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I am trying to partition a usb 3 drive but for some reason parted can't properly set the start sector. The drive is identical to multiple other sata drives, the only difference is that it's inside a usb 3 enclosure with 2 port hub integrated. I wouldn't have though it would matter.

Here are the steps I always used before:

sudo parted /dev/sd?

mklabel gpt

mkpart primary 0% 100%

quit

Here is fdisk -l output of the last 2 drives:

Disk /dev/sdk: 7.3 TiB, 8001563222016 bytes, 15628053168 sectors

Units: sectors of 1 * 512 = 512 bytes

Sector size (logical/physical): 512 bytes / 4096 bytes

I/O size (minimum/optimal): 4096 bytes / 4096 bytes

Disklabel type: gpt

Disk identifier: DB93D173-858A-475C-81CD-DB616E91C110



Device     Start         End     Sectors  Size Type

/dev/sdk1   2048 15628053134 15628051087  7.3T Linux filesystem





Disk /dev/sdl: 7.3 TiB, 8001563221504 bytes, 15628053167 sectors

Units: sectors of 1 * 512 = 512 bytes

Sector size (logical/physical): 512 bytes / 4096 bytes

I/O size (minimum/optimal): 4096 bytes / 33553920 bytes

Disklabel type: gpt

Disk identifier: B3791850-76F8-4CE2-B1CC-DF40886292CE



Device     Start         End     Sectors  Size Type

/dev/sdl1  65535 15628000379 15627934845  7.3T Linux filesystem



Partition 1 does not start on physical sector boundary.

Second drive is the problematic one.

Performance really seems to take a big hit as formatting to ext4 takes a long time (never waited to finish) where normally it would only take seconds. Why is this happening? How can I get proper alignment?

The only other difference I can think of is that it was originally formatted as ntfs with some un-partitioned space. I also ran this command to clear any leftover partitions: dd if=/dev/zero of=/dev/sdl bs=512 count=10000 with no luck.

Using optimal alignment doesnt work either:

sudo parted -a optimal /dev/sdl mkpart primary 0% 100%





Warning: You requested a partition from 0.00B to 8002GB (sectors 0..15628053166).

The closest location we can manage is 17.4kB to 1048kB (sectors 34..2047).

Is this still acceptable to you?

The optimal I/O size of the second drive is much larger than that of the first one; that is probably what is causing the issue. This article from 2013 suggests to manually align partitions starting at (Optimal I/O + Alignment Offset) / Physical Block Size = starting slice, and reading how parted words nowadays it seems like this was rolled in to how parted works by default. Now, performing that math on your parameters returns 8191.875 as the starting slice, which is probably not a valid sector address.

It seems most likely to me that your USB enclosure is misrepresenting the optimal I/O of the drive. I would try manually specifying the starting sector as 2048, matching the first drive, when you make the partition try using mkpart primary 2048s 100%. That should work around it.

If you have the opportunity you can check this beforehand by plugging the drive into a computer without the USB enclosure and then checking /sys/block/[drive]/queue/optimal_io_size if it exists. If it doesn't match, the USB enclosure is probably misreporting the drive's capabilities.

This was an issue in fdisk in util-linux. I reported to upstream quite sometime ago and it has been fixed:

https://github.com/karelzak/util-linux/commit/acb7651f8897ae73d0f45dd75bc87630001c61b9

So if you use fdisk in util-linux v2.27-rc1 or later to create partitions, you would not experience the problem.

I am not sure if parted has the same problem, if it does, it should probably introduce similar hack. (So file a bug report to upstream if you want to get it fixed: http://savannah.gnu.org/projects/parted/)

EDIT: Just notice that you are using GPT on both disks. IIRC gdisk does not suffer from this problem because it doesn't calculate alignment using the optimal i/o size, instead it statically defaults to 2048 and allows you to set it to any value range from 1 - 65536 (x -> l).