AutoDock-GPU: AutoDock for GPUs and other accelerators

  • Gradient-based local search methods (e.g. ADADELTA), as well as an improved version of Solis-Wets from AutoDock 4.
  • It targets platforms based on GPU as well as multicore CPU accelerators.
  • Observed speedups of up to 4x (quad-core CPU) and 56x (GPU) over the original serial AutoDock 4.2 (Solis-Wets) on CPU. The Cuda version is currently even faster than the OpenCL version.
  • A batched ligand pipeline to run virtual screenings on the same receptor (both OpenCL and Cuda)

Interactive mode

Request 1 GPU (k40m) from tesla.q 

$ qlogin -q tesla.q -lh_vmem=10G

Load Autodock module: 

$ module load gpu/autodock

Run Autodock GPU: 

$ autodock_gpu_128wi ...

Batch mode

#!/bin/bash
#$ -N test_sge
#$ -o $JOB_NAME.$JOB_ID.out
#$ -q tesla.q ## by default 1 GPU will be allocated
#$ -l h_vmem=10G 
## lancement de l'application 
 
module load gpu/autodock
autodock_gpu_128wi params...