On 11/09/2016 03:52 PM, Tracy Reed wrote:
I have booted the machine the the SATA
drive in and with it out. It only boots properly with the drive out. But
the NVMe device and OS partition is always hd0,msd0s1.

I recently have done experiments like you describe.
Your added drive should be in a SATA slot higher numbered than the first one
on your motherboard.  Most motherboards assign /dev/sda to the first one.

I found that wiping the added drive
stopped the bad influence an added drive has on my working system.
The added drive was being picked up as the one to boot from.

A handy tool for wiping a disk is:

sgdisk -Z "/dev/disk/by-id/ata-XXXX"

where ata-XXXX is the ID label of the disk you are certain you want to be 
zeroed out.

that will take away partition table and GPT boot sector and a bios boot sector 
whichever kind it was.

If it still gives trouble, use badblocks to wipe out everything:

badblocks -wsv /dev/disk/by-id/ata-XXXX

badblocks writes on and covers the whole disk surface as above, so it could 
take along time.

You could add [ last_block ] [ first_block ]
to make it just zero out one end of the drive.

use gdisk to get the blocks to use for first, last.  A MBR is before the first 
sector, so
setting last block to be close to first block and using first block from gdisk 
should speed
up zeroing the boot partitions of a terabyte drive...

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