Question and context:
In the MBR partition table of distros like for example ubuntu-16.04-desktop-amd64.iso, why does a GPT partition appear to overlap the primary boot partition? This seems to generate errors if I try, in any way, to edit the partition table.
I want to edit the MBR to add USB persistence (as described elsewhere), and must add a partition or enlarge the boot partition.
I believe this used to work, but the overlapped GPT #2 partition in this and similar distros appears to badly confuse fdisk, sfdisk, parted, gparted, and partprobe.
My machine is a MBR, and not a GPT bios.
What am I missing?
Here is the distro's MBR partition table (directly from the ISO file):
cat ubuntu-16.04-desktop-amd64.iso | xxd | head -32 | tail -5
00001b0: 28db 2b00 0000 0000 708e 0e0e 0000 8000 (.+.....p....... 00001c0: 0100 0058 e0fa 0000 0000 6048 2c00 00fe ...X......`H,... 00001d0: ffff effe ffff 4411 2c00 8012 0000 0000 ......D.,....... 00001e0: 0000 0000 0000 0000 0000 0000 0000 0000 ................ 00001f0: 0000 0000 0000 0000 0000 0000 0000 55aa ..............U.
(To decode this see https://en.wikipedia.org/wiki/Master_boot_record.)
The table starts at address 01be, where you see "80", for the #1 primary boot partition.
Then notice the "ef" at address 01d2 which denotes the #2 primary partition as being type=GPT.
Here's a breakdown of the table by partition (little endian):
partition#1 (normal MBR): 80 = 'boot' partition flag 00 01 00 = starting HSC (head, sector, cylindar) 00 = partition type ("Empty partition entry") 58 e0 fa = last HSC (head, sector, cylindar) 0000 0000 = LBA (logical block address) of first absolute sector in the 6048 2c00 = number of sectors in partition partition #2 (GPT): 00 = non-boot partition fe ff ff = starting HSC (head, sector, cylindar) ef = partition type ("EFI system partition") fe ff ff = last HSC 4411 2c00 = LBA (logical block adr) of first abs sector in part. 8012 0000 = number of sectors in partition
Attempts to edit partition table:
fdiskreports that these partitions overlap. Note how the beginning of sdb2  is inside of sdb1 [0-2955679] from
sudo fdisk -l /dev/sdb
Disk /dev/sdb: 14.5 GiB, 15527313408 bytes, 30326784 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 Disklabel type: dos Disk identifier: 0x40a863e7 Device Boot Start End Sectors Size Id Type /dev/sdb1 * 0 2955679 2955680 1.4G 0 Empty /dev/sdb2 2927216 2931951 4736 2.3M ef EFI (FAT-12/16/32)
From what I've read, it's ok to have a GPT partition, but not for partitions to overlap.
When I try to dd the iso to a usb stick, the trouble begins. The stick boots Ubuntu live ok, but I can not edit the partition table without errors (that is while not booted and not mounted), no matter which partition editor I try.
Furthermore, I can't even delete the partition table and return the USB stick to normal without the following lengthy procedure:
dd if=/dev/zero of=/dev/sdb bs=[something like 512 or 2048; doesn't matter] count=[some large number like 100000^]
^Smaller numbers don't always seem to fix this. I suspect you need to not only wipe out the primary fs blocks, but the secondary ones also.
and then use
fdiskto make a new ms-dos partition table on the stick.
Note, if I don't do the dd above to wipe before creating a new partition table, I get the following error message or similar when I try to edit the partition map (from either debian8 or ubuntu-16):
Libparted Warning The driver descriptor says the physical block size is 2048 bytes, but Linux says it is 512 bytes.
Also from ubuntu-12, I get this most enlightening message:
gparted -l /dev/sdb: libparted : 2.3 Could not stat device -l -- No such file or directory. /dev/sdb contains GPT signatures, indicating that it has a GPT table. However, it does not have a valid fake msdos partition table, as it should. Perhaps it was corrupted -- possibly by a program that doesn't understand GPT partition tables. Or perhaps you deleted the GPT table, and are now using an msdos partition table. Is this a GPT partition table? Both the primary and backup GPT tables are corrupt. Try making a fresh table, and using Parted's rescue feature to recover partitions.
So how do I edit the distro's MBR?
BTW, I'm NOT asking how to fix the overlap, as this is the way the distro actually is, and from the looks of it, has been for some time, (I also looked at Ub-v16, 14 and 12), rather I'm looking to figure out how to edit it if possible.
Could this be caused by too many applications of isohybrid (used to add a ms-dos MBR to a CDROM 9660 iso so it can boot on a USB)?
Is there an other, possibly newer partition table editor to use?
Is there a different, perhaps older, Ubuntu distro which doesn't have this issue?