First of all I don't have a Mac Pro... yet, but I do have a fair bit of experience with Macs as I have an iMac.
So you want to install Ubuntu on one HDD of the multiple HDD's in your Mac Pro, Well First you will need to make shure that you are able to back up you OS X partition so if something does go wrong you can always restore it. The second thing you need to do is to open Disk Utillity to partition the Hard Drive that you want to use, to do so open your Applications folder and open the Utilities folder inside there, inside you will find Disk Utility, another way you can do this is by pressing Command and Space together and then typing Disk Utility and pressing Enter. Lets say you are using the second HDD to install Ubuntu, this will usually be the second HDD in the list and have the identifier of disk1, you have to select that Disk and then select the Partition tab, in the drop down list that says "Current Layout" Select "2 Partitions", Click on the "Options" button and make shure that GUID Partition Map is selected then click Done, rename the first partition to Ubuntu and set its partition format to MS DOS FAT, rename the second partition to Linux Swap and and set the partition format to MS DOS FAT, next you will need to set the size of the Swap partition to 2 - 4GB's whichever one you want the swap to be, this makes shure that the Linux Swap isn't half of your HDD, next click "Partition" (It may help to turn off you computer and remove all hard drives except the First HDD in slot "1" and the hard drive that you wish to install Ubuntu on to minimise confusion). Once this is done you may insert your Ubuntu disk into the DVD drive and turn off your computer, If you want you can remove the OS X HDD in slot "1" so that Ubuntu only sees the HDD that you want to install to. When turning on your computer make shure you are holding down the Option/Alt key on your keyboard as this will open the OS selection menu, use your mouse or keyboard to select the "Windows" disk icon not the "EFI" disk icon, this will start the Ubuntu live CD so you can start the installation, pick either "Try Ubuntu Now" or "Install Ubuntu", I personally pick "Try Ubuntu Now" so I can setup Wifi, change some settings before installing, Go though setup as usuall until you get to the screen that says Choose installation type, Click "Something Else" instead of erasing the entire disk, once on the next screen you will need to select the First Partition of /dev/sdb (or /dev/sda if you chose to remove the OS X HDD before installing), click Change and set the partition type to ext4, set the mount point to "/" and check the Format option, click done and select the second partition, this partition should be 2-4 GB as it is the swap partition, set the partition type to Linux Swap and click done, next make shure the boot loader is set to install on /dev/sdb (or /dev/sda if you took all other HDD's out before hand), finally make shure that the first partition is highlighted and click Install, continue installation as usual until it finishes, when finished don't restart your computer as you will need to shut it down so you can insert the HDD with OS X on it if it was removed and then start up your computer, at this stage your computer will start up to OS X and not Ubuntu, this is fine as you will need to install rEFIt in order to be able to boot Ubuntu, to do so goto
http://refit.sourceforge.net/ and download the .DMG file from there, open the DMG file and select the installer file that is inside it, continue with the installation of rEFIt, make shure you check "Macintosh HD" as the install destination or it may stuff up your computer or just won't work properly. Once done you will be prompted to restart your computer, when booting nothing will show up and OS X will start as usual, your will need to restart a second time for the rEFIt menu to show up, once your Mac has restarted rEFIt should have shown up on your screen and you can select either Mac OS X or Linux, don't select Linux yet as you will need to open the Partition Tool at the bottom of your screen, it may or may not say that your partition table needs resyncing, if so type y and press Enter if not press Enter anyway, reboot once more than Select either OS X or Linux, Enjoy!
This method if done properly should work as the Mac EFI automatically knows if the BIOS emulation layer needs to be used and rEFIt handles booting Linux more better the the Mac EFI does, please note that rEFIt, even thou works very well, is outdated and may not work with future updates of OS X, but for now it works fine and is the best way to run Ubuntu on a Mac, hope this helps you on your quest to Triple boot OS X, Ubuntu and Windows on your new Mac Pro!
Best regards, supermariofan25
P.S. If this method doesn't work then try setting the Partition Table Map to Master Boot Record instead. Disclaimer, I have not tried this method before as I currently don't have a Mac with multiple hard drives and should only be used as a guide line so please do proceed at your own risk, I will update or remove this post later on when I do have access to a Macintosh with multiple hard drives in the near future. Therefore I do highly recommend that you make a backup of you entire OS X HDD with Time Machine on an external HDD before proceeding so that if anything does seem to go wrong then you can restore your Mac to its original condition.
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