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Is there a significance to installing the SDD in bay 1? I just installed mine, but I left the original HDD in bay 1, but the computer still restarted using the SDD automatically after I installed OX X onto it. Does it run faster if it's in bay 1?

I wouldn't imagine so? It might just be for organization. After all, they're all SATA 2 ports. There shouldn't be a speed boost anywhere
 
Ohhhh dilemma... Sorry to keep adding to this thread, I'm just trying to make up my mind. This will end up being my most expensive and fastest computer to date (most I've ever spent is $1600 on my MacBook Pro, and $1100 on a desktop).

I much prefer working in Mac OS X, but can't help but think I'd get more for my money if I went with Windows 10 (I already have a license too). I would be spending around $2500 on the desktop, and just feel like I have much more access to better things with building my own. SATA 3 for a start, and the option for more than 6 hard drives in this method, plus more pci slots (not having to waste one on a USB 3 card is a big bonus), but then it's Windows... And I prefer OS X.... Not sure what to do here...

I hear you. I'm feel the same. I really would rather use OS X on my desktop, but there is nothing in the current Mac desktop range that interests me. Mini is too gutless, particularly the GPU, iMac doesn't come with a 40" screen, and I can't justify the cost of a new Mac Pro for my usage. So I'll keep using my 09 Mac Pro until it can't be kept at a performance level I'm happy with for a cost I'm prepared to pay. At the moment I'm very happy with how fast it feels in general use. Nothing feels slow, apart from when I need to run a Windows program, and the parallels VM isn't already running, so I have to wait for Windows to boot.

In my opinion, the thing that makes the biggest difference to how snappy a computer feels in general use is the hard drive, or SSD. (Assuming you have enough RAM). The fastest Mac Pro running off a slow spinning drive will feel slower than an entry level Mac Mini or iMac that has even a low end SSD in it. Sure, doing heavy processing will be faster on the Pro, but it won't feel fast to use. That's why the next thing I spend money on for my Mac will likely be a PCIe SSD. I don't feel an urgent need to do it now, my SATA3 SSD (on an Apricorn SATA3 card) is fine, but that is what makes modern Macs feel fast.

I still have CPU, GPU, and SSD option available to me when I feel I need more speed. But there will come a time, I hope is still a few years away, when the return on investment for upgrading is no longer favourable. I just hope by then Apple have got some more interesting Macs available. I really don't want to go back to Windows!
 
Is there a significance to installing the SDD in bay 1? I just installed mine, but I left the original HDD in bay 1, but the computer still restarted using the SDD automatically after I installed OX X onto it. Does it run faster if it's in bay 1?

It's a boot sequence issue . A cMP will look for a bootable device in HDD Bay 1 first . I just completed a CPU Tray upgrade for a client , who has a Mac Pro 4,1 (2009) . He had an older Samsung SSD in Bay 3 with El Cap installed . I switch that drive to HDD Bay 1 and shaved about 7 seconds off the cold boot time . Could have been an issue with just that drive , but I've always had good luck with Bay 1 populated with an OS X bootable drive .
 
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It's a boot sequence issue . A cMP will look for a bootable device in HDD Bay 1 first . I just completed a CPU Tray upgrade for a client , who has a Mac Pro 4,1 (2009) . He had an older Samsung SSD in Bay 3 with El Cap installed . I switch that drive to HDD Bay 1 and shaved about 7 seconds off the cold boot time . Could have been an issue with just that drive , but I've always had good luck with Bay 1 populated with an OS X bootable drive .

Could you not just select the boot drive from Startup Disk under System Prefs and get around the problem that way?
 
Could you not just select the boot drive from Startup Disk under System Prefs and get around the problem that way?

It must have something to do with a faster initialization speed of the Mac's Boot ROM during Start Up , when the boot drive is installed in HDD Bay 1 . It actually is quicker and when clients have a Start Up issue one of the things I look for is where the boot drive is installed . The last client that had an issue with this , had a SSD installed in HDD Bay 3 and that drive was already selected as the Start Up drive in System Preferences . When his Mac booted , it struggled to find a bootable device for several seconds (so long a time , it actually gave that flashing ? symbol .) Then found the drive and the Start Up process continued normally . The Mac also performed normally once in an OS X session . And I even tried PRAMing and resetting his motherboard . This did not improve anything . So, I removed the drive from HDD Bay 3 and placed it into Bay 1 and it booted fast and without issue . It could have something to do with SIP (he was using EL Cap) . But I have seen this optimization situation enough that HDD Bay 1 is my preferred location to install a bootable device .
 
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