Towards Exascale Scientific Metadata Management

Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability of metadata that describe the scientific datasets. Existing workflow engines have been capturing a limited form of metadata to provide provenance information about the identity and lineage of the data. However, much of the data produced by simulations, experiments, and analyses still need to be annotated manually in an ad hoc manner by domain scientists. Systematic and transparent acquisition of rich metadata becomes a crucial prerequisite to sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and domain-agnostic metadata management infrastructure that can meet the demands of extreme-scale science is notable by its absence. To address this gap in scientific data management research and practice, we present our vision for an integrated approach that (1) automatically captures and manipulates information-rich metadata while the data is being produced or analyzed and (2) stores metadata within each dataset to permeate metadata-oblivious processes and to query metadata through established and standardized data access interfaces. We motivate the need for the proposed integrated approach using applications from plasma physics, climate modeling and neuroscience, and then discuss research challenges and possible solutions

Parallel in situ indexing for data-intensive computing

As computing power increases exponentially, vast amount of data is created by many scientific re- search activities. However, the bandwidth for storing the data to disks and reading the data from disks has been improving at a much slower pace. These two trends produce an ever-widening data access gap. Our work brings together two distinct technologies to address this data access issue: indexing and in situ processing. From decades of database research literature, we know that indexing is an effective way to address the data access issue, particularly for accessing relatively small fraction of data records. As data sets increase in sizes, more and more analysts need to use selective data access, which makes indexing an even more important for improving data access. The challenge is that most implementations of in- dexing technology are embedded in large database management systems (DBMS), but most scientific datasets are not managed by any DBMS. In this work, we choose to include indexes with the scientific data instead of requiring the data to be loaded into a DBMS. We use compressed bitmap indexes from the FastBit software which are known to be highly effective for query-intensive workloads common to scientific data analysis. To use the indexes, we need to build them first. The index building procedure needs to access the whole data set and may also require a significant amount of compute time. In this work, we adapt the in situ processing technology to generate the indexes, thus removing the need of read- ing data from disks and to build indexes in parallel. The in situ data processing system used is ADIOS, a middleware for high-performance I/O. Our experimental results show that the indexes can improve the data access time up to 200 times depending on the fraction of data selected, and using in situ data processing system can effectively reduce the time needed to create the indexes, up to 10 times with our in situ technique when using identical parallel settings

The Next Generation of EMPRESS: A Metadata Management System For Accelerated Scientific Discovery at Exascale

Scientific data sets have grown rapidly in recent years, outpacing the growth in memory and network bandwidths. This I/O bottleneck has made it increasingly difficult for scientists to read and search outputted datasets in an attempt to find features of interest. In this paper, we will present the next generation of EMPRESS, a scalable metadata management service that offers the following solution: users can tag features of interest and search these tags without having to read in the associated datasets. EMPRESS provides, in essence, a digital scientific notebook where scientists can write down observations and highlight interesting results, and an efficient way to search these annotations. EMPRESS also provides storage-system independent physical metadata, providing a portable way for users to read both metadata and the associated data. EMPRESS offers scalability through two different deployment modes: local , which runs on the compute nodes and dedicated, which uses a set of dedicated, shared-nothing servers. EMPRESS also provides robust fault tolerance and transaction management, which is crucial to supporting workflows

Improving I/O Performance for Exascale Applications through Online Data Layout Reorganization

The applications being developed within the U.S. Exascale Computing Project (ECP) to run on imminent Exascale computers will generate scientific results with unprecedented fidelity and record turn-around time. Many of these codes are based on particle-mesh methods and use advanced algorithms, especially dynamic load-balancing and mesh-refinement, to achieve high performance on Exascale machines. Yet, as such algorithms improve parallel application efficiency, they raise new challenges for I/O logic due to their irregular and dynamic data distributions. Thus, while the enormous data rates of Exascale simulations already challenge existing file system write strategies, the need for efficient read and processing of generated data introduces additional constraints on the data layout strategies that can be used when writing data to secondary storage. We review these I/O challenges and introduce two online data layout reorganization approaches for achieving good tradeoffs between read and write performance. We demonstrate the benefits of using these two approaches for the ECP particle-in-cell simulation WarpX, which serves as a motif for a large class of important Exascale applications. We show that by understanding application I/O patterns and carefully designing data layouts we can increase read performance by more than 80 percent

Real-time visualization of parallel simulations in CERN material design

This work presents the implementation of the in situ visualization module for multiscale-multiphysics simulation code FEMOCS and demonstrates its behavior in the simulation of vacuum breakdown. The visualization module makes it possible to observe in real-time the course of the simulation in FEMOCS and makes it more straightforward to set up a new simulation or develop additional features into the code. The first and second chapters briefly introduce the vacuum breakdown phenomenon and describe general aspects of numerical simulations. The third chapter describes the in situ method as a way of improving FEMOCS. The fourth and fifth chapters present the final solution and the impact of the solution on the overall running time of the simulation

HSP-Wrap: The Design and Evaluation of Reusable Parallelism for a Subclass of Data-Intensive Applications

There is an increasing gap between the rate at which data is generated by scientific and non-scientific fields and the rate at which data can be processed by available computing resources. In this paper, we introduce the fields of Bioinformatics and Cheminformatics; two fields where big data has become a problem due to continuing advances in the technologies that drives these fields: such as gene sequencing and small ligand exploration. We introduce high performance computing as a means to process this growing base of data in order to facilitate knowledge discovery. We enumerate goals of the project including reusability, efficiency, reliability, and scalability. We then describe the implementation of a software scheduler which aims to improve input and output performance of a targeted collection of informatics tools, as well as the profiling and optimization needed to tune the software. We evaluate the performance of the software with a scalability study of the Bioinformatics tools BLAST, HMMER, and MUSCLE; as well as the Cheminformatics tool DOCK6