SICSA Concordance Challenge:Using Groovy and the JCSP Library

Jon Kerridge

Software Environment• Groovy

– A Java based scripting language• Direct support for Lists and Maps

– Executes on a standard JVM

• JCSP– A CSP based library for Java– Process definitions independent of how the system will be executed– Enables multicore parallelism– Parallelism over a distributed system with TCP/IP interconnect– Executes on a standard JVM

• A set of Groovy Helper Classes have been created to permit easier access to the JCSP library

Hardware Environment• A network of multicore PCs• Network is 100Mbits / sec• Each processor has

– Intel Core 2 Duo E8400 operating at 3.0 Ghz– 2 cores– 2 threads ( no hyper-threading )– FSB 1333MHz– L2 cache 6MB– 2 Gbytes memory

Why Use a Distributed System?• Regardless of the application may need to use more than one

processing node• Better to start with an inherently parallel distributed design• Bolting on distributed parallelism afterwards is always very difficult• Scalability• Enables easier overlapping of operations, particularly file I/O

Architecture

Read File Process

Worker Worker Worker Worker

There can be any number of workers; in these experiments 4, 8 and 12Bi-directional CSP channel communication in Client-Server Design

Primary Design Criteria• Ensure all data structures are separable in some parameter

– N in this case– Reduces contention for memory access; – Hence easier to parallelise

• Keep loops simple– Easier to parallelise

Read File process• Reads parameters

– input file name, N value, Minimum number of repetitions to be output– Number of workers and Block size

• Operation– Reads input file, tokenises into space delimited words– Forms a block of such words ensuring an overlap of N-1 words between blocks– Sends a block to each worker in turn

– Merges the final partial concordance of each worker and writes final concordance to an output file

• Will be removed in the final version

Initial Experiments• The relationship between Block Size and the Number of Workers

governs how much processing can be overlapped with the initial file input

• It was discovered that for Block Size = 6144 gave the best performance for 4 or 8 workers

• Provided the only work undertaken was – removal of punctuation and – the initial calculation of the equivalent integer value for each word

Worker – Initial Phase

• Reads input blocks from Read File process– Removes punctuation – saving as bare words– Calculates integer equivalent value for each word by summing its ASCII characters

• This is also the N = 1 sequence value– These operations are overlapped with input and the same process in each worker

• For each block– Calculate the integer value for each sequence of length 2 up to N by adding word

values and store it in a Sequence list

• The integer values generated by this processing will generate duplicate values for different words and different sequences

Worker – Local Map Generation• For each Sequence in each Block

– Produce a Map of the Sequence value with the corresponding entry of a Map comprising the corresponding word strings with an entry of the places where that word string is found in the input file

– Save this in a structure that is indexed by N and each contains a list of the Maps produced above

• For each worker produce a composite Map combining the individual Maps– Save this in a structure indexed by N– This is the Concordance for this worker

Worker – Merge Phase• For each of the N partial Concordances

– Sort the integer keys into descending order– For each Key in the Nth partial Concordance

• Send the corresponding Map Entry to the Reader• The Map Entry contains a Map of the word sequences and locations within file

– This will be modified in the final version that overlaps the merge / output phase

Worker - Parallelisation• Each Worker can be parallelised by N• Data structures indexed by N can be written to in parallel

– Provided each element of the parallel only accesses a single value of N– Access to any shared structures is read only

• Thus depending on the number of available Threads (T) in the Worker’s Processor each of these operations can be carried out in parallel

• Thus the design is scalable in N and T

Parallelising the Worker’s Joindef localNPrimaryMapList = [] // holds concordance for each N valuefor ( n in 1..N)localNPrimaryMapList[n] = new PrimaryKeyMap() for ( s in 0..<startIndexes.size()){

/* sequential versionfor ( n in 1..N){defs.initPrimaryMap( localNPrimaryMapList[n],

localEqualWordMapListN[n][s])}*/def procNet = (1..N).collect { n -> new InitialJoiner( primaryMap: localNPrimaryMapList[n],

otherMap: localEqualWordMapListN[n][s])}new PAR(procNet).run()

}

InitialJoiner – Process Definition

class InitialJoiner implements CSProcess {

// this is a non-standard CSP process as it has no channels!// relies on the fact that the primaryMap can be written to by this// process exclusively

def primaryMapdef otherMap

void run(){defs.initPrimaryMap( primaryMap, otherMap)

}}

Creating Equal Block Maps - Sequentialdef localEqualWordMapListN = [] // contains an element for each N valuefor ( i in 1..N) localEqualWordMapListN[i] = [] def maxLength = BL - N for ( WordBlock wb in wordBlocks) {

/* sequential version that iterates through the sequenceBlockList for ( SequenceBlock sb in wb.sequenceBlockList){

// one sb for each value of Ndef length = maxLengthdef sequenceLength = sb.sequenceList.size()if ( sequenceLength < maxLength) length = sequenceLength def equalMap = defs.extractEqualValues ( length,

wb.startIndex, sb.sequenceList)def equalWordMap = defs.extractUniqueSequences ( equalMap, sb.Nvalue, wb.startIndex, wb.bareWords)localEqualWordMapListN[sb.Nvalue] << equalWordMap

}}

Creating Equal Block Maps - Paralleldef localEqualWordMapListN = [] // contains an element for each N valuefor ( i in 1..N) localEqualWordMapListN[i] = [] def maxLength = BL - N for ( WordBlock wb in wordBlocks) {

def procNet = (1..N).collect { n -> new ExtractEqualMaps( n: n,

maxLength: maxLength, startIndex: wb.startIndex, sequenceList: wb.sequenceBlockList[n-1].sequenceList, words: wb.bareWords, localMap: localEqualWordMapListN[n]) }

new PAR(procNet).run() }}

ExtractEqualMaps – Process Definitionclass ExtractEqualMaps implements CSProcess { def n def maxLength def startIndex def sequenceList def words def localMap

void run(){def length = maxLengthdef sequenceLength = sequenceList.size()if ( sequenceLength < maxLength) length = sequenceLengthdef equalMap = defs.extractEqualValues ( length, startIndex,

sequenceList)def equalWordMap = defs.extractUniqueSequences ( equalMap,

n, startIndex, words)localMap << equalWordMap

}}

Parallelisation Effect• The presented results have the parallel version of the InitialJoiner

deployed in both versions• The effect of the previous Parallelisation is immediately observable in

the results– Worker Style 1 has the sequential version to create the Equal Maps– Worker Style 2 has the parallel version to create the Equal Maps

• The system does allow the user to choose whether to output sequences that occur only once– All results presented do NOT output a sequence if it occurs only once

Results times in msecs – Bible

Worker Style Workers N

Worker Distribute

Worker Equal

Worker Join

Worker Merge

Worker Total  

Reader Distribute

Reader Merge

Reader Total  

Output File Size

KB1 4 3 3,749 138,263 1,147 19,263 162,421   3,045 159,205 162,250   17,7981 8 3 3,389 69,584 708 21,702 95,383   2,997 92,269 95,266   17,798

2 4 3 3,046 53,600 1,030 18,647 76,323   2,592 73,701 76,293   17,7982 8 3 4,629 27,559 597 21,758 54,543   3,761 50,159 53,920   17,7982 8 6 4,245 65,481 1,291 53,736 124,753   3,308 121,186 124,494   25,810

2 12 2 6,209 11,772 221 11,756 29,957   4,790 23,807 28,597   12,5932 12 3 4,750 17,957 319 21,008 44,034   4,026 39,423 43,449   17,7982 12 4 4,870 25,560 670 30,945 62,044   4,042 57,393 61,435   21,4122 12 5 5,030 34,292 651 42,030 82,003   4,089 77,928 82,017   23,9262 12 6 5,057 43,544 1,048 53,247 102,896   4,041 98,287 102,328   25,810

Commentary – Worker Equal Speedup• Speedup is Tslower / Tfaster

• For N = 3 Workers = 4 and 8– Speedup of Worker Style 2 (parallel) over Worker Style 1 (sequential)– W = 4: 2.58 and W= 8: 2.52– Solely due to the parallelisation of Extract Equal Maps using available threads (2)

• For N = 3 and Workers = 4, 8 and 12– Speedup due to additional workers

  W = 8 W = 12

W = 4 1.94 2.98

W = 8   1.53

Commentary - Overall

Merge Effects• For N = 3

– The Merge time is very similar

– Demonstrates that the Reader is the bottleneck

Merge Parallelisation• There is an option here to

parallelise more by undertaking merges in parallel

Worker Total Time  Speedup  W = 8 W = 12

W = 4 1.40 1.73W = 8   1.24

Overlapped Merge / Output Architecture

Reader

Worker

Worker

Merge N = 1

Merge N = 2

Merge N = 3

Commentary on Revised Architecture• The workers output each of the N Primary maps in parallel to the

respective Merge process– Each worker has N processes that output the entries in each primary key map in

descending sorted order– One merge process per N value– Each Merge process writes its own file

• When the worker has finished– Sends a message to Reader informing it of termination– This enables calculation of overall time

• The architecture implements the CSP Client-Server design pattern thereby guaranteeing freedom from deadlock

Results – Overlapped Merge (msecs)

Worker Style Workers N

Worker Distribute

Worker Equal

Worker Join

Worker Merge

Worker Total  

Reader Distribute

Reader Merge

Reader Total  

Output File Size KB

2 12 3 4,750 17,957 319 21,008 44,034   4,026 39,423 43,449   17,798

2 12 6 5,057 43,544 1,048 53,247102,89

6   4,041 98,287102,32

8   25,810

Bible

3 12 3 2,969 18,124 324 10,902 32,319   2,731 29,501 32,232   6,297 N = 1

3 12 6 3,202 44,342 1,082 15,239 63,866   2,715 61,049 63,809   6,297 N = 1

WaD

3 12 6 1,338 17,090 308 8,625 27,361   1,140 26,162 27,302   2,044 N = 1

Speedup Calculations

Worker 2 to Worker 3• Merge Speedup• Bible

Speedup on Input File• Compare Bible to WaD

– Overall times

Bible Speedup

N=6 3.49

N = 3 1.93

W = 12

N = 6 Words Time

Bible 802,300 63,809

WaD 268,500 27,302

Ratio 2.99 2.34

Conclusion• Utilisation of access to shared memory needs to be considered when

designing the algorithm– This was done from the outset with the choice of data structures

• The parallelisation of sequential sections is relatively straightforward– Provided there are no memory access violations between parallel processes– The JCSP Library made this particularly easy

• The resulting system is scalable in – The number of Workers– The value of N and the number of available Threads – 31 threads used in this implementation

• The creation of Equal maps needs to be further parallelised

Further Work• The School has recently installed a new multi-node system

– 18 nodes each with Dual Quad Hyper-threading processor • 16 threads in each Node• Hence N = 16 can be undertaken in one pass

– 16GB memory– 250 Gb local disk– Gigabit Ethernet communications infrastructure

• Its obvious what I shall be doing!