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


1. When executing megadock-gpu-dp or megadock-gpu, you get the following error:

error while loading shared libraries:{ver}: cannot open shared object file: No such file or directory
Answer: You need to add the path to the CUDA libraries to your $LD_LIBRARY_PATH environment variable. For example,
$ export LD_LIBRARY_PATH=/usr/local/cuda/lib64:${LD_LIBRARY_PATH}

2. Which versions of CUDA can I use? (GPU vesion)

Answer: MEGADOCK 4.0 has been tested on CUDA versions 5.0, 5.5, 6.0, 6.5, 7.0 and 7.5.

3. MPI_ABORT? (MPI version)

Answer: It's a feature. Please find master.log (-lg option) file and check that the all docking jobs are finished normally.

4. How to install FFTW3?

Answer: You download current version of FFTW3 from and install according to the following procedure.
 $ tar xzf fftw-3.X.X.tar.gz
 $ cd fftw-3.X.X
 $ ./configure --enable-float --enable-sse2 --prefix=/as/you/like
  (--enable-sse, --enable-sse2 or --enable-avx option enable the compilation of SIMD core for SSE, SSE2 or AVX, respectively.)
  (if you use intel compiler, add the option "CC=icc".)
 $ make
 $ make check
 $ make install
In this case, you set FFTW_INSTALL_PATH /as/you/like written in Makefile.
FFTW_INSTALL_PATH ?= /as/you/like 

5. Docking scores are different by CPU version and GPU version.

Answer: Because of precision of GPUs, the results of docking scores are slightly different by CPU version and GPU version. The differences are only approximately 0.001% (from 0.01 to 0.02 in docking score value) and have no impact on the docking results.

6. Can I use the MEGADOCK 4.0 freely?

Answer: The MEGADOCK 4.0 program is freely available to all academic and non-profit users under the GPLv3 licence. When you use MEGADOCK 4.0, please cite the paper:

Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0 : an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. Bioinformatics,30(22): 3281-3283, 2014.

7. Can I use the old versions of MEGADOCK?

Answer: Yes, you can use the old versions, but we would suggest using MEGADOCK 4.0.1. Current version is faster than old one by code optimization. Moreover, some bugs are fixed in current version.

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