1.1 --- a/runtime/pom.xml	Sat Dec 01 21:21:42 2012 +0200
     1.2 +++ b/runtime/pom.xml	Fri Dec 07 18:13:07 2012 +0200
     1.3 @@ -408,6 +408,27 @@
     1.4  					</execution>
     1.5  				</executions>
     1.6  			</plugin>
     1.7 +			
     1.8 +			<!--  retain permissions -->
     1.9 +			<plugin>
    1.10 +				<groupId>org.apache.maven.plugins</groupId>
    1.11 +				<artifactId>maven-antrun-plugin</artifactId>
    1.12 +				<version>1.6</version>
    1.13 +				<executions>
    1.14 +					<execution>
    1.15 +						<id>process-classes</id>
    1.16 +						<phase>process-classes</phase>
    1.17 +						<configuration>
    1.18 +							<target>
    1.19 +								<chmod file="target/classes/pg_restart_clear_caches.sh" perm="777" />
    1.20 +							</target>
    1.21 +						</configuration>
    1.22 +						<goals>
    1.23 +							<goal>run</goal>
    1.24 +						</goals>
    1.25 +					</execution>
    1.26 +				</executions>
    1.27 +			</plugin>
    1.28  		</plugins>
    1.29  	</build>
    1.30  </project>

     2.1 --- a/runtime/src/main/java/eu/earthobservatory/runtime/generaldb/Strabon.java	Sat Dec 01 21:21:42 2012 +0200
     2.2 +++ b/runtime/src/main/java/eu/earthobservatory/runtime/generaldb/Strabon.java	Fri Dec 07 18:13:07 2012 +0200
     2.3 @@ -225,7 +225,7 @@
     2.4  		logger.info("[Strabon.query] Executing query: \n{}", queryString);
     2.5  		
     2.6  		// check for null stream
     2.7 -		if (out == null) {
     2.8 +		if ((out == null) && (resultsFormat != org.openrdf.query.resultio.Format.EXP)) {
     2.9  			logger.error("[Strabon.query] Cannot write to null stream.");
    2.10  			
    2.11  			return false;
    2.12 @@ -255,13 +255,14 @@
    2.13  				long t2 = System.nanoTime();
    2.14  				
    2.15  				while (result.hasNext()) {
    2.16 +					String r = result.toString();
    2.17  					results++;
    2.18  				}
    2.19  				
    2.20  				long t3 = System.nanoTime();
    2.21  	
    2.22 -				//return new long[]{t2-t1, t3-t2, t3-t1, results};
    2.23 -				break;
    2.24 +				return new long[]{t2-t1, t3-t2, t3-t1, results};
    2.25 +				//break;
    2.26  				
    2.27  		default:
    2.28  			// get the writer for the specified format

     3.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     3.2 +++ b/runtime/src/main/java/eu/earthobservatory/utils/ExperimentsReal.java	Fri Dec 07 18:13:07 2012 +0200
     3.3 @@ -0,0 +1,225 @@
     3.4 +package eu.earthobservatory.utils;
     3.5 +
     3.6 +import java.io.BufferedWriter;
     3.7 +import java.io.File;
     3.8 +import java.io.FileWriter;
     3.9 +import java.io.IOException;
    3.10 +import java.net.URL;
    3.11 +import java.sql.Connection;
    3.12 +import java.sql.DriverManager;
    3.13 +import java.sql.ResultSet;
    3.14 +import java.sql.SQLException;
    3.15 +import java.sql.Statement;
    3.16 +import java.text.DecimalFormat;
    3.17 +import java.util.SortedSet;
    3.18 +import java.util.TreeSet;
    3.19 +
    3.20 +import org.apache.log4j.chainsaw.Main;
    3.21 +import org.openrdf.query.MalformedQueryException;
    3.22 +import org.openrdf.query.QueryEvaluationException;
    3.23 +import org.openrdf.query.QueryLanguage;
    3.24 +import org.openrdf.query.TupleQuery;
    3.25 +import org.openrdf.query.TupleQueryResult;
    3.26 +import org.openrdf.query.TupleQueryResultHandlerException;
    3.27 +import org.openrdf.repository.RepositoryException;
    3.28 +
    3.29 +
    3.30 +import eu.earthobservatory.runtime.monetdb.Strabon;
    3.31 +
    3.32 +public class ExperimentsReal {
    3.33 +	
    3.34 +	private static Strabon strabon = null;
    3.35 +
    3.36 +	/**
    3.37 +	 * @param args
    3.38 +	 * @throws Exception
    3.39 +	 */
    3.40 +	public static void main(String[] args) throws Exception {
    3.41 +
    3.42 +		if (args.length < 6) {
    3.43 +			System.err.println("Usage: eu.ist.semsorgrid4env.strabon.ExperimentReal <HOST> <PORT> <DATABASE> <USERNAME> <PASSWORD> <LOG_PATH>");
    3.44 +			System.err.println("       where <HOST>         is the postgis database host to connect to");
    3.45 +			System.err.println("             <PORT>         is the port to connect to on the database host");
    3.46 +			System.err.println("             <DATABASE>     is the spatially enabled postgis database that Strabon will use as a backend, ");
    3.47 +			System.err.println("             <USERNAME>     is the username to use when connecting to the database ");
    3.48 +			System.err.println("             <PASSWORD>     is the password to use when connecting to the database");
    3.49 +			System.err.println("             <LOG_PATH>     where to store the logs");
    3.50 +			System.exit(0);
    3.51 +		}
    3.52 +
    3.53 +		String host = args[0];
    3.54 +		Integer port = new Integer(args[1]);
    3.55 +		String db = args[2];
    3.56 +		String user = args[3];
    3.57 +		String passwd = args[4];
    3.58 +		String logPath = args[5];
    3.59 +
    3.60 +		String[] queries = {
    3.61 +				//Q1: members of Congress after Clinton.
    3.62 +				"select distinct ?name2 where  { ?x1  <http://xmlns.com/foaf/0.1/name> \"William Clinton\" .  ?x1 <http://www.rdfabout.com/rdf/schema/politico/hasRole> ?term1 ?t1 .   ?x2  <http://xmlns.com/foaf/0.1/name> ?name2 .  ?x2 <http://www.rdfabout.com/rdf/schema/politico/hasRole> ?term2 ?t2 .   FILTER(<http://strdf.di.uoa.gr/ontology#afterPeriod>(?t2, ?t1)) } ",
    3.63 +				//Q2: members of Congress, that there isn't another member of Congress after them.
    3.64 +				"select distinct ?name where { ?x1 <http://www.rdfabout.com/rdf/schema/politico/hasRole> ?term1 ?t1 .  ?x1  <http://xmlns.com/foaf/0.1/name> ?name . optional {?x2 <http://www.rdfabout.com/rdf/schema/politico/hasRole> ?term2 ?t2 . FILTER(<http://strdf.di.uoa.gr/ontology#afterPeriod>(?t2, ?t1)) .  } FILTER(!bound(?x2)) } ",
    3.65 +				//Q3: members of Congress in [1-1-1863, 1-1-1864].
    3.66 +				"select distinct ?name where { ?x1 <http://www.rdfabout.com/rdf/schema/politico/hasRole> ?term1 ?t1 .  ?x1  <http://xmlns.com/foaf/0.1/name> ?name .  FILTER(<http://strdf.di.uoa.gr/ontology#PeriodContains>(?t1, \"[1-1-1863 00:00:00, 1-1-1864 00:00:00]\"^^<http://strdf.di.uoa.gr/ontology#validTime>)) } " ,
    3.67 +		};
    3.68 +		
    3.69 +		int repetitions = 5;
    3.70 +
    3.71 +		try {
    3.72 +			for (int qno = 0; qno < queries.length; qno++) {
    3.73 +
    3.74 +				String queryString = queries[qno];
    3.75 +
    3.76 +				long coldtime = 0;
    3.77 +				long warmtime = 0;
    3.78 +				long results = 0;
    3.79 +
    3.80 +				// cold runs
    3.81 +				long[][] coldruns = new long[repetitions][4];
    3.82 +				for (int i = 0; i < repetitions; i++) {
    3.83 +					strabon = new Strabon(db, user, passwd, port, host, true);
    3.84 +					coldruns[i] = (long[])run("cold", queryString, i);
    3.85 +					strabon.close();
    3.86 +					strabon = null;
    3.87 +					
    3.88 +					URL script = Main.class.getResource("/pg_restart_clear_caches.sh");
    3.89 +					String restart_script = script.toString().substring(5);
    3.90 +					
    3.91 +					Process p = Runtime.getRuntime().exec(restart_script);
    3.92 +					p.waitFor();
    3.93 +					System.gc();
    3.94 +					Thread.sleep(5000);
    3.95 +				}
    3.96 +
    3.97 +				//Strabon strabon = new Strabon(db, user, passwd, port, host, true, cachepath);
    3.98 +				strabon = new Strabon(db, user, passwd, port, host, true);
    3.99 +
   3.100 +				// warm runs
   3.101 +				long[][] warmruns = new long[repetitions][4];
   3.102 +				// warm up caches
   3.103 +				long[] onerun = (long[])run("warm", queryString, 0);
   3.104 +				results = onerun[3];
   3.105 +
   3.106 +				for (int i = 0; i < repetitions; i++) {
   3.107 +					warmruns[i] = (long[])run("warm", queryString, i);
   3.108 +				}
   3.109 +
   3.110 +				strabon.close();
   3.111 +				strabon = null;
   3.112 +
   3.113 +				// sort results
   3.114 +				SortedSet<Long> coldtimes = new TreeSet<Long>();
   3.115 +				for (int i = 0; i < repetitions; i++) {
   3.116 +					coldtimes.add(coldruns[i][2]);
   3.117 +				}
   3.118 +
   3.119 +				SortedSet<Long> warmtimes = new TreeSet<Long>();
   3.120 +				for (int i = 0; i < repetitions; i++) {
   3.121 +					warmtimes.add(warmruns[i][2]);
   3.122 +				}
   3.123 +
   3.124 +				// calculate median
   3.125 +				int i = 0;
   3.126 +				for (Long long1 : coldtimes) {
   3.127 +					i++;
   3.128 +					if ((repetitions % 2 == 1) && ((repetitions/2+1) == i)) {
   3.129 +						coldtime = long1;
   3.130 +					} else if ((repetitions % 2 == 0) && ((repetitions/2) == i)) { 
   3.131 +						coldtime = long1;
   3.132 +					} else if ((repetitions % 2 == 0) && ((repetitions/2+1) == i)) {	
   3.133 +						coldtime = coldtime + long1;
   3.134 +						coldtime = coldtime / 2;
   3.135 +					}
   3.136 +				}
   3.137 +
   3.138 +				i = 0;
   3.139 +				for (Long long1 : warmtimes) {
   3.140 +					i++;
   3.141 +					if ((repetitions % 2 == 1) && ((repetitions/2+1) == i)) {
   3.142 +						warmtime = long1;
   3.143 +					} else if ((repetitions % 2 == 0) && ((repetitions/2) == i)) {
   3.144 +						warmtime = long1;
   3.145 +					} else if ((repetitions % 2 == 0) && ((repetitions/2+1) == i)) {
   3.146 +						warmtime = warmtime + long1;
   3.147 +						warmtime = warmtime / 2;
   3.148 +					}
   3.149 +				}
   3.150 +
   3.151 +				// print logs
   3.152 +				FileWriter fstream;
   3.153 +				BufferedWriter out;
   3.154 +				try {
   3.155 +
   3.156 +					fstream = new FileWriter(logPath + "/warm_key_q" + (qno+1),
   3.157 +							true);
   3.158 +					out = new BufferedWriter(fstream);
   3.159 +					out.write("GARBAGE " + results + " " + warmtime + "\n");
   3.160 +					out.close();
   3.161 +
   3.162 +					fstream = new FileWriter(logPath + "/warm_key_q" + (qno+1)
   3.163 +							+ "_long", true);
   3.164 +					out = new BufferedWriter(fstream);
   3.165 +					for (int j = 0; j < repetitions; j++) {
   3.166 +						out.write("GARBAGE " + results + " " + warmruns[j][0]
   3.167 +								+ " " + warmruns[j][1] + " " + warmruns[j][2]
   3.168 +										+ "\n");
   3.169 +					}
   3.170 +					out.close();
   3.171 +
   3.172 +					fstream = new FileWriter(logPath + "/cold_key_q" + (qno+1),
   3.173 +							true);
   3.174 +					out = new BufferedWriter(fstream);
   3.175 +					out.write("GARBAGE " + results + " " + coldtime + "\n");
   3.176 +					out.close();
   3.177 +
   3.178 +					fstream = new FileWriter(logPath + "/cold_key_q" + (qno+1)
   3.179 +							+ "_long", true);
   3.180 +					out = new BufferedWriter(fstream);
   3.181 +					for (int j = 0; j < repetitions; j++) {
   3.182 +						out.write("GARBAGE " + results + " " + coldruns[j][0]
   3.183 +								+ " " + coldruns[j][1] + " " + coldruns[j][2]
   3.184 +										+ "\n");
   3.185 +					}
   3.186 +					out.close();
   3.187 +				} catch (Exception e) {
   3.188 +					System.err.println("Error: " + e.getMessage());
   3.189 +				}
   3.190 +			}
   3.191 +
   3.192 +		} catch (MalformedQueryException e) {
   3.193 +			System.out.println("Please use a well-formed query");
   3.194 +			e.printStackTrace();
   3.195 +		} catch (QueryEvaluationException e) {
   3.196 +			e.printStackTrace();
   3.197 +		} catch (TupleQueryResultHandlerException e) {
   3.198 +			e.printStackTrace();
   3.199 +		} catch (IOException e) {
   3.200 +			e.printStackTrace();
   3.201 +		}
   3.202 +	}
   3.203 +
   3.204 +	private static long[] run(String cacheState, String query, int repetition) throws Exception {
   3.205 +
   3.206 +		System.out.println("Executing query. Caches: " + cacheState + ". Repetition: " + repetition);
   3.207 +
   3.208 +		long[] resp = (long[])strabon.query(query, org.openrdf.query.resultio.Format.EXP, null);
   3.209 +		
   3.210 +//		Statement st;
   3.211 +//		System.out.println("Evaluating query (naive).");
   3.212 +//		long t1 = System.nanoTime();
   3.213 +//		TupleQuery tupleQuery = repo.getConnection().prepareTupleQuery(QueryLanguage.SPARQL, query);
   3.214 +//		TupleQueryResult result = tupleQuery.evaluate();
   3.215 +//		long t2 = System.nanoTime();
   3.216 +//		int results = 0;
   3.217 +//		while(result.hasNext()) {
   3.218 +//			String rrrr = result.next().toString();
   3.219 +//			results++;
   3.220 +//		}
   3.221 +//		long t3 = System.nanoTime();
   3.222 +//		System.out.println("Evaluated query (naive). results="+results);
   3.223 +//		resp = new long[]{t2-t1, t3-t2, t3-t1,results};
   3.224 +		
   3.225 +		return resp;
   3.226 +
   3.227 +	}
   3.228 +}

     4.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     4.2 +++ b/runtime/src/main/resources/pg_restart_clear_caches.sh	Fri Dec 07 18:13:07 2012 +0200
     4.3 @@ -0,0 +1,8 @@
     4.4 +#!/bin/bash
     4.5 +DIR="$( cd -P "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
     4.6 +
     4.7 +service postgresql stop
     4.8 +sync && echo 3 > /proc/sys/vm/drop_caches;
     4.9 +service postgresql start
    4.10 +echo "clearing cache... `date`"
    4.11 +sleep 1;

     5.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     5.2 +++ b/scripts/experiments/exp	Fri Dec 07 18:13:07 2012 +0200
     5.3 @@ -0,0 +1,20 @@
     5.4 +#!/bin/bash
     5.5 +INITPATH="$( cd -P "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
     5.6 +source $INITPATH/setenv
     5.7 +
     5.8 +#DBNAME=$1
     5.9 +
    5.10 +cd $LOG_PATH;
    5.11 +dirs=`ls -1d $DBNAME* | sort | tail -n 1`;
    5.12 +maxdir=${dirs/$DBNAME-/''};
    5.13 +maxdir=`echo $maxdir | sed 's/^0//'`;
    5.14 +dir=`printf "%02d" $((++maxdir))`;
    5.15 +
    5.16 +if [ -z $dir ] ; then dir="01"; fi
    5.17 +
    5.18 +mkdir $DBNAME-$dir;
    5.19 +
    5.20 +cd $STRABONEXP_PATH;
    5.21 +CPATH=$(JARS=(*.jar); IFS=:; echo "${JARS[*]}")
    5.22 +java -Xmx10G -cp $CPATH eu.earthobservatory.utils.ExperimentsReal  $HOST $PORT $DBNAME $USERNAME $PASSWORD $LOG_PATH/$DBNAME-$dir 1> $LOG_PATH/$DBNAME-$dir/$DBNAME.out 2>$LOG_PATH/$DBNAME-$dir/$DBNAME.err
    5.23 +cd $INITPATH;

     6.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     6.2 +++ b/scripts/experiments/setenv	Fri Dec 07 18:13:07 2012 +0200
     6.3 @@ -0,0 +1,7 @@
     6.4 +#!/bin/bash
     6.5 +export DBTYPE=strabon #monet, postgres, rdf3x, strabon, naive
     6.6 +export HOST='localhost'
     6.7 +export PORT='5432'
     6.8 +export USERNAME='strabon'
     6.9 +export PASSWORD='strabon'
    6.10 +export LOG_PATH="/home/strabon/experiments/logs-$DBTYPE"