GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations

Abstract

Molecular dynamics methodologies comprise a vital research tool for structural biology. Molecular dynamics has benefited from technological advances in computing, such as multi-core CPUs and graphics processing units (GPUs), but harnessing the full power of hybrid GPU/CPU computers remains difficult. The generalized Born/solvent-accessible surface area implicit solvent model (GB/SA) stands to benefit from hybrid GPU/CPU computers, employing the GPU for the GB calculation and the CPU for the SA calculation. Here, we explore the computational challenges facing GB/SA calculations on hybrid GPU/CPU computers and demonstrate how NAMD, a parallel molecular dynamics program, is able to efficiently utilize GPUs and CPUs simultaneously for fast GB/SA simulations. The hybrid computation principles demonstrated here are generally applicable to parallel applications employing hybrid GPU/CPU calculations.

Figure 1

Hybrid GB/SA decomposition. (A) Simulated protein glycogen phosphorylase. (B) Protein decomposed into a 3D grid of atom-groups. (C) LCPO force work unit involving a 2 × 2 × 2 set of 8 adjacent atom-groups. The force work unit calculates forces for the inner 1/8th core of atoms (red) due to overlap with neighbors (red and blue). (D) Thread block design for GB force calculation on GPU multiprocessor. Each thread (vertical line) calculates the force on one group-I atom (red) due to interactions (blue) with group-J atoms (green); group-J atoms are loaded 32 at a time, in order 1-3, for coalesced and, therefore, accelerated memory access.

Figure 2

Benchmarked protein systems. (A) Villin headpiece (PDB ID 1YRI) with 582 atoms; (B) flavodoxin (PDB ID 2W5U) with 2,412 atoms; (C) glycogen phosphorylase (PDB ID 1GPB) with 13,340 atoms; (D) RuBisCO (PDB ID 1IR2) with 74,926 atoms.

Figure 3

NAMD’s GB/SA calculation for the 1GPB system. (A) Performance on 16 CPUs only. (B) Performance on 16 CPUs with 1 GPU added. Colors represent calculations being performed on the processors: three phases of GB calculation (see text); SA calculation; idle time; communication. (C) Detailed view of host CPU switching between communicating with the GPU and performing the SA calculation; arrows represent the transfer of data between host CPU and GPU; for GB phase 1, 2 and 3 calculations: (a) host CPU initializes the GB calculation on the GPU; (b) GPU calculates a GB phase while (c) host CPU performs SA calculations. (D) Detailed view of how switching without SA partitioning slows performance.

Figure 4

Simulation speed, in seconds/time step, for the 1IR2 benchmark system on 0-4 GPUs and 1-32 CPU cores; speeds for in vacuo (red), GB (green) and GB/SA (blue) calculations are shown. Both the seconds/step and processor cores axes are logarithmic.

Figure 5

Surface area during eight GB/SA simulations of the 2W5U system employing different surface tension parameter values. The final surface area for each GB/SA simulation is listed at right; shown is also the final surface area resulting from the simulation with explicit (TIP3P) solvent.