NAMD Wiki: NamdAtSDSC
Batch scripts for NAMD on Trestles are maintained in
The IBM-SP build of NAMD should run on Blue Horizon.
See also NamdOnAIX.
The BlueGeneL build of NAMD (binaries not available) should work on Intimidata, but you will probably want the latest cvs versions of NAMD and charm (not the charm-5.9) tree, at least until NAMD 2.6b2 is released.
See also NamdOnBlueGene.
Justin Gullingsrud reports as follows:
I've had good results improving the scaling on Datastar. Adding the following environment variables got me to 0.05 s/step on 128 nodes, a factor of two improvement over what I was getting before:
Decreasing the polling interval from 400ms to 10 got me from 0.1 s/step down to 0.07; increasing the eager limit got me down to 0.05. This means I'm now getting 70% efficiency on 128 processors.
Now that I think about it, I can probably use the same parameters to improve scaling on Blue Horizon as well. Any other suggestions would be welcome.