BarrierPoint: sampled simulation of multi-threaded applications

Sampling is a well-known technique to speed up architectural simulation of long-running workloads while maintaining accurate performance predictions. A number of sampling techniques have recently been developed that extend well- known single-threaded techniques to allow sampled simulation of multi-threaded applications. Unfortunately, prior work is limited to non-synchronizing applications (e.g., server throughput workloads); requires the functional simulation of the entire application using a detailed cache hierarchy which limits the overall simulation speedup potential; leads to different units of work across different processor architectures which complicates performance analysis; or, requires massive machine resources to achieve reasonable simulation speedups. In this work, we propose BarrierPoint, a sampling methodology to accelerate simulation by leveraging globally synchronizing barriers in multi-threaded applications. BarrierPoint collects microarchitecture-independent code and data signatures to determine the most representative inter-barrier regions, called barrierpoints. BarrierPoint estimates total application execution time (and other performance metrics of interest) through detailed simulation of these barrierpoints only, leading to substantial simulation speedups. Barrierpoints can be simulated in parallel, use fewer simulation resources, and define fixed units of work to be used in performance comparisons across processor architectures. Our evaluation of BarrierPoint using NPB and Parsec benchmarks reports average simulation speedups of 24.7x (and up to 866.6x) with an average simulation error of 0.9% and 2.9% at most. On average, BarrierPoint reduces the number of simulation machine resources needed by 78x

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

An efficient MPI/OpenMP parallelization of the Hartree-Fock method for the second generation of Intel Xeon Phi processor

Modern OpenMP threading techniques are used to convert the MPI-only Hartree-Fock code in the GAMESS program to a hybrid MPI/OpenMP algorithm. Two separate implementations that differ by the sharing or replication of key data structures among threads are considered, density and Fock matrices. All implementations are benchmarked on a super-computer of 3,000 Intel Xeon Phi processors. With 64 cores per processor, scaling numbers are reported on up to 192,000 cores. The hybrid MPI/OpenMP implementation reduces the memory footprint by approximately 200 times compared to the legacy code. The MPI/OpenMP code was shown to run up to six times faster than the original for a range of molecular system sizes.Comment: SC17 conference paper, 12 pages, 7 figure

PaPaS: A Portable, Lightweight, and Generic Framework for Parallel Parameter Studies

The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward since they may need multiple processing tasks and iterations. Furthermore, parameter and performance studies are common approaches used to characterize a simulation, often requiring traversal of a large parameter space. High-performance computers offer practical resources at the expense of users handling the setup, submission, and management of jobs. This work presents the design of PaPaS, a portable, lightweight, and generic workflow framework for conducting parallel parameter and performance studies. Workflows are defined using parameter files based on keyword-value pairs syntax, thus removing from the user the overhead of creating complex scripts to manage the workflow. A parameter set consists of any combination of environment variables, files, partial file contents, and command line arguments. PaPaS is being developed in Python 3 with support for distributed parallelization using SSH, batch systems, and C++ MPI. The PaPaS framework will run as user processes, and can be used in single/multi-node and multi-tenant computing systems. An example simulation using the BehaviorSpace tool from NetLogo and a matrix multiply using OpenMP are presented as parameter and performance studies, respectively. The results demonstrate that the PaPaS framework offers a simple method for defining and managing parameter studies, while increasing resource utilization.Comment: 8 pages, 6 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

MERIC and RADAR generator: tools for energy evaluation and runtime tuning of HPC applications

This paper introduces two tools for manual energy evaluation and runtime tuning developed at IT4Innovations in the READEX project. The MERIC library can be used for manual instrumentation and analysis of any application from the energy and time consumption point of view. Besides tracing, MERIC can also change environment and hardware parameters during the application runtime, which leads to energy savings. MERIC stores large amounts of data, which are difficult to read by a human. The RADAR generator analyses the MERIC output files to find the best settings of evaluated parameters for each instrumented region. It generates a Open image in new window report and a MERIC configuration file for application production runs