New Fault Tolerant Multicast Routing Techniques to Enhance Distributed-Memory Systems Performance

Distributed-memory systems are a key to achieve high performance computing and the most favorable architectures used in advanced research problems. Mesh connected multicomputer are one of the most popular architectures that have been implemented in many distributed-memory systems. These systems must support communication operations efficiently to achieve good performance. The wormhole switching technique has been widely used in design of distributed-memory systems in which the packet is divided into small flits. Also, the multicast communication has been widely used in distributed-memory systems which is one source node sends the same message to several destination nodes. Fault tolerance refers to the ability of the system to operate correctly in the presence of faults. Development of fault tolerant multicast routing algorithms in 2D mesh networks is an important issue. This dissertation presents, new fault tolerant multicast routing algorithms for distributed-memory systems performance using wormhole routed 2D mesh. These algorithms are described for fault tolerant routing in 2D mesh networks, but it can also be extended to other topologies. These algorithms are a combination of a unicast-based multicast algorithm and tree-based multicast algorithms. These algorithms works effectively for the most commonly encountered faults in mesh networks, f-rings, f-chains and concave fault regions. It is shown that the proposed routing algorithms are effective even in the presence of a large number of fault regions and large size of fault region. These algorithms are proved to be deadlock-free. Also, the problem of fault regions overlap is solved. Four essential performance metrics in mesh networks will be considered and calculated; also these algorithms are a limited-global-information-based multicasting which is a compromise of local-information-based approach and global-information-based approach. Data mining is used to validate the results and to enlarge the sample. The proposed new multicast routing techniques are used to enhance the performance of distributed-memory systems. Simulation results are presented to demonstrate the efficiency of the proposed algorithms

Hierarchical Dynamic Loop Self-Scheduling on Distributed-Memory Systems Using an MPI+MPI Approach

Computationally-intensive loops are the primary source of parallelism in scientific applications. Such loops are often irregular and a balanced execution of their loop iterations is critical for achieving high performance. However, several factors may lead to an imbalanced load execution, such as problem characteristics, algorithmic, and systemic variations. Dynamic loop self-scheduling (DLS) techniques are devised to mitigate these factors, and consequently, improve application performance. On distributed-memory systems, DLS techniques can be implemented using a hierarchical master-worker execution model and are, therefore, called hierarchical DLS techniques. These techniques self-schedule loop iterations at two levels of hardware parallelism: across and within compute nodes. Hybrid programming approaches that combine the message passing interface (MPI) with open multi-processing (OpenMP) dominate the implementation of hierarchical DLS techniques. The MPI-3 standard includes the feature of sharing memory regions among MPI processes. This feature introduced the MPI+MPI approach that simplifies the implementation of parallel scientific applications. The present work designs and implements hierarchical DLS techniques by exploiting the MPI+MPI approach. Four well-known DLS techniques are considered in the evaluation proposed herein. The results indicate certain performance advantages of the proposed approach compared to the hybrid MPI+OpenMP approach

Methodology for malleable applications on distributed memory systems

A la portada logo BSC(English) The dominant programming approach for scientific and industrial computing on clusters is MPI+X. While there are a variety of approaches within the node, denoted by the ``X'', Message Passing interface (MPI) is the standard for programming multiple nodes with distributed memory. This thesis argues that the OmpSs-2 tasking model can be extended beyond the node to naturally support distributed memory, with three benefits: First, at small to medium scale the tasking model is a simpler and more productive alternative to MPI. It eliminates the need to distribute the data explicitly and convert all dependencies into explicit message passing. It also avoids the complexity of hybrid programming using MPI+X. Second, the ability to offload parts of the computation among the nodes enables the runtime to automatically balance the loads in a full-scale MPI+X program. This approach does not require a cost model, and it is able to transparently balance the computational loads across the whole program, on all its nodes. Third, because the runtime handles all low-level aspects of data distribution and communication, it can change the resource allocation dynamically, in a way that is transparent to the application. This thesis describes the design, development and evaluation of OmpSs-2@Cluster, a programming model and runtime system that extends the OmpSs-2 model to allow a virtually unmodified OmpSs-2 program to run across multiple distributed memory nodes. For well-balanced applications it provides similar performance to MPI+OpenMP on up to 16 nodes, and it improves performance by up to 2x for irregular and unbalanced applications like Cholesky factorization. This work also extended OmpSs-2@Cluster for interoperability with MPI and Barcelona Supercomputing Center (BSC)'s state-of-the-art Dynamic Load Balance (DLB) library in order to dynamically balance MPI+OmpSs-2 applications by transparently offloading tasks among nodes. This approach reduces the execution time of a microscale solid mechanics application by 46% on 64 nodes and on a synthetic benchmark, it is within 10% of perfect load balancing on up to 8 nodes. Finally, the runtime was extended to transparently support malleability for pure OmpSs-2@Cluster programs and interoperate with the Resources Management System (RMS). The only change to the application is to explicitly call an API function to control the addition or removal of nodes. In this regard we additionally provide the runtime with the ability to semi-transparently save and recover part of the application status to perform checkpoint and restart. Such a feature hides the complexity of data redistribution and parallel IO from the user while allowing the program to recover and continue previous executions. Our work is a starting point for future research on fault tolerance. In summary, OmpSs-2@Cluster expands the OmpSs-2 programming model to encompass distributed memory clusters. It allows an existing OmpSs-2 program, with few if any changes, to run across multiple nodes. OmpSs-2@Cluster supports transparent multi-node dynamic load balancing for MPI+OmpSs-2 programs, and enables semi-transparent malleability for OmpSs-2@Cluster programs. The runtime system has a high level of stability and performance, and it opens several avenues for future work.(Español) El modelo de programación dominante para clusters tanto en ciencia como industria es actualmente MPI+X. A pesar de que hay alguna variedad de alternativas para programar dentro de un nodo (indicado por la "X"), el estandar para programar múltiples nodos con memoria distribuida sigue siendo Message Passing Interface (MPI). Esta tesis propone la extensión del modelo de programación basado en tareas OmpSs-2 para su funcionamiento en sistemas de memoria distribuida, destacando 3 beneficios principales: En primer lugar; a pequeña y mediana escala, un modelo basado en tareas es más simple y productivo que MPI y elimina la necesidad de distribuir los datos explícitamente y convertir todas las dependencias en mensajes. Además, evita la complejidad de la programacion híbrida MPI+X. En segundo lugar; la capacidad de enviar partes del cálculo entre los nodos permite a la librería balancear la carga de trabajo en programas MPI+X a gran escala. Este enfoque no necesita un modelo de coste y permite equilibrar cargas transversalmente en todo el programa y todos los nodos. En tercer lugar; teniendo en cuenta que es la librería quien maneja todos los aspectos relacionados con distribución y transferencia de datos, es posible la modificación dinámica y transparente de los recursos que utiliza la aplicación. Esta tesis describe el diseño, desarrollo y evaluación de OmpSs-2@Cluster; un modelo de programación y librería que extiende OmpSs-2 permitiendo la ejecución de programas OmpSs-2 existentes en múltiples nodos sin prácticamente necesidad de modificarlos. Para aplicaciones balanceadas, este modelo proporciona un rendimiento similar a MPI+OpenMP hasta 16 nodos y duplica el rendimiento en aplicaciones irregulares o desbalanceadas como la factorización de Cholesky. Este trabajo incluye la extensión de OmpSs-2@Cluster para interactuar con MPI y la librería de balanceo de carga Dynamic Load Balancing (DLB) desarrollada en el Barcelona Supercomputing Center (BSC). De este modo es posible equilibrar aplicaciones MPI+OmpSs-2 mediante la transferencia transparente de tareas entre nodos. Este enfoque reduce el tiempo de ejecución de una aplicación de mecánica de sólidos a micro-escala en un 46% en 64 nodos; en algunos experimentos hasta 8 nodos se pudo equilibrar perfectamente la carga con una diferencia inferior al 10% del equilibrio perfecto. Finalmente, se implementó otra extensión de la librería para realizar operaciones de maleabilidad en programas OmpSs-2@Cluster e interactuar con el Sistema de Manejo de Recursos (RMS). El único cambio requerido en la aplicación es la llamada explicita a una función de la interfaz que controla la adición o eliminación de nodos. Además, se agregó la funcionalidad de guardar y recuperar parte del estado de la aplicación de forma semitransparente con el objetivo de realizar operaciones de salva-reinicio. Dicha funcionalidad oculta al usuario la complejidad de la redistribución de datos y las operaciones de lectura-escritura en paralelo, mientras permite al programa recuperar y continuar ejecuciones previas. Este es un punto de partida para futuras investigaciones en tolerancia a fallos. En resumen, OmpSs-2@Cluster amplía el modelo de programación de OmpSs-2 para abarcar sistemas de memoria distribuida. El modelo permite la ejecución de programas OmpSs-2 en múltiples nodos prácticamente sin necesidad de modificarlos. OmpSs-2@Cluster permite además el balanceo dinámico de carga en aplicaciones híbridas MPI+OmpSs-2 ejecutadas en varios nodos y es capaz de realizar maleabilidad semi-transparente en programas OmpSs-2@Cluster puros. La librería tiene un niveles de rendimiento y estabilidad altos y abre varios caminos para trabajos futuro.Arquitectura de computador

SVM Support in the Vienna Fortran Compilation System

Vienna Fortran, a machine-independent language extension to Fortran which allows the user to write programs for distributed-memory systems using global addresses, provides the forall-loop construct for specifying irregular computations that do not cause inter-iteration dependences. Compilers for distributed-memory systems generate code that is based on runtime analysis techniques and is only efficient if, in addition, aggressive compile-time optimizations are applied. Since these optimizations are difficult to perform we propose to generate shared virtual memory code instead that can benefit from appropriate operating system or hardware support. This paper presents the shared virtual memory code generation, compares both approaches and gives first performance results

ScalaParBiBit: Scaling the Binary Biclustering in Distributed-Memory Systems

[Abstract] Biclustering is a data mining technique that allows us to find groups of rows and columns that are highly correlated in a 2D dataset. Although there exist several software applications to perform biclustering, most of them suffer from a high computational complexity which prevents their use in large datasets. In this work we present ScalaParBiBit, a parallel tool to find biclusters on binary data, quite common in many research fields such as text mining, marketing or bioinformatics. ScalaParBiBit takes advantage of the special characteristics of these binary datasets, as well as of an efficient parallel implementation and algorithm, to accelerate the biclustering procedure in distributed-memory systems. The experimental evaluation proves that our tool is significantly faster and more scalable that the state-of-the-art tool ParBiBit in a cluster with 32 nodes and 768 cores. Our tool together with its reference manual are freely available at https://github.com/fraguela/ScalaParBiBit.This research was supported by the Ministry of Science and Innovation of Spain (TIN2016-75845-P and PID2019-104184RB-I00, AEI/FEDER/EU, 10.13039/ 501100011033), and by the Xunta de Galicia co-founded by the European Regional Development Fund (ERDF) under the Consolidation Programme of Competitive Reference Groups (ED431C 2017/04). We acknowledge also the support from the Centro Singular de Investigación de Galicia “CITIC”, funded by Xunta de Galicia and the European Union (European Regional Development Fund- Galicia 2014-2020 Program), by grant ED431G 2019/01. We also acknowledge the Centro de Supercomputación de Galicia (CESGA) for the usage of their resourcesXunta de Galicia; ED431C 2017/04Xunta de Galicia; ED431G 2019/0

Scalable Graph Convolutional Network Training on Distributed-Memory Systems

Graph Convolutional Networks (GCNs) are extensively utilized for deep learning on graphs. The large data sizes of graphs and their vertex features make scalable training algorithms and distributed memory systems necessary. Since the convolution operation on graphs induces irregular memory access patterns, designing a memory- and communication-efficient parallel algorithm for GCN training poses unique challenges. We propose a highly parallel training algorithm that scales to large processor counts. In our solution, the large adjacency and vertex-feature matrices are partitioned among processors. We exploit the vertex-partitioning of the graph to use non-blocking point-to-point communication operations between processors for better scalability. To further minimize the parallelization overheads, we introduce a sparse matrix partitioning scheme based on a hypergraph partitioning model for full-batch training. We also propose a novel stochastic hypergraph model to encode the expected communication volume in mini-batch training. We show the merits of the hypergraph model, previously unexplored for GCN training, over the standard graph partitioning model which does not accurately encode the communication costs. Experiments performed on real-world graph datasets demonstrate that the proposed algorithms achieve considerable speedups over alternative solutions. The optimizations achieved on communication costs become even more pronounced at high scalability with many processors. The performance benefits are preserved in deeper GCNs having more layers as well as on billion-scale graphs.Comment: To appear in PVLDB'2

Extending the HybridThread SMP Model for Distributed Memory Systems

Memory Hierarchy is of growing importance in system design today. As Moore\u27s Law allows system designers to include more processors within their designs, data locality becomes a priority. Traditional multiprocessor systems on chip (MPSoC) experience difficulty scaling as the quantity of processors increases. This challenge is common behavior of memory accesses in a shared memory environment and causes a decrease in memory bandwidth as processor numbers increase. In order to provide the necessary levels of scalability, the computer architecture community has sought to decentralize memory accesses by distributing memory throughout the system. Distributed memory offers greater bandwidth due to decoupled access paths. Today\u27s million gate Field Programmable Gate Arrays (FPGA) offer an invaluable opportunity to explore this type of memory hierarchy. FPGA vendors such as Xilinx provide dual-ported on-chip memory for decoupled access in addition to configurable sized memories. In this work, a new platform was created around the use of dual-ported SRAMs for distributed memory to explore the possible scalability of this form of memory hierarchy. However, developing distributed memory poses a tremendous challenge: supporting a linear address space that allows wide applicability to be achieved. Many have agreed that a linear address space eases the programmability of a system. Although the abstraction of disjointed memories via underlying architecture and/or new programming presents an advantage in exploring the possibilities of distributed memory, automatic data partitioning and migration remains a considerable challenge. In this research this challenge was dealt with by the inclusion of both a shared memory and distributed memory model. This research is vital because exposing the programmer to the underlying architecture while providing a linear address space results in desired standards of programmability and performance alike. In addition, standard shared memory programming models can be applied allowing the user to enjoy full scalable performance potential

SMusket: Spark-based DNA error correction on distributed-memory systems

©2020 Elsevier B.V. All rights reserved. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/bync-nd/4.0/. This version of the article has been accepted for publication in Future Generation Computer Systems. The Version of Record is available online at https://doi.org/10.1016/j.future.2019.10.038This is the accepted version of: R. R. Expósito, J. González-Domínguez, and J. Touriño, "SMusket: Sparkbased DNA error correction on distributed-memory systems", Future Generation Computer Systems, vol. 111, pp. 698-713, 2020, https://doi.org/10.1016/j.future.2019.10.038[Abstract]: Next-Generation Sequencing (NGS) technologies have revolutionized genomics research over the last decade, bringing new opportunities for scientists to perform groundbreaking biological studies. Error correction in NGS datasets is considered an important preprocessing step in many workflows as sequencing errors can severely affect the quality of downstream analysis. Although current error correction approaches provide reasonably high accuracies, their computational cost can be still unacceptable when processing large datasets. In this paper we propose SparkMusket (SMusket), a Big Data tool built upon the open-source Apache Spark cluster computing framework to boost the performance of Musket, one of the most widely adopted and top-performing multithreaded correctors. Our tool efficiently exploits Spark features to implement a scalable error correction algorithm intended for distributed-memory systems built using commodity hardware. The experimental evaluation on a 16-node cluster using four publicly available datasets has shown that SMusket is up to 15.3 times faster than previous state-of-the-art MPI-based tools, also providing a maximum speedup of 29.8 over its multithreaded counterpart. SMusket is publicly available under an open-source license at https://github.com/rreye/smusketThis work was supported by the Ministry of Economy, Industry and Competitiveness of Spain and FEDER, Spain funds of the European Union (project TIN2016-75845-P, AEI/FEDER/EU); and by Xunta de Galicia, Spain (projects ED431G/01 and ED431C 2017/04).Xunta de galicia; ED431G/01Xunta de Galicia; ED431C 2017/0

MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems

This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of recordJorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt; MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems, Bioinformatics, Volume 32, Issue 24, 15 December 2016, Pages 3826–3828, https://doi.org/10.1093/bioinformatics/btw558is available online at: https://doi.org/10.1093/bioinformatics/btw558[Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively