Dear Amber Users,
I am using a GTX470 card under Linux RH 4.8. I have installed and tested both the Cuda SDK and Amber 11.
The deviceQuery program produces the expected output. This card supports Cuda 2.0, just like the GTX480. There is no Windows OS on the hard drive, only Linux. The host machine is an AMD Phenom II Quad processor with 8 GB ram, and a 650 W power supply. The machine has only one video card, but all my runs are done via remote access without logging in to the console via x-windows. If I set the machine to default run level 3 in the inittab file to prevent X-windows from starting, then the deviceQuery program fails. The driver apparently needs run level 5.
I have successfully run about four 20 ns trajectories on a 6 kDa protein with explicit TIP3P water for a total of 25,000 atoms, water included. However, when I attempt to run a larger protein with a total of 63,000 or 68,000 atoms (water included), I get the "Error: the launch timed out and was terminated launching kernel
kPMEGetGridWeights" that has been reported here by Wookyung. This error occurs whether I run an NVT or an NPT ensemble, anywhere from 0.1 ns to 1 ns of the run. I have not seen the error during the preliminary energy minimization steps before MD.
If pmemd.cuda is allocating more memory than the card has (1.3 GB for the GTX 470, vs about 1.5 GB for the GTX480), then I would expect the run to terminate consistently at the same point every time, but the program terminates at seemingly random times. Restarting the run yields the same behavior - about another ns can be accumulated before the error creeps up again.
I plan to increase the number of atoms from 25,000 upwards to see at what size the error begins to generate an idea of what size problems can be done on this card. However, I would like to understand what is going on. Thanks for any feedback.
Sergio Aragon/SFSU
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Received on Thu Aug 26 2010 - 17:30:05 PDT
