Java OpenMP patternlets and exemplar

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "Patternlets/MPI/notebook"]
 	path = Patternlets/MPI/notebook
 	url = https://github.com/rkurniawati/mpiC.git
+[submodule "Patternlets/pyjama"]
+	path = Patternlets/pyjama
+	url = https://github.com/rkurniawati/pyjama-patternlets.git

Exemplars/DrugDesign/DDPyjama.java

@@ -0,0 +1,157 @@
+import java.util.Random;
+
+public class DDPyjama {
+    static Random rand = new Random(42);
+
+    static String[] cannedLigands = 
+        {"razvex", "qudgy", "afrs", "sst", "pgfht", "rt", 
+        "id", "how", "aaddh",  "df", "os", "hid", 
+        "sad", "fl", "rd", "edp", "dfgt", "spa"};
+
+    // Ligand Score pair
+    static class LSPair {
+        String ligand;
+        int score;
+
+        public LSPair(String ligand, int score) {
+            this.ligand = ligand;
+            this.score = score;
+        }
+
+        @Override
+        public String toString() {
+            return "["+ligand+","+score+"]";
+        }
+    }
+
+    // returns arbitrary string of lower-case letters of length at most max_ligand
+    static String makeLigand(int maxLigandLength) {
+
+        int len = rand.nextInt(maxLigandLength+1);
+        if (len == 0) len++; // don't create a 0-character ligand
+
+        StringBuilder sb = new StringBuilder();
+        for (int i = 0;  i < len;  i++) 
+            sb.append((char) ('a' + rand.nextInt(26)));  
+        return sb.toString();
+    }
+
+    private static String[] generateLigands(int numLigands, int maxLigandLength, boolean useCanned) {
+        // If we use canned ligands, use as many of them as we can, then fill the rest with randomly generated ligands. 
+        // Otherwise, create a set of ligands whose length randomly varies from 1 to args.maxLigand
+
+        String[] result = new String[numLigands];
+
+        if (useCanned) {
+            for(int i = 0; i < Math.min(numLigands, cannedLigands.length); i++) {
+                result[i] = cannedLigands[i];
+            }
+        }
+
+        for(int i = useCanned ? cannedLigands.length : 0; i < numLigands; i++) {
+            result[i] = makeLigand(maxLigandLength);
+        }
+        return result;
+    }
+
+    public static void main(String[] args) {
+
+        if (args.length != 4) {
+            System.out.println("Usage DDPyjama numThreads numLigands maxLigandLength protein useCanned printLigands");
+
+            // the example string below is one of Dijkstra's famous quotes
+            System.out.println("   Example: java -cp .:Pyjama.jar DDPyjama 4 10 8 \"Simplicity is a great virtue but it requires hard work to achieve it and education to appreciate it\" false true\n");
+        }
+
+        int numThreads = 4;
+        if (args.length >= 1) {
+            numThreads = Integer.parseInt(args[0]);
+        }
+
+        int numLigands = 12;
+        if (args.length >= 2) {
+            numLigands = Integer.parseInt(args[1]);
+        }
+
+        int maxLigandLength = 6;
+        if (args.length >= 3) {
+            maxLigandLength = Integer.parseInt(args[2]);
+        }
+
+        String protein = "the cat in the hat wore the hat to the cat hat party";
+
+        if (args.length >= 4) {
+            protein = args[3];
+        }
+
+        System.out.println("Number of threads: " + numThreads);
+        System.out.println("Number of ligands: "+numLigands);
+        System.out.println("Max ligand length: "+ maxLigandLength);
+        System.out.println("Protein: "+ protein);
+        System.out.println();
+
+        // Things to do: 
+        // 1. Generate the requested numLigands w/ maxLigandLength
+        // 2. Calculate the matching score for each ligand vs the given protein
+        //    Score is calculated based on the number of character in the ligand that
+        //    appears in the same order in the protein. 
+        // 3. Find the ligand(s) with the highest score
+
+        long start = System.currentTimeMillis();
+        String[] ligands = generateLigands(numLigands, maxLigandLength, args.length >= 5 && args[4].equals("true"));
+
+        // print the ligands if desired
+        if (args.length >= 6 && args[5].equals("true")) {
+            System.out.println("Here are the ligands");
+            for(String l : ligands) {
+                System.out.println(l);
+            }
+        }
+
+        // map each ligand to (ligand, score)
+        // also keep track of the maxScore 
+        LSPair[] ligandsWScore = new LSPair[numLigands];
+        int maxScore = 0;
+
+        //#omp parallel for num_threads(numThreads) shared(numLigands, ligands, ligandsWScore, protein) reduction(max:maxScore) schedule(dynamic)
+        for(int i = 0; i < numLigands; i++) {
+            String ligand = ligands[i];
+            int score = calcScore(ligand, protein);
+            ligandsWScore[i] = new LSPair(ligand, score);
+            maxScore = Math.max(maxScore, score);
+        }
+
+        // find the ligands whose score is maxScore
+        // this is a reduce operation
+        StringBuilder sb = new StringBuilder();
+        for(int i = 0; i < numLigands; i++) {
+            if (ligandsWScore[i].score == maxScore) {
+                if (sb.length() > 0) sb.append(", ");
+                sb.append(ligandsWScore[i].ligand);
+            }
+        }
+
+        long end = System.currentTimeMillis();
+        System.out.println("The maximum score is " + maxScore);
+        System.out.println("Achieved by ligand(s) "+ sb.toString());
+        System.out.println("Calculation time " + (end-start) + " ms");
+    }
+
+    /**
+     * Match a ligand (str1) and the protein. Count the number of characters in str1
+     * that appear in the same seq in str2 (there can be any number of intervening chars)
+     * @param str1 first string
+     * @param str2 second string
+     * @return number of matches
+     */
+    private static int calcScore(String str1, String str2) {
+        // no match if either is empty string
+        if (str1.length() == 0 || str2.length() == 0) return 0;
+
+        if (str1.charAt(0) == str2.charAt(0)) {
+            return 1 + calcScore(str1.substring(1), str2.substring(1));
+        }
+        return Math.max(
+            calcScore(str1, str2.substring(1)), calcScore(str1.substring(1), str2));
+    }
+}

Exemplars/DrugDesign/Makefile

@@ -17,6 +17,18 @@ dd_threads: dd_threads.cpp
 dd_mpi:  dd_mpi.cpp
 	mpiCC -std=c++11 -o dd_mpi dd_mpi.cpp
 
+Pyjama.jar:
+	wget https://www.csc.tntech.edu/pdcincs/resources/modules/tools/updated/Pyjama.zip
+	unzip -o Pyjama.zip
+	cp Pyjama/Pyjama*.jar Pyjama.jar
+	rm -r -f Pyjama.zip Pyjama
+
+DDPyjama.class:	DDPyjama.java Pyjama.jar
+	java -jar Pyjama.jar DDPyjama.java
+
+DDPyjama:	DDPyjama.class
+	java -cp .:Pyjama.jar DDPyjama $(ARGS)
+
 clean:
-	rm -f dd_serial dd_omp_static dd_omp_dynamic dd_threads dd_mpi
+	rm -f dd_serial dd_omp_static dd_omp_dynamic dd_threads dd_mpi Pyjama.jar DDPyjama*class