Heat Map Implementation

.classpath

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+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src/main/scala"/>
+	<classpathentry kind="src" path="src/test/scala"/>
+	<classpathentry kind="src" path="src/main/java"/>
+	<classpathentry kind="con" path="org.scala-ide.sdt.launching.SCALA_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="C:/Users/jfc.EECS/.ivy2/cache/org.scala-tools.testing/scalacheck_2.9.1/jars/scalacheck_2.9.1-1.9.jar"/>
+	<classpathentry kind="lib" path="C:/Users/jfc.EECS/.ivy2/cache/org.scalatest/scalatest/jars/scalatest-1.4.RC2.jar"/>
+	<classpathentry kind="lib" path="C:/Users/jfc.EECS/.ivy2/cache/org.scala-lang/jline/jars/jline-2.9.1.jar"/>
+	<classpathentry kind="lib" path="C:/Users/jfc.EECS/.ivy2/cache/junit/junit/jars/junit-4.5.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jhdf5.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/ptplot.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcublas-0.5.0RC.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcuda-0.5.0RC.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcufft-0.5.0RC.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcurand-0.5.0RC.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcusparse-0.5.0RC.jar"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>BIDMat</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.scala-ide.sdt.core.scalabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.scala-ide.sdt.core.scalanature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

Copyright.txt

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+Copyright (c) 2012, Regents of the University of California
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * Neither the name of the <organization> nor the
+      names of its contributors may be used to endorse or promote products
+      derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

INSTALLING.txt

@@ -0,0 +1,28 @@
+BIDMat is a set of Scala, Java and native code libraries. To run it, you need:
+
+* A java runtime, version 1.5 or later.
+
+* An Installation of the Scala language, which you can get from here: http://www.scala-lang.org/
+  You need Scala 2.9.1 or later. We have tested extensively on 2.9.1 and 2.9.2.
+
+* A 64bit Intel machine (Linux, Windows, and *soon* Mac), if you plan to use any native
+  code acceleration. We have tested on Windows 7 and RedHat Enterprise Linux 6. 
+  You should set Mat.noMKL=true in scala if you dont have one. A lot of
+  the code will still work, but that's really not the point of the library.
+
+* To use these libraries with a CUDA GPU, you need a CUDA-enabled GPU device. The code has
+  been developed for GTX 600-series, and this is the ideal platform. The code should work
+  with Tesla K10 devices, which share the same GPU chip as the 680/690 which is our
+  main platform. Most operations will work also with 500-series and we are working to add
+  the others. 
+
+* You need the [http://developer.nvidia.com/cuda/cuda-downloads NVIDIA CUDA driver and the
+  CUDA Toolkit] from the NVIDIA website. This version is based on CUDA 4.2. CUDA 5.0 supported
+  should appear soon. 
+
+In Linux, you should just be able to run the "bidmat" script from the top-level
+directory. If that doesnt work, its probably because $JAVA_HOME is not set in your
+environment. You can set it inside the script instead.
+
+On windows you will need to set the system PATH variable to include the lib subdirectory,
+which is at <root_dir>/BIDMat/lib/win64, and which contains the native code dlls

README.md

@@ -1,4 +1,7 @@
 
+NOTE: Documentation for BIDMat is available here: 
+http://bid.berkeley.edu/BIDMat/index.php/Main_Page
+
 BIDMat is a matrix library intended to support large-scale exploratory
 data analysis and to accelerate production deployment on single
 machines or clusters.  While there are many excellent tools exist to
@@ -12,17 +15,19 @@ of a high-end programming language including good general-purpose data
 sructures. And also of Scala's compiler-based REPL (Read-Eval-Print Loop). 
 
 2. To leverage native machine performance through native libraries
-(Intel MKL, HDF5 and string/XML processing). Java/Scala are excellent
-high-level languages, but are one or two orders of magnitude away from
-native performance in some key areas: especially matrix algebra and
-string processing, and below the bar to a lesser degree in File-IO.
+(Intel MKL, HDF5, CUDA and string/XML processing). Java/Scala are
+excellent high-level languages, but are one or two orders of magnitude
+away from native performance in some key areas: especially matrix
+algebra and string processing, and below the bar to a lesser degree in
+File-IO.
 
 3. To leverage GPU hardware and GPU-based data as a first-class
 object.  GPUs now offer large improvements (again one or more orders
 of magnitude) over CPU performance in many areas that are relevant to
 data mining: matrix algebra, transcendental functions, random number
-generation, network and graph algorithms and even natural language
-parsing. Our own work suggests that the list is going to continue to
-grow, and that GPU acceleration will fairly soon be a requirement for
-competitive performance in most algorithms.
+generation. These advantages in low-level operations carry over to
+network and graph algorithms and even natural language parsing. Our
+own work suggests that the list is going to continue to grow, and that
+GPU acceleration will fairly soon be a requirement for competitive
+performance in most algorithms.
 

bidmat

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+#!/bin/bash
+export BIDMAT_ROOT="$( cd -P "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+export BIDMAT_ROOT="$( echo ${BIDMAT_ROOT} | sed s+/cygdrive/c+c:+ )" 
+# This is only needed/works on Linux
+export LD_LIBRARY_PATH="${BIDMAT_ROOT}/lib/linux64:${BIDMAT_ROOT}/lib/linux64/JCUDA5.0:/usr/local/cuda-5.0/lib64:${LD_LIBRARY_PATH}" 
+# export JAVA_HOME="" # Set here if not set in environment
+export JAVA_OPTS="-Xmx12G -Xms128M" # Set as much memory as possible
+# Fix these if needed
+export JCUDA_VERSION="0.5.0RC"
+export JCUDA_LIBDIR=${BIDMAT_ROOT}/lib
+export LIBDIR=${BIDMAT_ROOT}/lib
+
+export BIDMAT_LIBS="${BIDMAT_ROOT}/BIDMat.jar;${LIBDIR}/ptplot.jar;${LIBDIR}/ptplotapplication.jar;${LIBDIR}/jhdf5.jar"
+export JCUDA_LIBS="${JCUDA_LIBDIR}/jcuda-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcublas-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcufft-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcurand-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcusparse-${JCUDA_VERSION}.jar"
+
+export ALL_LIBS="${BIDMAT_LIBS};${JCUDA_LIBS};${JAVA_HOME}/lib/tools.jar"
+
+if [ ! "$OS" = "Windows_NT" ]; then
+    export ALL_LIBS=`echo "${ALL_LIBS}" | sed 's/;/:/g'`
+fi
+
+scala -nobootcp -cp "${ALL_LIBS}" -Yrepl-sync -i ${LIBDIR}/bidmat_init.scala

bidmat.cmd

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+@ECHO OFF
+:: Set JAVA_HOME here if not set in environment
+:: SET JAVA_HOME= 
+:: Set as much memory as possible
+(SET JAVA_OPTS=-Xmx12G -Xms128M)
+:: Fix these if needed
+SET JCUDA_VERSION=0.5.0RC
+SET JCUDA_LIBDIR=%CD%\lib
+SET LIBDIR=%CD%\lib
+SET PATH=%LIBDIR%\win64;%LIBDIR%\win64\JCUDA5.0;%PATH%
+
+
+SET BIDMAT_LIBS=%CD%\BIDMat.jar;%LIBDIR%\ptplot.jar;%LIBDIR%\ptplotapplication.jar;%LIBDIR%\jhdf5.jar
+
+SET JCUDA_LIBS=%JCUDA_LIBDIR%\jcuda-%JCUDA_VERSION%.jar;%JCUDA_LIBDIR%\jcublas-%JCUDA_VERSION%.jar;%JCUDA_LIBDIR%\jcufft-%JCUDA_VERSION%.jar;%JCUDA_LIBDIR%\jcurand-%JCUDA_VERSION%.jar;%JCUDA_LIBDIR%\jcusparse-%JCUDA_VERSION%.jar
+
+SET ALL_LIBS=%BIDMAT_LIBS%;%JCUDA_LIBS%;%JAVA_HOME%\lib\tools.jar
+echo %ALL_LIBS%
+
+scala -nobootcp -cp "%ALL_LIBS%" -Yrepl-sync -i %LIBDIR%\bidmat_init.scala

bidmat4.2

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+#!/bin/bash
+export BIDMAT_ROOT=`pwd`
+# This is only needed/works on Linux
+export LD_LIBRARY_PATH="${BIDMAT_ROOT}/lib/linux64:${BIDMAT_ROOT}/lib/linux64/JCUDA4.2:/usr/local/cuda-4.2/lib64:${LD_LIBRARY_PATH}" 
+# export JAVA_HOME="" # Set here if not set in environment
+export JAVA_OPTS="-Xmx12G -Xms128M" # Set as much memory as possible
+# Fix these if needed
+export JCUDA_VERSION="0.4.2"
+export JCUDA_LIBDIR=${BIDMAT_ROOT}/lib
+export LIBDIR=${BIDMAT_ROOT}/lib
+
+export BIDMAT_LIBS="${BIDMAT_ROOT}/BIDMat.jar;${LIBDIR}/ptplot.jar;${LIBDIR}/ptplotapplication.jar;${LIBDIR}/jhdf5.jar"
+export JCUDA_LIBS="${JCUDA_LIBDIR}/jcuda-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcublas-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcufft-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcurand-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcusparse-${JCUDA_VERSION}.jar"
+
+export ALL_LIBS="${BIDMAT_LIBS};${JCUDA_LIBS};${JAVA_HOME}/lib/tools.jar"
+
+if [ ! "$OS" = "Windows_NT" ]; then
+    export ALL_LIBS=`echo "${ALL_LIBS}" | sed 's/;/:/g'`
+fi
+
+scala -nobootcp -cp "${ALL_LIBS}" -Yrepl-sync -i ${LIBDIR}/bidmat_init.scala

build.sbt

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+
+name := "BIDMat"
+
+version := "0.1.0"
+
+organization := "edu.berkeley.bid"
+
+scalaVersion := "2.9.1"
+
+resolvers ++= Seq(
+  "Scala Tools Snapshots" at "http://scala-tools.org/repo-snapshots/"
+)
+
+libraryDependencies <<= (scalaVersion, libraryDependencies) { (sv, deps) =>
+  deps :+ ("org.scala-lang" % "scala-compiler" % sv)
+}
+
+libraryDependencies += "org.scala-lang" % "jline" % "2.9.1"
+
+libraryDependencies += "org.scalatest" %% "scalatest" % "1.8" % "test"
+
+libraryDependencies += "org.scala-tools.testing" %% "scalacheck" % "1.9" % "test"
+
+libraryDependencies += "junit" % "junit" % "4.5" % "test"
+
+credentials += Credentials(Path.userHome / ".ivy2" / ".credentials")
+
+javacOptions ++= Seq("-source", "1.5", "-target", "1.5")
+
+scalacOptions ++= Seq("-deprecation","-target:jvm-1.5")
+
+initialCommands := scala.io.Source.fromFile("lib/bidmat_init.scala").getLines.mkString("\n")
+
+javaOptions += "-Xmx12g"
+
+seq(ProguardPlugin.proguardSettings :_*)
+
+proguardOptions ++= Seq (
+  "-keep class scala.** { *; }",
+  "-keep class org.jfree.** { *; }",
+  keepMain("scala.tools.nsc.MainGenericRunner"),
+  keepLimitedSerializability,
+  keepAllScala,
+  "-keep class ch.epfl.** { *; }",
+  "-keep interface scala.ScalaObject"
+)
+
+