Merge branch 'master' of pwning.de:/hgraph

.gitignore

@@ -1,4 +1,5 @@
 *.o
 *~
 dist/setup-config
+*.hi
 

dist/build/autogen/Paths_hgraph.hs

@@ -7,8 +7,6 @@ module Paths_hgraph (
 import qualified Control.Exception as Exception
 import Data.Version (Version(..))
 import System.Environment (getEnv)
-import Prelude
-
 catchIO :: IO a -> (Exception.IOException -> IO a) -> IO a
 catchIO = Exception.catch
 
@@ -17,10 +15,10 @@ version :: Version
 version = Version {versionBranch = [0,0,1], versionTags = []}
 bindir, libdir, datadir, libexecdir :: FilePath
 
-bindir     = "/home/sdressel/.cabal/bin"
+bindir     = "/homes/sdressel/.cabal/bin"
-libdir     = "/home/sdressel/.cabal/lib/hgraph-0.0.1/ghc-7.6.3"
+libdir     = "/homes/sdressel/.cabal/lib/hgraph-0.0.1/ghc-7.4.1"
-datadir    = "/home/sdressel/.cabal/share/hgraph-0.0.1"
+datadir    = "/homes/sdressel/.cabal/share/hgraph-0.0.1"
-libexecdir = "/home/sdressel/.cabal/libexec"
+libexecdir = "/homes/sdressel/.cabal/libexec"
 
 getBinDir, getLibDir, getDataDir, getLibexecDir :: IO FilePath
 getBinDir = catchIO (getEnv "hgraph_bindir") (\_ -> return bindir)

dist/build/autogen/cabal_macros.h

@@ -1,11 +1,11 @@
 /* DO NOT EDIT: This file is automatically generated by Cabal */
 
-/* package QuickCheck-2.6 */
+/* package QuickCheck-2.4.2 */
-#define VERSION_QuickCheck "2.6"
+#define VERSION_QuickCheck "2.4.2"
 #define MIN_VERSION_QuickCheck(major1,major2,minor) (\
   (major1) <  2 || \
-  (major1) == 2 && (major2) <  6 || \
+  (major1) == 2 && (major2) <  4 || \
-  (major1) == 2 && (major2) == 6 && (minor) <= 0)
+  (major1) == 2 && (major2) == 4 && (minor) <= 2)
 
 /* package Stream-0.4.6.1 */
 #define VERSION_Stream "0.4.6.1"
@@ -21,33 +21,33 @@
   (major1) == 0 && (major2) <  13 || \
   (major1) == 0 && (major2) == 13 && (minor) <= 0)
 
-/* package base-4.6.0.1 */
+/* package base-4.5.0.0 */
-#define VERSION_base "4.6.0.1"
+#define VERSION_base "4.5.0.0"
 #define MIN_VERSION_base(major1,major2,minor) (\
   (major1) <  4 || \
-  (major1) == 4 && (major2) <  6 || \
+  (major1) == 4 && (major2) <  5 || \
-  (major1) == 4 && (major2) == 6 && (minor) <= 0)
+  (major1) == 4 && (major2) == 5 && (minor) <= 0)
 
-/* package bytestring-0.10.0.2 */
+/* package bytestring-0.9.2.1 */
-#define VERSION_bytestring "0.10.0.2"
+#define VERSION_bytestring "0.9.2.1"
 #define MIN_VERSION_bytestring(major1,major2,minor) (\
   (major1) <  0 || \
-  (major1) == 0 && (major2) <  10 || \
+  (major1) == 0 && (major2) <  9 || \
-  (major1) == 0 && (major2) == 10 && (minor) <= 0)
+  (major1) == 0 && (major2) == 9 && (minor) <= 2)
 
-/* package deepseq-1.3.0.1 */
+/* package deepseq-1.3.0.0 */
-#define VERSION_deepseq "1.3.0.1"
+#define VERSION_deepseq "1.3.0.0"
 #define MIN_VERSION_deepseq(major1,major2,minor) (\
   (major1) <  1 || \
   (major1) == 1 && (major2) <  3 || \
   (major1) == 1 && (major2) == 3 && (minor) <= 0)
 
-/* package ghc-7.6.3 */
+/* package ghc-7.4.1 */
-#define VERSION_ghc "7.6.3"
+#define VERSION_ghc "7.4.1"
 #define MIN_VERSION_ghc(major1,major2,minor) (\
   (major1) <  7 || \
-  (major1) == 7 && (major2) <  6 || \
+  (major1) == 7 && (major2) <  4 || \
-  (major1) == 7 && (major2) == 6 && (minor) <= 3)
+  (major1) == 7 && (major2) == 4 && (minor) <= 1)
 
 /* package monad-par-0.3.4.5 */
 #define VERSION_monad_par "0.3.4.5"
@@ -56,17 +56,17 @@
   (major1) == 0 && (major2) <  3 || \
   (major1) == 0 && (major2) == 3 && (minor) <= 4)
 
-/* package parallel-3.2.0.3 */
+/* package parallel-3.2.0.2 */
-#define VERSION_parallel "3.2.0.3"
+#define VERSION_parallel "3.2.0.2"
 #define MIN_VERSION_parallel(major1,major2,minor) (\
   (major1) <  3 || \
   (major1) == 3 && (major2) <  2 || \
   (major1) == 3 && (major2) == 2 && (minor) <= 0)
 
-/* package text-0.11.3.1 */
+/* package text-0.11.1.13 */
-#define VERSION_text "0.11.3.1"
+#define VERSION_text "0.11.1.13"
 #define MIN_VERSION_text(major1,major2,minor) (\
   (major1) <  0 || \
   (major1) == 0 && (major2) <  11 || \
-  (major1) == 0 && (major2) == 11 && (minor) <= 3)
+  (major1) == 0 && (major2) == 11 && (minor) <= 1)
 

references/pseudocode/pseudocode.tex

@@ -0,0 +1,103 @@
+\documentclass[11pt,a4paper]{scrartcl}
+\usepackage[ngerman]{babel} % Deutsches Wörterbuch usw.
+\usepackage[T1]{fontenc}
+\usepackage[utf8]{inputenc}
+\usepackage{times} % Skalierbarer und lesbarer Zeichensatz
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage[usenames,dvipsnames]{xcolor}
+\inputencoding{utf8} % Wir wollen UTF8(=keine Probleme mit Umlauten etc.)
+\parindent0em % Keine amerikanische Einrückung am Anfang von Paragraphen
+\usepackage[lmargin=2cm,rmargin=3.5cm,tmargin=2cm,bmargin=2cm]{geometry}
+\parindent0em
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+%opening
+\fancyhf{}
+\fancyhead[L]{\textbf{Message Passing Programming\\Parallele Algorithmen und Datenverarbeitung}}
+\fancyhead[R]{\textbf{Stefan Dresselhaus\\Thomas Pajenkamp}}
+\fancyfoot[C]{\thepage}
+\fancyfoot[R]{24. November 2013}
+
+\usepackage{algorithm}
+\usepackage[noend]{algpseudocode}
+
+\newcommand{\abs}[1]{\ensuremath{\left\lvert#1\right\rvert}}
+\newcommand{\norm}[1]{\ensuremath{\left\lVert#1\right\rVert}}
+\newcommand{\mean}[1]{\ensuremath{\overline{#1}}}
+\newcommand{\transp}[1]{\ensuremath{#1^{\mathsf{T}}}}
+
+% Ende der Voreinstellungen
+\begin{document}
+
+%\title{Message Passing Programming}
+%\author{Stefan Dresselhaus \and Thomas Pajenkamp}
+%\date{24. November 2013}
+%\maketitle
+
+\section*{Heuristik für \glqq{}Densely-connected Biclustering\grqq{}}
+
+\begin{algorithm*}
+\caption{Densely-connected Biclustering}
+\begin{algorithmic}[1]
+\Function{testHomogenity}{$A$, $\omega$, $\delta$, $g$}
+ \State $l \gets (\transp{A})_{g_0}$, $l \gets u$
+ \ForAll {nodes $i$ from $g \setminus \lbrace g_0\rbrace$}
+   \ForAll {dimensions $d$ of attribute matrix $A$}
+     \State $l \gets \min\lbrace l_d, A_{id}\rbrace$, $u \gets \max\lbrace l_d, A_{id}\rbrace$
+   \EndFor
+ \EndFor
+ \State $c \gets 0$
+ \ForAll {dimensions $d$ of attribute matrix $A$}
+    \If {$\abs{u_d - l_d} \leq \omega_d $}
+      \State $c \gets c+1$
+      \If {$c \geq \delta$}
+        \State \Return {true}
+      \EndIf
+    \EndIf
+ \EndFor
+ \Return {false}
+\EndFunction
+\end{algorithmic}
+\begin{algorithmic}[1]
+\Function{preprocessGraph}{$M$, $A$, $\omega$, $\delta$}
+ \State $G \gets \emptyset$
+ \ForAll {rows $i$ of adjascency matrix $M$}
+   \ForAll {columns $j$ of adjascency matrix $M$}
+     \If {$M_{ij} = 1$}
+       \If {\Call{testHomogenity}{$A$, $\omega$, $\delta$, $\lbrace i , j\rbrace$}}
+         \State $G \gets G \cup \lbrace \lbrace i, j\rbrace \rbrace$
+       \Else
+         \State $M_{ij} = 0$, $M_{ji} = 0$
+       \EndIf
+     \EndIf
+   \EndFor
+ \EndFor
+ \Return {$G$}
+\EndFunction
+\end{algorithmic}
+\begin{algorithmic}[1]
+\Function{DCB}{$M$, $A$, $\alpha$, $\omega$, $\delta$}
+ \State $G \gets $ \Call{preprocessGraph}{$M$, $A$, $\omega$, $\delta$}
+ \State $F \gets \emptyset$
+ \While {$G \neq \emptyset$}
+   \State $G' \gets G$, $G \gets \emptyset$
+   \ForAll {node sets $g$ in $G'$}
+     \State $b \gets \text{true}$
+     \ForAll {connected nodes $h$ with $h > \max g$}
+       \State $\hat{g} \gets g \cup \lbrace h\rbrace$
+       \If {\Call{testHomogenity}{$A$, $\omega$, $\delta$, $\hat{g}$} $\wedge$ \Call{graphDensity}{$M$, $\hat{g}$} $\leq$ $\alpha$}
+         \State $G \gets G \cup \lbrace \hat{g} \rbrace$
+         \State $b \gets \text{false}$
+       \EndIf
+     \EndFor
+     \If {$b$}
+       \State $F \gets F \cup \lbrace g\rbrace$
+     \EndIf
+   \EndFor
+ \EndWhile
+\EndFunction
+\end{algorithmic}
+\end{algorithm*}
+
+\end{document}

src/Main.hs

@@ -20,7 +20,7 @@ module Main (
 import Control.Monad (unless)
 import Control.Parallel.Strategies
 import Control.DeepSeq
-import Data.List
+import qualified Data.List as L
 import System.Exit (exitFailure)
 import System.Environment
 import Test.QuickCheck.All (quickCheckAll)
@@ -32,43 +32,50 @@ import Data.Either (lefts, rights)
 import Debug.Trace
 import qualified Data.Text as T
 import Data.Text.Encoding
-import Stream hiding (map)
+--import Stream hiding (map) --same as Data.Stream imported above?
-import qualified Data.Array.Accelerate as A
+import Data.Array.Accelerate hiding (not)
 -- change to Data.Array.Accelerate.CUDA as I and link accelerate-cuda to use GPU instead of CPU
 -- depends on accelerate-cuda package in cabal, which needs the installed CUDA-stuff form
 -- nVidia (nvcc, header-files, ...) and the propriatary driver
 import Data.Array.Accelerate.Interpreter as I
-type Matrix e = A.Array A.DIM2 e
+type Matrix e = Array DIM2 e
 
-type Attr  = Matrix A.Int8
+type Attr  = Matrix Int8
+-- Adjecency-Matrix
+type Adj   = Matrix Int8
+-- Vector of the Adjecency-Matrix
+type AdjV  = Vector Int8
+newtype Constraints = Matrix Float
 -- Graph consists of a Vector denoting which colums of the matrix represents wich originating
 -- column in the global adjencency-matrix, the reduces adjencency-matrix of the graph, a
 -- matrix of constraints and a scalar denoting the density
-newtype Constraints = Matrix A.Float
+type Density = Scalar Float
-type Density = A.Scalar A.Float
-type Graph = (A.Vector A.Int8, Matrix A.Int8, Constraints, Density)
--- Adjecency-Matrix
-type Adj   = Matrix A.Int8
--- Vector of the Adjecency-Matrix
-type AdjV  = A.Vector A.Int8
 
-expand :: [Graph]-> Adj -> Attr ->[Graph]
+-- Graph
+type Graph = (Vector Int8, Adj, Constraints, Density)
+
+-- Vector of Graphs
+type MultiGraph e = (Vector Int8, Array DIM3 e, Constraints, Density)
+
+
+
+expand :: Acc (MultiGraph Int8)-> Acc Adj -> Acc Attr -> Acc (MultiGraph Int8)
 expand g a att = undefined
 
 -- constraint gets a Graph and an Attribute-Matrix and yields true, if the Graph still fulfills
 -- all constraints defined via the Attribute-Matrix.
-constraint :: Graph -> Attr -> Bool
+constraint :: Acc Graph -> Acc Attr -> Acc (Scalar Bool)
 constraint g a = undefined
 
 
 -- addPoint gets a graph and a tuple of an adjecancy-Vector with an int wich column of the
 -- Adjacency-Matrix the Vector should represent to generate further Graphs
-addPoint :: Graph -> (Adj, Int) -> [Graph]
+addPoint :: Acc Graph -> Acc (Adj, (Scalar Int)) -> Acc (MultiGraph Int8)
-addPoint g (a, n) = undefined
+addPoint g a = undefined
 
 
 -- addablePoints yields all valid addititonsto a Graph
-addablePoints :: Adj -> Graph-> [(Adj, Int)]
+addablePoints :: Acc Adj -> Acc Graph-> Acc (Vector Int8)
 addablePoints a g = undefined
 
 
@@ -109,11 +116,11 @@ createOutput :: [[Int]] -> B.ByteString
 createOutput a = encodeUtf8 (createOutput' a)
 
 createOutput' :: [[Int]] -> T.Text
-createOutput' [a] = T.intercalate (T.singleton ',') (map (T.pack . show) a)
+createOutput' [a] = T.intercalate (T.singleton ',') (L.map (T.pack . show) a)
 createOutput' (a:as) = T.append
                                     (T.append
                                             (T.intercalate (T.singleton ',')
-                                            (map (T.pack . show) a))
+                                            (L.map (T.pack . show) a))
                                      (T.singleton '\n'))
                                (createOutput' as)
 
@@ -134,17 +141,18 @@ exeMain = do
             [adj, attr] -> Prelude.mapM B.readFile [adj, attr]
             _ -> error "Wrong arguments given"
     -- read file and clean
-    adjMat <- return $ filter (not . emptyLine) (T.lines (decodeUtf8 (head input)))
+    adjMat <- return $ L.filter (not . emptyLine) (T.lines (decodeUtf8 (head input)))
+    attrMat <- return $ L.filter (not . emptyLine) (T.lines (decodeUtf8 ((head . L.tail) input)))
 
     inputLines <- return $ length adjMat
     -- TODO: concat with foldl1' kills us later -> use presized/preallocated array so we
     --       dont copy that much lateron. Best would be Matrix Int
     -- unrefined_graph::[Either [Int] String] - [Int] is Adjacency-Line, String is parse-Error
-    unrefined_graph <- return $ (map (traceEvent "mapping" . createGraph) adjMat)
+    unrefined_graph <- return $ (L.map (traceEvent "mapping" . createGraph) adjMat)
                                         +|| (parBuffer 100 rdeepseq) --run parallel, evaluate fully
     --egraph <- return $ graphFolder unrefined_graph
 
-    (graph, log, lines) <- return $ ((foldl1' ((traceEvent "concatenating graph") . (++)) (lefts unrefined_graph), -- concatenated graph
+    (graph, log, lines) <- return $ ((L.foldl1' ((traceEvent "concatenating graph") . (++)) (lefts unrefined_graph), -- concatenated graph
                                 traceEvent "concatenating log" T.intercalate (T.singleton '\n') (rights unrefined_graph), -- concat error-log
                                 traceEvent "getting length" length unrefined_graph) -- number of elements in graph
                                                     -- in parallel