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Tag Archives: parallel
Including juicy stuff on using a cluster of Apple Machines for grid computing , seasonality forecasting (Yet Another Package For Time Series )
But I kind of liked Sumo too-
Sumo is a fully-functional web application template that exposes an authenticated user’s R session within java server pages.
Sumo: An Authenticating Web Application with an Embedded R Session by Timothy T. Bergsma and Michael S. Smith Abstract Sumo is a web application intended as a template for developers. It is distributed as a Java ‘war’ file that deploys automatically when placed in a Servlet container’s ‘webapps’
directory. If a user supplies proper credentials, Sumo creates a session-specific Secure Shell connection to the host and a user-specific R session over that connection. Developers may write dynamic server pages that make use of the persistent R session and user-specific file space.
and for Apple fanboys-
We created the xgrid package (Horton and Anoke, 2012) to provide a simple interface to this distributed computing system. The package facilitates use of an Apple Xgrid for distributed processing of a simulation with many independent repetitions, by simplifying job submission (or grid stuffing) and collation of results. It provides a relatively thin but useful layer between R and Apple’s ‘xgrid’ shell command, where the user constructs input scripts to be run remotely. A similar set of routines, optimized for parallel estimation of JAGS (just another Gibbs sampler) models is available within the runjags package (Denwood, 2010). However, with the exception of runjags, none of the previously mentioned packages support parallel computation over an Apple Xgrid.
Hmm I guess parallel computing enabled by Wifi on mobile phones would be awesome too ! So would be anything using iOS . See the rest of the R Journal at http://journal.r-project.org/current.html
Here is an interview with James G Kobielus, who is the Senior Program Director, Product Marketing, Big Data Analytics Solutions at IBM. Special thanks to Payal Patel Cudia of IBM’s communication team,for helping with the logistics for this.
Ajay -What are the specific parts of the IBM Platform that deal with the three layers of Big Data -variety, velocity and volume
James-Well first of all, let’s talk about the IBM Information Management portfolio. Our big data platform addresses the three layers of big data to varying degrees either together in a product , or two out of the three or even one of the three aspects. We don’t have separate products for the variety, velocity and volume separately.
Let us define these three layers-Volume refers to the hundreds of terabytes and petabytes of stored data inside organizations today. Velocity refers to the whole continuum from batch to real time continuous and streaming data.
Variety refers to multi-structure data from structured to unstructured files, managed and stored in a common platform analyzed through common tooling.
For Volume-IBM has a highly scalable Big Data platform. This includes Netezza and Infosphere groups of products, and Watson-like technologies that can support petabytes volume of data for analytics. But really the support of volume ranges across IBM’s Information Management portfolio both on the database side and the advanced analytics side.
For real time Velocity, we have real time data acquisition. We have a product called IBM Infosphere, part of our Big Data platform, that is specifically built for streaming real time data acquisition and delivery through complex event processing. We have a very rich range of offerings that help clients build a Hadoop environment that can scale.
Our Hadoop platform is the most real time capable of all in the industry. We are differentiated by our sheer breadth, sophistication and functional depth and tooling integrated in our Hadoop platform. We are differentiated by our streaming offering integrated into the Hadoop platform. We also offer a great range of modeling and analysis tools, pretty much more than any other offering in the Big Data space.
Attached- Jim’s slides from Hadoop World
Ajay- Any plans for Mahout for Hadoop
Jim- I cant speak about product plans. We have plans but I cant tell you anything more. We do have a feature in Big Insights called System ML, a library for machine learning.
Ajay- How integral are acquisitions for IBM in the Big Data space (Netezza,Cognos,SPSS etc). Is it true that everything that you have in Big Data is acquired or is the famous IBM R and D contributing here . (see a partial list of IBM acquisitions at at http://www.ibm.com/investor/strategy/acquisitions.wss )
Jim- We have developed a lot on our own. We have the deepest R and D of anybody in the industry in all things Big Data.
For example – Watson has Big Insights Hadoop at its core. Apache Hadoop is the heart and soul of Big Data (see http://www-01.ibm.com/software/data/infosphere/hadoop/ ). A great deal that makes Big Insights so differentiated is that not everything that has been built has been built by the Hadoop community.
We have built additions out of the necessity for security, modeling, monitoring, and governance capabilities into BigInsights to make it truly enterprise ready. That is one example of where we have leveraged open source and we have built our own tools and technologies and layered them on top of the open source code.
Yes of course we have done many strategic acquisitions over the last several years related to Big Data Management and we continue to do so. This quarter we have done 3 acquisitions with strong relevance to Big Data. One of them is Vivisimo (http://www-03.ibm.com/press/us/en/pressrelease/37491.wss ).
Vivisimo provides federated Big Data discovery, search and profiling capabilities to help you figure out what data is out there,what is relevance of that data to your data science project- to help you answer the question which data should you bring in your Hadoop Cluster.
We also did Varicent , which is more performance management and we did TeaLeaf , which is a customer experience solution provider where customer experience management and optimization is one of the hot killer apps for Hadoop in the cloud. We have done great many acquisitions that have a clear relevance to Big Data.
Netezza already had a massively parallel analytics database product with an embedded library of models called Netezza Analytics, and in-database capabilties to massively parallelize Map Reduce and other analytics management functions inside the database. In many ways, Netezza provided capabilities similar to that IBM had provided for many years under the Smart Analytics Platform (http://www-01.ibm.com/software/data/infosphere/what-is-advanced-analytics/ ) .
There is a differential between Netezza and ISAS.
ISAS was built predominantly in-house over several years . If you go back a decade ago IBM acquired Ascential Software , a product portfolio that was the heart and soul of IBM InfoSphere Information Manager that is core to our big Data platform. In addition to Netezza, IBM bought SPSS two years back. We already had data mining tools and predictive modeling in the InfoSphere portfolio, but we realized we needed to have the best of breed, SPSS provided that and so IBM acquired them.
Cognos- We had some BI reporting capabilities in the InfoSphere portfolio that we had built ourselves and also acquired for various degrees from prior acquisitions. But clearly Cognos was one of the best BI vendors , and we were lacking such a rich tool set in our product in visualization and cubing and so for that reason we acquired Cognos.
There is also Unica – which is a marketing campaign optimization which in many ways is a killer app for Hadoop. Projects like that are driving many enterprises.
Ajay- How would you rank order these acquisitions in terms of strategic importance rather than data of acquisition or price paid.
Jim-Think of Big Data as an ecosystem that has components that are fitted to particular functions for data analytics and data management. Is the database the core, or the modeling tool the core, or the governance tools the core, or is the hardware platform the core. Everything is critically important. We would love to hear from you what you think have been most important. Each acquisition has helped play a critical role to build the deepest and broadest solution offering in Big Data. We offer the hardware, software, professional services, the hosting service. I don’t think there is any validity to a rank order system.
Ajay-What are the initiatives regarding open source that Big Data group have done or are planning?
Jim- What we are doing now- We are very much involved with the Apache Hadoop community. We continue to evolve the open source code that everyone leverages.. We have built BigInsights on Apache Hadoop. We have the closest, most up to date in terms of version number to Apache Hadoop ( Hbase,HDFS, Pig etc) of all commercial distributions with our BigInsights 1.4 .
We have an R library integrated with BigInsights . We have a R library integrated with Netezza Analytics. There is support for R Models within the SPSS portfolio. We already have a fair amount of support for R across the portfolio.
Ajay- What are some of the concerns (privacy,security,regulation) that you think can dampen the promise of Big Data.
Jim- There are no showstoppers, there is really a strong momentum. Some of the concerns within the Hadoop space are immaturity of the technology, the immaturity of some of the commercial offerings out there that implement Hadoop, the lack of standardization for formal sense for Hadoop.
There is no Open Standards Body that declares, ratifies the latest version of Mahout, Map Reduce, HDFS etc. There is no industry consensus reference framework for layering these different sub projects. There are no open APIs. There are no certifications or interoperability standards or organizations to certify different vendors interoperability around a common API or framework.
The lack of standardization is troubling in this whole market. That creates risks for users because users are adopting multiple Hadoop products. There are lots of Hadoop deployments in the corporate world built around Apache Hadoop (purely open source). There may be no assurance that these multiple platforms will interoperate seamlessly. That’s a huge issue in terms of just magnifying the risk. And it increases the need for the end user to develop their own custom integrated code if they want to move data between platforms, or move map-reduce jobs between multiple distributions.
Also governance is a consideration. Right now Hadoop is used for high volume ETL on multi structured and unstructured data sources, or Hadoop is used for exploratory sand boxes for data scientists. These are important applications that are a majority of the Hadoop deployments . Some Hadoop deployments are stand alone unstructured data marts for specific applications like sentiment analysis like.
Hadoop is not yet ready for data warehousing. We don’t see a lot of Hadoop being used as an alternative to data warehouses for managing the single version of truth of system or record data. That day will come but there needs to be out there in the marketplace a broader range of data governance mechanisms , master data management, data profiling products that are mature that enterprises can use to make sure their data inside their Hadoop clusters is clean and is the single version of truth. That day has not arrived yet.
One of the great things about IBM’s acquisition of Vivisimo is that a piece of that overall governance picture is discovery and profiling for unstructured data , and that is done very well by Vivisimo for several years.
What we will see is vendors such as IBM will continue to evolve security features inside of our Hadoop platform. We will beef up our data governance capabilities for this new world of Hadoop as the core of Big Data, and we will continue to build up our ability to integrate multiple databases in our Hadoop platform so that customers can use data from a bit of Hadoop,some data from a bit of traditional relational data warehouse, maybe some noSQL technology for different roles within a very complex Big Data environment.
That latter hybrid deployment model is becoming standard across many enterprises for Big Data. A cause for concern is when your Big Data deployment has a bit of Hadoop, bit of noSQL, bit of EDW, bit of in-memory , there are no open standards or frameworks for putting it all together for a unified framework not just for interoperability but also for deployment.
There needs to be a virtualization or abstraction layer for unified access to all these different Big Data platforms by the users/developers writing the queries, by administrators so they can manage data and resources and jobs across all these disparate platforms in a seamless unified way with visual tooling. That grand scenario, the virtualization layer is not there yet in any standard way across the big data market. It will evolve, it may take 5-10 years to evolve but it will evolve.
So, that’s the concern that can dampen some of the enthusiasm for Big Data Analytics.
You can read more about Jim at http://www.linkedin.com/pub/james-kobielus/6/ab2/8b0 or
follow him on Twitter at http://twitter.com/jameskobielus
You can read more about IBM Big Data at http://www-01.ibm.com/software/data/bigdata/
Just got the email-more software is good news!
Revolution R Enterprise 6.0 for 32-bit and 64-bit Windows and 64-bit Red Hat Enterprise Linux (RHEL 5.x and RHEL 6.x) features an updated release of the RevoScaleR package that provides fast, scalable data management and data analysis: the same code scales from data frames to local, high-performance .xdf files to data distributed across a Windows HPC Server cluster or IBM Platform Computing LSF cluster. RevoScaleR also allows distribution of the execution of essentially any R function across cores and nodes, delivering the results back to the user.
Detailed information on what’s new in 6.0 and known issues:
and from the manual-lots of function goodies for Big Data
- IBM Platform LSF Cluster support [Linux only]. The new RevoScaleR function, RxLsfCluster, allows you to create a distributed compute context for the Platform LSF workload manager.
- Azure Burst support added for Microsoft HPC Server [Windows only]. The new RevoScaleR function, RxAzureBurst, allows you to create a distributed compute context to have computations performed in the cloud using Azure Burst
- The rxExec function allows distributed execution of essentially any R function across cores and nodes, delivering the results back to the user.
- functions RxLocalParallel and RxLocalSeq allow you to create compute context objects for local parallel and local sequential computation, respectively.
- RxForeachDoPar allows you to create a compute context using the currently registered foreach parallel backend (doParallel, doSNOW, doMC, etc.). To execute rxExec calls, simply register the parallel backend as usual, then set your compute context as follows: rxSetComputeContext(RxForeachDoPar())
- rxSetComputeContext and rxGetComputeContext simplify management of compute contexts.
- rxGlm, provides a fast, scalable, distributable implementation of generalized linear models. This expands the list of full-featured high performance analytics functions already available: summary statistics (rxSummary), cubes and cross tabs (rxCube,rxCrossTabs), linear models (rxLinMod), covariance and correlation matrices (rxCovCor),
binomial logistic regression (rxLogit), and k-means clustering (rxKmeans)example: a Tweedie family with 1 million observations and 78 estimated coefficients (categorical data)
took 17 seconds with rxGlm compared with 377 seconds for glm on a quadcore laptop
and easier working with R’s big brother SAS language
RevoScaleR high-performance analysis functions will now conveniently work directly with a variety of external data sources (delimited and fixed format text files, SAS files, SPSS files, and ODBC data connections). New functions are provided to create data source objects to represent these data sources (RxTextData, RxOdbcData, RxSasData, and RxSpssData), which in turn can be specified for the ‘data’ argument for these RevoScaleR analysis functions: rxHistogram, rxSummary, rxCube, rxCrossTabs, rxLinMod, rxCovCor, rxLogit, and rxGlm.
you can analyze a SAS file directly as follows:
# Create a SAS data source with information about variables and # rows to read in each chunk
sasDataFile <- file.path(rxGetOption(“sampleDataDir”),”claims.sas7bdat”)
sasDS <- RxSasData(sasDataFile, stringsAsFactors = TRUE,colClasses = c(RowNum = “integer”),rowsPerRead = 50)
# Compute and draw a histogram directly from the SAS file
rxHistogram( ~cost|type, data = sasDS)
# Compute summary statistics
rxSummary(~., data = sasDS)
# Estimate a linear model
linModObj <- rxLinMod(cost~age + car_age + type, data = sasDS)
# Import a subset into a data frame for further inspection
subData <- rxImport(inData = sasDS, rowSelection = cost > 400,
varsToKeep = c(“cost”, “age”, “type”))
The installation instructions and instructions for getting started with Revolution R Enterprise & RevoDeployR for Windows: http://www.revolutionanalytics.com/downloads/instructions/windows.php
A virtual Easter egg is an intentional hidden message, in-joke, or feature in a work such as a computer program, web page, video game, movie, book, or crossword. The term was coined — according to Warren Robinett — by Atari after they were pointed to the secret message left by Robinett in the game Adventure. It draws a parallel with the custom of the Easter egg hunt observed in many Western nations as well as the last Russian imperial family’s tradition of giving elaborately jeweled egg-shaped creations by Carl Fabergé which contained hidden surprises
I like this
and these two
on 32 bit R type
and on any version try four question marks
Perhaps the prettiest eggs are the demos in animation package.
But there is magic in asking for help on internal functions in R
and you get the sobering thought that you probably are a R Muggle
Call an Internal Function
.Internal performs a call to an internal code which is built in to the R interpreter.
Only true R wizards should even consider using this function, and only R developers can add to the list of internal functions.
||a call expression|
I liked that I could see the actual internal functions in svn at http://svn.r-project.org/R/trunk/src/main/names.c
The opening of the internals document floored me.
It must have been a curious year in 2003-4 when the copyright of R was held (briefly it seems) by the R Foundation and also by the R Development Core Team. (which sounds better?)
* R : A Computer Language for Statistical Data Analysis * Copyright (C) 1995, 1996 Robert Gentleman and Ross Ihaka * Copyright (C) 1997--2012 The R Development Core Team * Copyright (C) 2003, 2004 The R Foundation
R help discourages for loop
Try ??for or ?for
you go into a loop till you hit escapeIf you want more-just write .Internal(inspect(ls())) at the end of your R program.
A recent announcement showing Teradata partnering with KXEN and Revolution Analytics for Teradata Analytics.
The Latest in Open Source Emerging Software Technologies
Teradata provides customers with two additional open source technologies – “R” technology from Revolution Analytics for analytics and GeoServer technology for spatial data offered by the OpenGeo organization – both of which are able to leverage the power of Teradata in-database processing for faster, smarter answers to business questions.
In addition to the existing world-class analytic partners, Teradata supports the use of the evolving “R” technology, an open source language for statistical computing and graphics. “R” technology is gaining popularity with data scientists who are exploiting its new and innovative capabilities, which are not readily available. The enhanced “R add-on for Teradata” has a 50 percent performance improvement, it is easier to use, and its capabilities support large data analytics. Users can quickly profile, explore, and analyze larger quantities of data directly in the Teradata Database to deliver faster answers by leveraging embedded analytics.
Teradata has partnered with Revolution Analytics, the leading commercial provider of “R” technology, because of customer interest in high-performing R applications that deliver superior performance for large-scale data. “Our innovative customers understand that big data analytics takes a smart approach to the entire infrastructure and we will enable them to differentiate their business in a cost-effective way,” said David Rich, chief executive officer, Revolution Analytics. “We are excited to partner with Teradata, because we see great affinity between Teradata and Revolution Analytics – we embrace parallel computing and the high performance offered by multi-core and multi-processor hardware.”
The Teradata Data Lab empowers business users and leading analytic partners to start building new analytics in less than five minutes, as compared to waiting several weeks for the IT department’s assistance.
“The Data Lab within the Teradata database provides the perfect foundation to enable self-service predictive analytics with KXEN InfiniteInsight,” said John Ball, chief executive officer, KXEN. “Teradata technologies, combined with KXEN’s automated modeling capabilities and in-database scoring, put the power of predictive analytics and data mining directly into the hands of business users. This powerful combination helps our joint customers accelerate insight by delivering top-quality models in orders of magnitude faster than traditional approaches.”
Read more at