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r3878 - in trunk/src/main: java/fr/ifremer/isisfish java/fr/ifremer/isisfish/ui/input resources
by echatellier＠users.forge.codelutin.com Dec. 20, 2013

Dec. 20, 2013

Author: echatellier Date: 2013-12-20 17:00:44 +0100 (Fri, 20 Dec 2013) New Revision: 3878 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3878 Log: fixes #4054: Ajouter la distribution de recrutement par zone et de distribution de reproduction en facteur Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesEditorUI.jaxx trunk/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesUI.jaxx trunk/src/main/resources/sensitivity.properties Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2013-12-12 14:00:40 UTC (rev 3877) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2013-12-20 16:00:44 UTC (rev 3878) @@ -117,7 +117,7 @@ * migration de donnees demande automatiquement un changement de version * d'application. */ - protected final static Version version = new Version(4, 2, 1, 2); + protected final static Version version = new Version(4, 2, 1, 3); protected final static Version majorVersion = new Version(version.getNumber(0)); protected final static Version databaseVersion = new Version( Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesEditorUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesEditorUI.jaxx 2013-12-12 14:00:40 UTC (rev 3877) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesEditorUI.jaxx 2013-12-20 16:00:44 UTC (rev 3878) @@ -192,7 +192,9 @@ <cell columns='3' fill='both' weightx='1.0' weighty='0.5'> <org.nuiton.math.matrix.gui.MatrixPanelEditor id='fieldPopulationMappingZoneReproZoneRecru' constructorParams='false' enabled='{isActive()}' - onMatrixChanged="populationMappingZoneReproZoneRecruMatrixChanged(event)" /> + onMatrixChanged="populationMappingZoneReproZoneRecruMatrixChanged(event)" + decorator='boxed' + _sensitivityBean='{fr.ifremer.isisfish.entities.Population.class}' _sensitivityMethod='"MappingZoneReproZoneRecru"' /> </cell> </row> </Table> Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesUI.jaxx =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesUI.jaxx 2013-12-12 14:00:40 UTC (rev 3877) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesUI.jaxx 2013-12-20 16:00:44 UTC (rev 3878) @@ -43,6 +43,12 @@ getSaveVerifier().addCurrentPanel(popZones); }*/ + +@Override +public void setLayer(boolean active) { + super.setLayer(active); + popZones.setLayer(active); +} ]]> </script> <JPanel id='body'> @@ -50,8 +56,7 @@ <row> <cell columns="2" fill='both' weightx='1.0' weighty='1'> <PopulationZonesEditorUI id='popZones' constructorParams='this' - bean='{getBean()}' active='{isActive()}' decorator='boxed' - _sensitivityBean='{Population.class}' _sensitivityMethod='"MappingZoneReproZoneRecru"'/> + bean='{getBean()}' active='{isActive()}'/> </cell> </row> <row> Modified: trunk/src/main/resources/sensitivity.properties =================================================================== --- trunk/src/main/resources/sensitivity.properties 2013-12-12 14:00:40 UTC (rev 3877) +++ trunk/src/main/resources/sensitivity.properties 2013-12-20 16:00:44 UTC (rev 3878) @@ -42,6 +42,7 @@ Population.groupMin Population.growth Population.growthReverse +Population.mappingZoneReproZoneRecru Population.maturityOgiveEquation Population.meanWeight Population.monthGapBetweenReproRecrutement @@ -54,6 +55,7 @@ PopulationSeasonInfo.migrationEquation PopulationSeasonInfo.emigrationEquation PopulationSeasonInfo.immigrationEquation +PopulationSeasonInfo.reproductionDistribution Selectivity.equation SetOfVessels.fixedCosts SetOfVessels.numberOfVessels

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r3877 - trunk
by maven-release＠users.forge.codelutin.com Dec. 12, 2013

Dec. 12, 2013

Author: maven-release Date: 2013-12-12 15:00:40 +0100 (Thu, 12 Dec 2013) New Revision: 3877 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3877 Log: [maven-release-plugin] prepare for next development iteration Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2013-12-12 14:00:26 UTC (rev 3876) +++ trunk/pom.xml 2013-12-12 14:00:40 UTC (rev 3877) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.2.1.2</version> + <version>4.2.1.3-SNAPSHOT</version>  <dependencies> @@ -739,9 +739,9 @@   <scm> - <connection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.1.2</connection> - <developerConnection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.1.2</developerConnection> - <url>http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.1.2</url> + <connection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/trunk</connection> + <developerConnection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/trunk</developerConnection> + <url>http://svn.forge.codelutin.com/svn/isis-fish/trunk</url> </scm> <repositories>

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r3876 - in tags: . isis-fish-4.2.1.2
by maven-release＠users.forge.codelutin.com Dec. 12, 2013

Dec. 12, 2013

Author: maven-release Date: 2013-12-12 15:00:26 +0100 (Thu, 12 Dec 2013) New Revision: 3876 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3876 Log: [maven-release-plugin] copy for tag isis-fish-4.2.1.2 Added: tags/isis-fish-4.2.1.2/ Property changes on: tags/isis-fish-4.2.1.2 ___________________________________________________________________ Added: svn:ignore + maven.log target velocity.log .classpath .project isis-fish.ipr isis-fish.iws isis-fish.iml .settings bin nbproject Inputs_Langoustine Added: svn:mergeinfo + /branches/4.1:3601-3670

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r3875 - trunk
by maven-release＠users.forge.codelutin.com Dec. 12, 2013

Dec. 12, 2013

Author: maven-release Date: 2013-12-12 15:00:02 +0100 (Thu, 12 Dec 2013) New Revision: 3875 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3875 Log: [maven-release-plugin] prepare release isis-fish-4.2.1.2 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2013-12-12 10:25:59 UTC (rev 3874) +++ trunk/pom.xml 2013-12-12 14:00:02 UTC (rev 3875) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.2.1.2-SNAPSHOT</version> + <version>4.2.1.2</version>  <dependencies> @@ -739,9 +739,9 @@   <scm> - <connection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/trunk</connection> - <developerConnection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/trunk</developerConnection> - <url>http://svn.forge.codelutin.com/svn/isis-fish/trunk</url> + <connection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.1.2</connection> + <developerConnection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.1.2</developerConnection> + <url>http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.1.2</url> </scm> <repositories>

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r3874 - trunk
by echatellier＠users.forge.codelutin.com Dec. 12, 2013

Dec. 12, 2013

Author: echatellier Date: 2013-12-12 11:25:59 +0100 (Thu, 12 Dec 2013) New Revision: 3874 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3874 Log: Update parent Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2013-12-12 10:20:46 UTC (rev 3873) +++ trunk/pom.xml 2013-12-12 10:25:59 UTC (rev 3874) @@ -6,7 +6,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>4.3</version> + <version>4.4</version> </parent> <groupId>fr.ifremer</groupId>

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r3873 - trunk/src/main/java/fr/ifremer/isisfish/util
by echatellier＠users.forge.codelutin.com Dec. 12, 2013

Dec. 12, 2013

Author: echatellier Date: 2013-12-12 11:20:46 +0100 (Thu, 12 Dec 2013) New Revision: 3873 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3873 Log: Add license headers Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java 2013-12-12 10:17:26 UTC (rev 3872) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java 2013-12-12 10:20:46 UTC (rev 3873) @@ -1,3 +1,28 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2013 Ifremer, Code Lutin, Benjamin Poussin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ + package fr.ifremer.isisfish.util; import fr.ifremer.isisfish.types.TimeStep; Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2013-12-12 10:17:26 UTC (rev 3872) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2013-12-12 10:20:46 UTC (rev 3873) @@ -1,16 +1,35 @@ +/* + * #%L + * IsisFish + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2013 Ifremer, Code Lutin, Benjamin Poussin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ package fr.ifremer.isisfish.util; - import com.google.common.cache.Cache; import com.google.common.cache.CacheBuilder; import com.google.common.cache.Weigher; import fr.ifremer.isisfish.types.TimeStep; -import java.io.BufferedWriter; -import java.io.FileWriter; -import java.io.Writer; import java.util.Collection; import org.apache.commons.lang3.ClassUtils; -import org.apache.commons.lang3.ObjectUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixND;

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r3872 - trunk/src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com Dec. 12, 2013

Dec. 12, 2013

Author: bpoussin Date: 2013-12-12 11:17:26 +0100 (Thu, 12 Dec 2013) New Revision: 3872 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3872 Log: prevent '/ by zero' and refuse to adjuste cache to 0. Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2013-12-12 09:50:22 UTC (rev 3871) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2013-12-12 10:17:26 UTC (rev 3872) @@ -197,28 +197,32 @@ * @param amount new size of cache in byte */ public void adjustedCache(long amount){ - // on estime le nombre d'entree necessaire pour ce volume de donnees - long bytePerStep = totalCached / Math.max(1, numberStepCached); - long entriesPerStep = numberCached / Math.max(1, numberStepCached); + if (amount == 0) { + log.info("Cache size not ajusted because 0 is not acceptable amount"); + } else { + // on estime le nombre d'entree necessaire pour ce volume de donnees + long bytePerStep = totalCached / Math.max(1, numberStepCached); + long entriesPerStep = numberCached / Math.max(1, numberStepCached); - long initialCapacity = amount * entriesPerStep / Math.max(1, bytePerStep); - long stepEquivalent = initialCapacity / entriesPerStep; + long initialCapacity = amount * entriesPerStep / Math.max(1, bytePerStep); + long stepEquivalent = initialCapacity / Math.max(1, entriesPerStep); - // use amount as new size for cache - // if this new size is less than maxCache, use it - // to keep more memory for JVM - sizeCache = Math.min(this.maxCache, amount); + // use amount as new size for cache + // if this new size is less than maxCache, use it + // to keep more memory for JVM + sizeCache = Math.min(this.maxCache, amount); + + CacheBuilder builder = CacheBuilder.newBuilder(); + builder.maximumWeight(sizeCache); + builder.weigher(isisWeigher); + if (initialCapacity > 0) { + builder.initialCapacity((int)initialCapacity); + } + cache = builder.build(); - CacheBuilder builder = CacheBuilder.newBuilder(); - builder.maximumWeight(sizeCache); - builder.weigher(isisWeigher); - if (initialCapacity > 0) { - builder.initialCapacity((int)initialCapacity); + log.info(String.format("Cache size ajusted to %s (equivalent to %s step need)", + StringUtil.convertMemory(sizeCache), stepEquivalent)); } - cache = builder.build(); - - log.info(String.format("Cache size ajusted to %s (equivalent to %s step need)", - StringUtil.convertMemory(sizeCache), stepEquivalent)); } /**

1 0

r3871 - trunk
by echatellier＠users.forge.codelutin.com Dec. 12, 2013

Dec. 12, 2013

Author: echatellier Date: 2013-12-12 10:50:22 +0100 (Thu, 12 Dec 2013) New Revision: 3871 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3871 Log: Fix sun signatures Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2013-12-08 18:57:15 UTC (rev 3870) +++ trunk/pom.xml 2013-12-12 09:50:22 UTC (rev 3871) @@ -398,8 +398,6 @@ <version>15.0</version> </dependency> - -  <dependency> <groupId>junit</groupId> @@ -530,6 +528,8 @@ <maven.jar.main.class>fr.ifremer.isisfish.IsisFish</maven.jar.main.class> <license.licenseName>gpl_v3</license.licenseName> <license.organizationName>Ifremer, Codelutin</license.organizationName> + <signatureArtifactId>java16-sun</signatureArtifactId> + <signatureVersion>1.9</signatureVersion>  <jaxxVersion>2.4.2</jaxxVersion>

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r3870 - trunk/src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com Dec. 8, 2013

Dec. 8, 2013

Author: bpoussin Date: 2013-12-08 19:57:15 +0100 (Sun, 08 Dec 2013) New Revision: 3870 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3870 Log: doesn't use 'removeStep' to detect step change, use directly 'put' and 'clear' this prevent DefaultSimulator modification which would result in a malfunction of the cache Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2013-12-06 17:32:33 UTC (rev 3869) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2013-12-08 18:57:15 UTC (rev 3870) @@ -40,9 +40,9 @@ * <p> * @author poussin * @version $Revision$ - * <p> - * Last update: $Date$ by : - * $Author$ + <p> + Last update: $Date$ by : + $Author$ */ public class IsisCache { @@ -220,6 +220,8 @@ * <p> */ public String printStatistiqueAndClear() { + cacheBackend.clear(); + StringBuilder result = new StringBuilder(); result.append("--- Cache Statistiques ---\n"); result.append("Total call: ").append(totalCall).append("\n"); @@ -231,7 +233,6 @@ result.append("Cache usage: ").append(percent).append("%\n"); result.append(cacheBackend.getStat()); result.append("--------------------\n"); - cacheBackend.clear(); System.out.println(result.toString()); return result.toString(); Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2013-12-06 17:32:33 UTC (rev 3869) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2013-12-08 18:57:15 UTC (rev 3870) @@ -3,14 +3,18 @@ import com.google.common.cache.Cache; import com.google.common.cache.CacheBuilder; -import com.google.common.cache.CacheStats; import com.google.common.cache.Weigher; import fr.ifremer.isisfish.types.TimeStep; +import java.io.BufferedWriter; +import java.io.FileWriter; +import java.io.Writer; import java.util.Collection; import org.apache.commons.lang3.ClassUtils; +import org.apache.commons.lang3.ObjectUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.math.matrix.MatrixND; +import org.nuiton.util.StringUtil; /** * Cache qui reserve de la place pour l'equivalent de N pas de temps dans le cache. @@ -86,9 +90,8 @@ } } - backend.totalCached += result; - backend.biggestCached = Math.max(backend.biggestCached, result); - + backend.addStat(result); + result = Math.max(1024, result); // min to 1ko return result; } @@ -98,51 +101,146 @@ protected IsisWeigher isisWeigher; protected long maxMemory; protected long maxCache; - /** le total en octet mis en backend */ + protected long sizeCache; + + /** the last step use to put value in cache */ + protected TimeStep lastStep = null; + /** if true size of cache has been recomputed */ + protected boolean adjusted = false; + + /** le total en octet mis en cache au precedent pas de temps*/ + protected long totalLastStepCached = 0; + + // STATISTIQUE PAR ENTREE DANS LE CACHE + /** le total en d'element mis en cache */ + protected long numberCached = 0; + /** le total en octet mis en cache */ protected long totalCached = 0; - /** la plus grosse donnee mis en backend */ - protected int biggestCached = 0; - protected boolean ajusted = false; + /** la plus petite donnee mis en cache */ + protected long smallestCached = Long.MAX_VALUE; + /** la plus grosse donnee mis en cache */ + protected long biggestCached = 0; + // for variance + double delta = 0; + double mean = 0; + double M2 = 0; + + // STATISTIQUE PAR PAS DE TEMPS + /** le total en d'element mis en cache */ + protected long numberStepCached = 0; + /** le total en octet mis en cache */ + protected long totalStepCached = 0; + /** la plus petite donnee mis en cache */ + protected long smallestStepCached = Long.MAX_VALUE; + /** la plus grosse donnee mis en cache */ + protected long biggestStepCached = 0; + + // for variance + double stepDelta = 0; + double stepMean = 0; + double stepM2 = 0; + + + public IsisCacheBackendOnGuava() { isisWeigher = new IsisWeigher(this); - // TODO poussin 20131117 300Mo and 500Mo must be refined + maxMemory = Runtime.getRuntime().maxMemory(); - maxCache = maxMemory - 300*1024*1024; // isis need about 300M - maxCache = Math.max(maxCache, 500*1024*1024); // to do simulation we need 500M minimum + maxCache = maxMemory - 500*1024*1024; // isis need about 500M + maxCache = Math.max(maxCache, 200*1024*1024); // to do simulation we need 200M cache - // create first cache, this cache is juste for one step (see removeStep) - cache = CacheBuilder.newBuilder() - .maximumWeight(maxCache) - .weigher(isisWeigher) - .build(); + // create first cache, this cache is juste for one step + adjustedCache(maxCache); } + public void addStat(long value) { + numberCached++; + totalCached = totalCached + value; + + // compute variance + delta = value - mean; + mean = mean + delta/numberCached; + M2 = M2 + delta * (value - mean); + + biggestCached = Math.max(biggestCached, value); + smallestCached = Math.min(smallestCached, value); + } + + public void addStepStat(long value) { + numberStepCached++; + totalStepCached = totalStepCached + value; + + // compute variance + stepDelta = value - stepMean; + stepMean = stepMean + stepDelta/numberStepCached; + stepM2 = stepM2 + stepDelta * (value - stepMean); + + biggestStepCached = Math.max(biggestStepCached, value); + smallestStepCached = Math.min(smallestStepCached, value); + } + @Override public void clear() { cache.invalidateAll(); + // clear is assimilate to step change (last step end) + // useful to finalize variance computation for last step + changeStep(); } @Override public void removeStep(Object o) { - // after first step, use information to resize cache - if (!ajusted) { - Cache<String, Object> oldCache = cache; - // compute new size for cache with data from the first step - // if this new size is less than old maxCache, use it - // to keep more memory for JVM - maxCache = Math.min(maxCache, totalCached * CACHE_STEP); // keep place for 3 step - cache = CacheBuilder.newBuilder() - .maximumWeight(maxCache) - .weigher(isisWeigher) - .initialCapacity((int)oldCache.size() * 3) - .build(); + } - log.info(String.format("Cache size ajusted to %sMo (equivalent to %s step need)", - maxCache/1024/1024, CACHE_STEP)); + /** + * resizes the cache if amount is not greater than autorized maxCache + * @param amount new size of cache in byte + */ + public void adjustedCache(long amount){ + // on estime le nombre d'entree necessaire pour ce volume de donnees + long bytePerStep = totalCached / Math.max(1, numberStepCached); + long entriesPerStep = numberCached / Math.max(1, numberStepCached); + + long initialCapacity = amount * entriesPerStep / Math.max(1, bytePerStep); + long stepEquivalent = initialCapacity / entriesPerStep; + + // use amount as new size for cache + // if this new size is less than maxCache, use it + // to keep more memory for JVM + sizeCache = Math.min(this.maxCache, amount); + + CacheBuilder builder = CacheBuilder.newBuilder(); + builder.maximumWeight(sizeCache); + builder.weigher(isisWeigher); + if (initialCapacity > 0) { + builder.initialCapacity((int)initialCapacity); } + cache = builder.build(); + + log.info(String.format("Cache size ajusted to %s (equivalent to %s step need)", + StringUtil.convertMemory(sizeCache), stepEquivalent)); } + /** + * Previent le cache, qu'on change de TimeStep et qu'il peut faire + * du travail s'il en a besoin. + * + * - calcul de statistique + * - ajustement de la taille du cache + */ + public void changeStep() { + // on est passe au pas de temps suivant + long stepAmount = totalCached - totalLastStepCached; + totalLastStepCached = totalCached; + addStepStat(stepAmount); + + // after first step, use information to resize cache + if (!adjusted) { + adjustedCache(stepAmount * CACHE_STEP); // keep place for 3 step + adjusted = true; + } + } + @Override public Object get(TimeStep step, String key) { Object result = cache.getIfPresent(key); @@ -152,23 +250,37 @@ @Override public void put(TimeStep step, String key, Object value) { cache.put(key, value); + if (step != null) { + if (lastStep == null) { + lastStep = step; + } else if (lastStep.getStep() != step.getStep()) { + // if step differ, this indicate new Step + changeStep(); + lastStep = step; + } + } } @Override public String getStat() { - CacheStats stat = cache.stats(); - long evictionCount = stat.evictionCount(); - long hitCount = stat.hitCount(); - double hitRate = stat.hitRate(); - long missCount = stat.missCount(); - double missRate = stat.missRate(); + long mean = totalCached / Math.max(1, numberCached); + long stepMean = totalStepCached / Math.max(1, numberStepCached); + double variance = M2/Math.max(1, numberCached - 1); + double stepVariance = stepM2/Math.max(1, numberStepCached - 1); + + double standardDeviation = Math.sqrt(variance); + double stepStandardDeviation = Math.sqrt(stepVariance); + return String.format("%s - \n" - + "\tmaxMemory: %s, cacheMemory: %s, totalCached: %s, biggestCached: %s\n", -// + "\t evictionCount: %s, hitCount: %s, hitRate: %s, missCount: %s, missRate: %s\n", + + "\tmaxMemory: %s, cacheMemory: %s, totalCached: %s, numberStep: %s, numberEntries: %s\n" + + "\tStep min: %s, max: %s, mean: %s, standard deviation: %s\n" + + "\tEntry min: %s, max: %s, mean: %s, standard deviation: %s\n", getClass().getSimpleName(), - maxMemory, maxCache, totalCached, biggestCached, - evictionCount, hitCount, hitRate, missCount, missRate); + StringUtil.convertMemory(maxMemory), StringUtil.convertMemory(sizeCache), StringUtil.convertMemory(totalCached), numberStepCached, numberCached, + StringUtil.convertMemory(smallestStepCached), StringUtil.convertMemory(biggestStepCached), StringUtil.convertMemory(stepMean), StringUtil.convertMemory((long)stepStandardDeviation), + StringUtil.convertMemory(smallestCached), StringUtil.convertMemory(biggestCached), StringUtil.convertMemory(mean), StringUtil.convertMemory((long)standardDeviation) + ); }

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r3869 - trunk/src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com Dec. 6, 2013

Dec. 6, 2013

Author: bpoussin Date: 2013-12-06 18:32:33 +0100 (Fri, 06 Dec 2013) New Revision: 3869 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3869 Log: amelioration du cache guava (calcul la taille en fonction du premier pas de temps) Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2013-12-05 14:37:17 UTC (rev 3868) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2013-12-06 17:32:33 UTC (rev 3869) @@ -229,6 +229,7 @@ percent = 100 * cacheUsed / totalCall; } result.append("Cache usage: ").append(percent).append("%\n"); + result.append(cacheBackend.getStat()); result.append("--------------------\n"); cacheBackend.clear(); Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java 2013-12-05 14:37:17 UTC (rev 3868) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java 2013-12-06 17:32:33 UTC (rev 3869) @@ -20,6 +20,12 @@ void removeStep(Object key); + /** + * get specific backend cache statistic + * @return backend specific string cache stat representation + */ + String getStat(); + static public interface Factory { IsisCacheBackend createNew(); } Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2013-12-05 14:37:17 UTC (rev 3868) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2013-12-06 17:32:33 UTC (rev 3869) @@ -3,6 +3,7 @@ import com.google.common.cache.Cache; import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheStats; import com.google.common.cache.Weigher; import fr.ifremer.isisfish.types.TimeStep; import java.util.Collection; @@ -12,6 +13,11 @@ import org.nuiton.math.matrix.MatrixND; /** + * Cache qui reserve de la place pour l'equivalent de N pas de temps dans le cache. + * + * Une premiere instanciation du cache est faite. Puis apres le premier pas + * de temps on regarde la taille des objets ayant ete ajoutes au cache pour + * recalculer la nouvelle taille pour permettre de stocker N pas de temps. * * @author poussin * @version $Revision$ @@ -28,6 +34,10 @@ final static public int DOUBLE_SIZE = 8; final static public int CHAR_SIZE = 2; + /** number of time steps to cache by interpolating from the first step*/ + // perhaps allow the configuration + static public int CACHE_STEP = 3; + static public class IsisCacheBackendOnGuavaFactory implements IsisCacheBackend.Factory { @Override public IsisCacheBackend createNew() { @@ -37,49 +47,74 @@ static public Factory factory = new IsisCacheBackendOnGuavaFactory(); + static public class IsisWeigher implements Weigher<String, Object> { + + protected IsisCacheBackendOnGuava backend; + public IsisWeigher(IsisCacheBackendOnGuava backend) { + this.backend = backend; + } + + @Override + public int weigh(String key, Object value) { + int result = key.length() * CHAR_SIZE; + if (value instanceof MatrixND) { + // MatrixND + // on prend le nombre de case de la matrice pour sa taille + // on ne tient pas compte des dimensions qui sont des objets + // utilises ailleurs + int[] dim = ((MatrixND)value).getDim(); + int size = 1; + for (int i=0; i<dim.length; i++) { + size *= dim[i]; + } + result += size * DOUBLE_SIZE; // size is wrong, because depend on matrix type (float or double) + } else if (value instanceof Collection) { + // List<Zone|Pop|Str|Metier|Cell> + // on prend la taille de la collection, car la donnees + // elle meme qu'elle soit dans le backend ou non est + // certainement utilisee ailleur, donc seul la taille + // des pointeurs dans la collection est prise ici + result += ((Collection)value).size() * POINTER_SIZE; + } else if (value instanceof Number) { + // int| double + // seulement une valeur, on ajoute 1 + result += 1 * DOUBLE_SIZE; + } else { + // a priori, il n'y a pas d'autre type de donnee + if (value != null) { + log.info("Cache can't compute value size of " + ClassUtils.getPackageCanonicalName(value, "null")); + } + } + + backend.totalCached += result; + backend.biggestCached = Math.max(backend.biggestCached, result); + + result = Math.max(1024, result); // min to 1ko + return result; + } + } + protected Cache<String, Object> cache; + protected IsisWeigher isisWeigher; + protected long maxMemory; + protected long maxCache; + /** le total en octet mis en backend */ + protected long totalCached = 0; + /** la plus grosse donnee mis en backend */ + protected int biggestCached = 0; + protected boolean ajusted = false; public IsisCacheBackendOnGuava() { + isisWeigher = new IsisWeigher(this); // TODO poussin 20131117 300Mo and 500Mo must be refined - long max = Runtime.getRuntime().maxMemory() - 300*1024*1024; // isis need about 300M - max = Math.max(max, 500*1024*1024); // to do simulation we need 500M minimum + maxMemory = Runtime.getRuntime().maxMemory(); + maxCache = maxMemory - 300*1024*1024; // isis need about 300M + maxCache = Math.max(maxCache, 500*1024*1024); // to do simulation we need 500M minimum + + // create first cache, this cache is juste for one step (see removeStep) cache = CacheBuilder.newBuilder() - .maximumWeight(max) - .weigher(new Weigher<String, Object>(){ - @Override - public int weigh(String key, Object value) { - int result = key.length() * CHAR_SIZE; - if (value instanceof MatrixND) { - // MatrixND - // on prend le nombre de case de la matrice pour sa taille - // on ne tient pas compte des dimensions qui sont des objets - // utilises ailleurs - int[] dim = ((MatrixND)value).getDim(); - int size = 1; - for (int i=0; i<dim.length; i++) { - size *= dim[i]; - } - result += size * DOUBLE_SIZE; // size is wrong, because depend on matrix type (float or double) - } else if (value instanceof Collection) { - // List<Zone|Pop|Str|Metier|Cell> - // on prend la taille de la collection, car la donnees - // elle meme qu'elle soit dans le cache ou non est - // certainement utilisee ailleur, donc seul la taille - // des pointeurs dans la collection est prise ici - result += ((Collection)value).size() * POINTER_SIZE; - } else if (value instanceof Number) { - // int| double - // seulement une valeur, on ajoute 1 - result += 1 * DOUBLE_SIZE; - } else { - // a priori, il n'y a pas d'autre type de donnee - if (value != null) { - log.info("Cache can't compute value size of " + ClassUtils.getPackageCanonicalName(value, "null")); - } - } - return result; - } - }) + .maximumWeight(maxCache) + .weigher(isisWeigher) .build(); } @@ -90,7 +125,22 @@ @Override public void removeStep(Object o) { - // do nothing, can"t search step in cache without change cache behavior + // after first step, use information to resize cache + if (!ajusted) { + Cache<String, Object> oldCache = cache; + // compute new size for cache with data from the first step + // if this new size is less than old maxCache, use it + // to keep more memory for JVM + maxCache = Math.min(maxCache, totalCached * CACHE_STEP); // keep place for 3 step + cache = CacheBuilder.newBuilder() + .maximumWeight(maxCache) + .weigher(isisWeigher) + .initialCapacity((int)oldCache.size() * 3) + .build(); + + log.info(String.format("Cache size ajusted to %sMo (equivalent to %s step need)", + maxCache/1024/1024, CACHE_STEP)); + } } @Override @@ -103,6 +153,23 @@ public void put(TimeStep step, String key, Object value) { cache.put(key, value); } + + @Override + public String getStat() { + CacheStats stat = cache.stats(); + long evictionCount = stat.evictionCount(); + long hitCount = stat.hitCount(); + double hitRate = stat.hitRate(); + long missCount = stat.missCount(); + double missRate = stat.missRate(); + return String.format("%s - \n" + + "\tmaxMemory: %s, cacheMemory: %s, totalCached: %s, biggestCached: %s\n", +// + "\t evictionCount: %s, hitCount: %s, hitRate: %s, missCount: %s, missRate: %s\n", + getClass().getSimpleName(), + maxMemory, maxCache, totalCached, biggestCached, + evictionCount, hitCount, hitRate, missCount, missRate); + } + } Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java 2013-12-05 14:37:17 UTC (rev 3868) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java 2013-12-06 17:32:33 UTC (rev 3869) @@ -135,7 +135,11 @@ public void removeStep(Object o) { cache.remove(o); } - + + @Override + public String getStat() { + return String.format("%s - no specific stat\n", getClass().getSimpleName()); + } }

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