1. Moved break statement in utils.cc to correct position

2. Tested sandbox with regions
3. Lots of profiling code from previous commit exists

public/c++/VectorPairHMM/LoadTimeInitializer.cc

@@ -10,6 +10,9 @@ LoadTimeInitializer::LoadTimeInitializer()		//will be called when library is loa
 #ifndef DISABLE_FTZ
   //Very important to get good performance - enable FTZ, converts denormals to 0
   _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);
+  cout << "FTZ enabled - may decrease accuracy if denormal numbers encountered\n";
+#else
+  cout << "FTZ is not set - may slow down performance if denormal numbers encountered\n";
 #endif
   m_sumNumReads = 0;
   m_sumSquareNumReads = 0;

public/c++/VectorPairHMM/Sandbox.java

@@ -272,7 +272,7 @@ public class Sandbox {
         //System.err.println(e);
       //}
       Sandbox t = new Sandbox();
-      t.doEverythingNative(args[0]);
-      //t.parseSandboxFile(args[0]);
+      //t.doEverythingNative(args[0]);
+      t.parseSandboxFile(args[0]);
     }
 }

public/c++/VectorPairHMM/pairhmm-1-base.cc

@@ -9,14 +9,14 @@ using namespace std;
 
 int main(int argc, char** argv)
 {
-#define BATCH_SIZE 5
+#define BATCH_SIZE 10000
   if(argc < 2)
   {
     cerr << "Needs path to input file as argument\n";
     exit(0);
   }
   do_compute(argv[1]);
-#if 0
+  return 0;
   bool use_old_read_testcase = false;
   if(argc >= 3 && string(argv[2]) == "1")
     use_old_read_testcase = true;
@@ -56,7 +56,6 @@ int main(int argc, char** argv)
   testcase tc_in;
   int break_value = 0;
   tc_vector.clear();
-  g_load_time_initializer.open_sandbox();
   while(1)
   {
     break_value = use_old_read_testcase ? read_testcase(&tc_in, fptr) : 
@@ -144,8 +143,6 @@ int main(int argc, char** argv)
     fclose(fptr);
   else
     ifptr.close();
-  g_load_time_initializer.close_sandbox();
-#endif
   return 0;  
 }
 

public/c++/VectorPairHMM/utils.cc

@@ -79,9 +79,13 @@ int read_testcase(testcase *tc, FILE* ifp)
 	int x, size = 0;
 	ssize_t read;
 
-	read = getline(&line, (size_t *) &size, ifp == 0 ? stdin : ifp);
+
+        read = getline(&line, (size_t *) &size, ifp == 0 ? stdin : ifp);
 	if (read == -1)
-		return -1;
+        {
+          free(line);
+          return -1;
+        }
 
 
 	tc->hap = (char *) malloc(size);
@@ -326,7 +330,7 @@ void do_compute(char* filename)
   long long accum_values[NUM_PAPI_COUNTERS] = { 0, 0, 0, 0 };
 
 #endif
-#define BATCH_SIZE 100000
+#define BATCH_SIZE 10000
   bool use_old_read_testcase = true;
   unsigned chunk_size = 100;
   std::ifstream ifptr;
@@ -396,25 +400,25 @@ void do_compute(char* filename)
 #ifdef CHECK_UNDERFLOW
         if (result_avxf < MIN_ACCEPTED)
 #else
-        if(false)
+          if(false)
 #endif
-        {
+          {
 #ifdef COUNT_EXCEPTIONS
-          if(fp_exception)
-            ++fp_single_exceptions_reexecute;
+            if(fp_exception)
+              ++fp_single_exceptions_reexecute;
 #endif
-          double result_avxd = g_compute_full_prob_double(&(tc_vector[i]), 0);
-          result = log10(result_avxd) - log10(ldexp(1.0, 1020.0));
-          ++num_double_executions;
-        }
-        else
-        {
+            double result_avxd = g_compute_full_prob_double(&(tc_vector[i]), 0);
+            result = log10(result_avxd) - log10(ldexp(1.0, 1020.0));
+            ++num_double_executions;
+          }
+          else
+          {
 #ifdef COUNT_EXCEPTIONS
-          if(fp_exception)
-            ++fp_single_exceptions_continue;
+            if(fp_exception)
+              ++fp_single_exceptions_continue;
 #endif
-          result = (double)(log10f(result_avxf) - log10f(ldexpf(1.f, 120.f)));
-        }
+            result = (double)(log10f(result_avxf) - log10f(ldexpf(1.f, 120.f)));
+          }
         results_vec[i] = result;
       }
 #ifdef USE_PAPI
@@ -459,12 +463,12 @@ void do_compute(char* filename)
 #endif
       for(unsigned i=0;i<num_testcases;++i)
       {
-        delete tc_vector[i].rs;
-        delete tc_vector[i].hap;
-        delete tc_vector[i].q;
-        delete tc_vector[i].i;
-        delete tc_vector[i].d;
-        delete tc_vector[i].c;
+        free(tc_vector[i].rs);
+        free(tc_vector[i].hap);
+        free(tc_vector[i].q);
+        free(tc_vector[i].i);
+        free(tc_vector[i].d);
+        free(tc_vector[i].c);
       }
       total_count += num_testcases;
       num_testcases = 0;
@@ -473,9 +477,9 @@ void do_compute(char* filename)
       results_vec.clear();
       //curr_batch_size = rand()%BATCH_SIZE + 4;     //min batch size
       curr_batch_size = BATCH_SIZE;
-      if(break_value < 0)
-        break;
     }
+    if(break_value < 0)
+      break;
   }
 
   baseline_results.clear();