fixed redistribute option

ddcap · Apr 17, 2015 · 75854f6 · 75854f6
1 parent e82c955
commit 75854f6
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Showing 2 changed files with 34 additions and 27 deletions.
diff --git a/halvade/src/be/ugent/intec/halvade/tools/AlignerInstance.java b/halvade/src/be/ugent/intec/halvade/tools/AlignerInstance.java
@@ -62,12 +62,14 @@ public abstract class AlignerInstance {
     protected boolean keep = false;
     protected ChromosomeSplitter splitter;
     protected int containerMinusTasksLeft;
+    protected int containers;
     protected boolean redistribute;
 
 
     protected AlignerInstance(Mapper.Context context, String bin) throws IOException, URISyntaxException {
         AlignerInstance.context = context;
         header = null;
+        containers = HalvadeConf.getMapContainerCount(context.getConfiguration());
         containerMinusTasksLeft = HalvadeConf.lessTasksLeftThanContainers(context.getConfiguration());
         redistribute = HalvadeConf.getRedistribute(context.getConfiguration());
         writableRecord = new SAMRecordWritable();
@@ -91,34 +93,36 @@ protected AlignerInstance(Mapper.Context context, String bin) throws IOException
     }
 
     protected void getIdleCores(Mapper.Context context) throws IOException {
-        int totalCores = HalvadeConf.getVcores(context.getConfiguration());
-        int usedCores = 0;
-        // run "ps -eo args"  and search for any process with bwa aln
-        // count the -t options of all bwa aln instances this is used cores;
-        String line;
-        Process p = Runtime.getRuntime().exec("ps -eo args");
-        BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream()));
-        while ((line = input.readLine()) != null) {
-            if(line.contains("bwa")) {
-                System.out.println(line); //<-- Parse data here.
-                if(line.contains("sampe") || line.contains("samse"))
-                    usedCores++;
-                else if (line.contains("aln")) {
-                    String[] cmd = line.split("\\s+");
-                    int i = 0;
-                    while (i < cmd.length && !cmd[i].equals("-t"))
-                        i++;
-                    int alnCores = 1;
-                    if (i + 1 < cmd.length)
-                        alnCores = Integer.parseInt(cmd[i+1]);
-                    Logger.DEBUG("Aln used cores: " + alnCores);
-                    usedCores += alnCores;
-                }
-            }
-        }
-        input.close();
+//        int totalCores = HalvadeConf.getVcores(context.getConfiguration());
+//        int usedCores = 0;
+//        // run "ps -eo args"  and search for any process with bwa aln
+//        // count the -t options of all bwa aln instances this is used cores;
+//        String line;
+//        Process p = Runtime.getRuntime().exec("ps -eo args");
+//        BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream()));
+//        while ((line = input.readLine()) != null) {
+//            if(line.contains("bwa")) {
+//                System.out.println(line); //<-- Parse data here.
+//                if(line.contains("sampe") || line.contains("samse"))
+//                    usedCores++;
+//                else if (line.contains("aln")) {
+//                    String[] cmd = line.split("\\s+");
+//                    int i = 0;
+//                    while (i < cmd.length && !cmd[i].equals("-t"))
+//                        i++;
+//                    int alnCores = 1;
+//                    if (i + 1 < cmd.length)
+//                        alnCores = Integer.parseInt(cmd[i+1]);
+//                    Logger.DEBUG("Aln used cores: " + alnCores);
+//                    usedCores += alnCores;
+//                }
+//            }
+//        }
+//        input.close();
 
-        threads = Math.max(threads, totalCores - usedCores);
+//        threads = Math.max(threads, totalCores - usedCores);
+        if (containerMinusTasksLeft > 0 ) threads = 6;
+//        if (containerMinusTasksLeft > containers/2) threads = 8;
     }
 
     protected int feedLine(String line, ProcessBuilderWrapper proc) throws IOException  {

diff --git a/halvade/src/be/ugent/intec/halvade/utils/HalvadeConf.java b/halvade/src/be/ugent/intec/halvade/utils/HalvadeConf.java
@@ -269,6 +269,9 @@ public static boolean addTaskRunning(Configuration conf, String val) throws IOEx
     public static void setMapContainerCount(Configuration conf, int val) {
         conf.setInt(totalContainers, val);
     }
+    public static int getMapContainerCount(Configuration conf) {
+        return conf.getInt(totalContainers, 1);
+    }
     public static int lessTasksLeftThanContainers(Configuration conf) throws IOException, URISyntaxException {
         int containers = conf.getInt(totalContainers, 1);        
         int tasks = 0;