Merge pull request #2 from vivo-project/develop

Update Develop
vivo-community · Jul 27, 2015 · 9bdaf1e · 9bdaf1e
2 parents ab88d9c + 0c6b240
commit 9bdaf1e
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diff --git a/.classpath b/.classpath
@@ -1,10 +1,33 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" output="build/classes" path="src/main/java"/>
-	<classpathentry excluding="**" kind="src" output="build/classes" path="src/main/resources"/>
-	<classpathentry kind="src" output="build/test-classes" path="src/test/java"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="src" output="build/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="build/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="build/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="con" path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="build/dependency/jena-sdb-1.3.6.jar"/>
 	<classpathentry kind="output" path="build/classes"/>
 </classpath>
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,9 @@
+.settings/*
 /build
 /logs
 */data
+*data/*
 */logs
 */previous-harvest
+*.DS_Store
+*errDest/*
diff --git a/AUTHORS b/AUTHORS
@@ -1,12 +1,13 @@
 Christopher Barnes		[email protected]
 Christopher Haines		[email protected]
-Yang Li					[email protected]
+Yang Li				[email protected]
 Narayan Raum			[email protected]
 Dale Scheppler			[email protected]
 Nicholas Skaggs			[email protected]
 Stephen V. Williams		[email protected]
-Eliza Chan				[email protected]
-James Pence				[email protected]
+Eliza Chan			[email protected]
+James Pence			[email protected]
 Michael Barbieri		[email protected]
-Brian Keese				[email protected]
-Christopher Westling	[email protected]
+Brian Keese			[email protected]
+Christopher Westling		[email protected]
+John Fereira			[email protected]
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,3 +1,5 @@
+1.5 Release
+       Update Description TBD (2/19/2014):
 1.3
 	Pubmed script updated for faster scoring
 	New Example Scripts

diff --git a/bin/harvester-changenamespace b/bin/harvester-changenamespace
@@ -6,9 +6,11 @@
 
 #update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
 #8G-12G on large vivo's seems to work well
-MIN_MEM=2g
-MAX_MEM=8g
+#MIN_MEM=2g
+#MAX_MEM=8g
 
+MIN_MEM=1g
+MAX_MEM=1g
 #Variable for optimizations to the Java virtual machine.
 #-server                                                Run in server mode, which takes longer to start but runs faster
 #-d64                                                   Use 64-bit JVM
@@ -19,8 +21,8 @@ MAX_MEM=8g
 #-XX:SurvivorRatio=16                   Shrink eden slightly (Normal is 25)
 #-Xnoclassgc                                    Disable collection of class objects
 #-XX:ParallelGCThreads=3                Maximum number of Parallel garbage collection tasks
-#HARVESTER_JAVA_OPTS="" 
-HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
+HARVESTER_JAVA_OPTS="" 
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
 HARVESTER_DIAGNOSTIC_OPTS=""
 #HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
 OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS $HARVESTER_DIAGNOSTIC_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"

diff --git a/bin/harvester-createimagefolders b/bin/harvester-createimagefolders
@@ -6,9 +6,11 @@
 
 #update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
 #8G-12G on large vivo's seems to work well
-MIN_MEM=2g
-MAX_MEM=8g
+#MIN_MEM=2g
+#MAX_MEM=8g
 
+MIN_MEM=1g
+MAX_MEM=1g
 #Variable for optimizations to the Java virtual machine.
 #-server                                                Run in server mode, which takes longer to start but runs faster
 #-d64                                                   Use 64-bit JVM
@@ -19,8 +21,8 @@ MAX_MEM=8g
 #-XX:SurvivorRatio=16                   Shrink eden slightly (Normal is 25)
 #-Xnoclassgc                                    Disable collection of class objects
 #-XX:ParallelGCThreads=3                Maximum number of Parallel garbage collection tasks
-#HARVESTER_JAVA_OPTS="" 
-HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
+HARVESTER_JAVA_OPTS="" 
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
 HARVESTER_DIAGNOSTIC_OPTS=""
 #HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
 OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS $HARVESTER_DIAGNOSTIC_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"

diff --git a/bin/harvester-csvfetch b/bin/harvester-csvfetch
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+#Copyright (c) 2010-2011 VIVO Harvester Team. For full list of contributors, please see the AUTHORS file provided.
+#All rights reserved.
+#This program and the accompanying materials are made available under the terms of the new BSD license which accompanies this distribution, and is available at http://www.opensource.org/licenses/bsd-license.html
+
+#update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
+#8G-12G on large vivo's seems to work well
+#MIN_MEM=2g
+#MAX_MEM=8g
+
+MIN_MEM=1g
+MAX_MEM=1g
+
+#Variable for optimizations to the Java virtual machine.
+#-server                                                Run in server mode, which takes longer to start but runs faster
+#-d64                                                   Use 64-bit JVM
+#-XX:+UseParallelOldGC                  Use high throughput parallel GC on old generation 
+#-XX:+DisableExplicitGC                 Prevent direct calls to garbage collection in the code
+#-XX:+UseAdaptiveGCBoundary             Allow young/old boundary to move
+#-XX:-UseGCOverheadLimit                Limit the amount of time that Java will stay in Garbage Collection before throwing an out of memory exception
+#-XX:SurvivorRatio=16                   Shrink eden slightly (Normal is 25)
+#-Xnoclassgc                                    Disable collection of class objects
+#-XX:ParallelGCThreads=3                Maximum number of Parallel garbage collection tasks
+HARVESTER_JAVA_OPTS="" 
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
+HARVESTER_DIAGNOSTIC_OPTS=""
+#HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
+OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS $HARVESTER_DIAGNOSTIC_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"
+
+#pass incoming params to java program
+java $OPTS -Dprocess-task=CSVFetch org.vivoweb.harvester.fetch.CSVFetch "$@"
diff --git a/bin/harvester-csvtojdbc b/bin/harvester-csvtojdbc
@@ -6,8 +6,11 @@
 
 #update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
 #8G-12G on large vivo's seems to work well
-MIN_MEM=2g
-MAX_MEM=8g
+#MIN_MEM=2g
+#MAX_MEM=8g
+
+MIN_MEM=1g
+MAX_MEM=1g
 
 #Variable for optimizations to the Java virtual machine.
 #-server                                                Run in server mode, which takes longer to start but runs faster
@@ -19,9 +22,9 @@ MAX_MEM=8g
 #-XX:SurvivorRatio=16                   Shrink eden slightly (Normal is 25)
 #-Xnoclassgc                                    Disable collection of class objects
 #-XX:ParallelGCThreads=3                Maximum number of Parallel garbage collection tasks
-#HARVESTER_JAVA_OPTS="" 
-HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
-HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
+HARVESTER_JAVA_OPTS="" 
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
+#HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
 OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS $HARVESTER_DIAGNOSTIC_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"
 
 #pass incoming params to java program

diff --git a/bin/harvester-csvtordf b/bin/harvester-csvtordf
@@ -6,8 +6,11 @@
 
 #update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
 #8G-12G on large vivo's seems to work well
-MIN_MEM=2g
-MAX_MEM=8g
+#MIN_MEM=2g
+#MAX_MEM=8g
+
+MIN_MEM=1g
+MAX_MEM=1g
 
 #Variable for optimizations to the Java virtual machine.
 #-server                                                Run in server mode, which takes longer to start but runs faster
@@ -19,9 +22,10 @@ MAX_MEM=8g
 #-XX:SurvivorRatio=16                   Shrink eden slightly (Normal is 25)
 #-Xnoclassgc                                    Disable collection of class objects
 #-XX:ParallelGCThreads=3                Maximum number of Parallel garbage collection tasks
-#HARVESTER_JAVA_OPTS="" 
-HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
-HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
+HARVESTER_JAVA_OPTS="" 
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
+HARVESTER_DIAGNOSTIC_OPTS=""
+#HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
 OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS $HARVESTER_DIAGNOSTIC_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"
 
 #pass incoming params to java program

diff --git a/bin/harvester-d2rmapfetch b/bin/harvester-d2rmapfetch
@@ -6,8 +6,11 @@
 
 #update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
 #8G-12G on large vivo's seems to work well
-MIN_MEM=2g
-MAX_MEM=8g
+#MIN_MEM=2g
+#MAX_MEM=8g
+
+MIN_MEM=1g
+MAX_MEM=1g
 
 #Variable for optimizations to the Java virtual machine.
 #-server                                                Run in server mode, which takes longer to start but runs faster
@@ -19,9 +22,10 @@ MAX_MEM=8g
 #-XX:SurvivorRatio=16                   Shrink eden slightly (Normal is 25)
 #-Xnoclassgc                                    Disable collection of class objects
 #-XX:ParallelGCThreads=3                Maximum number of Parallel garbage collection tasks
-#HARVESTER_JAVA_OPTS="" 
-HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
-HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
+HARVESTER_JAVA_OPTS="" 
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
+HARVESTER_DIAGNOSTIC_OPTS=""
+#HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
 OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS $HARVESTER_DIAGNOSTIC_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"
 
 #pass incoming params to java program

diff --git a/bin/harvester-databaseclone b/bin/harvester-databaseclone
@@ -6,8 +6,11 @@
 
 #update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
 #8G-12G on large vivo's seems to work well
-MIN_MEM=2g
-MAX_MEM=8g
+#MIN_MEM=2g
+#MAX_MEM=8g
+
+MIN_MEM=1g
+MAX_MEM=1g
 
 #Variable for optimizations to the Java virtual machine.
 #-server                                                Run in server mode, which takes longer to start but runs faster
@@ -19,9 +22,10 @@ MAX_MEM=8g
 #-XX:SurvivorRatio=16                   Shrink eden slightly (Normal is 25)
 #-Xnoclassgc                                    Disable collection of class objects
 #-XX:ParallelGCThreads=3                Maximum number of Parallel garbage collection tasks
-#HARVESTER_JAVA_OPTS="" 
-HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
-HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
+HARVESTER_JAVA_OPTS="" 
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
+HARVESTER_DIAGNOSTIC_OPTS=""
+#HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
 OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS $HARVESTER_DIAGNOSTIC_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"
 
 #pass incoming params to java program

diff --git a/bin/harvester-diff b/bin/harvester-diff
@@ -6,8 +6,8 @@
 
 #update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
 #8G-12G on large vivo's seems to work well
-MIN_MEM=10g
-MAX_MEM=10g
+MIN_MEM=1g
+MAX_MEM=1g
 
 #Variable for optimizations to the Java virtual machine.
 #-server						Run in server mode, which takes longer to start but runs faster
@@ -19,10 +19,10 @@ MAX_MEM=10g
 #-XX:SurvivorRatio=16			Shrink eden slightly (Normal is 25)
 #-Xnoclassgc					Disable collection of class objects
 #-XX:ParallelGCThreads=3		Maximum number of Parallel garbage collection tasks
-#HARVESTER_JAVA_OPTS=""
-HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
-#HARVESTER_DIAGNOSTIC_OPTS=""
-HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:-HeapDumpOnOutOfMemoryError"
+HARVESTER_JAVA_OPTS=""
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
+HARVESTER_DIAGNOSTIC_OPTS=""
+#HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:-HeapDumpOnOutOfMemoryError"
 OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS $HARVESTER_DIAGNOSTIC_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"
 
 #pass incoming params to java program

diff --git a/bin/harvester-elementsfetch b/bin/harvester-elementsfetch
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+# Copyright (c) 2012 Symplectic Ltd. All rights reserved.
+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+#update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
+#8G-12G on large vivo's seems to work well
+MIN_MEM=1g
+MAX_MEM=1g
+
+#Variable for optimizations to the Java virtual machine.
+#-server						Run in server mode, which takes longer to start but runs faster
+#-d64							Use 64-bit JVM
+#-XX:+UseConcMarkSweepGC		Use concurrent (low pause time) garbage collector
+#-XX:+DisableExplicitGC			Prevent direct calls to garbage collection in the code
+#-XX:+UseAdaptiveGCBoundary		Allow young/old boundary to move
+#-XX:MaxGCPauseMillis=500		Target maximum for garbage collection time
+#-XX:-UseGCOverheadLimit		Limit the amount of time that Java will stay in Garbage Collection before throwing an out of memory exception
+#-XX:SurvivorRatio=16			Shrink eden slightly (Normal is 25)
+#-Xnoclassgc					Disable collection of class objects
+#-XX:UseSSE=3					Use SSE3 Processor extensions
+#-XX:ParallelGCThreads=3		Maximum number of Parallel garbage collection tasks
+HARVESTER_JAVA_OPTS=""
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseConcMarkSweepGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:MaxGCPauseMillis=500 -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:UseSSE=3 -XX:ParallelGCThreads=3"
+OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"
+
+#pass incoming params to java program
+java $OPTS -Dprocess-task=ElementsFetch uk.co.symplectic.vivoweb.harvester.app.ElementsFetchAndTranslate "$@"
diff --git a/bin/harvester-h2console b/bin/harvester-h2console
@@ -6,8 +6,10 @@
 
 #update memory to match your hardware -- set both to be the same, in general the more memory the better, but too much can cause errors as well.
 #8G-12G on large vivo's seems to work well
-MIN_MEM=2g
-MAX_MEM=8g
+#MIN_MEM=2g
+#MAX_MEM=8g
+MIN_MEM=1g
+MAX_MEM=1g
 
 #Variable for optimizations to the Java virtual machine.
 #-server                                                Run in server mode, which takes longer to start but runs faster
@@ -19,9 +21,10 @@ MAX_MEM=8g
 #-XX:SurvivorRatio=16                   Shrink eden slightly (Normal is 25)
 #-Xnoclassgc                                    Disable collection of class objects
 #-XX:ParallelGCThreads=3                Maximum number of Parallel garbage collection tasks
-#HARVESTER_JAVA_OPTS="" 
-HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
-HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
+HARVESTER_JAVA_OPTS="" 
+#HARVESTER_JAVA_OPTS="-server -d64 -XX:+UseParallelOldGC -XX:+DisableExplicitGC -XX:+UseAdaptiveGCBoundary -XX:-UseGCOverheadLimit -XX:SurvivorRatio=16 -Xnoclassgc -XX:ParallelGCThreads=3"
+HARVESTER_DIAGNOSTIC_OPTS=""
+#HARVESTER_DIAGNOSTIC_OPTS="-XX:+PrintG -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:HeapDumpPath /data/vivo/harvester/harvester_1.3/bin/heap-dumps/ -XX:-HeapDumpOnOutOfMemoryError"
 OPTS="-Xms$MIN_MEM -Xmx$MAX_MEM $HARVESTER_JAVA_OPTS $HARVESTER_DIAGNOSTIC_OPTS -Dharvester-task=$HARVEST_NAME.$DATE"
 
 #pass incoming params to java program