The Architecture of Scidb

The Architecture of SciDB Michael Stonebraker, Paul Brown, Alex Poliakov, Suchi Raman Paradigm4, Inc. 186 Third Avenue Waltham, MA 02451 Abstract. SciDB is an open-source analytical database oriented toward the data management needs of scientists. As such it mixes statistical and linear algebra operations with data management ones, using a natural nested multi-dimensional array data model. We have been working on the code for two years, most recently with the help of venture capital backing. Release 11.06 (June 2011) is downloadable from our website (SciDB.org). This paper presents the main design decisions of SciDB. It focuses on our decisions concerning a high-level, SQL-like query language, the issues facing our query optimizer and executor and efficient storage management for arrays. The paper also discusses implementation of features not usually present in DBMSs, including version control, uncertainty and provenance. Keywords: scientific data management, multi-dimensional array, statistics, linear algebra 1 Introduction and Background The Large Synoptic Survey Telescope (LSST) [1] is the next “big science” astronomy project, a telescope being erected in Chile, which will ultimately collect and manage some 100 Petabytes of raw and derived data. In October 2007, the members of the LSST data management team realized the scope of their data management problem, and that they were uncertain how to move forward. As a result, they organized the first Extremely Large Data Base (XLDB-1) conference at the Stanford National Accelerator Laboratory [2]. Present were many scientists from a variety of natural science disciplines as well as representatives from large web properties. All reported the following requirements: Multi-petabyte amounts of data. In fact a recent scientist at a major university reported that 20 research groups at his university had more than a quarter of a petabyte each [3]. A preponderance of array data. Geospatial and temporal data such as satellite imagery, oceanographic data telescope data, telematics data and most simulation data 2 The Architecture of SciDB all are naturally modeled as arrays. Genomics data generated from high throughput sequencing machines are also naturally represented as arrays. Complex analytics. Traditional business intelligence has focused on simple SQL aggregates or windowing functions. In contrast, scientists need much more sophisticated capabilities. For example, satellite imagery can be reported at various resolutions and in different co-ordinate systems. As a result, earth scientists need to regrid such imagery in order to correlate the data from multiple satellites. In addition, most satellites cannot see through cloud cover. Hence, it is necessary to find the “best” cloud-free composite image from multiple passes of the satellite. These are representative of the complex operations required in this application area. A requirement for open source code. Every scientist we have talked to is adamant about this requirement. Seemingly, the experience of the Large Hadron Collider (LHC) project [4] with one proprietary DBMS vendor has “poisoned the well”. Hence, scientists require the option of fixing bugs and adding their own features, if the vendor of their chosen solution is unable, unwilling, or just slow to respond. In effect, only open source software is acceptable. A requirement for no overwrite. Scientists are equally adamant about never throwing anything away. For example, large portions of the earth are currently not very interesting to earth scientists. However, that could change in the future, so discarding currently uninteresting data is not an option. Also, they wish to keep erroneous data that has been subsequently corrected. The reason for this is to redo analyses on the data as it existed at the time the original analysis was done, i.e. they want auditability for their analyses. This is related to the provenance discussion below, and requires that all data be kept indefinitely. A requirement for provenance. If a data element looks suspicious, then scientists want to be able to trace backward through its derivation to find previous data that appears faulty. In other words, trace the error back to its source. Similarly, they would then want to find all of the derived data that came from this faulty item. In other words, they want the ability to do forward and backward derivation efficiently. One reason for this requirement is assistance in the error correction noted above. A second reason is to facilitate sharing. Different scientists generally cannot make use of derived data unless they know the algorithm that was used to create it. For example, consider the “best” cloud free image discussed above. There is no universal way to choose the best composite image, and any scientist who wants to use a composite image must know what algorithm was used to construct it. They want to find this information by exploring the provenance of the data of interest. A requirement for uncertainty. After all, every bit of scientific data comes with error bars. Current DBMSs were written to support the business market, and assume the data is perfect. Obviously, enterprises must know accurate salaries, in order to The Architecture of SciDB 3 write pay checks. Essentially all information collected from sensors (nearly 100% of science data) does not have this property. Furthermore, scientists may want to propagate error data through a sequence of calculations. A requirement for version control. There is no universal agreement on the cooking algorithms, which turn raw data into derived data sets. Hence, scientists would like to re-cook raw data for their study areas, retaining the conventional derivations for the rest of the data set. Although they can construct a complete copy of the data, with the required characteristics, it is wildly more efficient to delta their copies off of the conventional one, so the common data only appears once. Version control software has been supporting this functionality for years. At XLDB-1, there was a general feeling that RDBMSs would never meet the above requirements because they have: The wrong data model, The wrong operators, and Are missing required capabilities. Moreover, the RDBMS vendors appear not to be focused on the science market, because the business enterprise market is perceived to be larger. Hence, there was skepticism that these shortcomings would ever be addressed. A second theme of the meeting was the increasing difficulty of meeting big science requirements with “from the bare metal up” custom implementations. The software stack is simply getting too large. Several of the web properties indicated the scope of their custom efforts, and said “we are glad we have sufficient resources to move forward”. Also, there was frustration that every big science project re-grows the complete stack, leading to limited shared infrastructure. The Sloan Digital Sky Survey [5] was also noted as a clear exception, as they made use of SQLServer. In effect, the community was envious of the RDBMS market where a common set of features is used by nearly everybody and supported by multiple vendors. In summary, the mood was “Why can’t somebody do for science what RDBMS did for business?” As a result, Dave Dewitt and Mike Stonebraker said they would try to build a from- the-ground-up DBMS aimed at science requirements. Following XLDB-1, there were meetings to discuss detailed requirements and a collection of use cases written, leading to an overall design. This process was helped along by the LSST data management team who said, “If it works, we will try to use it”. We began writing code in late 2008, with a pick-up team of volunteers and research personnel. This led to a demo of an early version of SciDB at VLDB in Lyon, France in Sept 2009 [6]. We obtained venture capital support for the project, and additional assistance from NSF in 2010. This has allowed us to accelerate our efforts. We have 4 The Architecture of SciDB recently released SciDB 11.06 and are working toward a full featured high performance system in late 2011. We have been helped along the way by the subsequent annual XLDB meetings [7, 8, 9] where SciDB issues have been discussed in an open forum. This paper reports on the SciDB design and indicates the status of the current system. 2 SciDB Design In this section we present the major design decisions and our rationale for making them the way we did. We start with system assumptions in Section 2.1, followed by a data model discussion in Section 2.2. The query language is treated in Section 2.3. The optimizer and storage management components are treated respectively in Section 2.4 and 2.5. Other features, such as extensibility, uncertainty, version control and provenance are discussed at appropriate times. 2.1 System Assumptions It was pretty obvious that SciDB had to run on a grid (or cloud) of computers. A single node solution is clearly not going to make LSST happy. Also, there is universal acceptance of Linux in this community, so the OS choice is easy. Although we might have elected to code the system in Java, the feeling was that C++ was a better choice for high performance system software. The only point of contention among the team was whether to adopt a shared-disk or a shared-nothing architecture. On the one hand, essentially all of the recent parallel DBMSs have adopted a shared nothing model, where each node talks to locally attached storage. The query optimizer runs portions of the query on local data. In essence, one adopts a “send the query to the data” model, and strives for maximum parallelism. On the other hand, many of the recent supercomputers have used a shared-disk architecture. This appears to result from the premise that the science workload is computation intensive, and therefore the architecture should be CPU-focused rather than data focused.

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