At boot up there is no particular order the cards have to be in. If your monitor is connected to the "main" card then that's the card it will use.
You can run your main card in slot 3 but will drop to 8X because of the card in slot 2
Raid card in slot 1 would be 8x (but 8X anyways) because of the card in slot 2 which takes it down to 8X
8800GTS 512 Black Pearl would be slot 2 @ 8x which is always 8x anyways unless your running a single card in slot 2 then it will run at the full 16X, but you need to go into nvidia control panel and enable the 8800GTS as your physx card.
"Would it be possible to get video output from the "main" graphics card in slot 3 during boot? " If your monitor is connected to this "main" card that's what it will be. And work perfectly fine. Just remember to set your 8800 (in mvidia control panel)as your physx card.
You cannot run at 16X with slots 1 and 3 while there is a card in slot 2 or 4
The only way to run at 16X is if you remove the card in slot 2 or 4
Sorry i had to correct this i got alittle confused myself.

Thanks for your replies!!!

So it depends on whether I attach a monitor to my second graphics card, or not? For example, if I wanted to use more than two monitors at once (and therefore don't dedicate one card to PhysX in the driver), the card in the "lower" counting PCIe-slot would be primary (if monitors are attached to both cards)? Thus directing POST video output to the monitor connected to this card? I assume that I could then chose the monitor that Windows should use as primary from any one of the attached monitors throughout any card?
Just hypothesising... ;)

What's your opinion: is it worth keeping the 8800GTS 512 for PhysX? Considering the hassles with occupied expansion slots and power draw...
 
EDIT: Does using the PCIe x1-slot right below the chipset cooler affect the x16-slots in any way? Is it 2.0 or 1.1?

chizow

Moltenlava 
(this is what EVGA claims in the specs) but some are claiming that function is broken at the moment so it seems if any cards occupy PCIE x16 slots 2+4 they will affect PCIE x16 slots 1+3's bandwidth.

Yep, the x1 slot 2 and 4 operation with slot 1 and 3 are broken right now or the FAQ is wrong, I've posted a few request to look at it and also in the latest BIOS thread, hopefully it gets fixed in an update.

@ Killi, why not run the following config (copied Moltenlava's formatting)

PCIE x16 slot 1 = Primary Graphics Card @ x16 bandwidth 
PCIE x16 slot 2 = empty/vacant
PCIE x16 slot 3 = RAID Card @ x8 bandwidth
PCIE x16 slot 4 = PhysX Graphics Card @ x8 bandwidth

The PhysX card will hang off a bit at the bottom, but it should work as this is how a 2-slot GPU would need to be aligned in a 3-way + PhysX set-up.

Also, the PCIe x1 slot above PCIE x16 slot 1 does work properly and won't interfere with any of the x16 slot bandwidth, the problem is that the Classified's heatsink has a bump that makes virtually every single PCIe x1 expansion card incompatible other than the X-Fi Titanium.

I'd use your suggested configuration, if the RAID-card wasn't dual-slot... ;) (for cooling purposes; it gets way too hot if there's another card right next to it; furthermore I've got a waterblock on it's processor, which doesn't allow for a card in the neighbouring slot).
 
As for the PCIe x1-slot: I'm going to use EK's full board waterblock: does this eliminate the problem with not beeing able to use other cards than the X-Fi?

KILLI
I'd use your suggested configuration, if the RAID-card wasn't dual-slot... ;) (for cooling purposes; it gets way too hot if there's another card right next to it; furthermore I've got a waterblock on it's processor, which doesn't allow for a card in the neighbouring slot).
 
As for the PCIe x1-slot: I'm going to use EK's full board waterblock: does this eliminate the problem with not beeing able to use other cards than the X-Fi?

Ah sorry, didn't catch the part about the RAID card being dual-slot.  If its a custom cooler, have you tried using a single slot cooler and perhaps using something like a spot-cooler for directed airflow?  Otherwise, you're pretty much stuck no matter what.  Moltenlava's recommended configuration would work, but currently populating slot 1 and slot 2 drops slot 3 down to x8 also.
 
As for the x1 slot, yep, using a full board waterblock or using a custom chipset cooler (like the HR-05) would solve the clearance problem for that slot. 
 

hagatha

I have to chime in here... I've had the same issue... 260's in SLI and a hardware RAID card... When I populated the 2nd PCI-e slot with the RAID card it dropped both my 260's to 8x... There was a noticeable change in frame rates and games were kinda choppy... I pulled the RAID card and used the motherboard RAID (intel) and now things are back to where they were. Until the PCI-e architecture changes... I'll put my RAID aside.

hagatha

That's normal and expected for that configuration to drop at least one of the x16 slots to x8, as anything over x1 bandwidth would have to drop bandwidth to the two main PCIe slots.  The FAQ doesn't state differently, the problem is for people who want to use x1 cards in slot 2 and 4 which drops their PCIe lanes to x8 for slot 1 and 3. 
 
But yes, I do agree, the impact on gaming is noticeable even if it doesn't show up in FPS averages.  Most notable is much lower minimum FPS for greater sustained amounts of time, so for a game like Modern Warfare 2 with Vsync On that means I'm actually getting FPS lower than 60FPS with only x8 bandwidth when it never dropped below 60FPS with x16 bandwidth.  Its so bad that I've actually disabled one of my cards in the meantime as a single card @ x16 results in a better gaming experience than two cards @ x8 in SLI.....

Sorry, bear with me here ... I would also like to ask a question:

How can you tell your card(s) are running at their x16 Specifications? Also...

I have TWO GTX295 CO-OP's ... one in Slot 1, and the other in Slot 2

Are they both running at x16/x16? Or is one running at x8? Should I move the other CO-OP to slot 3?

KILLI

Thanks for your replies!!!

So it depends on whether I attach a monitor to my second graphics card, or not? For example, if I wanted to use more than two monitors at once (and therefore don't dedicate one card to PhysX in the driver), the card in the "lower" counting PCIe-slot would be primary (if monitors are attached to both cards)? Thus directing POST video output to the monitor connected to this card? I assume that I could then chose the monitor that Windows should use as primary from any one of the attached monitors throughout any card?
Just hypothesising... ;)

What's your opinion: is it worth keeping the 8800GTS 512 for PhysX? Considering the hassles with occupied expansion slots and power draw...
 
EDIT: Does using the PCIe x1-slot right below the chipset cooler affect the x16-slots in any way? Is it 2.0 or 1.1?

No the single PCI-E x1 slot below the NB cooler is seperate, it doesnt affect the bandwidth of the 4 PCI-E x16 slots, what i was talking about before was putting  a PCI-E x1 card (like a soundcard) in one of the PCI-E x16 slots, that should not affect bandwidth of the other PCI-E x16 slots but it seems it does.

As for hooking up multiple monitors in windows it will let you decide which one is the primary monitor and thus primary card, to save yourself any headaches though boot up and load into widnows first with just the 1 monitor hooked up to the primary card and thenshutdown, add the second monitor and boot up into windows again, that should make windows automatically use the card you want as the Primary Monitor card but you will still have the option in "Display options" to change that.

Keeping the PhysX card depends on how many games you play that fully use PhysX, games like Cryostasis, Batman AA are heavy on the PhysX and will benefit from a dedicated PhysX card, with the lower spec cards you may see around a 20% FPS increase using a dedicated PhysX card compared to having PhysX on the rendering cards up to as much as 40% FPS with something like a GTX 285 (witnessed this myself using my 2 GTX 295' in Quad SLI doing rendering+ physX compared to using the GTX 295's for Quad SLI rendering only and a GTX 285 for dedicated PhysX playing Cryostasis).

That said most games will play with decent enough FPS either way so its down to your personal taste really, i have removed the GTX 285 dedicated physx card for now but i guess once my GTX 295's start struggling with games to do both rendering/physx i may put it back.

jas85

How do you know if the card is running at 16 or 8x ?

thanks :)

GPUZ will show you.

-any fix to this as I just put a X-Fi Forte 7.1 into slot #2 and it dropped my first gtx285 to x8 and gpu #2 is still at x16.
J bios I think,

Dae-San Baek

Hey.

Ima noob. If I want to use a single graphics card only. Can i put it in slot 2 and get 16x?

Thanks

NO
Well that depends on what your calling slot two if your countint the 1X slot as slot 1 then Yes, slot two would be 16X , as long as the dependent 8X slot below it is empty. If your counting full PCIE slots only, the first one is 16X as long as the slot below it is empty and 8X if occupied, that second slot is 8x all the time , the slot below that is 16X as long as the 8X slot below that is empty, and that final slot is 8X. also above someone said something about 40 lanes, it's actualy 36 lanes, see diagram
i7 Architecture: