Scientific research
Discussion of how database and related technologies are used to support scientific research. Related subjects include:
Nested data structures keep coming up, especially for log files
Nested data structures have come up several times now, almost always in the context of log files.
- Google has published about a project called Dremel. Per Tasso Agyros, one of Dremel’s key concepts is nested data structures.
- Those arrays that the XLDB/SciDB folks keep talking about are meant to be nested data structures. Scientific data is of course log-oriented. eBay was very interested in that project too.
- Facebook’s log files have a big nested data structure flavor.
I don’t have a grasp yet on what exactly is happening here, but it’s something.
| Categories: Facebook, Google, Log analysis, Scientific research, Theory and architecture, eBay | 5 Comments |
Why you should go to XLDB4
Scientific data commonly:
- Comes in large volumes
- Is machine-generated
- Is augmented by synthetic and/or derived data
- Has a spatial and/or temporal structure
In those respects, it is akin to some of the hottest areas for big data analytics, including:
- Investment trade data – big, partly machine generated, augmented (often), temporal
- Web/network log data – big, machine-generated, post-processed into derived form, temporal
- Marketing analytic data – big, post-processed into derived form
- Genomic data
So when Jacek Becla started the XLDB conferences on the premise that scientific and big data analytic challenges have a lot in common, he had a point. There are several tough database problems that the science-focused folks have taken the leading in thinking about, but which are soon going to matter to the commercial world as well. And that’s one of two big reasons why you should consider participating in XLDB4, October 6-7, at the SLAC facility in Menlo Park, CA, as an attendee, sponsor, or both.
The other big reason is that it is important for the world that XLDB succeed. Read more
| Categories: Investment research and trading, Log analysis, Scientific research, Web analytics | Leave a Comment |
Notes on SciDB and scientific data management
I firmly believe that, as a community, we should look for ways to support scientific data management and related analytics. That’s why, for example, I went to XLDB3 in Lyon, France at my own expense. Eight months ago, I wrote about issues in scientific data management. Here’s some of what has transpired since then.
The main new activity I know of has been in the open source SciDB project. Read more
| Categories: Analytic technologies, Data warehousing, GIS and geospatial, Microsoft and SQL*Server, SciDB, Scientific research, Web analytics, eBay | 3 Comments |
Greenplum Single-Node Edition — sometimes free is a real cool price
Greenplum is announcing today that you can run Greenplum software on a single 8-core commodity server, free. First and foremost, that’s a strong statement that Greenplum wants enterprises to pay it for Greenplum’s parallelization/”private cloud” capabilities. Second, it may be an attractive gift to a variety of folks who want to extract insight from terabyte-scale databases of various kinds.
Greenplum Single-Node Edition:
- Is free of charge, although you can buy support.
- Has no restrictions on use, production or otherwise.
- Has no restrictions on database size.
- Is closed-source.
For those who want free, terabyte-scale data warehousing software, Greenplum Single-Node Edition may be quite appealing, considering that the main available alternatives are:
- General-purpose open-source DBMS, such as PostgreSQL and MySQL (lacking analytic DBMS performance and features)
- Infobright Community Edition (the other best choice – Infobright’s commercial sales success indicates the solidity of Infobright’s technology)
- Rough research-project code and other other questionable open source offerings
- Crippleware from other commercial analytic DBMS vendors (e.g., Teradata)
For example, comparing PostgreSQL-based Greenplum with PostgreSQL itself, Greenplum offers:
- The ability to scale out queries across all cores in your box (and no, pgpool is not a serious alternative)
- Storage alternatives such as columnar (I am told that EnterpriseDB recently stopped funding a project for a PostgreSQL columnar option)
| Categories: Analytic technologies, Data warehousing, EnterpriseDB and Postgres Plus, Greenplum, Infobright, Open source, PostgreSQL, Pricing, Scientific research | 11 Comments |
How 30+ enterprises are using Hadoop
MapReduce is definitely gaining traction, especially but by no means only in the form of Hadoop. In the aftermath of Hadoop World, Jeff Hammerbacher of Cloudera walked me quickly through 25 customers he pulled from Cloudera’s files. Facts and metrics ranged widely, of course:
- Some are in heavy production with Hadoop, and closely engaged with Cloudera. Others are active Hadoop users but are very secretive. Yet others signed up for initial Hadoop training last week.
- Some have Hadoop clusters in the thousands of nodes. Many have Hadoop clusters in the 50-100 node range. Others are just prototyping Hadoop use. And one seems to be “OEMing” a small Hadoop cluster in each piece of equipment sold.
- Many export data from Hadoop to a relational DBMS; many others just leave it in HDFS (Hadoop Distributed File System), e.g. with Hive as the query language, or in exactly one case Jaql.
- Some are household names, in web businesses or otherwise. Others seem to be pretty obscure.
- Industries include financial services, telecom (Asia only, and quite new), bioinformatics (and other research), intelligence, and lots of web and/or advertising/media.
- Application areas mentioned — and these overlap in some cases — include:
- Log and/or clickstream analysis of various kinds
- Marketing analytics
- Machine learning and/or sophisticated data mining
- Image processing
- Processing of XML messages
- Web crawling and/or text processing
- General archiving, including of relational/tabular data, e.g. for compliance
Scientific data sharing
I’ve been posting recently about some issues in scientific data management. One topic I haven’t addressed yet is policies around data sharing. Generally:
- Scientists, like other academics, have their research judged largely on the basis of their published papers.
- The data scientists capture benefits scientists’ careers mainly by informing and being used in their published papers.
- Scientists are correspondingly uninterested in, if not actively opposed to, sharing their data with the rest of the world
- Promptly (for the data they use to directly support their publications)
- Perhaps ever (for the rest of the data)
On the other hand, it’s blindingly obvious that the world as a whole would be better off with widespread scientific data sharing, provided that making data “free” doesn’t significantly undermine scientists’ incentives to capture it in the first place. And institutions such as funding agencies are taking note. Thus:
Scientific data management technology should be suitable for either of the scenarios:
- Data is widely shared among scientists.
- Data is jealously guarded by the scientists who first gather it.
| Categories: Data warehousing, Scientific research | 7 Comments |
Jacek Becla on issues in scientific data management
Just as Martin Kersten did, Jacek Becla emailed a response to my post on issues in scientific data management. With his permission, I’ve lightly edited his email too, and am posting it below, with some interspersed comments of my own. Read more
| Categories: Analytic technologies, Hadoop, MapReduce, Open source, Parallelization, SciDB, Scientific research | 3 Comments |
Martin Kersten on issues in scientific data management
Martin Kersten emailed a response to my post on issues in scientific data management. With his permission, I’ve lightly edited it, and am posting it below. Read more
| Categories: Analytic technologies, Clustering, Parallelization, SciDB, Scientific research | 3 Comments |
Issues in scientific data management
In the opinion of the leaders of the XLDB and SciDB efforts, key requirements for scientific data management include:
- A data model based on multidimensional arrays, not sets of tuples
- A storage model based on versions and not update in place
- Built-in support for provenance (lineage), workflows, and uncertainty
- Scalability to 100s of petabytes and 1,000s of nodes with high degrees of tolerance to failures
- Support for “external” data objects so that data sets can be queried and manipulated without ever having to be loaded into the database
- Open source in order to foster a community of contributors and to insure that data is never “locked up” — a critical requirement for scientists
However: Read more
HadoopDB
Despite a thoughtful heads-up from Daniel Abadi at the time of his original posting about HadoopDB, I’m just getting around to writing about it now. HadoopDB is a research project carried out by a couple of Abadi’s students. Further research is definitely planned. But it seems too early to say that HadoopDB will ever get past the “research and oh by the way the code is open sourced” stage and become a real code line — whether commercialized, open source, or both.
The basic idea of HadoopDB is to put copies of a DBMS at different nodes of a grid, and use Hadoop to parcel work among them. Major benefits when compared with massively parallel DBMS are said to be:
- Open/cheap/free
- Query fault-tolerance
- The related concept of tolerating node degradation that isn’t an outright node failure.
HadoopDB has actually been built with PostgreSQL. That version achieved performance well below that of a commercial DBMS “DBX”, where X=2. Column-store guru Abadi has repeatedly signaled his intention to try out HadoopDB with VectorWise at the nodes instead. (Recall that VectorWise is shared-everything.) It will be interesting to see how that configuration performs.
The real opportunity for HadoopDB, however, in my opinion may lie elsewhere. Read more