Accelerating sequential programs using FastFlow and self-offloading

FastFlow is a programming environment specifically targeting cache-coherent shared-memory multi-cores. FastFlow is implemented as a stack of C++ template libraries built on top of lock-free (fence-free) synchronization mechanisms. In this paper we present a further evolution of FastFlow enabling programmers to offload part of their workload on a dynamically created software accelerator running on unused CPUs. The offloaded function can be easily derived from pre-existing sequential code. We emphasize in particular the effective trade-off between human productivity and execution efficiency of the approach.Comment: 17 pages + cove

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

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.Comment: EASC 2014 conference proceedin

Emulating and evaluating hybrid memory for managed languages on NUMA hardware

Non-volatile memory (NVM) has the potential to become a mainstream memory technology and challenge DRAM. Researchers evaluating the speed, endurance, and abstractions of hybrid memories with DRAM and NVM typically use simulation, making it easy to evaluate the impact of different hardware technologies and parameters. Simulation is, however, extremely slow, limiting the applications and datasets in the evaluation. Simulation also precludes critical workloads, especially those written in managed languages such as Java and C#. Good methodology embraces a variety of techniques for evaluating new ideas, expanding the experimental scope, and uncovering new insights. This paper introduces a platform to emulate hybrid memory for managed languages using commodity NUMA servers. Emulation complements simulation but offers richer software experimentation. We use a thread-local socket to emulate DRAM and a remote socket to emulate NVM. We use standard C library routines to allocate heap memory on the DRAM and NVM sockets for use with explicit memory management or garbage collection. We evaluate the emulator using various configurations of write-rationing garbage collectors that improve NVM lifetimes by limiting writes to NVM, using 15 applications and various datasets and workload configurations. We show emulation and simulation confirm each other's trends in terms of writes to NVM for different software configurations, increasing our confidence in predicting future system effects. Emulation brings novel insights, such as the non-linear effects of multi-programmed workloads on NVM writes, and that Java applications write significantly more than their C++ equivalents. We make our software infrastructure publicly available to advance the evaluation of novel memory management schemes on hybrid memories

Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond

Various strategies to implement efficiently QMC simulations for large chemical systems are presented. These include: i.) the introduction of an efficient algorithm to calculate the computationally expensive Slater matrices. This novel scheme is based on the use of the highly localized character of atomic Gaussian basis functions (not the molecular orbitals as usually done), ii.) the possibility of keeping the memory footprint minimal, iii.) the important enhancement of single-core performance when efficient optimization tools are employed, and iv.) the definition of a universal, dynamic, fault-tolerant, and load-balanced computational framework adapted to all kinds of computational platforms (massively parallel machines, clusters, or distributed grids). These strategies have been implemented in the QMC=Chem code developed at Toulouse and illustrated with numerical applications on small peptides of increasing sizes (158, 434, 1056 and 1731 electrons). Using 10k-80k computing cores of the Curie machine (GENCI-TGCC-CEA, France) QMC=Chem has been shown to be capable of running at the petascale level, thus demonstrating that for this machine a large part of the peak performance can be achieved. Implementation of large-scale QMC simulations for future exascale platforms with a comparable level of efficiency is expected to be feasible