Mark Abraham

KTH Royal Institute of Technology, Theoretical Physics, Faculty Member

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On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations

Molecular dynamics is expected to produce accurate results over a wide range of conditions and ti... more Molecular dynamics is expected to produce accurate results over a wide range of conditions and timescales. However, this is not always the case since the field has been too reluctant to abandon historically popular techniques known to introduce artefacts. Two recent papers have suggested there are reliability issues in the GROMACS code since it no longer uses a legacy twin-range algorithm. Here, we show there are order-of-magnitude differences in accuracy favoring the modern Trotter decomposition, and that a force field relying on the old algorithm will have errors parametrized into the force field. Similarly, the suggestions about incorrect virial calculations turn out to be explained by insufficient accuracy in the default SHAKE settings used for GROMOS, while the GROMACS default choices are accurate. This highlights the importance of being more critical to error cancellation in simulations in order for algorithms and parameters to both gradually converge to more perfect ones.

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Sharing Data from Molecular Simulations

Given the need for modern researchers to produce open, reproducible scientific output, the lack o... more Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations have become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, and each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effective...

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Trends in Data Locality Abstractions for HPC Systems

IEEE Transactions on Parallel and Distributed Systems

The cost of data movement has always been an important concern in high performance computing (HPC... more The cost of data movement has always been an important concern in high performance computing (HPC) systems. It has now become the dominant factor in terms of both energy consumption and performance. Support for expression of data locality has been explored in the past, but those efforts have had only modest success in being adopted in HPC applications for various reasons. However, with the increasing complexity of the memory hierarchy and higher parallelism in emerging HPC systems, locality management has acquired a new urgency. Developers can no longer limit themselves to low-level solutions and ignore the potential for productivity and performance portability obtained by using locality abstractions. Fortunately, the trend emerging in recent literature on the topic alleviates many of the concerns that got in the way of their adoption by application developers. Data locality abstractions are available in the forms of libraries, data structures, languages and runtime systems; a common theme is increasing productivity without sacrificing performance. This paper examines these trends and identifies commonalities that can combine various locality concepts to develop a comprehensive approach to expressing and managing data locality on future large-scale high-performance computing systems.

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Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation

Journal of chemical theory and computation, Jan 20, 2015

Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for elect... more Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for electrostatics have been revolutionary to the precision and accuracy of molecular simulations in general. Despite the performance penalty associated with lattice summation electrostatics, few biomolecular simulations today are performed without it. There are increasingly strong arguments for moving in the same direction for Lennard-Jones (LJ) interactions, and by using geometric approximations of the combination rules in reciprocal space, we have been able to make a very high-performance implementation available in GROMACS. Here, we present a new way to correct for these approximations to achieve exact treatment of Lorentz-Berthelot combination rules within the cutoff, and only a very small approximation error remains outside the cutoff (a part that would be completely ignored without LJ-PME). This not only improves accuracy by almost an order of magnitude but also achieves absolute biomolecu...

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

by Mark Abraham and Szilárd Páll

GROMACS is one of the most widely used open-source and free software codes in chemistry, used pri... more GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.

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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

by Szilárd Páll, Carsten Kutzner, and Mark Abraham

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it ha... more GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.

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Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5

Journal of Computational Chemistry, 2011

Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations

Journal of Chemical Theory and Computation, 2008

We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD)... more We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD) simulations that make efficient use of the replica space, assess whether published applications are achieving such &amp;amp;quot;mixing&amp;amp;quot; efficiency, and provide a how-to guide to assist users to plan efficient REMD simulations. To address our first question, we introduce and discuss three metrics for assessing the number of replica-exchange attempts required to justify the use of a replica scheme and define a &amp;amp;quot;transit number&amp;amp;quot; as the lower bound for the length of an efficient simulation. Our literature survey of applications of REMD simulations of peptides in explicit solvent indicated that authors are not routinely reporting sufficient details of their simulation protocols to allow readers to make independent assessments of the impact of the method on their results, particularly whether mixing efficiency has been achieved. Necessary details include the expected or observed replica-exchange probability, together with the total number of exchange attempts, the exchange period, and estimates of the autocorrelation time of the potential energy. Our analysis of cases where the necessary information was reported suggests that in many of these simulations there are insufficient exchanges attempted or an insufficiently long period between them to provide confidence that the simulation length justifies the size of the replica scheme. We suggest guidelines for designing REMD simulation protocols to ensure mixing efficiency. Two key recommendations are that the exchange period should in general be larger than 1 ps and the number of exchange attempts should be chosen to significantly exceed the transit number for the replica scheme.

Performance enhancements for GROMACS nonbonded interactions on BlueGene

Journal of Computational Chemistry - JCC, 2011

... 4. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, AE; Berendsen, HJ J Comput C... more

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