Enable internal DIS job looping and port to new extra.h API

Changes to DIS code:
- field, pointer, transitive, and update's random initialization
  steps moved the main job loop (so that they run on fresh state
  each job).
- Moved free() calls outside of the job loop in matrix
- Removed loose clock() call in pointer
Misc fixes:
- Added input file for neighborhood
- Log status before, rather than after, printing in gen_input.py

8 files changed, 211 insertions, 209 deletions

diff --git a/dis/Field/field.c b/dis/Field/field.c
index 248f779..900d47b 100644
--- a/dis/Field/field.c
+++ b/dis/Field/field.c
@@ -86,55 +86,55 @@ int main(int argc, char **argv) {
     return (-1);
 
   randInit(seed);
-  for (l = 0; l < f; l++) {
-    field[l] = randInt(MIN_TOKEN_VALUE, MAX_TOKEN_VALUE);
-  }
 
-  startTime = time(NULL);
-  START_LOOP
+  for_each_job {
+    for (l = 0; l < f; l++) {
+      field[l] = randInt(MIN_TOKEN_VALUE, MAX_TOKEN_VALUE);
+    }
 
-  for (l = 0; l < n; l++) {
-    unsigned int index;
+    startTime = time(NULL);
 
-    token[l].subfields = 0;
-    token[l].stat[0].count = 0;
-    token[l].stat[0].sum = 0;
-    token[l].stat[0].min = MAX_TOKEN_VALUE;
+    for (l = 0; l < n; l++) {
+      unsigned int index;
 
-    index = 0;
-    while ((index < f) && (token[l].subfields < MAX_SUBFIELDS)) {
-      unsigned char offset;
-      offset = 0;
-      while ((field[index + offset] == token[l].delimiter[offset]) &&
-             (offset < token[l].length)) {
-        offset++;
-      }
+      token[l].subfields = 0;
+      token[l].stat[0].count = 0;
+      token[l].stat[0].sum = 0;
+      token[l].stat[0].min = MAX_TOKEN_VALUE;
 
-      if (offset == token[l].length) {
-        for (offset = 0; offset < token[l].length; offset++) {
-          field[index + offset] = (field[index + offset] +
-                                   field[(index + offset + mod_offset) % f]) %
-                                  (MAX_TOKEN_VALUE + 1);
+      index = 0;
+      while ((index < f) && (token[l].subfields < MAX_SUBFIELDS)) {
+        unsigned char offset;
+        offset = 0;
+        while ((field[index + offset] == token[l].delimiter[offset]) &&
+               (offset < token[l].length)) {
+          offset++;
         }
-        index += token[l].length - 1;
-        token[l].subfields++;
-        token[l].stat[token[l].subfields].count = 0;
-        token[l].stat[token[l].subfields].sum = 0;
-        token[l].stat[token[l].subfields].min = MAX_TOKEN_VALUE;
-      }
 
-      else {
-        token[l].stat[token[l].subfields].count++;
-        token[l].stat[token[l].subfields].sum += field[index];
-        if (token[l].stat[token[l].subfields].min > field[index])
-          token[l].stat[token[l].subfields].min = field[index];
+        if (offset == token[l].length) {
+          for (offset = 0; offset < token[l].length; offset++) {
+            field[index + offset] = (field[index + offset] +
+                                     field[(index + offset + mod_offset) % f]) %
+                                    (MAX_TOKEN_VALUE + 1);
+          }
+          index += token[l].length - 1;
+          token[l].subfields++;
+          token[l].stat[token[l].subfields].count = 0;
+          token[l].stat[token[l].subfields].sum = 0;
+          token[l].stat[token[l].subfields].min = MAX_TOKEN_VALUE;
+        }
+
+        else {
+          token[l].stat[token[l].subfields].count++;
+          token[l].stat[token[l].subfields].sum += field[index];
+          if (token[l].stat[token[l].subfields].min > field[index])
+            token[l].stat[token[l].subfields].min = field[index];
+        }
+        index++;
       }
-      index++;
+      token[l].subfields++;
     }
-    token[l].subfields++;
   }
-
-  STOP_LOOP
   endTime = time(NULL);
 
   volatile int sumAll = 0;
diff --git a/dis/Matrix/ver2/matrix.c b/dis/Matrix/ver2/matrix.c
index 2b075fb..5162579 100755
--- a/dis/Matrix/ver2/matrix.c
+++ b/dis/Matrix/ver2/matrix.c
@@ -407,13 +407,6 @@ void biConjugateGradient(double *value, int *col_ind, int *row_start,
   *actualError = error;
   *actualIteration = iteration;
 
-  free(tmpVector1);
-  free(tmpVector2);
-  free(tmpVector3);
-
-  free(vectorR);
-  free(vectorP);
-
   return;
 }
 
@@ -525,27 +518,34 @@ int main(int argc, char **argv) {
 
   randInit(seed);
 
-  START_LOOP
-  initMatrix(matrixA, dim, numberNonzero);
+  for_each_job {
+    initMatrix(matrixA, dim, numberNonzero);
 
-  create_CRS(matrixA, value, col_ind, row_start, dim, numberNonzero);
+    create_CRS(matrixA, value, col_ind, row_start, dim, numberNonzero);
 
-  initVector(vectorB, dim);
-  zeroVector(vectorX, dim);
+    initVector(vectorB, dim);
+    zeroVector(vectorX, dim);
 
-  beginTime = time(NULL);
+    beginTime = time(NULL);
 
-  actualError = 0;
-  actualIteration = 0;
+    actualError = 0;
+    actualIteration = 0;
 
-  biConjugateGradient(value, col_ind, row_start, vectorB, vectorX,
-                      errorTolerance, maxIterations, &actualError,
-                      &actualIteration, dim, vectorP, vectorR, nextVectorR,
-                      tmpVector1, tmpVector2, tmpVector3);
+    biConjugateGradient(value, col_ind, row_start, vectorB, vectorX,
+                        errorTolerance, maxIterations, &actualError,
+                        &actualIteration, dim, vectorP, vectorR, nextVectorR,
+                        tmpVector1, tmpVector2, tmpVector3);
 
-  STOP_LOOP
+  }
   endTime = time(NULL);
 
+  free(tmpVector1);
+  free(tmpVector2);
+  free(tmpVector3);
+
+  free(vectorR);
+  free(vectorP);
+
   sum = 0;
   for (k = 1; k < dim; k++) {
     sum += sum + *(vectorX + k);
diff --git a/dis/Neighborhood/neighborhood.c b/dis/Neighborhood/neighborhood.c
index 614b8e8..2d401d3 100644
--- a/dis/Neighborhood/neighborhood.c
+++ b/dis/Neighborhood/neighborhood.c
@@ -63,14 +63,14 @@ int main(int argc, char **argv) {
   image = malloc(sizeof(Pixel) * dimension * dimension);
   assert(image != NULL);
 
-  beginTime = time(NULL);
-  START_LOOP
-  createImage(image, dimension, maxPixel, numberLines, minThickness,
-              maxThickness);
+  for_each_job {
+    beginTime = time(NULL);
+    createImage(image, dimension, maxPixel, numberLines, minThickness,
+                maxThickness);
 
-  neighborhoodCalculation(image, dimension, distanceShort, distanceLong,
-                          &values, maxPixel);
-  STOP_LOOP
+    neighborhoodCalculation(image, dimension, distanceShort, distanceLong,
+                            &values, maxPixel);
+  }
   endTime = time(NULL);
   WRITE_TO_FILE
 
diff --git a/dis/Pointer/pointer.c b/dis/Pointer/pointer.c
index 3f3eefb..d97f276 100644
--- a/dis/Pointer/pointer.c
+++ b/dis/Pointer/pointer.c
@@ -82,68 +82,67 @@ int main(int argc, char **argv) {