Squashed commit of the sb-vbs branch.

Includes the SD-VBS benchmarks modified to:
- Use libextra to loop as realtime jobs
- Preallocate memory before starting their main computation
- Accept input via stdin instead of via argc

Does not include the SD-VBS matlab code.

Fixes libextra execution in LITMUS^RT.

8 files changed, 731 insertions, 0 deletions

diff --git a/SD-VBS/benchmarks/svm/src/c/cal_learned_func.c b/SD-VBS/benchmarks/svm/src/c/cal_learned_func.c
new file mode 100644
index 0000000..79fdd68
--- /dev/null
+++ b/SD-VBS/benchmarks/svm/src/c/cal_learned_func.c
@@ -0,0 +1,42 @@
+/********************************
+Author: Sravanthi Kota Venkata
+********************************/
+
+#include "svm.h"
+
+float cal_learned_func(int k, F2D* a, float* b, int N, F2D* Y, F2D* X, int dim)
+{
+    float s, ret;
+    int i, j, m, n;
+    F2D *temp, *temp1;
+
+    s=0;
+    for(i=0; i<N; i++)
+    {
+        if( subsref(a,i,0) > 0)
+        {
+            temp = fMallocHandle(1, X->width);
+            temp1 = fMallocHandle(1, X->width);
+
+            for(m=0; m<X->width; m++)
+            {
+                asubsref(temp,m) = subsref(X,i,m);
+                asubsref(temp1,m) = subsref(X,k,m);
+            }
+
+            s += asubsref(a,i) * asubsref(Y,i) * polynomial(3, temp, temp1, dim);
+
+            free(temp);
+            free(temp1);
+        }
+    }
+
+    s = s- arrayref(b,0);
+    ret = s;
+
+    return ret;
+}
+
+
+
+
diff --git a/SD-VBS/benchmarks/svm/src/c/examineExample.c b/SD-VBS/benchmarks/svm/src/c/examineExample.c
new file mode 100644
index 0000000..5335f35
--- /dev/null
+++ b/SD-VBS/benchmarks/svm/src/c/examineExample.c
@@ -0,0 +1,67 @@
+/********************************
+Author: Sravanthi Kota Venkata
+********************************/
+
+#include "svm.h"
+
+int examineExample(int i, F2D* a, float* b, float C, F2D* e, F2D* X, F2D* Y, float tolerance, int N, float eps, int dim)
+{
+    int  ret, j, k, m, n;
+    float E, r1, randVal;
+    float maxDiff, temp;
+
+    if( ( asubsref(a,i) > 0) && ( asubsref(a,i) <C) )
+        E = asubsref(e,i);
+    else
+        E = cal_learned_func(i, a, b, N, Y, X, dim) - asubsref(Y,i);
+
+    r1 = subsref(Y,i,0) * E;
+    if( ((r1 < (-1*tolerance)) && ( asubsref(a,i) < C)) || ((r1 >tolerance) && ( asubsref(a,i) > 0)) )
+    {
+        maxDiff = 0;
+        j = i;
+
+        for(k=0; k<N; k++)
+        {
+            if( ( asubsref(a,k) > 0) && ( asubsref(a,k) < C) )
+            {
+                temp = fabsf( E - asubsref(e,k));
+                if (temp > maxDiff)
+                    j = k;
+            }
+        }
+
+        if ( i!=j)
+        {
+            ret = takeStep(i, j, a, C, e, Y, X, eps, b, N, dim);
+            if(ret == 1)
+                return ret;
+        }
+
+        randVal = 1.0;
+        for( k= (randVal*(N-2)); k<N; k++)
+        {
+            if( ( asubsref(a,k) > 0) && ( asubsref(a,k) <C) )
+            {
+                ret = takeStep(i, k, a, C, e, Y, X, eps, b, N, dim);
+                if (ret == 1)
+                    return ret;
+            }
+        }
+
+        for(k=0; k<N; k++)
+        {
+            ret = takeStep(i, k, a, C, e, Y, X, eps, b, N, dim);
+            if(ret == 1)
+                return ret;
+        }
+    }
+
+    
+    ret = 0;
+    return ret;
+}
+
+
+
+
diff --git a/SD-VBS/benchmarks/svm/src/c/getAlphaFromTrainSet.c b/SD-VBS/benchmarks/svm/src/c/getAlphaFromTrainSet.c
new file mode 100644
index 0000000..681f2c6
--- /dev/null
+++ b/SD-VBS/benchmarks/svm/src/c/getAlphaFromTrainSet.c
@@ -0,0 +1,98 @@
+/********************************
+Author: Sravanthi Kota Venkata
+********************************/
+
+#include "svm.h"
+
+alphaRet* getAlphaFromTrainSet(int N, F2D* trn1, F2D* trn2, int iterations)
+{
+    float tolerance, C, eps, *b;
+    F2D *a_result, *b_result;
+    int NumChanged, r, ExamineAll, cnt, d, dim, ret, iter, i;
+    F2D *X, *Y;
+    F2D *a, *e;
+
+    b = malloc(sizeof(float));
+    alphaRet* alpha;
+    alpha = (alphaRet*)malloc(sizeof(alphaRet));
+    tolerance = 0.001;
+    C = 0.05;
+    d = -1;
+    dim = 256;
+    eps = 0.001;
+    a_result = fSetArray(iterations, N, 0);
+    b_result = fSetArray(iterations, 1, 0);
+    ret = 0;
+    
+    X = usps_read_partial( trn1, trn2, 0, 1, (N/iterations), iterations);
+    
+    for(iter=0; iter<iterations; iter++)
+    {
+        Y = usps_read_partial( trn1, trn2, iter, 0, N/iterations, iterations);
+        
+        a = fSetArray(N, 1, 0);
+        arrayref(b,0) = 0;                  /** check if ptr **/
+        e = fSetArray(N, 1, 0);
+        ExamineAll = 1;
+        cnt = 0;
+        NumChanged = 0;
+
+        while(NumChanged>0 || ExamineAll == 1)
+        {
+            cnt = cnt + 1;
+            NumChanged = 0;
+            if(ExamineAll == 1)
+            {
+                for(i=0; i<N; i++)
+                {
+                    ret = examineExample(i, a, b, C, e, X, Y, tolerance, N, eps, dim);
+                    NumChanged = NumChanged + ret;
+                }
+            }
+            else
+            {
+                for(i=0; i<N; i++)
+                {
+                    if( asubsref(a,i) > 0 && asubsref(a,i) <C )
+                    {
+                        ret = examineExample(i, a, b, C, e, X, Y, tolerance, N, eps, dim);
+                        NumChanged = NumChanged + ret;
+                    }
+                }
+            }
+            if(ExamineAll == 1)
+                ExamineAll = 0;
+            else if(NumChanged == 0)
+                ExamineAll = 1;
+        }
+