Improving the performance of GWW

In this report, we present the results of investigation into improving the per- formance of GWW, part of the Quantum Espresso suite of software for ab initio simulation. In particular, the 3D Fourier Transform was found to be a significant bottleneck to application scaling. Several alternative methods for the FFT transpose were implemented, and the performance of these was studied on HECToR (Phase 2a and 2b). Speedups of up to 400% (on 128 cores of HECToR Phase 2a) were demonstrated for the 3D FFT in isolation, which delivered benefits of in the range of 4-36% in full application benchmarks. A checkpoint and restart mechanism was also added to help jobs complete in under the 12 hour queue limit on HECToR

Improving the Performance of CP2K on the Cray XT

Paper presented at CUG 2010, EdinburghCP2K is a freely available and increasingly popular Density Functional Theory code for the simulation of a wide range of systems. It is heavily used on many Cray XT systems, including ‘HECToR’ in the UK and ‘Monte Rosa’ in Switzerland. We describe performance optimisations made to the code in several key areas, including 3D Fourier Transforms, and present the implementation of a load balancing scheme for multi-grids. These result in performance gains of around 30% on 256 cores (for a generally representative benchmark) and up to 300% on 1024 cores (for non-homogeneous systems). Early results from the implementation of hybrid MPI/OpenMP parallelism in the code are also presented

Improving the scalability of CP2K on multi-core systems

Six months of HECToR dCSE funding was given to implement mixed-mode OpenMP parallelism in CP2K, building on the results of an earlier successful dCSE project. Improved scalability of up to 8 times as many cores was demonstrated for a small benchmark, and a larger, inhomogeneous benchmark was shown to scale up to 9000+ cores. An increase in peak performance of up to 60% was also realised on HECToR Phase 2b. In addition, the performance of the code was studied on three generations of Cray systems - XT4, XT5 and XT6 - and under four different compilers

CP2K - Sparse Linear Algebra on 1000s of cores

CP2K is a freely available atomistic and molecular simulation code, able to study of a wide range of molecular and bulk materials with methods including classical potentials, density functional theory (DFT), Hartree-Fock and post-HF methods. Following two earlier dCSE projects, we report here on an additional 6 months of work to optimisise the DBCSR sparse matrix multiplication library embedded within CP2K. Efficient and scalable sparse matrix operations are shown to benefit existing users of the code by reducing time to solution for typical simulations, and has enabled development of new algorithms including for the fully linear scaling DFT based on density matrix iterations

Improving the performance of CP2K on HECToR

This report presents the results of a HECToR dCSE project to improve the performance of CP2K, a freely available and popular Density Functional Theory code, on HECToR. Building on a recently implemented domain decomposition method, further optimisation of the code was performed, and significant performance gains were measured - around 30% on 256 cores (for a generally representative benchmark) and up to 300% on 1024 cores (for non-homogenous systems). Detailed profiling of the code was also carried out, which has highlighted further opportunities to improve the performance of the code

MIST: a portable and efficient toolkit for molecular dynamics integration algorithm development

The main contribution of this thesis is MIST, the Molecular Integration Simula- tion Toolkit, a lightweight and efficient software library written in C++ which provides an abstract interface to common Molecular Dynamics codes, enabling rapid and portable development of new integration schemes for Molecular Dynamics. The initial release provides plug-in interfaces to NAMD-Lite, GROMACS, Amber and LAMMPS and includes several standard integration schemes, a constraint solver, temperature control using Langevin Dynamics, temperature and pressure control using Nosé-Hoover chains, and five advanced sampling schemes. I describe the architecture, functionality and internal details of the library and the C and Fortran APIs which can be used to interface additional MD codes to MIST. As an example to future developers, each of the existing plug-ins and the integrators that are included with MIST are described. Brief instructions for compilation and use of the library are also given as a reference to users. The library is designed to be expressive, portable and performant, and I show via a range of test systems that MIST introduces negligible overheads for serial, parallel, and GPU-accelerated cases, except for Amber where the native integrators run directly on the GPU itself, but only run on the CPU in MIST. The capabilities of MIST for production-quality simulations are demonstrated through the use of a simulated tempering simulation to study the free energy landscape of Alanine-12 in both vacuum and detailed solvent conditions. I also present the evaluation and application of force-field and ab initio Molecular Dynamics to study the structural properties and behaviour of olivine melts. Three existing classical potentials for fayalite are tested and found to give lattice parameters and Radial Distribution Functions in good agreement with experimental data. For forsterite, lattice parameters at ambient pressure and temperature are slightly over-predicted by simulation (similar to other reported results in the literature). Likewise, higher-than expected thermal expansion coefficients and heat capacities are obtained from both ab initio and classical methods. The structure of both the crystal and melt are found to be in good agreement with experimental data. Several methodological improvements which could improve the accuracy of melting point determination and the thermal expansion coefficients are discussed