Make SD-VBS compatible with run_bench.sh and cleanup

SD-VBS:
- Run silently
- Fix some whitespace errors
- Don't duplicate extra.h
- Auto-detect if building with LITMUS-RT
- Disable result checking
- Add helper symlinks
Misc:
- Remove unused code from libextra
- Set some missing rt_param fields in libextra
- Disable CSV info dump from computeSMTslowdown.sh
- Widen scope of .gitignore on .txt files
- Include list of 2MB DIS pair benchmarks and inputs

25 files changed, 99 insertions, 583 deletions

diff --git a/.gitignore b/.gitignore
index 057a48b..0e0db96 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,6 +3,9 @@
 *.txt.clean
 # But not benchmark lists
 !*Names.txt
+# Special-case .txt handling for SD-VBS
+**/12345.txt
+!SD-VBS/benchmarks/**/*.txt
 
 # Ignore DIS benchmark binaries
 **/field
@@ -40,12 +43,7 @@
 **/statemate
 **/susan
 
-# Ignore random walk benchmark
-**/random_walk
-
-# Ignore misc debug and build outputs
-**/.gdb_history
-
+# Ignore SD-VBS binaries
 **/mser
 **/multi_ncut
 **/stitch
@@ -56,5 +54,10 @@
 **/sift
 **/localization
 **/disparity
-**/12345.txt
-!SD-VBS/**/*.txt
+
+# Ignore random walk benchmark
+**/random_walk
+
+# Ignore misc temporary files
+**/.gdb_history
+*.swp
diff --git a/SD-VBS/benchmarks/disparity/src/c/script_disparity.c b/SD-VBS/benchmarks/disparity/src/c/script_disparity.c
index 431c02c..7d45ada 100644
--- a/SD-VBS/benchmarks/disparity/src/c/script_disparity.c
+++ b/SD-VBS/benchmarks/disparity/src/c/script_disparity.c
@@ -28,9 +28,7 @@ int main(int argc, char* argv[])
     int WIN_SZ=8, SHIFT=64;
     FILE* fp;
     
-    printf("Image 1: ");
     scanf("%s", im1);
-    printf("Image 2: ");
     scanf("%s", im2);
 #ifdef CHECK
     char checkFile[100] = "./expected_C.txt";
@@ -86,17 +84,15 @@ int main(int argc, char* argv[])
     Iright_moved = iSetArray(paddedRows, paddedCols, 0);
 
     range = iMallocHandle(1, 2);
-    printf("starting..\n");
-    for_each_job{
-    retDisparity = getDisparity(imleft, imright, WIN_SZ, SHIFT, 
-                   minSAD, retDisp, halfWin,
-                   IrightPadded, IleftPadded, Iright_moved,
-                   retSAD, SAD, integralImg,
-                   range);
+    for_each_job {
+        retDisparity = getDisparity(imleft, imright, WIN_SZ, SHIFT,
+               minSAD, retDisp, halfWin,
+               IrightPadded, IleftPadded, Iright_moved,
+               retSAD, SAD, integralImg,
+               range);
     }
-    printf("ending\n");
 
-#ifdef CHECK   
+#ifdef CHECK
     /** Self checking - use expected.txt from data directory  **/
     {
         int tol, ret=0;
diff --git a/SD-VBS/benchmarks/localization/src/c/script_localization.c b/SD-VBS/benchmarks/localization/src/c/script_localization.c
index 3392320..ed37132 100644
--- a/SD-VBS/benchmarks/localization/src/c/script_localization.c
+++ b/SD-VBS/benchmarks/localization/src/c/script_localization.c
@@ -41,7 +41,6 @@ int main(int argc, char* argv[])
 
     char im1[100];
 
-    printf("Input txt File: ");
     scanf("%s", im1);
 
     fid = readFile(im1);
@@ -83,11 +82,10 @@ int main(int argc, char* argv[])
     F2D *randn;
 
     randn = randWrapper(n,3);
-    printf("start\n");
-    for_each_job{
-        fResetArray(pos,n, 3, 0);
-        fResetArray(vel,n, 3, 0);
-        fResetArray(ones,n,1,1);
+    for_each_job {
+        fResetArray(pos,n, 3, 0);
+        fResetArray(vel,n, 3, 0);
+        fResetArray(ones,n,1,1);
 
         {
             int j;
@@ -95,7 +93,7 @@ int main(int argc, char* argv[])
                 for(j=0; j<3; j++)
                     subsref(vel, i, j) += subsref(randn,i,j) * STDDEV_ODOVel;
 
-        }  
+        }
 
 
  
@@ -486,17 +484,15 @@ int main(int argc, char* argv[])
                 subsref(resultMat,1,icount) = velOut;
                 subsref(resultMat,2,icount) = posOut;
             }
-    
+
             fFreeHandle(sData);
-    
-        
+
             if (asubsref(isEOF,0) == 1)
                break;
         }
     }
-    printf("end..\n");
 
-#ifdef CHECK   
+#ifdef CHECK
     
     // Self checking - use expected.txt from data directory
     {
diff --git a/SD-VBS/benchmarks/mser/src/c/script_mser.c b/SD-VBS/benchmarks/mser/src/c/script_mser.c
index d4a98cd..3e98f86 100644
--- a/SD-VBS/benchmarks/mser/src/c/script_mser.c
+++ b/SD-VBS/benchmarks/mser/src/c/script_mser.c
@@ -33,7 +33,6 @@ int main(int argc, char* argv[])
 
     int ndims, nel, gdl, nmer;
 
-    printf("Input Image: ");
     scanf("%s", im1);
 
     I = readImage(im1);
@@ -74,19 +73,17 @@ int main(int argc, char* argv[])
 
 
     out = iMallocHandle(1, nmer);
-    printf("start\n");
-    for_each_job{
+    for_each_job {
         idx = mser(It, 2, subs_pt, nsubs_pt, strides_pt, visited_pt, dims, 
-                   joins_pt,
+                   joins_pt,
                    regions_pt,
-                   pairs_pt,
+                   pairs_pt,
                    forest_pt,
-                   acc_pt, ell_pt,
+                   acc_pt, ell_pt,
                    out);
     }
-    printf("end..\n");
-    
-#ifdef CHECK   
+
+#ifdef CHECK
     /** Self checking - use expected.txt from data directory  **/
     {
         int tol, ret=0;
diff --git a/SD-VBS/benchmarks/multi_ncut/src/c/script_multi_ncut.c b/SD-VBS/benchmarks/multi_ncut/src/c/script_multi_ncut.c
index e4f7912..77c6b71 100644
--- a/SD-VBS/benchmarks/multi_ncut/src/c/script_multi_ncut.c
+++ b/SD-VBS/benchmarks/multi_ncut/src/c/script_multi_ncut.c
@@ -28,7 +28,6 @@ int main(int argc, char* argv[])
 
     F2D *imageOut, *tempOut;
     F2D *edgeWeights, *in;
-    printf("Input image: ");
     scanf("%s", im1);
     im = readImage(im1);
 
@@ -50,13 +49,12 @@ int main(int argc, char* argv[])
     u->elts = (uni_elt*)malloc(sizeof(uni_elt)*num_vertices);
     output = iMallocHandle(height, width);
 
-    printf("start\n");
     for_each_job{
-        seg = segment_image(im, sigma, k, min_size, num_ccs, segments, edges, imageOut, tempOut, kernel, edgeWeights, in, ind, u, output);
-        out = seg;
+        seg = segment_image(im, sigma, k, min_size, num_ccs, segments, edges, imageOut, tempOut, kernel, edgeWeights, in, ind, u, output);
+        out = seg;
     }
-    printf("end..\n");
-#ifdef CHECK   
+
+#ifdef CHECK
     /** Self checking - use expected.txt from data directory  **/
     {
         int ret=0;
diff --git a/SD-VBS/benchmarks/sift/src/c/script_sift.c b/SD-VBS/benchmarks/sift/src/c/script_sift.c
index 0b2f106..ab39ae3 100644
--- a/SD-VBS/benchmarks/sift/src/c/script_sift.c
+++ b/SD-VBS/benchmarks/sift/src/c/script_sift.c
@@ -45,7 +45,6 @@ int main(int argc, char* argv[])
     unsigned int* startTime, *endTime, *elapsed;    
     
     char imSrc[100];
-    printf("Input image: ");
     scanf("%s", imSrc);
     im = readImage(imSrc);
     image = fiDeepCopy(im);
@@ -53,16 +52,14 @@ int main(int argc, char* argv[])
     cols = image->width;
 
 
-    printf("start\n");
     for_each_job{
         image = fiDeepCopy(im);
-        normalizeImage(image);
+        normalizeImage(image);
         /** Extract sift features for the normalized image **/
         frames = sift(image);
     }
-    printf("end..\n");
-   
-#ifdef CHECK   
+
+#ifdef CHECK
     {
         int ret=0;
         float tol = 0.2;
diff --git a/SD-VBS/benchmarks/stitch/src/c/script_stitch.c b/SD-VBS/benchmarks/stitch/src/c/script_stitch.c
index 00c9a93..b7611f1 100644
--- a/SD-VBS/benchmarks/stitch/src/c/script_stitch.c
+++ b/SD-VBS/benchmarks/stitch/src/c/script_stitch.c
@@ -16,16 +16,13 @@ int main(int argc, char* argv[])
     I2D *Icur;
     int i, j;
     char im1[100], im2[100];
-    
 
-    printf("Input image: ");
     scanf("%s", im1);
     Icur = readImage(im1);
     rows = Icur->height;
     cols = Icur->width;
-    
-    printf("start\n");
-    for_each_job{
+
+    for_each_job {
         v = harris(Icur);
         interestPnts = getANMS(v, 24);
         int1 = fMallocHandle(interestPnts->height, 1);
@@ -38,10 +35,8 @@ int main(int argc, char* argv[])
 
         Fcur = extractFeatures(Icur, int1, int2);  
     }
-    printf("end..\n");
-    
 
-#ifdef CHECK   
+#ifdef CHECK
     /** Self checking - use expected.txt from data directory  **/
     {
         int ret=0;
diff --git a/SD-VBS/benchmarks/svm/src/c/script_svm.c b/SD-VBS/benchmarks/svm/src/c/script_svm.c
index 62a264d..f1ce963 100644
--- a/SD-VBS/benchmarks/svm/src/c/script_svm.c
+++ b/SD-VBS/benchmarks/svm/src/c/script_svm.c
@@ -70,24 +70,23 @@ int main(int argc, char* argv[])
     #endif
 
 
-    printf("trn file 1: ");
+    // trn file 1
     scanf("%s", im1);
-    trn1 = readFile(im1);   
+    trn1 = readFile(im1);
 
-    printf("trn file 2: ");
+    // trn file 2
     scanf("%s", im1);
-    trn2 = readFile(im1);   
+    trn2 = readFile(im1);
 
-    printf("tst file 1: ");
+    // tst file 1
     scanf("%s", im1);
-    tst1 = readFile(im1);   
+    tst1 = readFile(im1);
 
-    printf("tst file 2: ");
+    // tst file 2
     scanf("%s", im1);
-    tst2 = readFile(im1);       
+    tst2 = readFile(im1);
 
-    printf("start.\n");
-    for_each_job{
+    for_each_job {
         alpha = getAlphaFromTrainSet(N, trn1, trn2, iter);
         a_result = alpha->a_result;
         b_result = alpha->b_result;
@@ -135,8 +134,8 @@ int main(int argc, char* argv[])
             asubsref(result,n) = maxs;
         }
     }
-    printf("end..\n");
-#ifdef CHECK   
+
+#ifdef CHECK
     /** Self checking - use expected.txt from data directory  **/
     {
         int ret=0;
diff --git a/SD-VBS/benchmarks/texture_synthesis/src/c/script_texture_synthesis.c b/SD-VBS/benchmarks/texture_synthesis/src/c/script_texture_synthesis.c
index 01ddefd..2ebb423 100644
--- a/SD-VBS/benchmarks/texture_synthesis/src/c/script_texture_synthesis.c
+++ b/SD-VBS/benchmarks/texture_synthesis/src/c/script_texture_synthesis.c
@@ -27,11 +27,10 @@ int  main(int argc, char **argv)
     image = fiDeepCopy(im);
     init_params(data);
 
-    printf("start.\n");
-    for_each_job{
+    for_each_job {
         create_texture(image, data);
     }
-    printf("end..\n");
+
 #ifdef CHECK
 {
     int ret=0;
@@ -59,7 +58,6 @@ I2D* parse_flags(int argc, char ** argv)
     I2D* image;
     char fileNm[256];
 
-    printf("Input image: ");
     scanf("%s", fileNm);
     image = readImage(fileNm);
     WIDTHin = image->width;
@@ -122,7 +120,7 @@ I2D* parse_flags(int argc, char ** argv)
     localx = 5;
     localy = 5;
 #endif
-    printf("Input size\t\t- (%dx%d)\n", HEIGHTin, WIDTHin);
+//    printf("Input size\t\t- (%dx%d)\n", HEIGHTin, WIDTHin);
 
 //    xloopin = malloc(2*WIDTHin*sizeof(int));
 //    yloopin = malloc(2*HEIGHTin*sizeof(int));
diff --git a/SD-VBS/benchmarks/tracking/src/c/script_tracking.c b/SD-VBS/benchmarks/tracking/src/c/script_tracking.c
index bb48ace..2938126 100644
--- a/SD-VBS/benchmarks/tracking/src/c/script_tracking.c
+++ b/SD-VBS/benchmarks/tracking/src/c/script_tracking.c
@@ -96,19 +96,16 @@ int main(int argc, char* argv[])
     for(count=1; count<=counter; count++)
     {
         /** Read image **/
-        printf("Input image %d: ", count);
-        scanf("%s", im1);
+        scanf("%s", im1);
         images[count - 1] = readImage(im1);
-        if(count == 1) Ic = readImage(im1);
+        if(count == 1) Ic = readImage(im1);
     }
 
 
     rows = Ic->height;
     cols = Ic->width;
     
-    printf("start\n");   
-    for_each_job{
-        
+    for_each_job {
         /** IMAGE PRE-PROCESSING **/
     
         /** Blur the image to remove noise - weighted avergae filter **/
@@ -230,8 +227,8 @@ int main(int argc, char* argv[])
             fFreeHandle(newpoints);
         }
     }
-    printf("end..\n");
-#ifdef CHECK   
+
+#ifdef CHECK
     /* Self checking */
     {
         int ret=0;
diff --git a/SD-VBS/common/c/extra.h b/SD-VBS/common/c/extra.h
deleted file mode 100644
index 8c67b33..0000000
--- a/SD-VBS/common/c/extra.h
+++ /dev/null
@@ -1,479 +0,0 @@
-/**
- * Copyright 2019 Sims Hill Osborne and 2020 Joshua Bakita
- *
- * This header provides facilities by which to separably run and time TACLeBench
- * To use this for paired task timing, define PAIRED (pass CFLAGS=-DPAIRED to make)
- **/
-#define _GNU_SOURCE
-#include <fcntl.h>     // For O_CREAT and O_RDWR
-#include <sched.h>     // For sched_yield()
-#include <semaphore.h> // For sem_{open, post, wait}()
-#include <stdio.h>
-#include <stdlib.h>    // For exit()
-#include <string.h>    // For strlen()
-#include <sys/mman.h>  // For mlockall()
-#include <unistd.h>    // For ftruncate()
-#include <time.h>
-
-// This is only visible if _GNU_SOURCE is defined, and that define does not
-// come along to places where this file is included. Address this by manually
-// forcing it into the global namespace.
-extern int sched_getcpu();
-
-// These constants correspond to the imx6q-sabredb platform
-#define LINE_SIZE 32
-#define L2_SIZE 16*2048*32
-
-#if __arm__
-#include <unistd.h>
-#include <sys/syscall.h>
-#endif
-
-#define LITMUS 1
-#define MC2 0
-#define MMDC_PROF 0
-
-#if LITMUS
-#include <litmus.h>
-#endif
-
-#if MMDC_PROF
-#include  "/media/speedy/litmus/tools/mmdc/mmdc.h"
-#endif
-
-#if LITMUS
-#define SET_UP LOAD_PARAMS SETUP_LITMUS
-#else
-#define SET_UP LOAD_PARAMS
-#endif
-
-#if MMDC_PROF
-#define LOAD_PARAMS LOAD_PARAMS_ITRL SETUP_MMDC
-#else
-#define LOAD_PARAMS LOAD_PARAMS_ITRL
-#endif
-
-// Store state globally so that the job can be outside main()
-// Arrays use float as a comprimise between overflow and size
-// Paired arrays use long longs as precision is more important for those times
-#ifdef PAIRED
-long long *_rt_start_time;
-long long *_rt_end_time;
-#else
-float *_rt_exec_time;
-#endif
-#if MMDC_PERF
-float *_rt_mmdc_read;
-float *_rt_mmdc_write;
-#endif
-long _rt_jobs_complete;
-long _rt_max_jobs;
-int _rt_core;
-int _rt_will_output;
-struct timespec _rt_start, _rt_end;
-
-char *_rt_run_id;
-char *_rt_our_prog_name;
-char *_rt_other_prog_name;
-char *_rt_other_core;
-#define _RT_FILENAME_LEN 64
-#define _BILLION (1000*1000*1000)
-#ifdef PAIRED
-char *_rt_barrier;
-sem_t *_rt_first_sem, *_rt_second_sem;
-int _rt_lock_id;
-#endif
-
-static void _rt_load_params_itrl(int argc, char **argv) {
-#ifdef PAIRED
-    if (argc != 8) {
-        fprintf(stderr, "Usage: %s <name> <loops> <my core> <other core> <other name> <runID> <lockID>", argv[0]);
-        fprintf(stderr, " <name> string for logging. Name of this task.\n");
-        fprintf(stderr, " <loops> integer number of iterations. -1 for infinite.\n");
-        fprintf(stderr, " <my core> UNUSED. Core is now auto-detected.\n");
-        fprintf(stderr, " <other core> integer for logging. Core of paired task.\n");
-        fprintf(stderr, " <other name> string for logging. Name of paired task.\n");
-        fprintf(stderr, " <runID> string to append with .txt to yield output file name.\n");
-        fprintf(stderr, " <lockID> 1 to indicate this is pair member 1, otherwise pair member 2.\n");
-        exit(1);
-    }
-#else
-    if (argc != 6) {
-        fprintf(stderr, "Usage: %s <name> <loops> <my core> <runID> <save results?>\n", argv[0]);
-        fprintf(stderr, " <name> string for logging. Name of this task.\n");
-        fprintf(stderr, " <loops> integer number of iterations. -1 for infinite.\n");
-        fprintf(stderr, " <my core> UNUSED. Core is now auto-detected.\n");
-        fprintf(stderr, " <runID> string to append with .txt to yield output file name.\n");
-        fprintf(stderr, " <save results?> 1 to save results, 0 to discard.\n");
-        exit(1);
-    }
-#endif
-    _rt_our_prog_name = argv[1];
-    _rt_max_jobs = atol(argv[2]);
-    _rt_core = sched_getcpu();
-#ifdef PAIRED
-    _rt_other_core = argv[4];
-    _rt_other_prog_name = argv[5];
-    _rt_run_id = argv[6];
-    _rt_lock_id = atoi(argv[7]);
-    // The paired version doesn't support disabling output (legacy compatibility)
-    _rt_will_output = 1;
-#else
-    _rt_other_core = "none";
-    _rt_other_prog_name = "none";
-    _rt_run_id = argv[4];
-    _rt_will_output = atoi(argv[5]);
-#endif /* PAIRED */
-    if (_rt_max_jobs < 0 && _rt_will_output != 0) {
-        fprintf(stderr, "Infinite loops only supported when _rt_will_output is disabled!\n");
-        exit(1);
-    }
-    if (strlen(_rt_run_id) + 5 > _RT_FILENAME_LEN) {
-        fprintf(stderr, "Run ID is too large! Keep it to less than %d characters.\n", _RT_FILENAME_LEN);
-        exit(1);
-    }
-#ifdef PAIRED
-    _rt_start_time = calloc(_rt_max_jobs * _rt_will_output, sizeof(long long));
-    _rt_end_time = calloc(_rt_max_jobs * _rt_will_output, sizeof(long long));
-    if (!_rt_end_time || !_rt_start_time) {
-        perror("Unable to allocate buffers for execution times");
-        exit(1);
-    }
-    _rt_first_sem = sem_open("/_libextra_first_sem", O_CREAT, 644, 0);
-    _rt_second_sem = sem_open("/_libextra_second_sem", O_CREAT, 644, 0);
-    if (_rt_first_sem == SEM_FAILED || _rt_second_sem == SEM_FAILED) {
-        perror("Error while creating semaphores");
-        exit(1);
-    }
-    int barrier_file = shm_open("/_libextra_barrier", O_CREAT | O_RDWR, 644);
-    if (barrier_file == -1) {
-        perror("Error while creating shared memory for barrier synchronization");
-        exit(1);
-    }
-    if (ftruncate(barrier_file, 1) == -1) {
-        perror("Error while setting size of shared memory for barrier synchronization");
-        exit(1);
-    }
-    _rt_barrier = mmap(NULL, 1, PROT_WRITE, MAP_SHARED, barrier_file, 0);
-    if (_rt_barrier == MAP_FAILED) {
-        perror("Error while mapping shared memory for barrier synchronization");
-        exit(1);
-    }
-    *_rt_barrier = 0;
-#else
-    _rt_exec_time = calloc(_rt_max_jobs * _rt_will_output, sizeof(float));
-    if (!_rt_exec_time) {
-        perror("Unable to allocate buffer for execution times");
-        exit(1);
-    }
-#endif /* PAIRED */
-    _rt_jobs_complete = 0;
-    mlockall(MCL_CURRENT || MCL_FUTURE);
-}
-#define LOAD_PARAMS_ITRL _rt_load_params_itrl(argc, argv);
-
-#define SETUP_MMDC \
-    _rt_mmdc_read = calloc(_rt_max_jobs * _rt_will_output, sizeof(float));\
-    _rt_mmdc_write = calloc(_rt_max_jobs * _rt_will_output, sizeof(float));\
-    if (!_rt_mmdc_read || !_rt_mmdc_write) {\
-        perror("Unable to allocate buffer for MMDC data");\
-        exit(1);\
-    }\
-    MMDC_PROFILE_RES_t mmdc_res;\
-    memset(&mmdc_res, 0, sizeof(MMDC_PROFILE_RES_t));\
-    int fd = open("/dev/mem", O_RDWR, 0);\
-    if (fd < 0) {\
-        perror("Unable to open /dev/mem");\
-        exit(1);\
-    }\
-    pMMDC_t mmdc = mmap(NULL, 0x4000, PROT_READ | PROT_WRITE, MAP_SHARED, fd, MMDC_P0_IPS_BASE_ADDR);\
-    if (mmdc == MAP_FAILED) {\
-        perror("Unable to map MMDC address space");\
-        exit(1);\
-    }\
-    mmdc->madpcr1 = axi_arm1;\
-    msync(&(mmdc->madpcr1),4,MS_SYNC);
-
-#define SETUP_LITMUS \
-    unsigned int wait = 0; \
-    if (be_migrate_to_domain(_rt_core) < 0) { \
-        perror("Unable to migrate to specified CPU"); \
-        exit(1); \
-    } \
-    struct rt_task rt_param; \
-    init_rt_task_param(&rt_param); \
-    /* Supposedly the next two parameters are irrelevant when reservations are enabled, but I'm leaving them anyway... */ \
-    rt_param.exec_cost = ms2ns(999); \
-    rt_param.period = ms2ns(1000); \
-    rt_param.priority = LITMUS_HIGHEST_PRIORITY; \
-    rt_param.cls = RT_CLASS_HARD; \
-    rt_param.release_policy = TASK_PERIODIC; \
-    rt_param.budget_policy = NO_ENFORCEMENT; \
-    rt_param.cpu = _rt_core; \
-    if (set_rt_task_param(gettid(), &rt_param) < 0) { \
-        perror("Unable to set real-time parameters"); \
-        exit(1); \
-    } \
-    if (init_litmus() != 0) { \
-        perror("init_litmus failed"); \
-        exit(1); \
-    } \
-    MC2_SETUP \
-    if (task_mode(LITMUS_RT_TASK) != 0) { \
-        perror("Unable to become real-time task"); \
-        exit(1); \
-    } \
-    if (wait && wait_for_ts_release() != 0) { \
-        perror("Unable to wait for taskset release"); \
-        exit(1); \
-    }
-
-#if MC2
-#define MC2_SETUP \
-
-    set_page_color(rt_param.cpu);
-#else
-#define MC2_SETUP
-#endif
-
-#define CLEANUP_LITMUS \
-    if (task_mode(BACKGROUND_TASK) != 0) { \
-        perror("Unable to become a real-time task"); \
-        exit(1); \
-    } \
-
-#if __arm__
-// On ARM, manually flush the cache
-#define FLUSH_CACHES \
-    volatile uint8_t buffer[L2_SIZE * 4]; \
-    for (uint32_t j = 0; j < 4; j++) \
-        for (uint32_t i = 0; i < L2_SIZE * 4; i += LINE_SIZE) \
-            buffer[i]++;
-#else
-// On x86 call the wbinvld instruction (it's in a kernel module due to it being ring-0)
-#define FLUSH_CACHES \
-    FILE *fp = fopen("/proc/wbinvd", "r");\
-    if (fp == NULL) {\
-        perror("Cache flush module interface cannot be opened");\
-        exit(1);\
-    }\
-    char dummy;\
-    if (fread(&dummy, 1, 1, fp) == 0) {\
-        perror("Unable to access cache flush module interface");\
-        exit(1);\
-    }\
-    fclose(fp);
-#endif
-
-// This semaphore-based synchronization is from Sims
-#define FIRST_UNLOCK \
-    if (_rt_lock_id == 1) {\
-        if (sem_post(_rt_second_sem) != 0) {\
-            perror("Unable to unlock second semaphore");\
-            exit(1);\
-        }\
-    } \
-    else {\
-        if (sem_post(_rt_first_sem) != 0) {\
-            perror("Unable to unlock first semaphore");\
-            exit(1);\
-        }\
-    } \
-
-#define FIRST_LOCK \
-    if (_rt_lock_id == 1) {\
-        if (sem_wait(_rt_first_sem) != 0) {\
-            perror("Unable to wait on first semaphore");\
-            exit(1);\
-        }\
-    }\
-    else {\
-        if (sem_wait(_rt_second_sem) != 0) {\
-            perror("Unable to wait on second semaphore");\
-            exit(1);\
-        }\
-    }
-
-// This ensures a very low difference between pair member start times
-#define BARRIER_SYNC \
-    if (__sync_bool_compare_and_swap(_rt_barrier, 0, 1)) {\
-        while (!__sync_bool_compare_and_swap(_rt_barrier, 0, 0)) {};\
-    }\
-    else {\
-        __sync_bool_compare_and_swap(_rt_barrier, 1, 0);\
-    }
-
-// Buffer timing result from a single job
-static void _rt_save_job_result() {
-    if (_rt_jobs_complete >= _rt_max_jobs) {
-        fprintf(stderr, "Max jobs setting too small! Trying to record job #%ld when we only have space for %ld jobs. Exiting...\n", _rt_jobs_complete, _rt_max_jobs);
-        exit(1);
-    }
-    if (_rt_jobs_complete > -1 && _rt_will_output) {
-#ifdef PAIRED
-        _rt_start_time[_rt_jobs_complete] = _rt_start.tv_sec;
-        _rt_start_time[_rt_jobs_complete] *= _BILLION;
-        _rt_start_time[_rt_jobs_complete] += _rt_start.tv_nsec;
-        _rt_end_time[_rt_jobs_complete] = _rt_end.tv_sec;
-        _rt_end_time[_rt_jobs_complete] *= _BILLION;
-        _rt_end_time[_rt_jobs_complete] += _rt_end.tv_nsec;
-#else
-        _rt_exec_time[_rt_jobs_complete] = _rt_end.tv_sec - _rt_start.tv_sec;
-        _rt_exec_time[_rt_jobs_complete] *= _BILLION;
-        _rt_exec_time[_rt_jobs_complete] += _rt_end.tv_nsec - _rt_start.tv_nsec;
-#endif /* PAIRED */
-#if MMDC_PROF
-        _rt_mmdc_read[_rt_jobs_complete] = mmdc_res.read_bytes;
-        _rt_mmdc_write[_rt_jobs_complete] = mmdc_res.write_bytes;
-#endif
-    }
-}
-
-// Save all buffered timing results to disk
-static void _rt_write_to_file() {
-    char fileName[_RT_FILENAME_LEN];
-    FILE *fp;
-    munlockall();
-    if (!_rt_will_output)
-        goto out;
-    strcpy(fileName, _rt_run_id);
-    strcat(fileName, ".txt");
-    fp = fopen(fileName, "a");
-    if (fp == NULL) {
-        perror("Unable to open output file");
-        exit(1);
-    }
-    // Baseline output uses a similar format with "none" for unused fields
-    for (int i = 0; i < _rt_jobs_complete; i++){
-        fprintf(fp, "%s %s %u %s %ld", _rt_our_prog_name, _rt_other_prog_name,
-            _rt_core, _rt_other_core, _rt_max_jobs);
-#ifdef PAIRED
-        // For unclear legacy reasons, paired tasks emit sec and ns separately
-        fprintf(fp, " %lld %lld %lld %lld",
-            _rt_start_time[i] / _BILLION, _rt_start_time[i] % _BILLION,
-            _rt_end_time[i] / _BILLION, _rt_end_time[i] % _BILLION);
-#else
-        fprintf(fp, " %.f", _rt_exec_time[i]);
-#endif /* PAIRED */
-        fprintf(fp, " %s %d %.f %.f\n",  _rt_run_id, i,
-#if MMDC_PROF
-            _rt_mmdc_read[i], _rt_mmdc_write[i]);
-#else
-            0.0, 0.0);
-#endif /* MMDC_PROF */
-    }
-    fclose(fp);
-out:
-#if LITMUS
-    CLEANUP_LITMUS
-#endif /* LITMUS */
-#ifdef PAIRED
-    munmap(_rt_barrier, 1);
-    shm_unlink("/_libextra_barrier");
-    sem_unlink("/_libextra_first_sem");
-    sem_unlink("/_libextra_second_sem");
-    free(_rt_start_time);
-    free(_rt_end_time);
-#else
-    free(_rt_exec_time);
-#endif /* PAIRED */
-#if MMDC_PROF
-    free(_rt_mmdc_read);
-    free(_rt_mmdc_write);
-#endif /* MMDC_PROF */
-}
-
-// Start a job
-static void _rt_start_loop() {
-#if LITMUS
-    if (sleep_next_period() != 0) {
-        perror("Unable to sleep for next period");
-    }
-#else
-    sched_yield();
-#endif /* LITMUS */
-#ifdef PAIRED
-    FIRST_UNLOCK
-    FIRST_LOCK
-#endif /* PAIRED */
-    FLUSH_CACHES
-#ifdef PAIRED
-    BARRIER_SYNC
-#endif /* PAIRED */
-#if MMDC_PROF
-    /* This disables profiling, resets the counters, clears the overflow bit, and enables profiling */
-    start_mmdc_profiling(mmdc);
-#endif /* MMDC_PROF */
-    clock_gettime(CLOCK_MONOTONIC, &_rt_start);
-}
-
-// Complete a job
-static void _rt_stop_loop() {
-    clock_gettime(CLOCK_MONOTONIC, &_rt_end);
-#if MMDC_PROF
-    /* This freezes the profiling and makes results available */
-    pause_mmdc_profiling(mmdc);
-    get_mmdc_profiling_results(mmdc, &mmdc_res);
-#endif /* MMDC_PROF */
-    _rt_save_job_result();
-    _rt_jobs_complete++;
-}
-
-/****** New API ******
- * Intended structure:
- *
- * |int main(int argc, char **argv) {
- * |  SET_UP
- * |  ...
- * |  for_each_job {
- * |    tacleInit();
- * |    tacleMain();
- * |  }
- * |  WRITE_TO_FILE
- * |}
- *
- * The main() function must call its parameters argc and argv for SET_UP to be
- * able to read them.
- * Only SET_UP necessarily has to be in main().
- *
- * We use some niche C features, here's a quick explaination:
- * 1. The && operator doesn't evaluate the right-hand side of the expression
- *    unless the left side evaluated to true. We use this to only execute 
- *    _rt_start_loop() when the loop will actually run.
- * 2. The comma operator executes the first expression and then throws away the
- *    result. We use this to call our void function from inside a comparison.
- */
-#define for_each_job \
-    for (; _rt_jobs_complete < _rt_max_jobs && (_rt_start_loop(),1); \
-         _rt_stop_loop())
-
-/****** Legacy API ******
- * Intended structure:
- *
- * |int main(int argc, char **argv) {
- * |  SET_UP
- * |  for (jobsComplete=0; jobsComplete<maxJobs; jobsComplete++){
- * |    START_LOOP
- * |    tacleInit();
- * |    tacleMain();
- * |    STOP_LOOP
- * |  }
- * |  WRITE_TO_FILE
- * |  tacleReturn
- * |}
- *
- * The main() function must call its parameters argc and argv for SET_UP to be
- * able to read them.
- */
-static int jobsComplete = 0;
-#define START_LOOP _rt_start_loop();
-#define STOP_LOOP _rt_stop_loop();
-#define WRITE_TO_FILE _rt_write_to_file();
-#define maxJobs _rt_max_jobs
-// Has been part of STOP_LOOP for quite some time
-#define SAVE_RESULTS \
-    #warning "The SAVE_RESULTS macro is deprecated and will soon be removed!";
-// Unclear if SLEEP is used anywhere.
-#define SLEEP \
-    #warning "The SLEEP macro is deprecated and may be removed!" \
-    nanosleep((const struct timespec[]){{0, 1000000}}, NULL);
diff --git a/SD-VBS/common/makefiles/Makefile.common b/SD-VBS/common/makefiles/Makefile.common
index 144adb2..9c28cfc 100644
--- a/SD-VBS/common/makefiles/Makefile.common
+++ b/SD-VBS/common/makefiles/Makefile.common
@@ -18,7 +18,7 @@ endif
 endif
 
 CC=gcc
-override CFLAGS += -DGCC -D$(INPUT) -pthread -DCHECK 
+override CFLAGS += -DGCC -D$(INPUT) -pthread -I../../../../..
 COMMON_DIR := $(TOP_DIR)/common/c
 M_COMMON := $(TOP_DIR)/common/matlab
 M_TOOLBOX=$(TOP_DIR)/common/toolbox
@@ -28,7 +28,11 @@ PRELOAD_TIMES_DIR := $(TOP_DIR)/preload-times/$(BMARK)
 MTIMING_DIR := $(TOP_DIR)/cycles/$(BMARK)
 BMARK_DIR := $(TOP_DIR)/benchmarks/$(BMARK)
 TOOL_DIR := $(TOP_DIR)/tools
-LIBLITMUS := /home/litmus/liblitmus
+LIBLITMUS ?= /home/litmus/liblitmus
+ifneq ($(shell grep "define LITMUS 1" ../../../../../extra.h),)
+        CFLAGS += -I${LIBLITMUS}/include
+        LDFLAGS += -L${LIBLITMUS} -llitmus
+endif
 #The options set below and specific to each benchmark. Disparity takes 2 input images, whereas Tracking can take any >1 input images =.
 
 # Variables exported from the benchmark specific Makefiles:
@@ -55,8 +59,8 @@ COMMON_SRC := $(wildcard $(COMMON_DIR)/*.c)
 # RULES
 
 EXE =
-INCLUDES = -I$(COMMON_DIR) -I$(C_DIR) -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
-COMPILE_C = $(CC) $(CFLAGS) $(INCLUDES) -O2
+INCLUDES = -I$(COMMON_DIR) -I$(C_DIR)
+COMPILE_C = $(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -O2
 #COMPILE_C = $(CC) $(CFLAGS) -DGENERATE_OUTPUT -lm -O2 $(INCLUDES)
 COMPILE_G = $(CC) $(CFLAGS) -g -lm $(INCLUDES)
 COMPILE_PG = $(COMPILE_G) -pg
@@ -107,7 +111,7 @@ compile-preload:
 compile: $(C_SRC)
         @echo 
         @echo -e "Benchmark\t\t- $(BMARK)"
-        @$(COMPILE_C) $(COMMON_SRC) $(C_SRC) -lrt -L$(LIBLITMUS) -llitmus -lm  -w -o $(BMARK)$(EXE)
+        @$(COMPILE_C) $(COMMON_SRC) $(C_SRC) -lrt -lm  -w -o $(BMARK)$(EXE)
 
 compile-prof: $(C_SRC)
         @echo 
diff --git a/SD-VBS/disparity_qcif b/SD-VBS/disparity_qcif
new file mode 120000
index 0000000..9874fe6
--- /dev/null
+++ b/SD-VBS/disparity_qcif
@@ -0,0 +1 @@
+benchmarks/disparity/data/qcif/disparity
\ No newline at end of file
diff --git a/SD-VBS/localization_qcif b/SD-VBS/localization_qcif
new file mode 120000
index 0000000..d81d27e
--- /dev/null
+++ b/SD-VBS/localization_qcif
@@ -0,0 +1 @@
+benchmarks/localization/data/qcif/localization
\ No newline at end of file
diff --git a/SD-VBS/mser_qcif b/SD-VBS/mser_qcif
new file mode 120000
index 0000000..8121c92
--- /dev/null
+++ b/SD-VBS/mser_qcif
@@ -0,0 +1 @@
+benchmarks/mser/data/qcif/mser
\ No newline at end of file
diff --git a/SD-VBS/multi_ncut_qcif b/SD-VBS/multi_ncut_qcif
new file mode 120000
index 0000000..e3f755f
--- /dev/null
+++ b/SD-VBS/multi_ncut_qcif
@@ -0,0 +1 @@
+benchmarks/multi_ncut/data/qcif/multi_ncut
\ No newline at end of file
diff --git a/SD-VBS/sd-vbsNames.txt b/SD-VBS/sd-vbsNames.txt
new file mode 100644
index 0000000..23b168d
--- /dev/null
+++ b/SD-VBS/sd-vbsNames.txt
@@ -0,0 +1,9 @@
+disparity_qcif                  echo -e "./benchmarks/disparity/data/qcif/1.bmp\\n./benchmarks/disparity/data/qcif/2.bmp"
+localization_qcif               echo "./benchmarks/localization/data/qcif/1.txt"
+mser_qcif                               echo "./benchmarks/mser/data/qcif/1.bmp"
+multi_ncut_qcif                 echo "./benchmarks/multi_ncut/data/qcif/1.bmp"
+sift_qcif                               echo "./benchmarks/sift/data/qcif/1.bmp"
+stitch_qcif                             echo "./benchmarks/stitch/data/qcif/1.bmp"
+svm_qcif                                echo -e "./benchmarks/svm/data/qcif/d16trn_1.txt\\n./benchmarks/svm/data/qcif/d16trn_2.txt\\n./benchmarks/svm/data/qcif/d16tst_1.txt\\n./benchmarks/svm/data/qcif/d16tst_2.txt"
+texture_synthesis_qcif  echo "./benchmarks/texture_synthesis/data/qcif/1.bmp"
+tracking_qcif                   echo -e "./benchmarks/tracking/data/qcif/1.bmp\\n./benchmarks/tracking/data/qcif/2.bmp\\n./benchmarks/tracking/data/qcif/3.bmp\\n./benchmarks/tracking/data/qcif/4.bmp"
diff --git a/SD-VBS/sift_qcif b/SD-VBS/sift_qcif
new file mode 120000
index 0000000..724930b
--- /dev/null
+++ b/SD-VBS/sift_qcif
@@ -0,0 +1 @@
+benchmarks/sift/data/qcif/sift
\ No newline at end of file
diff --git a/SD-VBS/stitch_qcif b/SD-VBS/stitch_qcif
new file mode 120000
index 0000000..0b05a84
--- /dev/null
+++ b/SD-VBS/stitch_qcif
@@ -0,0 +1 @@
+benchmarks/stitch/data/qcif/stitch
\ No newline at end of file
diff --git a/SD-VBS/svm_qcif b/SD-VBS/svm_qcif
new file mode 120000
index 0000000..a8dc348
--- /dev/null
+++ b/SD-VBS/svm_qcif
@@ -0,0 +1 @@
+benchmarks/svm/data/qcif/svm
\ No newline at end of file
diff --git a/SD-VBS/texture_synthesis_qcif b/SD-VBS/texture_synthesis_qcif
new file mode 120000
index 0000000..e198a53
--- /dev/null
+++ b/SD-VBS/texture_synthesis_qcif
@@ -0,0 +1 @@
+benchmarks/texture_synthesis/data/qcif/texture_synthesis
\ No newline at end of file
diff --git a/SD-VBS/tracking_qcif b/SD-VBS/tracking_qcif
new file mode 120000
index 0000000..683191e
--- /dev/null
+++ b/SD-VBS/tracking_qcif
@@ -0,0 +1 @@
+benchmarks/tracking/data/qcif/tracking
\ No newline at end of file
diff --git a/dis/disPairs2MbInNames.txt b/dis/disPairs2MbInNames.txt
new file mode 100644
index 0000000..a45ead4
--- /dev/null
+++ b/dis/disPairs2MbInNames.txt
@@ -0,0 +1,6 @@
+field_all                       ./gen_input.py field inputs/Field/in0 2097152
+matrix_all                      ./gen_input.py matrix inputs/Matrix/in0 2097152
+neighborhood_all        ./gen_input.py neighborhood inputs/Neighborhood/in0 2097152
+pointer_all                     ./gen_input.py pointer inputs/Pointer/in0 2097152
+transitive_all          ./gen_input.py transitive inputs/Transitive/in0 2097152
+update_all                      ./gen_input.py update inputs/Update/in0 2097152
diff --git a/extra.h b/extra.h
index 0d700ab..59ae97a 100644
--- a/extra.h
+++ b/extra.h
@@ -29,8 +29,7 @@ extern int sched_getcpu();
 #include <sys/syscall.h>
 #endif
 
-#define LITMUS 1
-#define MC2 0
+#define LITMUS 0
 #define MMDC_PROF 0
 
 #if LITMUS
@@ -202,10 +201,11 @@ static void _rt_load_params_itrl(int argc, char **argv) {
     } \
     struct rt_task rt_param; \
     init_rt_task_param(&rt_param); \
-    /* Supposedly the next two parameters are irrelevant when reservations are enabled, but I'm leaving them anyway... */ \
     rt_param.exec_cost = ms2ns(999); \
     rt_param.period = ms2ns(1000); \
-    rt_param.priority = LITMUS_HIGHEST_PRIORITY; \
+    rt_param.deadline = 0; \
+    rt_param.phase = 0; \
+    rt_param.priority = LITMUS_LOWEST_PRIORITY; \
     rt_param.cls = RT_CLASS_HARD; \
     rt_param.release_policy = TASK_PERIODIC; \
     rt_param.budget_policy = NO_ENFORCEMENT; \
@@ -218,7 +218,6 @@ static void _rt_load_params_itrl(int argc, char **argv) {
         perror("init_litmus failed"); \
         exit(1); \
     } \
-    MC2_SETUP \
     if (task_mode(LITMUS_RT_TASK) != 0) { \
         perror("Unable to become real-time task"); \
         exit(1); \
@@ -228,14 +227,6 @@ static void _rt_load_params_itrl(int argc, char **argv) {
         exit(1); \
     }
 
-#if MC2
-#define MC2_SETUP \
-
-    set_page_color(rt_param.cpu);
-#else
-#define MC2_SETUP
-#endif
-
 #define CLEANUP_LITMUS \
     if (task_mode(BACKGROUND_TASK) != 0) { \
         perror("Unable to become a real-time task"); \
diff --git a/smt_analysis/computeSMTslowdown.py b/smt_analysis/computeSMTslowdown.py
index 2cf58ac..aa7aa21 100755
--- a/smt_analysis/computeSMTslowdown.py
+++ b/smt_analysis/computeSMTslowdown.py
@@ -247,7 +247,7 @@ print(plt.hist(M_vals_to_plot, bins=10))
 ##### BELOW TEXT IS OLD OFFSET CODE (patched) #####
 ## This still works, but is hacky and deprecated ##
 ## PearsonR doesn't work though                  ##
-if not LEVEL_C_ANALYSIS:
+if not LEVEL_C_ANALYSIS and False:
     benchmarkNames = idx_to_name
     benchmarkCount = len(benchmarkNames)
     numJobs = len(paired_times[0][0])