23,469 research outputs found
MSREP: A Fast yet Light Sparse Matrix Framework for Multi-GPU Systems
Sparse linear algebra kernels play a critical role in numerous applications,
covering from exascale scientific simulation to large-scale data analytics.
Offloading linear algebra kernels on one GPU will no longer be viable in these
applications, simply because the rapidly growing data volume may exceed the
memory capacity and computing power of a single GPU. Multi-GPU systems nowadays
being ubiquitous in supercomputers and data-centers present great potentials in
scaling up large sparse linear algebra kernels. In this work, we design a novel
sparse matrix representation framework for multi-GPU systems called MSREP, to
scale sparse linear algebra operations based on our augmented sparse matrix
formats in a balanced pattern. Different from dense operations, sparsity
significantly intensifies the difficulty of distributing the computation
workload among multiple GPUs in a balanced manner. We enhance three mainstream
sparse data formats -- CSR, CSC, and COO, to enable fine-grained data
distribution. We take sparse matrix-vector multiplication (SpMV) as an example
to demonstrate the efficiency of our MSREP framework. In addition, MSREP can be
easily extended to support other sparse linear algebra kernels based on the
three fundamental formats (i.e., CSR, CSC and COO)
Next generation of Exascale-class systems: ExaNeSt project and the status of its interconnect and storage development
The ExaNeSt project started on December 2015 and is funded by EU H2020 research framework (call H2020-FETHPC-2014, n. 671553) to study the adoption of low-cost, Linux-based power-efficient 64-bit ARM processors clusters for Exascale-class systems. The ExaNeSt consortium pools partners with industrial and academic research expertise in storage, interconnects and applications that share a vision of an European Exascale-class supercomputer. The common goal is designing and implementing a physical rack prototype together with its cooling system, the non-volatile memory (NVM) architecture and a unified low-latency interconnect able to test different options for network and storage. Furthermore, the consortium goal is to provide real HPC applications to validate the system. In this paper we describe the unified data and storage network architecture, reporting on the status of development of different testbeds and highlighting preliminary benchmark results obtained through the execution of scientific, engineering and data analytics scalable application kernels
BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments
Advances in sequencing techniques have led to exponential growth in
biological data, demanding the development of large-scale bioinformatics
experiments. Because these experiments are computation- and data-intensive,
they require high-performance computing (HPC) techniques and can benefit from
specialized technologies such as Scientific Workflow Management Systems (SWfMS)
and databases. In this work, we present BioWorkbench, a framework for managing
and analyzing bioinformatics experiments. This framework automatically collects
provenance data, including both performance data from workflow execution and
data from the scientific domain of the workflow application. Provenance data
can be analyzed through a web application that abstracts a set of queries to
the provenance database, simplifying access to provenance information. We
evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree
assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a
RASopathy analysis workflow. We analyze each workflow from both computational
and scientific domain perspectives, by using queries to a provenance and
annotation database. Some of these queries are available as a pre-built feature
of the BioWorkbench web application. Through the provenance data, we show that
the framework is scalable and achieves high-performance, reducing up to 98% of
the case studies execution time. We also show how the application of machine
learning techniques can enrich the analysis process
Matrix Factorization at Scale: a Comparison of Scientific Data Analytics in Spark and C+MPI Using Three Case Studies
We explore the trade-offs of performing linear algebra using Apache Spark,
compared to traditional C and MPI implementations on HPC platforms. Spark is
designed for data analytics on cluster computing platforms with access to local
disks and is optimized for data-parallel tasks. We examine three widely-used
and important matrix factorizations: NMF (for physical plausability), PCA (for
its ubiquity) and CX (for data interpretability). We apply these methods to
TB-sized problems in particle physics, climate modeling and bioimaging. The
data matrices are tall-and-skinny which enable the algorithms to map
conveniently into Spark's data-parallel model. We perform scaling experiments
on up to 1600 Cray XC40 nodes, describe the sources of slowdowns, and provide
tuning guidance to obtain high performance
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