Mm_par2.0: An object-oriented molecular dynamics simulation program parallelized using a hierarchical scheme with MPI and OPENMP

Abstract

We have revised a general purpose parallel molecular dynamics simulation program mm_par using the object-oriented programming. We parallelized the revised version using a hierarchical scheme in order to utilize more processors for a given system size. The benchmark result will be presented here. New version program summary Program title: mm_par2.0 Catalogue identifier: ADXP_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADXP_v2_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2 390 858 No. of bytes in distributed program, including test data, etc.: 25 068 310 Distribution format: tar.gz Programming language: C++ Computer: Any system operated by Linux or Unix Operating system: Linux Classification: 7.7 External routines: We provide wrappers for FFTW [1], Intel MKL library [2] FFT routine, and Numerical recipes [3] FFT, random number generator, and eigenvalue solver routines, SPRNG [4] random number generator, Mersenne Twister [5] random number generator, space filling curve routine. Catalogue identifier of previous version: ADXP_v1_0 Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 560 Does the new version supersede the previous version?: Yes Nature of problem: Structural, thermodynamic, and dynamical properties of fluids and solids from microscopic scales to mesoscopic scales. Solution method: Molecular dynamics simulation in NVE, NVT, and NPT ensemble, Langevin dynamics simulation, dissipative particle dynamics simulation. Reasons for new version: First, object-oriented programming has been used, which is known to be open for extension and closed for modification. It is also known to be better for maintenance. Second, version 1.0 was based on atom decomposition and domain decomposition scheme [6] for parallelization. However, atom decomposition is not popular due to its poor scalability. On the other hand, domain decomposition scheme is better for scalability. It still has a limitation in utilizing a large number of cores on recent petascale computers due to the requirement that the domain size is larger than the potential cutoff distance. To go beyond such a limitation, a hierarchical parallelization scheme has been adopted in this new version and implemented using MPI [7] and OPENMP [8]. Summary of revisions: (1) Object-oriented programming has been used. (2) A hierarchical parallelization scheme has been adopted. (3) SPME routine has been fully parallelized with parallel 3D FFT using volumetric decomposition scheme [9]. K.J.O. thanks Mr. Seung Min Lee for useful discussion on programming and debugging. Running time: Running time depends on system size and methods used. For test system containing a protein (PDB id: 5DHFR) with CHARMM22 force field [10] and 7023 TIP3P [11] waters in simulation box having dimension 62.23 Å × 62.23 Å × 62.23 Å , the benchmark results are given in Fig. 1. Here the potential cutoff distance was set to 12 Å and the switching function was applied from 10 Å for the force calculation in real space. For the SPME [12] calculation, K 1 , K 2 , and K 3 were set to 64 and the interpolation order was set to 4. To do the fast Fourier transform, we used Intel MKL library. All bonds including hydrogen atoms were constrained using SHAKE/RATTLE algorithms [13,14]. The code was compiled using Intel compiler version 11.1 and mvapich2 version 1.5. Fig. 2 shows performance gains from using CUDA-enabled version [15] of mm_par for 5DHFR simulation in water on Intel Core2Quad 2.83 GHz and GeForce GTX 580. Even though mm_par2.0 is not ported yet for GPU, its performance data would be useful to expect mm_par2.0 performance on GPU. [Display omitted] [Display omitted]