Heat. What are you using to monitor? find one that is good and reliable.
Airflow. Location and space around your Mac in your work space.
ATTO card. It has its own fan. Does it have a utilty, thermal readings showing and fan speed?
And testing... one thing at a time.
Disconnect everything for testing.
SMC Reset you already did (mention such things).
If you really want to, then of course take out the ATTO too while testing.
And oh, are you running 10.8.2 or not?
Did it ship with AHT or does it run a test from ML Recovery Mode?
Thanks for reply. There is not an external heat problem. The temperature around the
system is about 55 degrees! I had the system turned off for a week or two, and turned it on. All periperals
were connected, etc i.e. normal operation. I powered the system on, and the power supply fans came on immediately! Once the system is running, I can sometimes cause fans to stop by putting system to sleep.
Also the fans may not come on for an hour or two. There is no way to predict or duplicate scenario.
There are several fans inside the Mac Pro. The ones you usually hear are NOT the Power Supply fans. The power supply fans are unique in that they are generally NOT controlled by software, but are controlled independently by temperature-sensing electronics inside the power supply. They seldom run at top speed unless they are clogged with dust and the power supply is overheating.
The ones you usually hear are in several different "Zones" inside the cabinet. They are set to maximum at power-on by "watchdog" Hardware. The running software will then to reset the fans to more reasonable speeds based on measured temperatures inside the cabinet. If the software stops resetting the fans to moderate speeds, Hardware takes over and sets them to maximum in an attept to minimize heat damage.
Fans coming on loudly may indicate excessive heat is building up in a particular Zone inside the cabinet, or that a sensor in a particular zone is not providing proper temperature measurements, or may indicate the software has crashed.