next up previous contents index
Next: Improving Parallel Scaling Up: Running NAMD Previous: CUDA GPU Acceleration   Contents   Index

Memory Usage

NAMD has traditionally used less than 100MB of memory even for systems of 100,000 atoms. With the reintroduction of pairlists in NAMD 2.5, however, memory usage for a 100,000 atom system with a 12A cutoff can approach 300MB, and will grow with the cube of the cutoff. This extra memory is distributed across processors during a parallel run, but a single workstation may run out of physical memory with a large system.

To avoid this, NAMD now provides a pairlistMinProcs config file option that specifies the minimum number of processors that a run must use before pairlists will be enabled (on fewer processors small local pairlists are generated and recycled rather than being saved, the default is ``pairlistMinProcs 1''). This is a per-simulation rather than a compile time option because memory usage is molecule-dependent.

Additional information on reducing memory usage may be found at http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction



http://www.ks.uiuc.edu/Research/namd/