Large-Scale Data Storage and Processing for Scientists with Hadoop

Large-Scale Data Storage and Processing for Scientists in The NetherlandsEvert.Lammerts@SARA.nlJanuary 21, 2011NBIC BioAssist Programmers Day

Super computingCloud computing Grid computing Cluster computing GPU computing BioAssist Programmers Day, January 21, 2011

Status Quo:Storage separate from Compute BioAssist Programmers Day, January 21, 2011

Case Study:Virtual Knowledge Studio http://simshelf2.virtualknowledgestudio.nl/activities/biggrid-wikipedia-experiment ● How do categories in WikiPedia evolve over time? (And how do they relate to internal links?) ● 2.7 TB raw text, single file ● Java application, searches for categories in Wiki markup, like [[Category:NAME]] ● Executed on the Grid BioAssist Programmers Day, January 21, 2011

1.1) Copy file from local 2.1) Stream file from Grid 3.1) Process all files in Machine to Grid storage Storage to single machine parallel: N machines 2.2) Cut into pieces of 10 GB run the Java application, 2.3) Stream back to Grid fetch a 10GB file as Storage input, processing it, and putting the result back BioAssist Programmers Day, January 21, 2011

Status Quo: Arrange your own (Data-)parallelism● Cut the dataset up in “processable chunks”: ● Size of chunk depending on local space on processing node... ● … on the total processing capacity available … ● … on the smallest unit of work (“largest grade of parallelism”)... ● … on the substance (sometimes you dont want many output files, e.g. when building a search index).● Submit the amount of jobs you consider necessary: ● To a cluster close to your data (270x10GB over WAN is a bad idea) ● Amount might depend on cluster capacity, amount of chunks, smallest unit of work, substance... When dealing with large data, lets say 100GB+, this is ERROR PRONE, TIME CONSUMING AND NOT FOR NEWBIES! BioAssist Programmers Day, January 21, 2011

2002 2004 2006Nutch* MR/GFS** Hadoop* http://nutch.apache.org/** http://labs.google.com/papers/mapreduce.html http://labs.google.com/papers/gfs.html BioAssist Programmers Day, January 21, 2011

2010/2011: A Hype in Productionhttp://wiki.apache.org/hadoop/PoweredBy BioAssist Programmers Day, January 21, 2011

BioAssist Programmers Day, January 21, 2011

Hadoop Distributed File System (HDFS)● Very large DFS. Order of magnitude: – 10k nodes – millions of files – PetaBytes of storage● Assumes “commodity hardware”: – redundancy through replication – failure handling and recovery● Optimized for batch processing: – locations of data exposed to computation – high aggregate bandwidth BioAssist Programmers Day, January 21, 2011 http://www.slideshare.net/jhammerb/hdfs-architecture

HDFS Continued...● Single Namespace for the entire cluster● Data coherency – Write-once-read-many model – Only appending is supported for existing files● Files are broken up in chunks (“blocks”) – Blocksizes ranging from 64 to 256 MB, depending on configuration – Blocks are distributed over nodes (a single FILE, existing of N blocks, is stored on M nodes) – Blocks are replicated and replications are distributed● Client accesses the blocks of a file at the nodes directly – This creates high aggregate bandwidth! BioAssist Programmers Day, January 21, 2011 http://www.slideshare.net/jhammerb/hdfs-architecture

HDFS NameNode & DataNodesNameNode DataNode● Manages File System Namespace ● A “Block Server” – Mapping filename to blocks – Stores data in local FS – Mapping blocks to DataNode – Stores metadata of a block (e.g. hash)● Cluster Configuration – Serve (meta)data to clients● Replication Management ● Facilitates pipeline to other DNs BioAssist Programmers Day, January 21, 2011

http://hadoop.apache.org/common/docs/r0.20.0/hdfs_shell.html Metadata operations ● Communicate with NN only – ls (see above), lsr, df, du, chmod, chown... etc. R/W (block) operations ● Communicate with NN and DNs – put, copyFromLocal, CopyToLocal, tail... etc. BioAssist Programmers Day, January 21, 2011

HDFS Application Programming Interface (API)● Enables programmers to access any HDFS from their code● Described at http://hadoop.apache.org/common/docs/r0.20.0/api/index.html● Written in (and thus available for) Java, but...● Is also exposed through Apache Thrift, so can be accessed from: ● C++, Python, PHP, Ruby, and others ● See http://wiki.apache.org/hadoop/HDFS-APIs● Has a separate C-API (libhdfs)So: you can enable your services to work with HDFS BioAssist Programmers Day, January 21, 2011

MapReduce● Is a framework for distributed (parallel) processing of large datasets● Provides a programming model● Lets users plug-in own code● Uses a common pattern: cat | grep | sort | unique > file input | map | shuffle | reduce > output● Is useful for large scale data analytics and processing BioAssist Programmers Day, January 21, 2011

MapReduce Continued...● Is great for processing large datasets! – Send computation to data, so little data over lines – Uses blocks stored in the DFS, so no splitting required (this is a bit more sophisticated depending on your input)● Handles parallelism for you – One map per block, if possible● Scales basically linearly – time_on_cluster = time_on_single_core / total_cores● Java, but streaming possible (plus others, see later) BioAssist Programmers Day, January 21, 2011

MapReduce JobTracker & TaskTrackersJobTracker TaskTracker● Holds job metadata ● Requests work from JT – Status of job – Fetch the code to execute from the DFS – Status of Tasks running on TTs – Apply job-specific configuration● Decides on scheduling ● Communicate with JT on tasks:● Delegates creation of InputSplits – Sending output, Killing tasks, Task updates, etc BioAssist Programmers Day, January 21, 2011

MapReduce clientBioAssist Programmers Day, January 21, 2011

MapReduce Application Programming Interface (API)● Enables programmers to write MapReduce jobs ● More info on MR jobs: http://www.slideshare.net/evertlammerts/infodoc-6107350● Enables programmers to communicate with a JobTracker ● Submitting jobs, getting statuses, cancelling jobs, etc● Described at http://hadoop.apache.org/common/docs/r0.20.0/api/index.html BioAssist Programmers Day, January 21, 2011

Case Study: Virtual Knowledge Studio1) Load file into 2) Submit code HDFS to MR BioAssist Programmers Day, January 21, 2011

Whats more on Hadoop?Lots!● Apache Pig http://pig.apache.org – Analyze datasets in a high level language, “Pig Latin” – Simple! SQL like. Extremely fast experiments. – N-stage jobs (MR chaining!)● Apache Hive http://hive.apache.org – Data Warehousing – Hive QL● Apache Hbase http://hbase.apache.org – BigTable implementation (Google) – In-memory operation – Performance good enough for websites (Facebook built its Messaging Platform on top of it)● Yahoo! Oozie http://yahoo.github.com/oozie/ – Hadoop workflow engine● Apache [AVRO | Chukwa | Hama | Mahout] and so on● 3rd Party: – ElephantBird – Clouderas Distribution for Hadoop – Hue – Yahoos Distribution for Hadoop BioAssist Programmers Day, January 21, 2011

Hadoop @ SARAA prototype cluster● Since December 2010● 20 cores for MR (TTs)● 110 TB gross for HDFS (DN) (55TB net)● Hue web-interface for job submission & management● SFTP interface to HDFS● Pig 0.8● Hive● Available for scientists / scientific programmers until May / June 2011Towards a production infrastructure?● Depending on results Its open for you all as well: ask me for an account! BioAssist Programmers Day, January 21, 2011

BioAssist Programmers Day, January 21, 2011

Hadoop for: ● Large-scale data storage and processing ● Fundamental difference: data locality! ● Small files? Dont, but... Hadoop Archives (HAR) ● Archival? Dont. Use tape storage. (We have lots!) ● Very fast analytics (Pig!) ● For data-parallel applications (not good at crossproducts – use Huygens or Lisa!) ● Legacy applications possible through piping / streaming (Weird dependencies? Use Cloud!)Well do another Hackathon on Hadoop. Interested? Send me a mail! BioAssist Programmers Day, January 21, 2011

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Large-Scale Data Storage and Processing for Scientists with Hadoop

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