an ultra-high-performance protein-protein docking for heterogeneous supercomputers

Requirements

Installation

You can use MEGADOCK 4.0 on (a) GPU cluster, (b) CPU cluster, (c) GPU single node and (d) CPU single node. Please see the appropriate instructions below.

(a) GPU cluster (GPU, MPI & OpenMP hybrid parallelization)

Extract tarball contents
      $ tar xzf megadock-4.1.1.tgz
      $ cd megadock-4.1.1
Edit Makefile
    CUDA_INSTALL_PATH ?= your/cuda/toolkit/install/path # default: /usr/local/cuda
    CUDA_SAMPLES_PATH ?= your/cuda/sdk/install/path     # default: /usr/local/cuda/samples
    FFTW_INSTALL_PATH ?= your/fftw/library/install/path # default: /usr/local
    CPPCOMPILER       ?= g++                            # default: g++ (or icpc, others)
    MPICOMPILER       ?= mpicxx                         # default: mpicxx (or others)
    OPTIMIZATION      ?= -O3                            # 
    OMPFLAG           ?= -fopenmp                       # default: -fopenmp (g++), or -openmp, -qopenmp (intel)
Compile
      $ make
A binary file megadock-gpu-dp will be generated.

(b) CPU cluster (MPI & OpenMP hybrid parallelization)

Extract tarball contents
      $ tar xzf megadock-4.1.1.tgz
      $ cd megadock-4.1.1
Edit Makefile
    FFTW_INSTALL_PATH ?= your/fftw/library/install/path # default: /usr/local
    CPPCOMPILER       ?= g++                            # default: g++ (or icpc, others)
    MPICOMPILER       ?= mpicxx                         # default: mpicxx (or others)
    OPTIMIZATION      ?= -O3                            # 
    OMPFLAG           ?= -fopenmp                       # default: -fopenmp (g++), or -openmp, -qopenmp (intel)
    
    USE_GPU := 0 
Compile
      $ make
A binary file megadock-dp will be generated.

(c) GPU single node (GPU parallelization)

Extract tarball contents
      $ tar xzf megadock-4.1.1.tgz
      $ cd megadock-4.1.1
Edit Makefile
    CUDA_INSTALL_PATH ?= your/cuda/toolkit/install/path # default: /usr/local/cuda
    CUDA_SAMPLES_PATH ?= your/cuda/sdk/install/path     # default: /usr/local/cuda/samples
    FFTW_INSTALL_PATH ?= your/fftw/library/install/path # default: /usr/local
    CPPCOMPILER       ?= g++                            # default: g++ (or icpc, others)
    OPTIMIZATION      ?= -O3                            # 
    OMPFLAG           ?= -fopenmp                       # default: -fopenmp (g++), or -openmp, -qopenmp (intel)
    
    USE_MPI := 0 
Compile
      $ make
A binary file megadock-gpu will be generated.

(d) CPU single node (OpenMP thread parallelization)

Extract tarball contents
      $ tar xzf megadock-4.1.1.tgz
      $ cd megadock-4.1.1
Edit Makefile
    FFTW_INSTALL_PATH ?= your/fftw/library/install/path # default: /usr/local
    CPPCOMPILER       ?= g++                            # default: g++ (or icpc, others)
    OPTIMIZATION      ?= -O3                            # 
    OMPFLAG           ?= -fopenmp                       # default: -fopenmp (g++), or -openmp, -qopenmp (intel)

    USE_GPU := 0
    USE_MPI := 0
Compile
      $ make
A binary file megadock will be generated.

Copyright © 2014-2019 Akiyama Laboratory, Tokyo Institute of Technology, All Rights Reserved.
Email: megadock @ bi.cs.* (please replace * with titech.ac.jp)
Last update: April 17, 2019