Automation of Determination of Optimal Intra-Compute Node Parallelism

Maximizing the productivity of modern multicore and manycore chips requires optimizing parallelism at the compute node level. This is, however, a complex multi-step process. It is an iterative method requiring determining optimal degrees of parallel scalability and optimizing memory access behavior. Further, there are multiple cases to be considered, programs which use only MPI or OpenMP and hybrid (MPI +OpenMP) programs. This paper presents a set of three coordinated workflows for determining the optimal parallelism at the program level for MPI programs and at the loop level for hybrid (MPI+OpenMP) cases. The paper also details mostly automated implementations of these workflows using the PerfExpert infrastructure. Finally the paper presents case studies demonstrating both the applicability and the effectiveness of optimizing parallelism at the compute node level. The results shown in the paper will provide valuable information to further advance in the full automation of the workflows. The software implementing the parallelism scalability optimization is open source and available for download.Texas Advanced Computing Center (TACC)Computer Science

Diagnose network failures via data-plane analysis

Diagnosing problems in networks is a time-consuming and error-prone process. Previous tools to assist operators primarily focus on analyzing control plane configuration. Configuration analysis is limited in that it cannot find bugs in router software, and is harder to generalize across protocols since it must model complex configuration languages and dynamic protocol behavior. This paper studies an alternate approach: diagnosing problems through static analysis of the data plane. This approach can catch bugs that are invisible at the level of configuration files, and simplifies unified analysis of a network across many protocols and implementations. We present Anteater, a tool for checking invariants in the data plane. Anteater translates high-level network invariants into boolean satisfiability problems, checks them against network state using a SAT solver, and reports counterexamples if violations have been found. Applied to a large campus network, Anteater revealed 23 bugs, including forwarding loops and stale ACL rules, with only five false positives. Nine of these faults are being fixed by campus network operators

Understanding the Scalability of Molecular Simulation Using Empirical Performance Modeling

The final authenticated publication is available online at https://doi.org/10.1007/978-3-030-17872-7_8.Molecular dynamics (MD) simulation allows for the study of static and dynamic properties of molecular ensembles at various molecular scales, from monatomics to macromolecules such as proteins and nucleic acids. It has applications in biology, materials science, biochemistry, and biophysics. Recent developments in simulation techniques spurred the emergence of the computational molecular engineering (CME) field, which focuses specifically on the needs of industrial users in engineering. Within CME, the simulation code ms2 allows users to calculate thermodynamic properties of bulk fluids. It is a parallel code that aims to scale the temporal range of the simulation while keeping the execution time minimal. In this paper, we use empirical performance modeling to study the impact of simulation parameters on the execution time. Our approach is a systematic workflow that can be used as a blue-print in other fields that aim to scale their simulation codes. We show that the generated models can help users better understand how to scale the simulation with minimal increase in execution time.BMBF, 01IH16008D, Verbundprojekt: TaLPas - Task-basierte Lastverteilung und Auto-Tuning in der PartikelsimulationDFG, 323299120, ExtraPeak - Automatische Leistungsmodellierung von HPC-Anwendungen mit multiplen Modellparameter

What broke where for distributed and parallel applications — a whodunit story

Detection, diagnosis and mitigation of performance problems in today\u27s large-scale distributed and parallel systems is a difficult task. These large distributed and parallel systems are composed of various complex software and hardware components. When the system experiences some performance or correctness problem, developers struggle to understand the root cause of the problem and fix in a timely manner. In my thesis, I address these three components of the performance problems in computer systems. First, we focus on diagnosing performance problems in large-scale parallel applications running on supercomputers. We developed techniques to localize the performance problem for root-cause analysis. Parallel applications, most of which are complex scientific simulations running in supercomputers, can create up to millions of parallel tasks that run on different machines and communicate using the message passing paradigm. We developed a highly scalable and accurate automated debugging tool called PRODOMETER, which uses sophisticated algorithms to first, create a logical progress dependency graph of the tasks to highlight how the problem spread through the system manifesting as a system-wide performance issue. Second, uses this logical progress dependence graph to identify the task where the problem originated. Finally, PRODOMETER pinpoints the code region corresponding to the origin of the bug. Second, we developed a tool-chain that can detect performance anomaly using machine-learning techniques and can achieve very low false positive rate. Our input-aware performance anomaly detection system consists of a scalable data collection framework to collect performance related metrics from different granularity of code regions, an offline model creation and prediction-error characterization technique, and a threshold based anomaly-detection-engine for production runs. Our system requires few training runs and can handle unknown inputs and parameter combinations by dynamically calibrating the anomaly detection threshold according to the characteristics of the input data and the characteristics of the prediction-error of the models. Third, we developed performance problem mitigation scheme for erasure-coded distributed storage systems. Repair operations of the failed blocks in erasure-coded distributed storage system take really long time in networked constrained data-centers. The reason being, during the repair operation for erasure-coded distributed storage, a lot of data from multiple nodes are gathered into a single node and then a mathematical operation is performed to reconstruct the missing part. This process severely congests the links toward the destination where newly recreated data is to be hosted. We proposed a novel distributed repair technique, called Partial-Parallel-Repair (PPR) that performs this reconstruction in parallel on multiple nodes and eliminates network bottlenecks, and as a result, greatly speeds up the repair process. Fourth, we study how for a class of applications, performance can be improved (or performance problems can be mitigated) by selectively approximating some of the computations. For many applications, the main computation happens inside a loop that can be logically divided into a few temporal segments, we call phases. We found that while approximating the initial phases might severely degrade the quality of the results, approximating the computation for the later phases have very small impact on the final quality of the result. Based on this observation, we developed an optimization framework that for a given budget of quality-loss, would find the best approximation settings for each phase in the execution

Software Verification and Graph Similarity for Automated Evaluation of Students' Assignments

In this paper we promote introducing software verification and control flow graph similarity measurement in automated evaluation of students' programs. We present a new grading framework that merges results obtained by combination of these two approaches with results obtained by automated testing, leading to improved quality and precision of automated grading. These two approaches are also useful in providing a comprehensible feedback that can help students to improve the quality of their programs We also present our corresponding tools that are publicly available and open source. The tools are based on LLVM low-level intermediate code representation, so they could be applied to a number of programming languages. Experimental evaluation of the proposed grading framework is performed on a corpus of university students' programs written in programming language C. Results of the experiments show that automatically generated grades are highly correlated with manually determined grades suggesting that the presented tools can find real-world applications in studying and grading

Systematic debugging methods for large-scale HPC computational frameworks

pre-printParallel computational frameworks for high-performance computing are central to the advancement of simulation-based studies in science and engineering. Finding and fixing bugs in these frameworks can be time consuming. If left unchecked, these bugs diminish the amount of new science performed. A systematic study of the Uintah Computational Framework investigates debugging approaches, leveraging the framework's modular structure