I recently re-installed debian etch onto a machine i have running as a server.

I setup software raid 1 on two drives connected directly to the motherboard SATA controller. The install went completely sucessfully, the machine boots, runs and disk redundancy works 100%.

I then inserted a PCI SATA controller with 3 drives connected which i plan use in JBOD for some extra storage.

When Linux boots, it recognises the PCI card first and hence assigns the three hard drives as sda, sdb and sdc, this offsets the two main hard drives to sdd+sde which stops the raid array being created properly and makes the machine unbootable.

If i unplug the drives from the PCI card, boot the machine and then hot-plug the drives, they show up as sdc, sdd and sde. This is what i want.

Is there a way of making linux use the onbord SATA controller first or disabling the PCI SATA card during boot?

I would rather not re-assign the raid array to use sdd and sde.

Sorry, this is more of a hardware issue, i should have probably put it in the hardware thread.

This is an issue with the BIOS; the kernel has nothing to do with the enumeration. If it can't be 'fixed' in BIOS, the simplest thing to do is remove the PCI SATA card, set up the system to assemble the RAID in the new configuration (a bit tricky since the initrd image must also be correctly updated), then plug in the SATA, etc etc. Keep a boot CD handy for fixing things.