I just recently upgraded the coolers on my Supermicro server and now it can't find the default boot device unless I unplug ALL of the drives except the boot drive.

This system is an older Supermicro SC846, 24-drive bay, 4U machine. I took it out of the rack, replaced the stock CPU heatsinks with some larger ones that have fans, then re-assembled and re-inserted the drives (in the same order they came out, they're labeled).

Now when I turn it on, the system boots to a screen:

Reboot and Select proper Boot device or insert boot media in selected Boot device and press a key

All of the drives are in the same bay as they always have been, but now the RAID controller won't load it by default.

The system has an LSI 3ware 9650SE-24M8. There are 12 hard drives and 1 SSD. The SSD is (and always has been) in slot 0 of the array and on the controller.

I went through the BIOS, but there's nothing that indicates which drive is the boot drive. Some internet searches indicates that the drive in Slot 0 should be the boot volume and I've confirmed this configuration.

The OS is Debian 9 with grub installed on /dev/sda, which correlates to slot-0 on the controller. I've also tried reinstalling Grub from Debian Rescue, but that had no effect. I also ran grub-update once I got into the system, but that didn't help either; I'm confident this is more of a BIOS issue, but I don't know how to fix it if so.

I found the manual for the 3ware controller which contains this information:

If you will install your OS on a disk or unit attached to the 3ware RAID controller, specify the controller as the boot device. (Note that if you configured more than one unit, the drive(s) specified as Unit 0 will be treated as the boot disk.)

Position the unit you want to be bootable at the top of the list of exportable units.

The boot disk is in slot 0. Is there something I need to do to refresh the boot-flag on the volume? Would this help with the BIOS when it scans the disks?

I have no idea how to fix this.

  • To start, yes this is before GRUB takes hold - so it's a BIOS issue. After that I can't help you much with this particular model. However, you may be able to define which of the drives or RAID abstractions are "the one who boots" via the LSI configuration utility (sometimes separate from the BIOS, accessible via a hotkey during boot).
    – Spooler
    Feb 27, 2018 at 2:44
  • Go into the 3ware BIOS and look around. Feb 27, 2018 at 3:17
  • I have gone through the 3ware BIOS a few times now. Maybe I've missed it, but I can't find anything that would provide how to indicate which device is the 'boot' volume.
    – Andrew
    Feb 27, 2018 at 14:40
  • All your arrays should appear in Exportable Units. Only spares should be listed in Available Drives; such drives are not bootable and won't be exposed to the OS. Feb 27, 2018 at 17:00
  • All drives are exported as JBOD. None show in the 'avaiable' drive section. I'm using an SSD as the boot volume and the other 12 drives in ZFS on Linux; the SSD is not in the ZFS pool(s), it's just a direct install of Debian 9 with Grub.
    – Andrew
    Feb 27, 2018 at 17:09

2 Answers 2


Well, I never quite figured this one one, but I ended up moving the drive off of the 3ware controller and instead have it hooked to an available SATA port on the motherboard directly. With this, I can specify the SATA disk over the 3ware controller and make that the first boot device.


I've had the same problem here... I was in shock, thinking I had to open the 16-disk-bay-server to plug the disk directly on the sata port...

So, went to the 3ware BIOS again (had gone at least 15 times before) after reading your text where says "Position the unit you want to be bootable at the top of the list of exportable units"... how it's done? so, i saw a "PGUP/PGDOWN TO ARRANGE" text at the bottom...


  1. Select with ENTER the array you want to move to the top (where the boot disk resides).

  2. PGUP the array, and it will go to the top.

F8 to save, reboot the system, and go to dance with your wife this night, it deserves a good celebration!!

PD: Who was the stupid who made this interface...

  • It's "enterprise", of course it's stupid! Sep 7, 2018 at 22:54

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