 41943040 sectors
Units = sectors of 1 * 512 = 512 bytes
Device Boot Start End Blocks Id System
/dev/sda1 * 63 208844 104391 83 Linux
/dev/sda2 208845 41929649 20860402+ 8e Linux LVM
fdisk -v
fdisk (util-linux 2.13-pre7)
</pre>
As far as I can tell, 6.3 and 5.8 have both partitions with sectors that are not a multiple of 8.
How can I avoid the message, even if it may just address a cosmetic issue?