How neuroscience is benefiting from distributed computing — and how computing might learn from neuroscience.
When we think about big data, we usually think about the web: the billions of users of social media, the sensors on millions of mobile phones, the thousands of contributions to Wikipedia, and so forth. Due to recent innovations, web-scale data can now also come from a camera pointed at a small, but extremely complex object: the brain. New progress in distributed computing is changing how neuroscientists work with the resulting data — and may, in the process, change how we think about computation. Read more…
New frameworks for interactive business analysis and advanced analytics fuel the rise in tabular data objects.
Long before the advent of “big data,” analysts were building models using tools like R (and its forerunners S/S-PLUS). Productivity hinged on tools that made data wrangling, data inspection, and data modeling convenient. Among R users, this meant proficiency with data frames — objects used to store data matrices that can hold both numeric and categorical data. A
data.frame is the data structure consumed by most R analytic libraries.
But not all data scientists use R, nor is R suitable for all data problems. I’ve been watching with interest the growing number of alternative data structures for business analysis and advanced analytics. These new tools are designed to handle much larger data sets and are frequently optimized for specific problems. And they all use idioms that are familiar to data scientists — either SQL-like expressions, or syntax similar to those used for R
Many more companies want to highlight how they're using Apache Spark in production.
One of the trends we’re following closely at Strata is the emergence of vertical applications. As components for creating large-scale data infrastructures enter their early stages of maturation, companies are focusing on solving data problems in specific industries rather than building tools from scratch. Virtually all of these components are open source and have contributors across many companies. Organizations are also sharing best practices for building big data applications, through blog posts, white papers, and presentations at conferences like Strata.
These trends are particularly apparent in a set of technologies that originated from UC Berkeley’s AMPLab: the number of companies that are using (or plan to use) Spark in production1 has exploded over the last year. The surge in popularity of the Apache Spark ecosystem stems from the maturation of its individual open source components and the growing community of users. The tight integration of high-performance tools that address different problems and workloads, coupled with a simple programming interface (in Python, Java, Scala), make Spark one of the most popular projects in big data. The charts below show the amount of active development in Spark:
For the second year in a row, I’ve had the privilege of serving on the program committee for the Spark Summit. I’d like to highlight a few areas where Apache Spark is making inroads. I’ll focus on proposals2 from companies building applications on top of Spark.
It's easier to "discover" features with tools that have broad coverage of the data science workflow
Interface languages: Python, R, SQL (and Scala)
This is a great time to be a data scientist or data engineer who relies on Python or R. For starters there are developer tools that simplify setup, package installation, and provide user interfaces designed to boost productivity (RStudio, Continuum, Enthought, Sense).
Increasingly, Python and R users can write the same code and run it against many different execution1 engines. Over time the interface languages will remain constant but the execution engines will evolve or even get replaced. Specifically there are now many tools that target Python and R users interested in implementations of algorithms that scale to large data sets (e.g., GraphLab, wise.io, Adatao, H20, Skytree, Revolution R). Interfaces for popular engines like Hadoop and Apache Spark are also available – PySpark users can access algorithms in MLlib, SparkR users can use existing R packages.
In addition many of these new frameworks go out of their way to ease the transition for Python and R users. wise.io “… bindings follow the Scikit-Learn conventions”, and as I noted in a recent post, with SFrames and Notebooks GraphLab, Inc. built components2 that are easy for Python users to learn.
Open source, distributed computing tools speedup an important processing pipeline for genomics data
As open source, big data tools enter the early stages of maturation, data engineers and data scientists will have many opportunities to use them to “work on stuff that matters”. Along those lines, computational biology and medicine are areas where skilled data professionals are already beginning to make an impact. I recently came across a compelling open source project from UC Berkeley’s AMPLab: ADAM is a processing engine and set of formats for genomics data.
Second-generation sequencing machines produce more detailed and thus much larger files for analysis (250+ GB file for each person). Existing data formats and tools are optimized for single-server processing and do not easily scale out. ADAM uses distributed computing tools and techniques to speedup key stages of the variant processing pipeline (including sorting and deduping):
Very early on the designers of ADAM realized that a well-designed data schema (that specifies the representation of data when it is accessed) was key to having a system that could leverage existing big data tools. The ADAM format uses the Apache Avro data serialization system and comes with a human-readable schema that can be accessed using many programming languages (including C/C++/C#, Java/Scala, php, Python, Ruby). ADAM also includes a data format/access API implemented on top of Apache Avro and Parquet, and a data transformation API implemented on top of Apache Spark. Because it’s built with widely adopted tools, ADAM users can leverage components of the Hadoop (Impala, Hive, MapReduce) and BDAS (Shark, Spark, GraphX, MLbase) stacks for interactive and advanced analytics.
The Delite framework has produced high-performance languages that target data scientists
An important reason why pydata tools and Spark appeal to data scientists is that they both cover many data science tasks and workloads (Spark users can move seamlessly between batch and streaming). Being able to use the same programming style and syntax for workflows that span a variety of tasks is a huge productivity boost. In the case of Spark (and Hadoop), the emergence of a variety of scalable analytic engines have made distributed computing applications much easier to build.
Delite: a framework for embedded, parallel, and high-performance DSLs
Another way to boost productivity is to use a family of high-performance languages that cover many data science tasks. Ideally you want languages that allow programmers to focus on applications (not on low-level details of parallel programming) and that can run efficiently on different machines and architectures1 (CPU, GPU). And just like pydata and Spark, syntax and context-switching shouldn’t get in the way of tackling complex data science workflows.
The Delite framework from Stanford’s Pervasive Parallelism Lab (PPL) has been used to produce a family of high-performance domain specific languages (DSLs) that target different data analysis tasks. DSLs are programming languages2 with restricted expressiveness (for a particular domain) and tend to be high-level in nature (they are often declarative and deterministic). Delite is a compiler and runtime infrastructure that allows language designers to use aggressive, domain-specific optimizations to deliver high-performance DSLs. Using Delite, the team at Stanford produced DSLs embedded in a functional language (Scala) with performance results comparable to hand-optimized implementations (e.g. MATLAB, LINQ) across different domains.
New tools make it easier for companies to process and mine streaming data sources
Stream processing was in the minds of a few people that I ran into over the past week. A combination of new systems, deployment tools, and enhancements to existing frameworks, are behind the recent chatter. Through a combination of simpler deployment tools, programming interfaces, and libraries, recently released tools make it easier for companies to process and mine streaming data sources.
Of the distributed stream processing systems that are part of the Hadoop ecosystem0, Storm is by far the most widely used (more on Storm below). I’ve written about Samza, a new framework from the team that developed Kafka (an extremely popular messaging system). Many companies who use Spark express interest in using Spark Streaming (many have already done so). Spark Streaming is distributed, fault-tolerant, stateful, and boosts programmer productivity (the same code used for batch processing can, with minor tweaks, be used for realtime computations). But it targets applications that are in the “second-scale latencies”. Both Spark Streaming and Samza have their share of adherents and I expect that they’ll both start gaining deployments in 2014.
Python and Scala are popular among members of several well-attended SF Bay Area Meetups
In exchange for getting personalized recommendations many Meetup members declare1 topics that they’re interested in. I recently looked at the topics listed by members of a few local, data Meetups that I’ve frequented. These Meetups vary in size from 600 to 2,000 total (and 400 to 1,100 active2) members.
How it All Started
Spark is a popular open source cluster computing engine for Big Data analytics and a central component of the Berkeley Data Analytics Stack (BDAS). It started as a research project in the UC Berkeley AMPLab and was developed with a focus on attracting production users as well as a diverse community of open source contributors. A community quickly began to grow around Spark, even as a young project in the AMPLab. Before long, this community began gathering at monthly meetups and using mailing lists to discuss development efforts and share their experiences using Spark. More recently the project entered the Apache Incubator.
This year, the core Spark team spun out of the AMPLab to found Databricks, a startup that is using Spark to build next-generation software for analyzing and extracting value from data. At Databricks, we are dedicated to the success of the Spark project and are excited to see the community growing rapidly. This growth demonstrates the need for a larger event that brings the entire community together beyond the meetups. Thus we began planning the first Spark Summit. The Summit will be structured like a super-sized meetup. Meetups typically consist of a single talk, a single sponsor, and dozens of attendees, whereas the Summit will consist of 30 talks, 18 sponsors, hundreds of attendees, and a full day of training exercises.
We understand that an open source project is only as successful as its underlying community. Therefore, we want the Summit to be a community driven event.
Behind the Scenes with the Summit Ops and the Program Committee
The first thing we did was bring in a third-party event producer with a track record of creating high quality open source community events. By separating out the event production we allowed all of the community leaders to share ownership of the technical portion of the event. For example, instead of inviting speakers directly, we hosted an open call for talk submissions. Then we assembled a Program Committee consisting of representatives from 12 of the leading organizations in the Spark community. Finally, the PC members voted on all of the talk submissions to decide the final summit agenda.
The event has been funded by assembling a sponsor network consisting of organizations within the community. With sponsors that are driving the development of the platform, the summit will be an environment that facilitates connections between developers with Spark skills and organizations searching for such developers. We decided that Databricks would participate in the Summit as a peer in this sponsor network.
The inaugural Spark Summit will feature a wide variety of real-world applications
When an interesting piece of big data technology gets introduced, early1 adopters tend to focus on technical features and capabilities. Applications get built as companies develop confidence that it’s reliable and that it really scales to large data volumes. That seems to be where Spark is today. With over 90 contributors from 25 companies, it has one of the largest developer communities among big data projects (second only to Hadoop MapReduce).
I recently became an advisor to Databricks (a startup commercializing Spark) and a member of the program committee for the inaugural Spark Summit. As I pored over submissions to Spark’s first community gathering, I learned how companies have come to rely on Spark, Shark, and other components of the Berkeley Data Analytics Stack (BDAS). Spark is at that stage where companies are deploying it, and the upcoming Spark Summit in San Francisco will showcase many real-world applications. These applications cut across many domains including advertising, marketing, finance, and academic/scientific research, but can generally be grouped into the following categories:
Data processing workflows: ETL and Data Wrangling
Many companies rely on a wide variety of data sources for their analytic products. That means cleaning, transforming, and fusing (unstructured) external data with internal data sources. Many companies – particularly startups – use Spark for these types of data processing workflows. There are even companies that have created simple user interfaces that open up batch data processing tasks to non-programmers.