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Your video card needs upgrading. Look into a HD 6850. It's ranked #1 in terms of bang for buck. 150 bucks with rebate. I am a longtime Nvidia fanboy and decided to go ATI this time due to cost per value with this card. Loving it thus far.

Ranked 12th overall for high end video cards..
http://www.videocardbenchmark.net/high_end_gpus.html

Ranked #1 per value for price
http://www.videocardbenchmark.net/gpu.php?gpu=Radeon+HD+6850
Don't listen to the members who don't know any better than to pooh-pooh your graphics setup and tell you to spend a lot of money for no benefit.

You're on target by thinking you have a heat problem. G80 cards run hot, but 80-90C at idle (that's what yours are running) is beyond just running hot.

Older cards may require you to pull the cooler, or at least pull the cover off of it (if the cover will come off without pulling the whole cooler) in order to clean it properly. This is well worthwhile for cards that have been in service in a dusty place for years. I was able to salvage two cards that had been overheating and causing BSODs this way.

If you have to pull the whole cooler off, you'll need thermal compound (Arctic Silver 5 or Arctic Cooling MX-4) for the GPU and thermal pads (a little harder to find) for the RAM chips in order to reassemble. Compared to the cost of a sidegrade to a 6850, that's peanuts.
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Marrius: The 4 cores are running at around 120 degrees each which seems normal. However, one graphics card is running at 177 degrees and the other is at 195 degrees. And that is when the game is not running so overheating may very well be the issue. I do know that one of the cards is perfectly clean, probably the cooler one, but the rest of the computer is dusty. Tomorrow I will clean it our carefully and hope that will help. Any other suggestions in cooling a system?
That's extremely hot, under game load your temps will be well over the GPUs threshold.

cjrgreen has some solid advice. Dust and thermal paste decay are very common problems when your hardware has been running for a few years. I'm assuming you've had those cards for quite some time now, which is fine, they just need a bit of a "service". Its a lot easier than it sounds, really just unscrewing some screws, smearing some paste and screwing it all back together, 10 minutes.
I'd go down the memory leak path. Make sure your drivers are updated.
I'm running a Radeon 4850 (AMD PCB) which idles at 85 Celsius and loads in Witcher 2 (1600 x 900, downscale med, bloom on, shafts on, min shadows, dangling limit, med decals, blur on) up to 115 Celsius. Has been like this since the beginning no problem. No crashes, no slowdowns, nothing - it's so hot it instablisters you when you touch the PC case in the back or the soundcard (3 centimeters above, in a pciex x 1 slot).

You can watch the framerate, temperature during gameplay, GPU speeds or loads with MSI Afterburner. Message me if you need help figuring out the settings of its overlay server.
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Marrius: The 4 cores are running at around 120 degrees each which seems normal. However, one graphics card is running at 177 degrees and the other is at 195 degrees. And that is when the game is not running so overheating may very well be the issue. I do know that one of the cards is perfectly clean, probably the cooler one, but the rest of the computer is dusty. Tomorrow I will clean it our carefully and hope that will help. Any other suggestions in cooling a system?
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Denominus: That's extremely hot, under game load your temps will be well over the GPUs threshold.

cjrgreen has some solid advice. Dust and thermal paste decay are very common problems when your hardware has been running for a few years. I'm assuming you've had those cards for quite some time now, which is fine, they just need a bit of a "service". Its a lot easier than it sounds, really just unscrewing some screws, smearing some paste and screwing it all back together, 10 minutes.
Yeah, it is that simple; the hardest part is finding the thermal pads for cards that are designed with gaps between the RAM chips and the cooler. You have to replace them; you can't re-use them. But getting the right thickness in a reasonable quantity (i.e. not in 15-meter rolls) takes some shopping.
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Marrius: I have read a lot of forums and suggestions, but can't figure out why the game is running so slow. At first it runs perfectly fine, but after a few minutes it is running so slow i can do anything. Even the mouse moves with a delay.

I run a lot of games on this computer and have never had any problems before running them at high settings.

I have tried many different resolution and graphic options. I have downloaded new video drivers. Nothing works.

Windows XP, media center edition, sp3
Intel Core 2 extreme CPU Q6800 @ 2.93GHz
4 GB RAM
nvidia geforce 8800 ultra

(I reposted because i forgot to mark it as a problem)
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NameLess1: an 8800 ultra is pretty much the minimum requirement for the game I'm not surprised it runs slow...well technically the 8800gt is the min but an ultra is basically a gt and 1/4th...
His card is actually fine. I run the game at 1920x1200 on max settings (minus UB ssao and motionblur) on a 9800 GT (which is very similar to his card) and get 18-35 FPS. Yes it's not high, but definitely playable.

Your card might be overheating and throttling down the clockspeeds after a while. (sometimes it downclocks without even overheating due to buggy drivers.) You should watch your GPU temperature and clockspeeds (evga precision software rocks for this) and see if anything unusual happens when the game gets laggy. For reference, my 9800 GT runs at around 60 celcius at full load.

If none of that helps, I would start looking at the CPU.
Post edited June 10, 2011 by PrayForDeath
I just went back and noticed the temps he posted. For an idle temp, that is way too high. By the time I was ready to end the game for the night, I noticed the temp om my GTX560ti was at 73C and kind of grimaced, then I realized that the card tends to run warmer than most crads and this game tends to heat things up a bit anyway, due to the demand. Also, the ambient room temps were up some, which adds to the Temp increase. The 8800's are usually a pretty cool running card, and at the gae of it, the suggestions about reapplying the thermal Compound is a good suggestion and checking on dust build up as well. It is possible that the fan itself could be getting a little weak ( they can be changed, but not always the easiest thing to find a replacement ).
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cjrgreen: Don't listen to the members who don't know any better than to pooh-pooh your graphics setup and tell you to spend a lot of money for no benefit.
Had to sign in just to quote this. On pretty much any game forum out there most people will only glance at the OP's specs, not even read his actual problem, and if they find the specs too low, immediately suggest a costly system upgrade. It's not really the way to "solve" anything other than earning bragging rights, if you can improve the situation on your current specs without paying any money.

That being said, it's definitely an overheating issue or something else. The game's playable at 30+ FPS for me on a 1,5 year old laptop with a Core 2 Duo T6600 2.2 Ghz, 4 GB RAM and a Mobility Radeon HD 4670 1 GB (Win 7 64 bit) on 1280x720 res, HIGH textures with no texture downscaling, other settings low except for medium decals and "near" LOD, cinematic depth of field (+gameplay), light shafts and bloom. And I think those are about the same level specs save for the worse CPU too, yet my system doesn't overheat from the game or anything. You might wanna check if any other games cause high temperatures too, because I doubt Witcher 2 would be the only game to cause such high temperatures.
When cleaning the dust off the inside of my computer, i found a think layer of dust completely blocking the vent on the cooling system. It wasn't in a position easy to see or i would have noticed it long ago. After cleaning it, the processors averaged 35 C each and both cards were about 75 C all after playing the game for an hour and a half straight with no problems at medium graphics. The GPU's were at 60 C idle. So that definitely was the problem.

Thank you to everyone who took the time to respond with suggestions. I truly appreciate everyone's help.