65 files changed, 1196 insertions, 1383 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
+# Ignore SD-VBS binaries
-**/random_walk
-# Ignore misc debug and build outputs
-**/.gdb_history
 **/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/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..ebc7523
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,6 @@
+[submodule "smt_analysis/plotille"]
+        path = smt_analysis/plotille
+        url = https://github.com/tammoippen/plotille.git
+[submodule "wbinvd"]
+        path = wbinvd
+        url = https://github.com/JoshuaJB/wbinvd.git
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 {
-    for_each_job{
+        retDisparity = getDisparity(imleft, imright, WIN_SZ, SHIFT,
-    retDisparity = getDisparity(imleft, imright, WIN_SZ, SHIFT, 
+               minSAD, retDisp, halfWin,
-                   minSAD, retDisp, halfWin,
+               IrightPadded, IleftPadded, Iright_moved,
-                   IrightPadded, IleftPadded, Iright_moved,
+               retSAD, SAD, integralImg,
-                   retSAD, SAD, integralImg,
+               range);
-                   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 {
-    for_each_job{
+        fResetArray(pos,n, 3, 0);
-        fResetArray(pos,n, 3, 0);
+        fResetArray(vel,n, 3, 0);
-        fResetArray(vel,n, 3, 0);
+        fResetArray(ones,n,1,1);
-        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);
+        seg = segment_image(im, sigma, k, min_size, num_ccs, segments, edges, imageOut, tempOut, kernel, edgeWeights, in, ind, u, output);
-        out = seg;
+        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..c0af2d7 100644
--- a/SD-VBS/benchmarks/tracking/src/c/script_tracking.c
+++ b/SD-VBS/benchmarks/tracking/src/c/script_tracking.c
@@ -93,22 +93,18 @@ int main(int argc, char* argv[])
    I2D* images[counter];
    /** Read input image **/
-    for(count=1; count<=counter; count++)
+    for(count=1; count<=counter; count++){
-    {
+        /** Read Image **/
-        /** Read image **/
+        scanf("%s", im1);
-        printf("Input image %d: ", count);
-        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 +226,7 @@ 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/makefiles/Makefile.common b/SD-VBS/common/makefiles/Makefile.common
index 144adb2..964ece6 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),)
+        override CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
+        override 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${LIBLITMUS}/arch/arm/include
+INCLUDES = -I$(COMMON_DIR) -I$(C_DIR)
-COMPILE_C = $(CC) $(CFLAGS) $(INCLUDES) -O2
+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/all_pairs/Makefile b/all_pairs/Makefile
index 0042372..592db70 100644
--- a/all_pairs/Makefile
+++ b/all_pairs/Makefile
@@ -1,7 +1,7 @@
-LIBLITMUS ?= /media/speedy/litmus/liblitmus
+LIBLITMUS ?= /playpen/mc2/liblitmus
 CC ?= gcc
-CFLAGS = -pthread -O2 -I.. -DPAIRED
+override CFLAGS += -pthread -O2 -I.. -DPAIRED
-LDFLAGS = -lrt
+LDFLAGS += -lrt
 COMMON = ../extra.h
 # Handle cases where we're also profiling with the MMDC on the i.MX6Q
@@ -11,8 +11,8 @@ endif
 # Include all the LITMUS^RT headers if we're using it
 ifneq ($(shell grep "define LITMUS 1" ../extra.h),)
-        CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
+        override CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
-        LDFLAGS += -L${LIBLITMUS} -llitmus
+        override LDFLAGS += -L${LIBLITMUS} -llitmus
 endif
 all: bin/cjpeg_wrbmp bin/huff_enc bin/gsm_enc bin/dijkstra bin/h264_dec bin/susan bin/adpcm_enc bin/rijndael_dec bin/huff_dec bin/rijndael_enc bin/gsm_dec bin/anagram bin/epic bin/ammunition bin/g723_enc bin/ndes bin/petrinet bin/statemate bin/cjpeg_transupp bin/mpeg2 bin/fmref bin/audiobeam bin/adpcm_dec
diff --git a/all_pairs/run_all_pairs.sh b/all_pairs/run_all_pairs.sh
deleted file mode 100755
index 2260216..0000000
--- a/all_pairs/run_all_pairs.sh
+++ /dev/null
@@ -1,168 +0,0 @@
-#!/bin/bash
-firstCore=$1
-secondCore=$2
-maxJobs=$3
-userRunID=$4
-tacleNames=tacleNames.txt
-if [ $# -lt 4 ]; then
-    echo "Usage $0 <first core ID> <second core ID> <number of iterations> <run ID> [TACLe names file] [--contend]"
-    exit
-fi
-if [ $# -gt 4 ]; then
-    echo "Using alternate list of TACLe benchmarks from $5"
-    tacleNames=$5
-fi
-if [ "$EUID" -ne 0 ]
-then
-    echo "You need to be root to enable interrupt isolation and real-time execution!"
-    exit
-fi
-echo "Making sure that binaries are up to date..."
-while read i; do
-    make bin/$i
-done < $tacleNames
-echo "Done. Disabling real-time throttling..."
-# Turn off rt throttling
-echo -1 > /proc/sys/kernel/sched_rt_runtime_us
-echo "Done. Redirecting all interrupts to core 0..."
-# Redirect all interrupts to core 0
-i=0
-for IRQ in /proc/irq/*
-do
-    # Skip default_smp_affinity
-    if [ -d $IRQ ]; then
-        irqList[$i]=$(cat $IRQ/smp_affinity_list)
-        echo 0 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
-# Read the names of each benchmark
-j=0
-while read i; do
-    tacleProg[$j]=$i
-    j=$(( $j + 1 ))
-done < $tacleNames
-echo "Done. Checking for wbinvd module..."
-if [[ ! -f "/proc/wbinvd" ]]; then
-    echo "ERROR: wbinvd module not loaded. Exiting..."
-    exit
-fi
-echo "Done. Setting cores $firstCore and $secondCore to 'performance'..."
-echo "performance" > /sys/devices/system/cpu/cpu$firstCore/cpufreq/scaling_governor
-echo "performance" > /sys/devices/system/cpu/cpu$secondCore/cpufreq/scaling_governor
-# Enable L3 isolation
-echo "Done. Enabling L3 isolation..."
-mount -t resctrl resctrl /sys/fs/resctrl
-mkdir -p /sys/fs/resctrl/benchmarks
-echo $firstCore > /sys/fs/resctrl/benchmarks/cpus_list
-echo $secondCore > /sys/fs/resctrl/benchmarks/cpus_list
-# Reset global bandwith control and remove L3 from global
-echo "L3:0=ffff;1=ffff;2=ffff;3=0000" > /sys/fs/resctrl/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/schemata
-# Alloc L3 to benchmark
-echo "L3:0=0000;1=0000;2=0000;3=ffff" > /sys/fs/resctrl/benchmarks/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks/schemata
-echo "Done. Verifying configuration with user..."
-# Generate file name string
-# We append to this as we parse the environment settings
-runID=$(date +"%b%d-%H")
-# Confirm configuration with user
-echo "=== Global Config ==="
-cat /sys/fs/resctrl/schemata
-echo "=== Core $firstCore and $secondCore Config ==="
-cat /sys/fs/resctrl/benchmarks/schemata
-if [[ $6 == "--contend" ]]; then
-    if [[ ! -f "/playpen/mc2/imx6q-thrasher/thrasher" ]]; then
-        echo "ERROR: thrasher binary not fonud. Exiting..."
-        exit
-    fi
-    echo "Will run 6 contending tasks"
-    runID=$runID-c
-else
-    runID=$runID-xc
-fi
-if uname -a | grep -q "mc2"; then
-    echo "MC^2 Autodetected. Cache coloring will be enabled."
-    runID=$runID-i
-else
-    echo "MC^2 not detected. Cache coloring will be DISABLED."
-    runID=$runID-xi
-fi
-if pwd | grep -qi dis; then
-    echo "Autodetected DIS. Will use script-level looping."
-fi
-echo "Results will be saved as $runID-$userRunID-A.txt and $runID-$userRunID-B.txt"
-echo "Press enter to confirm environment, Ctrl-C to exit..."
-read
-# Start contending tasks
-if [[ $6 == "--contend" ]]; then
-    echo "Done. Starting 6 contending tasks..."
-    # Run two contending tasks on each other CCX
-    taskset -c 1 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 2 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 5 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 6 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 9 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 10 /playpen/mc2/imx6q-thrasher/thrasher &
-fi
-sleep 1 # Wait for contending tasks to start
-echo "Done. Beginning benchmarks..."
-num_tests=$(wc -l < $tacleNames)
-for (( i = 0; i < $num_tests ; i++ ))
-do
-    for (( j = $i; j < $num_tests ; j++ ))  #loop through programs
-    do
-        # If using DIS, we have to iterate in the script as DIS won't do it for us
-        pwd | grep -qi dis
-        iters=$(python3 -c "print(int(not "$?")*("$maxJobs"-1))")
-        for ((k=0;k<=iters;k++)); do
-            # Autodetect MC^2
-            if uname -a | grep -q "mc2"; then
-                chrt -r 97 numactl -m 0 taskset -c $firstCore  ./bin/${tacleProg[$i]} ${tacleProg[$i]} $maxJobs $firstCore $secondCore ${tacleProg[$j]} $runID-$userRunID"-A" 1 & PID1=$!;
-                chrt -r 97 numactl -m 1 taskset -c $secondCore ./bin/${tacleProg[$j]} ${tacleProg[$j]} $maxJobs $secondCore $firstCore ${tacleProg[$i]} $runID-$userRunID"-B" 2 & PID2=$!;
-            else
-                chrt -r 97 taskset -c $firstCore  ./bin/${tacleProg[$i]} ${tacleProg[$i]} $maxJobs $firstCore $secondCore ${tacleProg[$j]} $runID-$userRunID-A 1 & PID1=$!;
-                chrt -r 97 taskset -c $secondCore ./bin/${tacleProg[$j]} ${tacleProg[$j]} $maxJobs $secondCore $firstCore ${tacleProg[$i]} $runID-$userRunID-B 2 & PID2=$!;
-            fi
-            wait $PID1 $PID2
-        done
-        echo ${tacleProg[$i]} ${tacleProg[$j]}
-    done
-    echo COMPLETE: ${tacleProg[$i]}
-done
-# End contending tasks
-if [[ $6 == "--contend" ]]; then
-    killall thrasher
-fi
-# Remove semaphores from system
-# Leaving them won't hurt these tests, but would be messy and is bad practice 
-# TODO: Do this directly in the benchmarks. They should clean up after themselves
-./bin/cleanupSemaphores
-# Put smp_affinty back the way it was
-i=0
-for IRQ in /proc/irq/*
-do
-    if [ -d $IRQ ]; then
-        echo ${irqList[$i]} 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
diff --git a/all_pairs/run_all_pairs_L3_ONLY.sh b/all_pairs/run_all_pairs_L3_ONLY.sh
deleted file mode 100755
index 8ed5eeb..0000000
--- a/all_pairs/run_all_pairs_L3_ONLY.sh
+++ /dev/null
@@ -1,170 +0,0 @@
-#!/bin/bash
-firstCore=$1
-secondCore=$2
-maxJobs=$3
-userRunID=$4
-tacleNames=tacleNames.txt
-if [ $# -lt 4 ]; then
-    echo "Usage $0 <first core ID> <second core ID> <number of iterations> <run ID> [TACLe names file] [--contend]"
-    exit
-fi
-if [ $# -gt 4 ]; then
-    echo "Using alternate list of TACLe benchmarks from $5"
-    tacleNames=$5
-fi
-if [ "$EUID" -ne 0 ]
-then
-    echo "You need to be root to enable interrupt isolation and real-time execution!"
-    exit
-fi
-echo "Making sure that binaries are up to date..."
-while read i; do
-    make bin/$i
-done < $tacleNames
-echo "Done. Disabling real-time throttling..."
-# Turn off rt throttling
-echo -1 > /proc/sys/kernel/sched_rt_runtime_us
-echo "Done. Redirecting all interrupts to core 0..."
-# Redirect all interrupts to core 0
-i=0
-for IRQ in /proc/irq/*
-do
-    # Skip default_smp_affinity
-    if [ -d $IRQ ]; then
-        irqList[$i]=$(cat $IRQ/smp_affinity_list)
-        echo 0 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
-# Read the names of each benchmark
-j=0
-while read i; do
-    tacleProg[$j]=$i
-    j=$(( $j + 1 ))
-done < $tacleNames
-echo "Done. Checking for wbinvd module..."
-if [[ ! -f "/proc/wbinvd" ]]; then
-    echo "ERROR: wbinvd module not loaded. Exiting..."
-    exit
-fi
-# Enable L3 isolation
-echo "Done. Enabling L3 isolation..."
-mount -t resctrl resctrl /sys/fs/resctrl
-mkdir -p /sys/fs/resctrl/benchmarks
-mkdir -p /sys/fs/resctrl/benchmarks2
-echo $firstCore > /sys/fs/resctrl/benchmarks/cpus_list
-echo $secondCore > /sys/fs/resctrl/benchmarks2/cpus_list
-# Reset global bandwith control and remove L3 from global
-echo "L3:0=ffff;1=ffff;2=ffff;3=0000" > /sys/fs/resctrl/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/schemata
-# Alloc half L3 to benchmark
-echo "L3:0=0000;1=0000;2=0000;3=ff00" > /sys/fs/resctrl/benchmarks/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks/schemata
-# Alloc other half L3 to benchmark2
-echo "L3:0=0000;1=0000;2=0000;3=00ff" > /sys/fs/resctrl/benchmarks2/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks2/schemata
-echo "Done. Verifying configuration with user..."
-# Generate file name string
-# We append to this as we parse the environment settings
-runID=$(date +"%b%d-%H")
-# Confirm configuration with user
-echo "=== Global Config ==="
-cat /sys/fs/resctrl/schemata
-echo "=== Core $firstCore Config ==="
-cat /sys/fs/resctrl/benchmarks/schemata
-echo "=== Core $secondCore Config ==="
-cat /sys/fs/resctrl/benchmarks2/schemata
-if [[ $6 == "--contend" ]]; then
-    if [[ ! -f "/playpen/mc2/imx6q-thrasher/thrasher" ]]; then
-        echo "ERROR: thrasher binary not found. Exiting..."
-        exit
-    fi
-    echo "Will run 6 contending tasks"
-    runID=$runID-c
-else
-    runID=$runID-xc
-fi
-if uname -a | grep -q "mc2"; then
-    echo "MC^2 Autodetected. Not supported by this script!."
-    exit
-else
-    echo "MC^2 not detected. Cache coloring will be enabled in the L3 only.."
-    runID=$runID-i3
-fi
-if pwd | grep -qi dis; then
-    echo "Autodetected DIS. Will use script-level looping."
-fi
-echo "Results will be saved as $runID-$userRunID-A.txt and $runID-$userRunID-B.txt"
-echo "Press enter to confirm environment, Ctrl-C to exit..."
-read
-# Start contending tasks
-if [[ $6 == "--contend" ]]; then
-    echo "Done. Starting 6 contending tasks..."
-    # Run two contending tasks on each other CCX
-    taskset -c 1 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 2 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 5 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 6 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 9 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 10 /playpen/mc2/imx6q-thrasher/thrasher &
-fi
-sleep 1 # Wait for contending tasks to start
-echo "Done. Beginning benchmarks..."
-num_tests=$(wc -l < $tacleNames)
-for (( i = 0; i < $num_tests ; i++ ))
-do
-    for (( j = $i; j < $num_tests ; j++ ))  #loop through programs
-    do
-        # If using DIS, we have to iterate in the script as DIS won't do it for us
-        pwd | grep -qi dis
-        iters=$(python3 -c "print(int(not "$?")*("$maxJobs"-1))")
-        for ((k=0;k<=iters;k++)); do
-            # Autodetect MC^2
-            if uname -a | grep -q "mc2"; then
-                chrt -r 97 numactl -m 0 taskset -c $firstCore  ./bin/${tacleProg[$i]} ${tacleProg[$i]} $maxJobs $firstCore $secondCore ${tacleProg[$j]} $runID-$userRunID"-A" 1 & PID1=$!;
-                chrt -r 97 numactl -m 1 taskset -c $secondCore ./bin/${tacleProg[$j]} ${tacleProg[$j]} $maxJobs $secondCore $firstCore ${tacleProg[$i]} $runID-$userRunID"-B" 2 & PID2=$!;
-            else
-                chrt -r 97 taskset -c $firstCore  ./bin/${tacleProg[$i]} ${tacleProg[$i]} $maxJobs $firstCore $secondCore ${tacleProg[$j]} $runID-$userRunID-A 1 & PID1=$!;
-                chrt -r 97 taskset -c $secondCore ./bin/${tacleProg[$j]} ${tacleProg[$j]} $maxJobs $secondCore $firstCore ${tacleProg[$i]} $runID-$userRunID-B 2 & PID2=$!;
-            fi
-            wait $PID1 $PID2
-        done
-        echo ${tacleProg[$i]} ${tacleProg[$j]}
-    done
-    echo COMPLETE: ${tacleProg[$i]}
-done
-# End contending tasks
-if [[ $6 == "--contend" ]]; then
-    killall thrasher
-fi
-# Remove semaphores from system
-# Leaving them won't hurt these tests, but would be messy and is bad practice 
-# TODO: Do this directly in the benchmarks. They should clean up after themselves
-./bin/cleanupSemaphores
-# Put smp_affinty back the way it was
-i=0
-for IRQ in /proc/irq/*
-do
-    if [ -d $IRQ ]; then
-        echo ${irqList[$i]} 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
diff --git a/all_pairs/source/anagram/anagram.c b/all_pairs/source/anagram/anagram.c
index fc8b6a8..feb9784 100644
--- a/all_pairs/source/anagram/anagram.c
+++ b/all_pairs/source/anagram/anagram.c
@@ -305,10 +305,10 @@ void anagram_ReadDict( void )
    _Pragma( "loopbound min 1 max 5" )
    while ( anagram_dictionary[ i ][ strlen ] != 0 )
      strlen ++;
-    len += strlen + 2;
+    len += strlen + 3;
  }
-  pchBase = anagram_pchDictionary = ( char * )anagram_malloc( len );
+  pchBase = anagram_pchDictionary = ( char * )anagram_malloc( len + 1 );
  _Pragma( "loopbound min 2279 max 2279" )
  for ( i = 0; i < anagram_DICTWORDS; i ++ ) {
@@ -346,7 +346,7 @@ void anagram_init( void )
 int anagram_return( void )
 {
  int i;
-  char const *answer = "duke rip amy";
+  char const *answer = "duke yip arm";
  for ( i = 0; i < 12; i++ )
    if ( answer[ i ] != anagram_buffer[ i ] )
diff --git a/all_pairs/source/anagram/anagram_stdlib.c b/all_pairs/source/anagram/anagram_stdlib.c
index c766a5e..5c9f3fc 100644
--- a/all_pairs/source/anagram/anagram_stdlib.c
+++ b/all_pairs/source/anagram/anagram_stdlib.c
@@ -126,7 +126,7 @@ void anagram_qsort( void *va, unsigned long n, unsigned long es )
 /* This must be redefined for each new benchmark */
-#define ANAGRAM_HEAP_SIZE 18000
+#define ANAGRAM_HEAP_SIZE 20388
 static char anagram_simulated_heap[ANAGRAM_HEAP_SIZE];
 static unsigned int anagram_freeHeapPos;
diff --git a/all_pairs/source/huff_enc/huff_enc.c b/all_pairs/source/huff_enc/huff_enc.c
index f2db552..6a0b901 100644
--- a/all_pairs/source/huff_enc/huff_enc.c
+++ b/all_pairs/source/huff_enc/huff_enc.c
@@ -153,6 +153,8 @@ void huff_enc_init( void )
 {
  huff_enc_input_pos = 0;
  huff_enc_output_pos = 0;
+  huff_enc_byte_nb_to_write = 0;
+  huff_enc_val_to_write = 0;
 }
diff --git a/all_pairs/source/rijndael_dec/rijndael_dec.c b/all_pairs/source/rijndael_dec/rijndael_dec.c
index c8f606b..5c0bea8 100644
--- a/all_pairs/source/rijndael_dec/rijndael_dec.c
+++ b/all_pairs/source/rijndael_dec/rijndael_dec.c
@@ -68,6 +68,7 @@ void rijndael_dec_init( void )
  rijndael_dec_fin.data = rijndael_dec_data;
  rijndael_dec_fin.size = 32768;
  rijndael_dec_fin.cur_pos = 0;
+  rijndael_dec_checksum = 0;
  unsigned i;
  volatile int x = 0;
diff --git a/all_pairs/tacleNames.txt b/all_pairs/tacleNames.txt
index 8f4845a..2e02966 100644
--- a/all_pairs/tacleNames.txt
+++ b/all_pairs/tacleNames.txt
@@ -1,19 +1,23 @@
 petrinet
-ndes
 statemate
-adpcm_dec
+ndes
+h264_dec
+huff_dec
 cjpeg_wrbmp
+fmref
+audiobeam
+adpcm_dec
 adpcm_enc
+g723_enc
+huff_enc
+gsm_dec
 cjpeg_transupp
-dijkstra
 epic
-fmref
+anagram
-gsm_dec
-h264_dec
-huff_enc
 rijndael_enc
 rijndael_dec
 gsm_enc
 susan
+dijkstra
 ammunition
 mpeg2
diff --git a/baseline/Makefile b/baseline/Makefile
index 40b57f4..a929bc6 100644
--- a/baseline/Makefile
+++ b/baseline/Makefile
@@ -1,6 +1,6 @@
-LIBLITMUS ?= /media/speedy/litmus/liblitmus
+LIBLITMUS ?= /playpen/mc2/liblitmus
 CC ?= gcc
-CFLAGS = -pthread -O2 -I..
+override CFLAGS = -pthread -O2 -I..
 LDFLAGS = -lrt
 COMMON = ../extra.h
@@ -11,8 +11,8 @@ endif
 # Include all the LITMUS^RT headers if we're using it
 ifneq ($(shell grep "define LITMUS 1" ../extra.h),)
-        CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
+        override CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
-        LDFLAGS += -L${LIBLITMUS} -llitmus
+        override LDFLAGS += -L${LIBLITMUS} -llitmus
 endif
 all: bin/cjpeg_wrbmp bin/huff_enc bin/gsm_enc bin/dijkstra bin/h264_dec bin/susan bin/adpcm_enc bin/rijndael_dec bin/huff_dec bin/rijndael_enc bin/gsm_dec bin/anagram bin/epic bin/ammunition bin/g723_enc bin/ndes bin/petrinet bin/statemate bin/cjpeg_transupp bin/mpeg2 bin/fmref bin/audiobeam bin/adpcm_dec
diff --git a/baseline/run_baseline_L3_ONLY.sh b/baseline/run_baseline_L3_ONLY.sh
deleted file mode 100755
index 4183653..0000000
--- a/baseline/run_baseline_L3_ONLY.sh
+++ /dev/null
@@ -1,152 +0,0 @@
-#!/bin/bash
-core=$1
-maxJobs=$2
-userRunID=$3
-tacleNames=tacleNames.txt
-if [ $# -lt 3 ]; then
-    echo "Usage $0 <core ID> <number of iterations> <run ID> [TACLe names file] [--contend]"
-    exit
-fi
-if [ $# -gt 3 ]; then
-    echo "Using alternate list of TACLe benchmarks from $4"
-    tacleNames=$4
-fi
-if [ "$EUID" -ne 0 ]
-then
-    echo "You need to be root to enable interrupt isolation and real-time execution!"
-    exit
-fi
-echo "Making sure that binaries are up to date..."
-while read i; do
-    make bin/$i
-done < $tacleNames
-echo "Done. Disabling real-time throttling..."
-# Turn off rt throttling
-echo -1 > /proc/sys/kernel/sched_rt_runtime_us
-echo "Done. Redirecting all interrupts to core 0..."
-# Redirect all interrupts to core 0
-i=0
-for IRQ in /proc/irq/*
-do
-    # Skip default_smp_affinity
-    if [ -d $IRQ ]; then
-        irqList[$i]=$(cat $IRQ/smp_affinity_list)
-        echo 0 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
-# Read the names of each benchmark
-j=0
-while read i; do
-    tacleProg[$j]=$i
-    j=$(( $j + 1 ))
-done < $tacleNames
-echo "Done. Checking for wbinvd module..."
-if [[ ! -f "/proc/wbinvd" ]]; then
-    echo "ERROR: wbinvd module not loaded. Exiting..."
-    exit
-fi
-# Enable L3 isolation
-echo "Done. Enabling L3 isolation..."
-mount -t resctrl resctrl /sys/fs/resctrl
-mkdir -p /sys/fs/resctrl/benchmarks
-echo $1 > /sys/fs/resctrl/benchmarks/cpus_list
-# Reset global bandwith control and remove L3 from global
-echo "L3:0=ffff;1=ffff;2=ffff;3=0000" > /sys/fs/resctrl/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/schemata
-# Alloc L3 to benchmark
-echo "L3:0=0000;1=0000;2=0000;3=00ff" > /sys/fs/resctrl/benchmarks/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks/schemata
-echo "Done. Verifying configuration with user..."
-# Generate file name string
-# We append to this as we parse the environment settings
-runID=$(date +"%b%d-%H")
-# Confirm configuration with user
-echo "=== Global Config ==="
-cat /sys/fs/resctrl/schemata
-echo "=== Core $1 Config ==="
-cat /sys/fs/resctrl/benchmarks/cpus_list
-cat /sys/fs/resctrl/benchmarks/schemata
-if [[ $5 == "--contend" ]]; then
-    if [[ ! -f "/playpen/mc2/imx6q-thrasher/thrasher" ]]; then
-        echo "ERROR: thrasher binary not fonud. Exiting..."
-        exit
-    fi
-    echo "Will run 6 contending tasks"
-    runID=$runID-c
-else
-    runID=$runID-xc
-fi
-if uname -a | grep -q "mc2"; then
-    echo "MC^2 Autodetected. NOT SUPPORTED. Exiting..."
-    exit
-else
-    echo "MC^2 not detected. 50% L3 allocation enabled."
-    runID=$runID-i3
-fi
-if pwd | grep -qi dis; then
-    echo "Autodetected DIS. Will use script-level looping."
-fi
-echo "Results will be saved as $runID-$userRunID.txt"
-echo "Press enter to confirm environment, Ctrl-C to exit..."
-read
-# Start contending tasks
-if [[ $5 == "--contend" ]]; then
-    echo "Done. Starting 6 contending tasks..."
-    # Run two contending tasks on each other CCX
-    taskset -c 1 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 2 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 5 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 6 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 9 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 10 /playpen/mc2/imx6q-thrasher/thrasher &
-fi
-sleep 1 # Wait for contending tasks to start
-echo "Done. Beginning benchmarks..."
-num_tests=$(wc -l < $tacleNames)
-for (( i = 0; i < $num_tests ; i++ ))
-do
-    # If using DIS, we have to iterate in the script as DIS won't do it for us
-    pwd | grep -qi dis
-    iters=$(python3 -c "print(int(not "$?")*("$maxJobs"-1))")
-    for ((k=0;k<=iters;k++)); do
-        # Check if we're using LITMUS^RT or not
-        if [[ -f source/extra.h ]] && grep -q "#define LITMUS 1" source/extra.h; then
-            ./bin/${tacleProg[$i]} ${tacleProg[$i]} $maxJobs $core $runID-$userRunID 1
-        else
-            # Interleave memory allocations between all nodes (only 1 node w/out MC^2)
-            chrt -r 97 numactl --interleave=all taskset -c $core ./bin/${tacleProg[$i]} ${tacleProg[$i]} $maxJobs $core $runID-$userRunID 1
-        fi
-    done
-    echo COMPLETE: ${tacleProg[$i]}
-done
-# End contending tasks
-if [[ $5 == "--contend" ]]; then
-    killall thrasher
-fi
-# Put smp_affinty back the way it was
-i=0
-for IRQ in /proc/irq/*
-do
-    if [ -d $IRQ ]; then
-        echo ${irqList[$i]} 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
diff --git a/baseline/source/anagram/anagram.c b/baseline/source/anagram/anagram.c
index fc8b6a8..feb9784 100644
--- a/baseline/source/anagram/anagram.c
+++ b/baseline/source/anagram/anagram.c
@@ -305,10 +305,10 @@ void anagram_ReadDict( void )
    _Pragma( "loopbound min 1 max 5" )
    while ( anagram_dictionary[ i ][ strlen ] != 0 )
      strlen ++;
-    len += strlen + 2;
+    len += strlen + 3;
  }
-  pchBase = anagram_pchDictionary = ( char * )anagram_malloc( len );
+  pchBase = anagram_pchDictionary = ( char * )anagram_malloc( len + 1 );
  _Pragma( "loopbound min 2279 max 2279" )
  for ( i = 0; i < anagram_DICTWORDS; i ++ ) {
@@ -346,7 +346,7 @@ void anagram_init( void )
 int anagram_return( void )
 {
  int i;
-  char const *answer = "duke rip amy";
+  char const *answer = "duke yip arm";
  for ( i = 0; i < 12; i++ )
    if ( answer[ i ] != anagram_buffer[ i ] )
diff --git a/baseline/source/anagram/anagram_stdlib.c b/baseline/source/anagram/anagram_stdlib.c
index c766a5e..5c9f3fc 100644
--- a/baseline/source/anagram/anagram_stdlib.c
+++ b/baseline/source/anagram/anagram_stdlib.c
@@ -126,7 +126,7 @@ void anagram_qsort( void *va, unsigned long n, unsigned long es )
 /* This must be redefined for each new benchmark */
-#define ANAGRAM_HEAP_SIZE 18000
+#define ANAGRAM_HEAP_SIZE 20388
 static char anagram_simulated_heap[ANAGRAM_HEAP_SIZE];
 static unsigned int anagram_freeHeapPos;
diff --git a/baseline/source/huff_enc/huff_enc.c b/baseline/source/huff_enc/huff_enc.c
index f2db552..6a0b901 100644
--- a/baseline/source/huff_enc/huff_enc.c
+++ b/baseline/source/huff_enc/huff_enc.c
@@ -153,6 +153,8 @@ void huff_enc_init( void )
 {
  huff_enc_input_pos = 0;
  huff_enc_output_pos = 0;
+  huff_enc_byte_nb_to_write = 0;
+  huff_enc_val_to_write = 0;
 }
diff --git a/baseline/source/rijndael_dec/rijndael_dec.c b/baseline/source/rijndael_dec/rijndael_dec.c
index c8f606b..5c0bea8 100644
--- a/baseline/source/rijndael_dec/rijndael_dec.c
+++ b/baseline/source/rijndael_dec/rijndael_dec.c
@@ -68,6 +68,7 @@ void rijndael_dec_init( void )
  rijndael_dec_fin.data = rijndael_dec_data;
  rijndael_dec_fin.size = 32768;
  rijndael_dec_fin.cur_pos = 0;
+  rijndael_dec_checksum = 0;
  unsigned i;
  volatile int x = 0;
diff --git a/baseline/summarize.py b/baseline/summarize.py
deleted file mode 100755
index 82f82d9..0000000
--- a/baseline/summarize.py
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/python3
-import sys
-f = sys.argv[1]
-res = {}
-mem_res = {}
-memw_res = {}
-samples = {}
-with open(f) as fp:
-    for line in fp:
-        s = line.split()
-        if s[0] not in res:
-            print(s[0])
-            res[s[0]] = int(s[5])
-            mem_res[s[0]] = int(s[8])
-            memw_res[s[0]] = int(s[9])
-            samples[s[0]] =int(s[4])
-        else:
-            res[s[0]] += int(s[5])
-            mem_res[s[0]] += int(s[8])
-            memw_res[s[0]] += int(s[9])
-print("Average times:")
-for r in res.keys():
-    print(res[r]/samples[r])
-print("Average memory read:")
-for r in mem_res.keys():
-    print(mem_res[r]/samples[r])
-print("Average memory write:")
-for r in memw_res.keys():
-    print(memw_res[r]/samples[r])
diff --git a/baseline/tacleNames.txt b/baseline/tacleNames.txt
index 8f4845a..2e02966 100644
--- a/baseline/tacleNames.txt
+++ b/baseline/tacleNames.txt
@@ -1,19 +1,23 @@
 petrinet
-ndes
 statemate
-adpcm_dec
+ndes
+h264_dec
+huff_dec
 cjpeg_wrbmp
+fmref
+audiobeam
+adpcm_dec
 adpcm_enc
+g723_enc
+huff_enc
+gsm_dec
 cjpeg_transupp
-dijkstra
 epic
-fmref
+anagram
-gsm_dec
-h264_dec
-huff_enc
 rijndael_enc
 rijndael_dec
 gsm_enc
 susan
+dijkstra
 ammunition
 mpeg2
diff --git a/dis/Makefile b/dis/Makefile
index df93116..d18761b 100755
--- a/dis/Makefile
+++ b/dis/Makefile
@@ -2,9 +2,9 @@
 # Build the DIS benchmarks with all-pairs or unpaired instrumentation
 # (I know that this Makefile is mildly evil and breaks so many rules
 # that a good Makefile should follow. Sorry - at least I have one.)
-LIBLITMUS ?= /media/speedy/litmus/liblitmus
+LIBLITMUS ?= /playpen/mc2/liblitmus
 CC ?= gcc
-CFLAGS += -pthread -O2 -I..
+override CFLAGS += -pthread -O2 -I..
 LDFLAGS = -lrt -lm
 COMMON = ../extra.h
@@ -15,8 +15,8 @@ endif
 # Include all the LITMUS^RT headers if we're using it
 ifneq ($(shell grep "define LITMUS 1" ../extra.h),)
-        CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
+        override CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
-        LDFLAGS += -L${LIBLITMUS} -llitmus
+        override LDFLAGS += -L${LIBLITMUS} -llitmus
 endif
 all: baseline
diff --git a/dis/bin/field_2mb b/dis/bin/field_2mb
deleted file mode 100755
index 31f2a8d..0000000
--- a/dis/bin/field_2mb
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/bash
-taskset -c 0 ./gen_input.py field inputs/Field/in0 2097152 | ./field $@
diff --git a/dis/bin/matrix_2mb b/dis/bin/matrix_2mb
deleted file mode 100755
index 72710ab..0000000
--- a/dis/bin/matrix_2mb
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/bash
-taskset -c 0 ./gen_input.py matrix inputs/Matrix/in4 2097152 | ./matrix $@ > /dev/null
diff --git a/dis/bin/neighborhood_2mb b/dis/bin/neighborhood_2mb
deleted file mode 100755
index 226bd98..0000000
--- a/dis/bin/neighborhood_2mb
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/bash
-taskset -c 0 ./gen_input.py neighborhood inputs/Neighborhood/in0 2097152 | ./neighborhood $@ > /dev/null
diff --git a/dis/bin/pointer_2mb b/dis/bin/pointer_2mb
deleted file mode 100755
index 3ce8f2b..0000000
--- a/dis/bin/pointer_2mb
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/bash
-taskset -c 0 ./gen_input.py pointer inputs/Pointer/in0 2097152 | ./pointer $@
diff --git a/dis/bin/transitive_2mb b/dis/bin/transitive_2mb
deleted file mode 100755
index b8bcf5a..0000000
--- a/dis/bin/transitive_2mb
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/bash
-taskset -c 0 ./gen_input.py transitive inputs/Transitive/in0 2097152 | ./transitive $@
diff --git a/dis/bin/update_2mb b/dis/bin/update_2mb
deleted file mode 100755
index 3bc33f4..0000000
--- a/dis/bin/update_2mb
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/bash
-taskset -c 0 ./gen_input.py update inputs/Update/in0 2097152 | ./update $@
diff --git a/dis/dis2MbInNames.txt b/dis/dis2MbInNames.txt
new file mode 100644
index 0000000..00e6a22
--- /dev/null
+++ b/dis/dis2MbInNames.txt
@@ -0,0 +1,6 @@
+field                   ./gen_input.py field inputs/Field/in0 2097152
+matrix                  ./gen_input.py matrix inputs/Matrix/in0 2097152
+neighborhood    ./gen_input.py neighborhood inputs/Neighborhood/in0 2097152
+pointer                 ./gen_input.py pointer inputs/Pointer/in0 2097152
+transitive              ./gen_input.py transitive inputs/Transitive/in0 2097152
+update                  ./gen_input.py update inputs/Update/in0 2097152
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/dis/run_dis.sh b/dis/run_dis.sh
deleted file mode 100755
index 78745ec..0000000
--- a/dis/run_dis.sh
+++ /dev/null
@@ -1,92 +0,0 @@
-#!/bin/bash
-core=$1
-maxJobs=$2
-runID=$3
-benchmark=${4,}
-template_input=inputs/$4/in0
-wss_settings=inputs/WSSS
-cache_settings=inputs/caches
-if [ $# -lt 4 ]; then
-    echo "Usage $0 <core ID> <number of iterations> <run ID> <benchmark> [template input] [DIS WSS file] [DIS cache file]"
-    exit
-fi
-if [ $# -gt 4 ]; then
-    echo "Using alternate input template from $5"
-    template_input=$5
-fi
-if [ $# -gt 5 ]; then
-    echo "Using alternate WSS settings from $6"
-    wss_settings=$6
-fi
-if [ $# -gt 6 ]; then
-    echo "Using alternate cache settings from $7"
-    cache_settings=$7
-fi
-echo "Making sure that binary is up to date..."
-make $benchmark
-echo "Done. Disabling real-time throttling..."
-# Turn off rt throttling
-echo -1 > /proc/sys/kernel/sched_rt_runtime_us
-echo "Done. Redirecting all interrupts to core 0..."
-# Redirect all interrupts to core 0
-i=0
-for IRQ in /proc/irq/*
-do
-    # Skip default_smp_affinity
-    if [ -d $IRQ ]; then
-        irqList[$i]=$(cat $IRQ/smp_affinity_list)
-        echo 0 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
-echo "Done. Checking for wbinvd module..."
-if [[ ! -f "/proc/wbinvd" ]]; then
-    echo "ERROR: wbinvd module not loaded. Exiting..."
-    exit
-fi
-# Enable L3 isolation
-echo "Done. Enabling L3 isolation..."
-mount -t resctrl resctrl /sys/fs/resctrl
-mkdir -p /sys/fs/resctrl/benchmarks
-echo $1 > /sys/fs/resctrl/benchmarks/cpus_list
-# Reset global bandwith control and remove L3 from global
-echo "L3:0=ffff;1=ffff;2=ffff;3=0000" > /sys/fs/resctrl/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/schemata
-# Alloc L3 to benchmark
-echo "L3:0=0000;1=0000;2=0000;3=ffff" > /sys/fs/resctrl/benchmarks/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks/schemata
-echo "Done. Beginning benchmarks..."
-# Execute the benchmark for each WSS and cache config
-while read j; do
-    echo $j > /sys/fs/resctrl/benchmarks/schemata
-    while read i; do
-        if grep -q "#define LITMUS 1" ../baseline/source/extra.h; then
-            echo "Using LITMUS-RT!"
-            ./gen_input.py $benchmark $template_input $i | numactl -m 0 ./$benchmark $benchmark-$i-$j $maxJobs $core $runID 1
-        else
-            ./gen_input.py $benchmark $template_input $i | chrt -r 97 numactl -m 0 taskset -c $core ./$benchmark $benchmark-$i-$j $maxJobs $core $runID 1
-        fi
-    done < $wss_settings
-done < $cache_settings
-# Put IRQs back as they were
-i=0
-for IRQ in /proc/irq/*
-do
-    if [ -d $IRQ ]; then
-        echo ${irqList[$i]} 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
diff --git a/dis/setup_mem_and_global.sh b/dis/setup_mem_and_global.sh
deleted file mode 100755
index 6bddb2f..0000000
--- a/dis/setup_mem_and_global.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-# Setup group
-mount -t resctrl resctrl /sys/fs/resctrl
-mkdir -p /sys/fs/resctrl/benchmarks
-echo 15 > /sys/fs/resctrl/benchmarks/cpus_list
-echo 31 > /sys/fs/resctrl/benchmarks/cpus_list
-# Remove mem from global domain and assign to local
-echo "L3:0=ffff;1=ffff;2=ffff;3=0000" > /sys/fs/resctrl/schemata
-echo "L3:0=ffff;1=ffff;2=ffff;3=ffff" > /sys/fs/resctrl/benchmarks/schemata
-if [[ $1 == "--bandwith" ]]; then
-    # Remove bandwidth from global domain
-    echo "MB:0=2;1=2;2=2;3=2" > /sys/fs/resctrl/schemata
-    echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks/schemata
-else
-    # Disable bandwidth control
-    echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/schemata
-    echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks/schemata
-fi
-echo "=== Global Config ==="
-cat /sys/fs/resctrl/schemata
-echo "=== Core 15 & 31 Config ==="
-cat /sys/fs/resctrl/benchmarks/schemata
diff --git a/extra.h b/extra.h
index 8c67b33..8c894f6 100644
--- a/extra.h
+++ b/extra.h
@@ -29,8 +29,13 @@ extern int sched_getcpu();
 #include <sys/syscall.h>
 #endif
+<<<<<<< HEAD
 #define LITMUS 1
 #define MC2 0
+=======
+// This is a proxy for "case study mode" now
+#define LITMUS 0
+>>>>>>> rtas20-wip
 #define MMDC_PROF 0
 #if LITMUS
@@ -41,18 +46,6 @@ extern int sched_getcpu();
 #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
@@ -82,50 +75,72 @@ char *_rt_other_core;
 char *_rt_barrier;
 sem_t *_rt_first_sem, *_rt_second_sem;
 int _rt_lock_id;
+#define _ID_SZ 128
+char _rt_sem1_name[_ID_SZ] = "/_libextra_first_sem-";
+char _rt_sem2_name[_ID_SZ] = "/_libextra_second_sem-";
+char _rt_shm_name[_ID_SZ] = "/_libextra_barrier-";
+#endif /* PAIRED */
+#if LITMUS
+long unsigned int _rt_period;
 #endif
 static void _rt_load_params_itrl(int argc, char **argv) {
 #ifdef PAIRED
-    if (argc != 8) {
+    if (argc != (8 + LITMUS*2) && argc != (9 + LITMUS*2)) {
-        fprintf(stderr, "Usage: %s <name> <loops> <my core> <other core> <other name> <runID> <lockID>", argv[0]);
+        fprintf(stderr, "Usage: %s <name> <loops> <my core> <other core> <other name> <runID> <save results?>", 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) {
+    if (argc != (6 + LITMUS*2)) {
        fprintf(stderr, "Usage: %s <name> <loops> <my core> <runID> <save results?>\n", argv[0]);
+#endif /* PAIRED */
        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, " <my core> integer core number. Only used for LITMUS-RT.\n");
+#ifdef PAIRED
+        fprintf(stderr, " <other core> integer for logging. Core of paired task.\n");
+        fprintf(stderr, " <other name> string for logging. Name of paired task.\n");
+#endif /* PAIRED */
        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");
+#ifdef PAIRED
+        fprintf(stderr, " <pairID> (optional).\n");
+#endif
+#if LITMUS
+        fprintf(stderr, " <task period> in ms\n");
+        fprintf(stderr, " <task criticality level> 0 for Level-A, 1 for Level-B, 2 for Level-C\n");
+#endif /* LITMUS */
        exit(1);
    }
-#endif
    _rt_our_prog_name = argv[1];
    _rt_max_jobs = atol(argv[2]);
+#if !LITMUS
    _rt_core = sched_getcpu();
+#else
+    _rt_core = atoi(argv[3]);
+#endif
 #ifdef PAIRED
    _rt_other_core = argv[4];
    _rt_other_prog_name = argv[5];
    _rt_run_id = argv[6];
-    _rt_lock_id = atoi(argv[7]);
+    _rt_will_output = atoi(argv[7]);
-    // The paired version doesn't support disabling output (legacy compatibility)
+    char *pairId;
-    _rt_will_output = 1;
+    int end;
+    if (argc > 8) {
+        pairId = argv[8];
+        end = 8;
+    } else {
+        pairId = "none";
+        end = 9;
+    }
 #else
    _rt_other_core = "none";
    _rt_other_prog_name = "none";
    _rt_run_id = argv[4];
    _rt_will_output = atoi(argv[5]);
+    int end = 6;
 #endif /* PAIRED */
    if (_rt_max_jobs < 0 && _rt_will_output != 0) {
-        fprintf(stderr, "Infinite loops only supported when _rt_will_output is disabled!\n");
+        fprintf(stderr, "Infinite loops only supported when output is disabled!\n");
        exit(1);
    }
    if (strlen(_rt_run_id) + 5 > _RT_FILENAME_LEN) {
@@ -133,32 +148,54 @@ static void _rt_load_params_itrl(int argc, char **argv) {
        exit(1);
    }
 #ifdef PAIRED
+    // __rt_sem2_name happens to be the longest
+    if (strlen(pairId) + strlen(_rt_sem2_name) > _ID_SZ) {
+        fprintf(stderr, "PairID is too long! Maximum length is %ld characters.\n", _ID_SZ - strlen(_rt_sem2_name));
+        exit(1);
+    }
    _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);
+    // Use PairID to create unique semaphore and shared memory paths
-    _rt_second_sem = sem_open("/_libextra_second_sem", O_CREAT, 644, 0);
+    strcat(_rt_sem1_name, pairId);
+    strcat(_rt_sem2_name, pairId);
+    strcat(_rt_shm_name, pairId);
+    _rt_first_sem = sem_open(_rt_sem1_name, O_CREAT, 644, 0);
+    _rt_second_sem = sem_open(_rt_sem2_name, 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);
+    // Create shared memory for barrier synchronization and infer lock ID
+    int barrier_file = shm_open(_rt_shm_name, O_CREAT | O_RDWR | O_EXCL, 644);
+    if (barrier_file == -1) {
+        // File already existed - we're the 2nd program and thus lock ID 2
+        _rt_lock_id = 2;
+        barrier_file = shm_open(_rt_shm_name, O_CREAT | O_RDWR, 644);
+    } else {
+        _rt_lock_id = 1;
+    }
    if (barrier_file == -1) {
        perror("Error while creating shared memory for barrier synchronization");
        exit(1);
    }
-    if (ftruncate(barrier_file, 1) == -1) {
+    if (ftruncate(barrier_file, 2) == -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);
+    _rt_barrier = mmap(NULL, 2, PROT_WRITE, MAP_SHARED, barrier_file, 0);
    if (_rt_barrier == MAP_FAILED) {
        perror("Error while mapping shared memory for barrier synchronization");
        exit(1);
    }
+    // If we're the 2nd user of this barrier, mark it as in-use
+    if (_rt_lock_id == 2 && !__sync_bool_compare_and_swap(_rt_barrier+1, 0, 1)) {
+        fprintf(stderr, "Pair ID already in use!\n");
+        exit(1);
+    }
    *_rt_barrier = 0;
 #else
    _rt_exec_time = calloc(_rt_max_jobs * _rt_will_output, sizeof(float));
@@ -169,8 +206,46 @@ static void _rt_load_params_itrl(int argc, char **argv) {
 #endif /* PAIRED */
    _rt_jobs_complete = 0;
    mlockall(MCL_CURRENT || MCL_FUTURE);
+#if LITMUS
+    _rt_period = strtoul(argv[end], NULL, 10);
+    unsigned int crit = atoi(argv[end+1]);
+    unsigned int wait = 1;
+    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);
+    rt_param.exec_cost = 0; // We disable budget enforcement, so this doesn't matter
+    rt_param.period = ms2ns(_rt_period);
+    rt_param.relative_deadline = 0;
+    rt_param.phase = 0;
+    rt_param.priority = LITMUS_LOWEST_PRIORITY;
+    rt_param.cls = crit;
+    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);
+    }
+    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);
+    }
+#endif /* LITMUS */
+#if MMDC_PROF
+    SETUP_MMDC
+#endif
 }
-#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));\
@@ -194,6 +269,7 @@ static void _rt_load_params_itrl(int argc, char **argv) {
    mmdc->madpcr1 = axi_arm1;\
    msync(&(mmdc->madpcr1),4,MS_SYNC);
+<<<<<<< HEAD
 #define SETUP_LITMUS \
    unsigned int wait = 0; \
    if (be_migrate_to_domain(_rt_core) < 0) { \
@@ -242,6 +318,8 @@ static void _rt_load_params_itrl(int argc, char **argv) {
        exit(1); \
    } \
+=======
+>>>>>>> rtas20-wip
 #if __arm__
 // On ARM, manually flush the cache
 #define FLUSH_CACHES \
@@ -305,28 +383,28 @@ static void _rt_load_params_itrl(int argc, char **argv) {
 // Buffer timing result from a single job
 static void _rt_save_job_result() {
+    if (!_rt_will_output)
+        return;
    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] = _rt_start.tv_sec;
-        _rt_start_time[_rt_jobs_complete] *= _BILLION;
+    _rt_start_time[_rt_jobs_complete] *= _BILLION;
-        _rt_start_time[_rt_jobs_complete] += _rt_start.tv_nsec;
+    _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] = _rt_end.tv_sec;
-        _rt_end_time[_rt_jobs_complete] *= _BILLION;
+    _rt_end_time[_rt_jobs_complete] *= _BILLION;
-        _rt_end_time[_rt_jobs_complete] += _rt_end.tv_nsec;
+    _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] = _rt_end.tv_sec - _rt_start.tv_sec;
-        _rt_exec_time[_rt_jobs_complete] *= _BILLION;
+    _rt_exec_time[_rt_jobs_complete] *= _BILLION;
-        _rt_exec_time[_rt_jobs_complete] += _rt_end.tv_nsec - _rt_start.tv_nsec;
+    _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_read[_rt_jobs_complete] = mmdc_res.read_bytes;
-        _rt_mmdc_write[_rt_jobs_complete] = mmdc_res.write_bytes;
+    _rt_mmdc_write[_rt_jobs_complete] = mmdc_res.write_bytes;
-#endif
+#endif /* MMDC_PROF */
-    }
 }
 // Save all buffered timing results to disk
@@ -365,13 +443,16 @@ static void _rt_write_to_file() {
    fclose(fp);
 out:
 #if LITMUS
-    CLEANUP_LITMUS
+    if (task_mode(BACKGROUND_TASK) != 0) {
+        perror("Unable to become a real-time task");
+        exit(1);
+    }
 #endif /* LITMUS */
 #ifdef PAIRED
-    munmap(_rt_barrier, 1);
+    munmap(_rt_barrier, 2);
-    shm_unlink("/_libextra_barrier");
+    sem_unlink(_rt_sem1_name);
-    sem_unlink("/_libextra_first_sem");
+    sem_unlink(_rt_sem2_name);
-    sem_unlink("/_libextra_second_sem");
+    shm_unlink(_rt_shm_name);
    free(_rt_start_time);
    free(_rt_end_time);
 #else
@@ -396,7 +477,9 @@ static void _rt_start_loop() {
    FIRST_UNLOCK
    FIRST_LOCK
 #endif /* PAIRED */
+#if !LITMUS
    FLUSH_CACHES
+#endif
 #ifdef PAIRED
    BARRIER_SYNC
 #endif /* PAIRED */
@@ -444,7 +527,7 @@ static void _rt_stop_loop() {
 *    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); \
+    for (; (_rt_max_jobs == -1 || _rt_jobs_complete < _rt_max_jobs) && (_rt_start_loop(),1); \
         _rt_stop_loop())
 /****** Legacy API ******
@@ -466,6 +549,7 @@ static void _rt_stop_loop() {
 * able to read them.
 */
 static int jobsComplete = 0;
+#define SET_UP _rt_load_params_itrl(argc, argv);
 #define START_LOOP _rt_start_loop();
 #define STOP_LOOP _rt_stop_loop();
 #define WRITE_TO_FILE _rt_write_to_file();
diff --git a/run_all_dis.sh b/run_all_dis.sh
deleted file mode 100755
index 5a6b6e1..0000000
--- a/run_all_dis.sh
+++ /dev/null
@@ -1,70 +0,0 @@
-#!/bin/bash
-# Run baselines for all the DIS tasks
-if [ "$EUID" -ne 0 ]
-then
-    echo "You need to be root to enable cache way and interrupt isolation!"
-    exit
-fi
-if uname -a | grep -q "mc2"; then
-    echo "MC^2 detected! Cache isolation will be enabled"
-    iso="i"
-else
-    echo "MC^2 not detected."
-    iso="xi"
-fi
-datestring=$(date +"%b%d-%H")
-if ! grep -q irqaffinity /proc/cmdline; then
-    /playpen/move_interrupts_off_core15.sh
-else
-    echo "performance" > /sys/devices/system/cpu/cpu15/cpufreq/scaling_governor
-fi
-WSSS=WSSS_maxstride2mb
-caches=caches_all
-# Consider re-enabling this only if you're interested in exploring bandwidth effects
-#./setup_mem_and_global.sh
-if [[ $1 == "--contend" ]]; then
-    echo "Will run 6 contending tasks"
-    echo "Files will be named $datestring-<benchmark name>-c-"$iso".txt"
-    echo "Please verify the above settings. Press enter to continue..."
-    read
-    # Run two contending tasks on each other CCX
-    taskset -c 1 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 2 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 5 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 6 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 9 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 10 /playpen/mc2/imx6q-thrasher/thrasher &
-    ./run_dis.sh 15 10 $datestring-field-c-$iso Field inputs/Field/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-field-c-$iso
-    ./run_dis.sh 15 10 $datestring-matrix-c-$iso Matrix inputs/Matrix/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-matrix-c-$iso
-    ./run_dis.sh 15 10 $datestring-neighborhood-c-$iso Neighborhood inputs/Neighborhood/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-neighborhood-c-$iso
-    ./run_dis.sh 15 10 $datestring-pointer-c-$iso Pointer inputs/Pointer/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-pointer-c-$iso
-    ./run_dis.sh 15 10 $datestring-transitive-c-$iso Transitive inputs/Transitive/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-transitive-c-$iso
-    ./run_dis.sh 15 10 $datestring-update-c-$iso Update inputs/Update/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-update-c-$iso
-    killall thrasher
-else
-    echo "Will run no contending tasks (use --contend for contending tasks)"
-    echo "Files will be named $datestring-<benchmark name>-xc-"$iso".txt"
-    echo "Please verify the above settings. Press enter to continue..."
-    read
-    killall thrasher
-    ./run_dis.sh 15 10 $datestring-field-xc-$iso Field inputs/Field/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-field-xc-$iso
-    ./run_dis.sh 15 10 $datestring-matrix-xc-$iso Matrix inputs/Matrix/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-matrix-xc-$iso
-    ./run_dis.sh 15 10 $datestring-neighborhood-xc-$iso Neighborhood inputs/Neighborhood/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-neighborhood-xc-$iso
-    ./run_dis.sh 15 10 $datestring-pointer-xc-$iso Pointer inputs/Pointer/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-pointer-xc-$iso
-    ./run_dis.sh 15 10 $datestring-transitive-xc-$iso Transitive inputs/Transitive/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-transitive-xc-$iso
-    ./run_dis.sh 15 10 $datestring-update-xc-$iso Update inputs/Update/in0 inputs/$WSSS inputs/$caches
-    ./postproc.sh $datestring-update-xc-$iso
-fi
diff --git a/run_all_sd-vbs.sh b/run_all_sd-vbs.sh
new file mode 100755
index 0000000..1f5948d
--- /dev/null
+++ b/run_all_sd-vbs.sh
@@ -0,0 +1,67 @@
+#!/bin/bash
+# Copyright 2020 Joshua Bakita
+# Runs SD-VBS in every configuration needed
+# for the paper and schedulability studies
+maxJobs=$1
+runID=$2
+if [ $# -lt 2 ]; then
+    echo "Usage $0 <number of iterations> <run ID>"
+    exit
+fi
+if [[ "$EUID" != 0 ]]; then
+    echo "You need to be root to enable spatial isolation!"
+    exit
+fi
+date
+# Run the pairs baseline and some comparisons to examine the effect of less cache
+echo "Building benchmarks in unpaired configuration..."
+cd SD-VBS/benchmarks
+make compile -j30 > /dev/null # Suppress noisy output
+cd ..
+echo "Done. Running experiments..."
+# Full L3, full L2 - xi is the baseline for the pairs
+baseXI=SD-VBS/$(date +"%b%d-%H")-c-xi-$runID.txt
+echo "" | ../run_bench.sh -m base -p 15 -l $maxJobs -b sd-vbsNames.txt -B -I xi $runID
+# Half L3, full L2 - i3 sees effect of half L3
+baseI3=SD-VBS/$(date +"%b%d-%H")-c-i3-$runID.txt
+echo "" | ../run_bench.sh -m base -p 15 -l $maxJobs -b sd-vbsNames.txt -B -I i3 $runID
+# Half L3, half L2 - additional effect of half L2
+baseI=SD-VBS/$(date +"%b%d-%H")-c-i-$runID.txt
+echo "" | ../run_bench.sh -m base -p 15 -l $maxJobs -b sd-vbsNames.txt -B -I i $runID
+date
+# Run the Level-C pairs
+pairC=SD-VBS/$(date +"%b%d-%H")-c-xi-async-$runID.txt
+echo "" | ../run_bench.sh -m pair -p 15 -P 31 -l $maxJobs -b sd-vbsNames.txt -B -I xi -A $runID
+date
+# Run the Level-A/-B pairs
+echo "Building benchmarks in paired configuration..."
+cd benchmarks
+make CFLAGS=-DPAIRED compile -j30 > /dev/null # Suppress noisy output
+cd ..
+echo "Done. Continuing experiments..."
+# No cache isolation
+pairXI=SD-VBS/$(date +"%b%d-%H")-c-xi-$runID"-A.txt and -B.txt"
+echo "" | ../run_bench.sh -m pair -p 15 -P 31 -l $maxJobs -b sd-vbsNames.txt -B -I xi $runID
+# Shared L2, split L3
+pairI3=SD-VBS/$(date +"%b%d-%H")-c-i3-$runID"-A.txt and -B.txt"
+echo "" | ../run_bench.sh -m pair -p 15 -P 31 -l $maxJobs -b sd-vbsNames.txt -B -I i3 $runID
+# Split L2, split L3
+pairI=SD-VBS/$(date +"%b%d-%H")-c-i-$runID"-A.txt and -B.txt"
+echo "" | ../run_bench.sh -m pair -p 15 -P 31 -l $maxJobs -b sd-vbsNames.txt -B -I i $runID
+date
+echo "==== DONE ===="
+echo "Results are in:"
+echo "- $baseXI"
+echo "- $baseI3"
+echo "- $baseI"
+echo "- $pairXI"
+echo "- $pairI3"
+echo "- $pairI"
+echo "- $pairC"
diff --git a/run_all_tacle.sh b/run_all_tacle.sh
new file mode 100755
index 0000000..51a9c24
--- /dev/null
+++ b/run_all_tacle.sh
@@ -0,0 +1,62 @@
+#!/bin/bash
+# Copyright 2020 Joshua Bakita
+# Runs TACLeBench in every configuration needed
+# for the paper and schedulability studies
+maxJobs=$1
+runID=$2
+if [ $# -lt 2 ]; then
+    echo "Usage $0 <number of iterations> <run ID>"
+    exit
+fi
+if [[ "$EUID" != 0 ]]; then
+    echo "You need to be root to enable spatial isolation!"
+    exit
+fi
+date
+# Run the pairs baseline and some comparisons to examine the effect of less cache
+cd baseline
+make all -j32
+# Full L3, full L2 - xi is the baseline for the pairs
+baseXI=baseline/$(date +"%b%d-%H")-c-xi-$runID.txt
+echo "" | ../run_bench.sh -m base -p 15 -l $maxJobs -b tacleNames.txt -B -I xi $runID
+# Half L3, full L2 - i3 sees effect of half L3
+baseI3=baseline/$(date +"%b%d-%H")-c-i3-$runID.txt
+echo "" | ../run_bench.sh -m base -p 15 -l $maxJobs -b tacleNames.txt -B -I i3 $runID
+# Half L3, half L2 - additional effect of half L2
+baseI=baseline/$(date +"%b%d-%H")-c-i-$runID.txt
+echo "" | ../run_bench.sh -m base -p 15 -l $maxJobs -b tacleNames.txt -B -I i $runID
+date
+# Run the Level-A/-B pairs
+cd ../all_pairs
+make all -j32
+# No cache isolation
+pairXI=all_pairs/$(date +"%b%d-%H")-c-xi-$runID"-A.txt and -B.txt"
+echo "" | ../run_bench.sh -m pair -p 15 -P 31 -l $maxJobs -b tacleNames.txt -B -I xi $runID
+# Shared L2, split L3
+pairI3=all_pairs/$(date +"%b%d-%H")-c-i3-$runID"-A.txt and -B.txt"
+echo "" | ../run_bench.sh -m pair -p 15 -P 31 -l $maxJobs -b tacleNames.txt -B -I i3 $runID
+# Split L2, split L3
+pairI=all_pairs/$(date +"%b%d-%H")-c-i-$runID"-A.txt and -B.txt"
+echo "" | ../run_bench.sh -m pair -p 15 -P 31 -l $maxJobs -b tacleNames.txt -B -I i $runID
+date
+# Run the Level-C pairs
+cd ../baseline
+pairC=baseline/$(date +"%b%d-%H")-c-xi-async-$runID.txt
+echo "" | ../run_bench.sh -m pair -p 15 -P 31 -l $maxJobs -b tacleNames.txt -B -I xi -A $runID
+date
+echo "==== DONE ===="
+echo "Results are in:"
+echo "- $baseXI"
+echo "- $baseI3"
+echo "- $baseI"
+echo "- $pairXI"
+echo "- $pairI3"
+echo "- $pairI"
+echo "- $pairC"
diff --git a/run_bench.sh b/run_bench.sh
index c5b67b6..ddc6bcc 100755
--- a/run_bench.sh
+++ b/run_bench.sh
@@ -1,30 +1,162 @@
 #!/bin/bash
+# Copyright 2020 Joshua Bakita
+# A unified script for timing:
+# - SMT pairs with synchronous launches (hard real-time methodolgy)
+# - SMT pairs with asynchronous launches (soft real-time methodolgy)
+# - Unpaired tasks
+# - The cache alloc vs WSS setting exploration for DIS
+# These can all be done with:
+# - No cache management
+# - L3 cache splitting
+# - L2+L3 cache splitting (if OS supported)
-core=$1
+if grep -q "#define LITMUS 1" ../extra.h ./extra.h 2> /dev/null; then
-maxJobs=$2
+    LITMUS=1
-userRunID=$3
+fi
-tacleNames=tacleNames.txt
+if [ $# -lt 5 ]; then
+    echo "Usage $0 -m MODE -p CPU -l LOOPS -b FILE [-B] [-I] RUN_ID"
+    echo " -m base|dis|pair  Which benchmarking mode to use"
+    echo " -p CPU       Which CPU to run each benchmark on"
+    echo " -l LOOPS     How many loops of each benchmark to do"
+    echo " -b FILE      List of benchmarks to execute. Optional tab-"
+    echo "              delimited 2nd column specifies an input"
+    echo "              generation command (fed to bench via stdin)"
+    echo " -B           Enable background contenders on other CCXes"
+    echo " -I xi|i3|i   Isolation mode: none (xi) (default), way-based"
+    echo "              L3-only (i3), or color-based L2+L3 (i)"
+    echo "Mode base requires no additional options."
+    echo "Mode dis does not support the 2nd col. of -b and needs:"
+    echo " -W FILE      List of working set sizes to pass gen_input.py"
+    echo " -T FILE      Input template to pass to gen_input.py"
+    echo " -C FILE      List of cache configurations to test"
+    echo "Mode pair options:"
+    echo " -P CPU       CPU to run the 2nd benchmark on"
+    echo " -A           Async. (Don't synchronize the pair at job"
+    echo "              boundries.) Typically used SMT in soft realtime"
+fi
+# Name options similarly to rtspin
+while getopts “m:p:l:b:BI:W:T:C:P:A” opt; do
+  case $opt in
+# Required
+    m) mode=$OPTARG ;;
+    p) core=$OPTARG ;;
+    l) maxJobs=$OPTARG ;;
+    b) benchNames=$OPTARG ;;
+# Optional
+    B) contend=1 ;;
+    I) iso_mode=$OPTARG ;;
+# DIS
+    W) wss_settings=$OPTARG ;;
+    T) template_input=$OPTARG ;;
+    C) cache_settings=$OPTARG ;;
+# Pair
+    P) core_two=$OPTARG ;;
+    A) async=1 ;;
+  esac
+done
+# Reset to read operands
+shift $((OPTIND -1))
+userRunID=$1
+# Required argument checking
+if [[ "$mode" != "base" && "$mode" != "dis" && $mode != pair ]]; then
+    echo "Invalid argument: MODE must be either 'base' or 'dis'"
+    exit
+fi
+if [[ ! -v core ]] || [[ ! -v maxJobs ]] || [[ ! -v benchNames ]]; then
+    echo "Missing argument: -p, -l, and -b are required"
+    exit
+fi
+if [[ ! -f "$benchNames" ]]; then
+    echo "Invalid argument: $benchNames des not exist"
+    exit
+fi
+if [[ ! -v userRunID ]]; then
+    echo "Missing argument: RUN_ID is required"
+    exit
+fi
+# DIS argument checking
+if [[ "$mode" == "dis" ]] && [[ ! -v wss_settings || ! -v template_input || -z $cache_settings ]]; then
+    echo "Missing argument: DIS needs -W FILE -T FILE and -C FILE"
+    exit
+fi
+if [[ "$mode" == "dis" ]] && [[ ! -f "$wss_settings" ]]; then
+    echo "Invalid argument: $wss_settings does not exist"
+    exit
+fi
+if [[ "$mode" == "dis" ]] && [[ ! -f "$template_input" ]]; then
+    echo "Invalid argument: $template_input does not exist"
+    exit
+fi
+if [[ "$mode" == "dis" ]] && [[ ! -f "$cache_settings" ]]; then
+    echo "Invalid argument: $cache_settings does not exist"
+    exit
+fi
-if [ $# -lt 3 ]; then
+# Pair argument checking
-    echo "Usage $0 <core ID> <number of iterations> <run ID> [TACLe names file] [--contend]"
+if [[ "$mode" == "pair" && ! -v core_two ]]; then
+    echo "Missing argument: mode=pair reqires -P"
+    exit
+fi
+if [[ "$mode" != "pair" ]] && [[ -v async || -v core_two ]]; then
+    echo "Invalid argument: -A and -P require mode=pair"
    exit
 fi
-if [ $# -gt 3 ]; then
+# Additional checks
-    echo "Using alternate list of TACLe benchmarks from $4"
+if [[ $userRunID == "" ]]; then
-    tacleNames=$4
+    echo "Missing argument: a run ID is required"
+    exit
+fi
+if [[ -v contend && ! -f "/playpen/mc2/imx6q-thrasher/thrasher" ]]; then
+    echo "ERROR: cannot find thrasher binary for -B. Exiting..."
+    exit
+fi
+if [[ $iso_mode == "i" && ! $(uname -a | grep "mc2") ]]; then
+    echo "Isolation mode 'i' requires the MC^2 kernel. Exiting..."
+    exit
 fi
-if [ "$EUID" -ne 0 ]
+# Check permissions and update state
-then
+if [[ "$EUID" != 0 ]]; then
    echo "You need to be root to enable interrupt isolation and real-time execution!"
    exit
 fi
-echo "Making sure that binaries are up to date..."
+echo "Loading benchmark names and input..."
+# Read the names of each benchmark and load input.
+# This might look a bit scary, but all it does is
+# separate the two fields (1 or more tabs in-between),
+# save the benchmark name, and execute the input
+# command (storing its output in-memory for later).
+j=0
+IFS=$'\r\n'
 while read i; do
-    make bin/$i
+    bench[$j]=$(echo $i | tr -s "\t" | cut -f1)
-done < $tacleNames
+    input[$j]=$(eval $(echo $i | tr -s "\t" | cut -s -f2))
+    j=$(( $j + 1 ))
+done < $benchNames
+echo "Making sure that binaries are up to date..."
+for b in ${bench[@]}; do
+    # Build "bin/bench" if bin directory
+    if [[ -d bin ]]; then
+        make bin/$b
+    fi
+    # If that failed, try a different name
+    if [[ "$?" != 0 || ! -d bin ]]; then
+        make $b
+    fi
+    # If bench is still not in bin or curr dir, fail
+    if [[ ! -f "./$b" && ! -f "./bin/$b" ]]; then
+        echo "Unable to find benchmark $b"
+        exit
+    fi
+done
 echo "Done. Disabling real-time throttling..."
 # Turn off rt throttling
@@ -43,12 +175,34 @@ do
    i=$(( $i + 1 ))
 done
-# Read the names of each benchmark
+echo "Done. Creating cleanup handler..."
-j=0
+function cleanup {
-while read i; do
+    # End contending tasks
-    tacleProg[$j]=$i
+    if [[ -v contend ]]; then
-    j=$(( $j + 1 ))
+        killall thrasher
-done < $tacleNames
+    fi
+    # Restore cache access to everyone
+    echo "L3:0=ffff;1=ffff;2=ffff;3=ffff" > /sys/fs/resctrl/schemata
+    if [[ -e /sys/fs/resctrl/benchmarks ]]; then
+        echo "" > /sys/fs/resctrl/benchmarks/cpus_list
+    fi
+    if [[ -e /sys/fs/resctrl/benchmarks2 ]]; then
+        echo "" > /sys/fs/resctrl/benchmarks2/cpus_list
+    fi
+    # Put smp_affinty back the way it was
+    i=0
+    for IRQ in /proc/irq/*
+    do
+        if [ -d $IRQ ]; then
+            echo ${irqList[$i]} 2> /dev/null > $IRQ/smp_affinity_list
+        fi
+        i=$(( $i + 1 ))
+    done
+}
+# This sets the cleanup function to be called when we exit for any reason
+trap cleanup EXIT
 echo "Done. Checking for wbinvd module..."
 if [[ ! -f "/proc/wbinvd" ]]; then
@@ -56,21 +210,51 @@ if [[ ! -f "/proc/wbinvd" ]]; then
    exit
 fi
-echo "Done. Setting cores $firstCore and $secondCore to 'performance'..."
+echo "Done. Setting cores to 'performance'..."
-echo "performance" > /sys/devices/system/cpu/cpu15/cpufreq/scaling_governor
+echo "performance" > /sys/devices/system/cpu/cpu$core/cpufreq/scaling_governor
-echo "performance" > /sys/devices/system/cpu/cpu31/cpufreq/scaling_governo
+if [[ -v core_two ]]; then
+    echo "performance" > /sys/devices/system/cpu/cpu$core_two/cpufreq/scaling_governor
+fi
 # Enable L3 isolation
-echo "Done. Enabling L3 isolation..."
+echo "Done. Setting up L3 isolation..."
 mount -t resctrl resctrl /sys/fs/resctrl
-mkdir -p /sys/fs/resctrl/benchmarks
-echo $1 > /sys/fs/resctrl/benchmarks/cpus_list
 # Reset global bandwith control and remove L3 from global
 echo "L3:0=ffff;1=ffff;2=ffff;3=0000" > /sys/fs/resctrl/schemata
 echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/schemata
 # Alloc L3 to benchmark
-echo "L3:0=0000;1=0000;2=0000;3=ffff" > /sys/fs/resctrl/benchmarks/schemata
+# (this logic is safe when $core_two is empty)
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks/schemata
+if [[ $iso_mode == "i" ]]; then
+    # With "i" we rely on numactl to do isolation
+    # Full L3 access from both cores
+    mkdir -p /sys/fs/resctrl/benchmarks
+    # Must write both at the same time. Appends unsupported!
+    echo $core,$core_two > /sys/fs/resctrl/benchmarks/cpus_list
+    echo "L3:0=0000;1=0000;2=0000;3=ffff" > /sys/fs/resctrl/benchmarks/schemata
+    # But each core is bound to its own numa mem node
+    numa_arg0="--membind=0"
+    numa_arg1="--membind=1"
+elif [[ $iso_mode == "i3" ]]; then
+    # With "i3" we rely on resctrl to do isolation
+    mkdir -p /sys/fs/resctrl/benchmarks
+    mkdir -p /sys/fs/resctrl/benchmarks2
+    echo $core > /sys/fs/resctrl/benchmarks/cpus_list
+    echo $core_two > /sys/fs/resctrl/benchmarks2/cpus_list
+    echo "L3:0=0000;1=0000;2=0000;3=ff00" > /sys/fs/resctrl/benchmarks/schemata
+    echo "L3:0=0000;1=0000;2=0000;3=00ff" > /sys/fs/resctrl/benchmarks2/schemata
+    # Disable numa-based isolation
+    numa_arg0="--interleave=all"
+    numa_arg1="--interleave=all"
+else
+    iso_mode="xi"
+    # No isolation via numactl or resctrl
+    mkdir -p /sys/fs/resctrl/benchmarks
+    echo $core,$core_two > /sys/fs/resctrl/benchmarks/cpus_list
+    echo "L3:0=0000;1=0000;2=0000;3=ffff" > /sys/fs/resctrl/benchmarks/schemata
+    # Disable numa-based isolation
+    numa_arg0="--interleave=all"
+    numa_arg1="--interleave=all"
+fi
 echo "Done. Verifying configuration with user..."
 # Generate file name string
@@ -80,34 +264,47 @@ runID=$(date +"%b%d-%H")
 # Confirm configuration with user
 echo "=== Global Config ==="
 cat /sys/fs/resctrl/schemata
-echo "=== Core $1 Config ==="
+echo "=== NUMA Config ==="
+echo "    '$numa_arg0' and '$numa_arg1'"
+echo "=== Core $(cat /sys/fs/resctrl/benchmarks/cpus_list) Config ==="
 cat /sys/fs/resctrl/benchmarks/schemata
-if [[ $5 == "--contend" ]]; then
+if [[ -v core_two && $(cat /sys/fs/resctrl/benchmarks2/cpus_list) ]]; then
-    if [[ ! -f "/playpen/mc2/imx6q-thrasher/thrasher" ]]; then
+    echo "=== Core $(cat /sys/fs/resctrl/benchmarks2/cpus_list) Config ==="
-        echo "ERROR: thrasher binary not fonud. Exiting..."
+    cat /sys/fs/resctrl/benchmarks2/schemata
-        exit
+fi
-    fi
+if [[ -v contend ]]; then
    echo "Will run 6 contending tasks"
    runID=$runID-c
 else
    runID=$runID-xc
 fi
-if uname -a | grep -q "mc2"; then
-    echo "MC^2 Autodetected. Cache coloring and interleaving will be enabled."
+runID=$runID-$iso_mode
-    runID=$runID-i
+if [[ -v async ]]; then
+    echo "Will use asynchronous job pairing"
+    runID=$runID-async
+fi
+if [[ $mode == "pair" && ! -v async ]]; then
+    echo "Results will be saved as $runID-$userRunID-A.txt and $runID-$userRunID-B.txt"
 else
-    echo "MC^2 not detected."
+    echo "Results will be saved as $runID-$userRunID.txt"
-    runID=$runID-xi
 fi
-if pwd | grep -qi dis; then
-    echo "Autodetected DIS. Will use script-level looping."
+if [[ $core == 0 || "$core_two" == 0 ]]; then
+    echo "!!!!! DANGER !!!!!"
+    echo "! Running real-time tasks on core 0 will conflict with interrupt"
+    echo "! handling and likely freeze your system! Only continue if you know"
+    echo "! exactly what you're doing!!"
+    echo "!!!!!!!!!!!!!!!!!!"
 fi
-echo "Results will be saved as $runID-$userRunID.txt"
 echo "Press enter to confirm environment, Ctrl-C to exit..."
 read
 # Start contending tasks
-if [[ $5 == "--contend" ]]; then
+if [[ -v contend ]]; then
    echo "Done. Starting 6 contending tasks..."
    # Run two contending tasks on each other CCX
    taskset -c 1 /playpen/mc2/imx6q-thrasher/thrasher &
@@ -120,37 +317,82 @@ fi
 sleep 1 # Wait for contending tasks to start
 echo "Done. Beginning benchmarks..."
-num_tests=$(wc -l < $tacleNames)
+# Output coloring
-for (( i = 0; i < $num_tests ; i++ ))
+FAIL_COLOR="\033[0;31m"
-do
+GOOD_COLOR="\033[0;32m"
-    # If using DIS, we have to iterate in the script as DIS won't do it for us
+RESET_COLOR="\033[0m"
-    pwd | grep -qi dis
-    iters=$(python3 -c "print(int(not "$?")*("$maxJobs"-1))")
+# For each benchmark
-    for ((k=0;k<=iters;k++)); do
+for (( i = 0; i < ${#bench[@]} ; i++ )); do
+    # Search for the benchmark in this directory, than /bin
+    if [[ -f ${bench[$i]} ]]; then
+        prefix="."
+    else
+        prefix="./bin"
+    fi
+    if [[ "$mode" == "base" ]]; then
+        # Just run the benchmark if TACLeBench
        # Check if we're using LITMUS^RT or not
-        if [[ -f source/extra.h ]] && grep -q "#define LITMUS 1" source/extra.h; then
+        if [[ -v $LITMUS ]]; then
-            ./bin/${tacleProg[$i]} ${tacleProg[$i]} $maxJobs $core $runID-$userRunID 1
+            echo "${input[$i]}" | numactl $numa_arg0 $prefix/${bench[$i]} ${bench[$i]} $maxJobs $core $runID-$userRunID 1
        else
-            # Interleave memory allocations between all nodes (only 1 node w/out MC^2)
+            # Remember: Unpaired tasks always get access to all colors (so we --interleave all)
-            chrt -r 97 numactl --interleave=all taskset -c $core ./bin/${tacleProg[$i]} ${tacleProg[$i]} $maxJobs $core $runID-$userRunID 1
+            echo "${input[$i]}" | chrt -r 97 numactl $numa_arg0 taskset -c $core $prefix/${bench[$i]} ${bench[$i]} $maxJobs $core $runID-$userRunID 1
-#chrt -r 97 numactl -m 0 taskset -c $core ./bin/${tacleProg[$i]} ${tacleProg[$i]} $maxJobs $core $runID-$userRunID-NOINTERLEAVE 1
        fi
-    done
+    elif [[ "$mode" == "dis" ]]; then
-    echo COMPLETE: ${tacleProg[$i]}
+        # Loop through each WSS and cache config if DIS
-done
+        while read j; do # For cache setting
+            echo $j > /sys/fs/resctrl/benchmarks/schemata
-# End contending tasks
+            while read ii; do # For WSS setting
-if [[ $5 == "--contend" ]]; then
+                if [[ -v $LITMUS ]]; then
-    killall thrasher
+                    ./gen_input.py ${bench[$i]} inputs/${bench[$i]^}/$template_input $ii | numactl $numa_arg0 $prefix/${bench[$i]} $bench[$i]}-$ii-$j $maxJobs $core $runID 1
-fi
+                else
+                    ./gen_input.py ${bench[$i]} inputs/${bench[$i]^}/$template_input $ii | chrt -r 97 numactl $numa_arg0 taskset -c $core $prefix/${bench[$i]} ${bench[$i]}-$ii-$j $maxJobs $core $runID 1
-# Put smp_affinty back the way it was
+                fi
-i=0
+            done < $wss_settings
-for IRQ in /proc/irq/*
+        done < $cache_settings
-do
+    elif [[ "$mode" == "pair" ]]; then
-    if [ -d $IRQ ]; then
+        # Only async truly needs to do all-pairs
-        echo ${irqList[$i]} 2> /dev/null > $IRQ/smp_affinity_list
+        if [[ ! -v async ]]; then
+            start=$i
+        else
+            start=0
+        fi
+        for (( j = $start; j < ${#bench[@]} ; j++ )); do
+            if [[ ! -v async ]]; then
+                # Synchronize between pairs - original hard real-time SMT approach
+                if [[ -v $LITMUS ]]; then
+                    echo "${input[$i]}" | numactl $numa_arg0 taskset -c $core $prefix/${bench[$i]} ${bench[$i]} $maxJobs $core $core_two ${bench[$j]} $runID-$userRunID-A 1 & PID1=$!;
+                    echo "${input[$j]}" | numactl $numa_arg1 taskset -c $core_two $prefix/${bench[$j]} ${bench[$j]} $maxJobs $core_two $core ${bench[$i]} $runID-$userRunID-B 2 & PID2=$!;
+                else
+                    echo "${input[$i]}" | chrt -r 97 numactl $numa_arg0 taskset -c $core $prefix/${bench[$i]} ${bench[$i]} $maxJobs $core $core_two ${bench[$j]} $runID-$userRunID-A 1 & PID1=$!;
+                    echo "${input[$j]}" | chrt -r 97 numactl $numa_arg1 taskset -c $core_two $prefix/${bench[$j]} ${bench[$j]} $maxJobs $core_two $core ${bench[$i]} $runID-$userRunID-B 2 & PID2=$!;
+                fi
+                # We launched them asynchronously, so we have to wait
+                wait $PID1 $PID2
+            else
+                # No synchronization between pairs - original soft real-time SMT approach
+                if [[ -v $LITMUS ]]; then
+                    echo "${input[$j]}" | numactl $numa_arg0 taskset -c $core $prefix/${bench[$j]} ${bench[$j]} -1 $core NULL 0 & PID1=$!;
+                    echo "${input[$i]}" | numactl $numa_arg1 taskset -c $core_two $prefix/${bench[$i]} ${bench[$i]}"+"${bench[$j]} $maxJobs $core_two $runID-$userRunID 1 & PID2=$!;
+                else
+                    echo "${input[$j]}" | chrt -r 97 numactl $numa_arg0 taskset -c $core $prefix/${bench[$j]} ${bench[$j]} -1 $core NULL 0 & PID1=$!;
+                    echo "${input[$i]}" | chrt -r 97 numactl $numa_arg1 taskset -c $core_two $prefix/${bench[$i]} ${bench[$i]}"+"${bench[$j]} $maxJobs $core_two $runID-$userRunID 1 & PID2=$!;
+                fi
+                wait $PID2
+                kill $PID1
+            fi
+            if [[ $? != 0 ]]; then
+                echo -e ${FAIL_COLOR}FAILED${RESET_COLOR}: ${bench[$i]} ${bench[$j]}
+            else
+                echo -e ${GOOD_COLOR}COMPLETE${RESET_COLOR}: ${bench[$i]} ${bench[$j]}
+            fi
+        done
+    fi
+    if [[ $? != 0 ]]; then
+        echo -e ${FAIL_COLOR}FAILED${RESET_COLOR}: ${bench[$i]}
+    else
+        echo -e ${GOOD_COLOR}COMPLETE${RESET_COLOR}: ${bench[$i]}
    fi
-    i=$(( $i + 1 ))
 done
diff --git a/run_dis_cache_vs_wss.sh b/run_dis_cache_vs_wss.sh
new file mode 100755
index 0000000..2a7991e
--- /dev/null
+++ b/run_dis_cache_vs_wss.sh
@@ -0,0 +1,67 @@
+#!/bin/bash
+# Run baselines for all the DIS tasks
+if [ "$EUID" -ne 0 ]
+then
+    echo "You need to be root to enable cache way and interrupt isolation!"
+    exit
+fi
+if uname -a | grep -q "mc2"; then
+    echo "MC^2 detected! Cache isolation will be enabled"
+    iso="i"
+else
+    echo "MC^2 not detected."
+    iso="xi"
+fi
+cd dis
+WSSS=WSSS_maxstride2mb
+caches=caches_all
+if [[ $1 == "--contend" ]]; then
+    echo "Will run 6 contending tasks"
+    echo "Files will be named $datestring-<benchmark name>-10-c-"$iso".txt"
+    echo "Please verify the above settings. Press enter to continue..."
+    read
+    echo "field" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -B -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 field-10
+    ./postproc.sh $datestring-field-10-c-$iso
+    echo "matrix" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -B -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 matrix-10
+    ./postproc.sh $datestring-matrix-10-c-$iso
+    echo "neighborhood" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -B -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 neighborhood-10
+    ./postproc.sh $datestring-neighborhood-10-c-$iso
+    echo "pointer" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -B -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 pointer-10
+    ./postproc.sh $datestring-pointer-10-c-$iso
+    echo "transitive" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -B -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 transitive-10
+    ./postproc.sh $datestring-transitive-10-c-$iso
+    echo "update" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -B -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 update-10
+    ./postproc.sh $datestring-update-10-c-$iso
+else
+    echo "Will run no contending tasks (use --contend for contending tasks)"
+    echo "Files will be named $datestring-<benchmark name>-10-xc-"$iso".txt"
+    echo "Please verify the above settings. Press enter to continue..."
+    read
+    echo "field" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 field-10
+    ./postproc.sh $datestring-field-10-xc-$iso
+    echo "matrix" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 matrix-10
+    ./postproc.sh $datestring-matrix-10-xc-$iso
+    echo "neighborhood" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 neighborhood-10
+    ./postproc.sh $datestring-neighborhood-10-xc-$iso
+    echo "pointer" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 pointer-10
+    ./postproc.sh $datestring-pointer-10-xc-$iso
+    echo "transitive" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 transitive-10
+    ./postproc.sh $datestring-transitive-10-xc-$iso
+    echo "update" > /tmp/disNames.txt
+    ../run_bench.sh -p 15 -l 10 -b /tmp/disNames.txt -W WSSS -C caches -T in0 update-10
+    ./postproc.sh $datestring-update-10-xc-$iso
+fi
diff --git a/run_everything.sh b/run_everything.sh
deleted file mode 100755
index 8d46ad7..0000000
--- a/run_everything.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-maxJobs=$1
-runID=$2
-if [ $# -lt 2 ]; then
-    echo "Usage $0 <number of iterations> <run ID>"
-    exit
-fi
-date
-cd baseline
-make all
-../interference-benchmark/deactivateCoresSMT.bash
-./run_baseline.sh 15 $maxJobs $runID
-date
-cd ../all_pairs
-../../interference-benchmark/activateCores.bash
-make all
-./run_all_pairs.sh 15 31 $maxJobs $runID
-date
diff --git a/run_tacle_rtss20.sh b/run_tacle_rtss20.sh
deleted file mode 100755
index 6770c55..0000000
--- a/run_tacle_rtss20.sh
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/bin/bash
-# Copyright 2020 Joshua Bakita
-# This script runs the baselines and Level-A/B and Level-C all_pairs for TACLe w/out MC^2
-if uname -a | grep -q mc2; then
-    echo "You need to run this without MC^2!"
-    exit
-fi
-if [ "$EUID" -ne 0 ]; then
-    echo "You need to be root to enable interrupt isolation and real-time execution!"
-    exit
-fi
-echo "This will run the contended and uncontended TACLe baseline, all-pairs, and Level-C micro-benchamarks in non-interactive mode."
-echo "Please press enter to confirm (Ctrl-C to abort)..."
-read
-echo "performance" > /sys/devices/system/cpu/cpu15/cpufreq/scaling_governor
-echo "performance" > /sys/devices/system/cpu/cpu31/cpufreq/scaling_governor
-cd baseline
-baseNo=baseline/$(date +"%b%d-%H")-xc-xi-1k.txt
-echo "" | ./run_baseline.sh 15 1001 1k ../all_pairs/tacleNames.txt
-baseYes=baseline/$(date +"%b%d-%H")-c-xi-1k.txt
-echo "" | ./run_baseline.sh 15 1001 1k ../all_pairs/tacleNames.txt --contend
-cd ../all_pairs
-pairsNo=all_pairs/$(date +"%b%d-%H")-xc-xi-1k
-echo "" | ./run_all_pairs.sh 15 31 1001 1k ./tacleNames.txt
-pairsYes=all_pairs/$(date +"%b%d-%H")-c-xi-1k
-echo "" | ./run_all_pairs.sh 15 31 1001 1k ./tacleNames.txt --contend
-cd ../baseline
-echo "" | ../smt_analysis_rtss20/run_all_pairs_Level-C_TACLe.sh 15 31 1001 1k ./tacleNames.txt
-cNo=all_pairs/$(date +"%b%d-%H")-xc-xi-1k-LC-TACLe.txt
-echo "" | ../smt_analysis_rtss20/run_all_pairs_Level-C_TACLe.sh 15 31 1001 1k ./tacleNames.txt --contend
-cYes=all_pairs/$(date +"%b%d-%H")-c-xi-1k-LC-TACLe.txt
-echo "==== DONE ==="
-echo "Results are in:"
-echo "- "$baseNo
-echo "- "$baseYes
-echo "- "$pairsNo" (A/B)"
-echo "- "$pairsYes" (A/B)"
-echo "- "$cNo
-echo "- "$cYes
diff --git a/smt_analysis/computeLCslowdown.py b/smt_analysis/computeLCslowdown.py
new file mode 100755
index 0000000..bcd22da
--- /dev/null
+++ b/smt_analysis/computeLCslowdown.py
@@ -0,0 +1,73 @@
+#!/usr/bin/python3
+import numpy as np
+import sys
+import plotille.plotille as plt
+from libSMT import *
+TIMING_ERROR = 1000 #ns
+ASYNC_FORMAT = False
+def print_usage():
+    print("This program takes in the all-pairs and baseline SMT data and computes the worst-case slowdown against any other task when SMT is enabled.", file=sys.stderr)
+    print("Level-A/B usage: {} <file -A> <file -B> <baseline file>".format(sys.argv[0]), file=sys.stderr)
+    print("Level-C usage: {} <continuous pairs> <baseline file>".format(sys.argv[0]), file=sys.stderr)
+# Check that we got the right number of parameters
+if len(sys.argv) < 3:
+    print_usage()
+    exit()
+if len(sys.argv) > 3:
+    print("Reading file using synchronous pair format...")
+    print("Are you sure you want to do this? For the RTAS'21 paper, L-A/-B pairs should use the other script.")
+    input("Press enter to continue, Ctrl+C to exit...")
+else:
+    print("Reading file using asynchronous pair format...")
+    ASYNC_FORMAT = True
+assert_valid_input_files(sys.argv[1:-1], print_usage)
+# Pull in the data
+if not ASYNC_FORMAT:
+    baseline_times, baseline_sample_cnt, baseline_max_times = load_baseline(sys.argv[3])
+    paired_times, paired_offsets, name_to_idx, idx_to_name = load_paired(sys.argv[1], sys.argv[2], len(list(baseline_times.keys())))
+    for key in baseline_times:
+        print(key,max(baseline_times[key]))
+else:
+    baseline_times, baseline_sample_cnt, baseline_max_times = load_baseline(sys.argv[2])
+    paired_times, name_to_idx, idx_to_name = load_fake_paired(sys.argv[1])
+# We work iff the baseline was run for the same set of benchmarks as the pairs were
+assert_base_and_pair_keys_match(baseline_times, name_to_idx)
+# Only consider benchmarks that are at least an order of magnitude longer than the timing error
+reliableNames = []
+for i in range(0, len(name_to_idx)):
+    benchmark = idx_to_name[i]
+    if min(baseline_times[benchmark]) > TIMING_ERROR * 10:
+        reliableNames.append(benchmark)
+# Compute worst-case SMT slowdown for each benchmark
+print("Bench           Mi")
+# Print rows
+sample_f = np.mean # Change this to np.mean to use mean values in Mi generation
+M_vals = []
+for b1 in reliableNames:
+    print("{:<14.14}:".format(b1), end=" ")
+    max_mi = 0
+    # Scan through everyone we ran against and find our maximum slowdown
+    for b2 in reliableNames:
+        time_with_smt = sample_f(paired_times[name_to_idx[b1]][name_to_idx[b2]])
+        time_wout_smt = sample_f(baseline_times[b1])
+        M = time_with_smt / time_wout_smt
+        max_mi = max(max_mi, M)
+    print("{:>10.3}".format(max_mi), end=" ")
+    M_vals.append(max_mi)
+    print("")
+# Print some statistics about the distribution
+print("Average: {:>5.3} with standard deviation {:>5.3} using `{}`".format(np.mean(M_vals), np.std(M_vals), sample_f.__name__))
+Ms = np.asarray(M_vals, dtype=np.float32)
+print(np.sum(Ms <= 1), "of", len(M_vals), "M_i values are at most one -", 100*np.sum(Ms <= 1)/len(M_vals), "percent")
+print(np.sum(Ms > 2), "of", len(M_vals), "M_i values are greater than two -", 100*np.sum(Ms > 2)/len(M_vals), "percent")
+M_vals_to_plot = Ms
+print(plt.hist(M_vals_to_plot, bins=10))
diff --git a/smt_analysis/computeSMTslowdown.py b/smt_analysis/computeSMTslowdown.py
new file mode 100755
index 0000000..805def1
--- /dev/null
+++ b/smt_analysis/computeSMTslowdown.py
@@ -0,0 +1,155 @@
+#!/usr/bin/python3
+from typing import List, Any
+import numpy as np
+from scipy import stats
+import sys
+import plotille.plotille as plt
+TIMING_ERROR = 1000 #ns
+LEVEL_C_ANALYSIS = False
+from libSMT import *
+def print_usage():
+    print("This program takes in the all-pairs and baseline SMT data and computes how much each program is slowed when SMT in enabled.", file=sys.stderr)
+    print("Level-A/B usage: {} <file -A> <file -B> <baseline file> --cij".format(sys.argv[0]), file=sys.stderr)
+    print("Level-C usage: {} <continuous pairs> <baseline file>".format(sys.argv[0]), file=sys.stderr)
+# Check that we got the right number of parameters
+if len(sys.argv) < 3:
+    print_usage()
+    exit()
+if len(sys.argv) > 3:
+    print("Analyzing results using Level-A/B methodology...")
+else:
+    print("Analyzing results using Level-C methodology...")
+    LEVEL_C_ANALYSIS = True
+assert_valid_input_files(sys.argv[1:-1], print_usage);
+# Print Cij values rather than Mij
+TIMES_ONLY = len(sys.argv) > 4 and "--cij" in sys.argv[4]
+OK_PAIRS_ONLY = len(sys.argv) > 4 and "--cij-ok" in sys.argv[4]
+# Pull in the data
+if not LEVEL_C_ANALYSIS:
+    baseline_times, baseline_sample_cnt, baseline_max_times = load_baseline(sys.argv[3])
+    paired_times, paired_offsets, name_to_idx, idx_to_name = load_paired(sys.argv[1], sys.argv[2], len(list(baseline_times.keys())))
+    for key in baseline_times:
+        print(key,max(baseline_times[key]))
+else:
+    # Paired times use an abuse of the baseline file format
+    baseline_times, baseline_sample_cnt, baseline_max_times = load_baseline(sys.argv[2])
+    paired_times, name_to_idx, idx_to_name = load_fake_paired(sys.argv[1])
+# We work iff the baseline was run for the same set of benchmarks as the pairs were
+assert_base_and_pair_keys_match(baseline_times, name_to_idx)
+# Only consider benchmarks that are at least an order of magnitude longer than the timing error
+reliableNames = []
+for i in range(0, len(name_to_idx)):
+    benchmark = idx_to_name[i]
+    if min(baseline_times[benchmark]) > TIMING_ERROR * 10:
+        reliableNames.append(benchmark)
+# Compute SMT slowdown for each benchmark
+# Output format: table, each row is one benchmark and each column is one benchmark
+#                each cell is base1 + base2*m = pair solved for m, aka (pair - base1) / base2
+# Print table header
+print("Bench          ", end=" ")
+for name in reliableNames:
+    if not TIMES_ONLY: print("{:<10.10}".format(name), end=" ")
+    if TIMES_ONLY: print("{:<12.12}".format(name), end=" ")
+print()
+# Print rows
+sample_f = max # Change this to np.mean to use mean values in Mij generation
+M_vals = []
+for b1 in reliableNames:
+    if not TIMES_ONLY: print("{:<14.14}:".format(b1), end=" ")
+    if TIMES_ONLY: print("{:<14.14}:".format(b1), end=" ")
+    for b2 in reliableNames:
+        if not LEVEL_C_ANALYSIS:
+            Ci = max(sample_f(baseline_times[b1]), sample_f(baseline_times[b2]))
+            Cj = min(sample_f(baseline_times[b1]), sample_f(baseline_times[b2]))
+            Cij = sample_f(paired_times[name_to_idx[b1]][name_to_idx[b2]])
+            if False:
+                M = np.std(paired_times[name_to_idx[b1]][name_to_idx[b2]]) / np.mean(paired_times[name_to_idx[b1]][name_to_idx[b2]])
+            else:
+                M = (Cij - Ci) / Cj
+            if Cij and Cj * 10 > Ci: # We don't pair tasks with more than a 10x difference in length
+                M_vals.append(M)
+                if not TIMES_ONLY: print("{:>10.3}".format(M), end=" ")
+            else:
+                if not TIMES_ONLY: print("{:>10}".format("N/A"), end=" ")
+            if TIMES_ONLY and (not OK_PAIRS_ONLY or Cj * 10 > Ci):
+                print("{:>12}".format(Cij), end=" ")
+            elif OK_PAIRS_ONLY and Cj * 10 <= Ci:
+                print("{:>12}".format("0"), end=" ")
+        else:
+            time_with_smt = sample_f(paired_times[name_to_idx[b1]][name_to_idx[b2]])
+            time_wout_smt = sample_f(baseline_times[b1])
+            M = time_with_smt / time_wout_smt
+            M_vals.append(M)
+            print("{:>10.3}".format(M), end=" ")
+    print("")
+# Print some statistics about the distribution
+print("Average: {:>5.3} with standard deviation {:>5.3} using `{}`".format(np.mean(M_vals), np.std(M_vals), sample_f.__name__))
+Ms = np.asarray(M_vals, dtype=np.float32)
+if not LEVEL_C_ANALYSIS:
+    print(np.sum(Ms <= 0), "of", len(M_vals), "M_i:j values are at most zero -", 100*np.sum(Ms <= 0)/len(M_vals), "percent")
+    print(np.sum(Ms > 1), "of", len(M_vals), "M_i:j values are greater than one -", 100*np.sum(Ms > 1)/len(M_vals), "percent")
+    M_vals_to_plot = Ms[np.logical_and(Ms > 0, Ms <= 1)]
+else:
+    print(np.sum(Ms <= 1), "of", len(M_vals), "M_i:j values are at most one -", 100*np.sum(Ms <= 1)/len(M_vals), "percent")
+    print(np.sum(Ms > 2), "of", len(M_vals), "M_i:j values are greater than two -", 100*np.sum(Ms > 2)/len(M_vals), "percent")
+    M_vals_to_plot = Ms
+print("Using Sim's analysis, average: {:>5.3} with standard deviation {:>5.3} using `{}`".format(np.mean(list(M_vals_to_plot)), np.std(list(M_vals_to_plot)), sample_f.__name__))
+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 and False:
+    benchmarkNames = idx_to_name
+    benchmarkCount = len(benchmarkNames)
+    numJobs = len(paired_times[0][0])
+    reliableNames=["ndes", "cjpeg_wrbmp", "adpcm_enc", "cjpeg_transupp", "epic", "gsm_dec", "h264_dec", "huff_enc", "rijndael_enc", "rijndael_dec", "gsm_enc", "ammunition", "mpeg2"]
+    #stats.pearsonr(time[b1][b2], oList),
+    with open("weakRelPairs_offset.csv", mode="w+") as f3:
+        print("Benchmark1", "Benchmark2", "minOffset", "maxOffset", "meanOffset", "meddOffset", "stdOffset", "minLength", "maxLength", sep=",", file=f3)
+        for b1 in range (0, benchmarkCount):
+            for b2 in range (0, benchmarkCount):
+                if benchmarkNames[b1] in reliableNames and benchmarkNames[b2] in reliableNames:
+                    #exclude last job due to inccurate timing
+                    oList = paired_offsets[b1][b2][:numJobs-1]
+                    jList = paired_times[b1][b2][:numJobs-1]
+#                   plt.scatter(oList, jList)
+#                   plt.title(benchmarkNames[b1] + ", " + benchmarkNames[b2])
+#                   plt.show()
+#                   print(benchmarkNames[b1], benchmarkNames[b2], min(oList), max(oList), np.mean(oList), np.median(oList), np.std(oList), stats.pearsonr(jList, oList), stats.spearmanr(jList, oList),  sep=",", file=f3)
+                    print(benchmarkNames[b1], benchmarkNames[b2], min(oList), max(oList), np.mean(oList), np.median(oList), np.std(oList), min(jList), max(jList),  sep=",", file=f3)
+"""
+#with open("reliableGraphs.csv", mode="x") as f3:
+        for b1 in range(0, benchmarkCount):
+            for b2 in range(0, benchmarkCount):
+                if benchmarkNames[b1] in reliableNames and benchmarkNames[b2] in reliableNames:
+                    oList = offset[b1][b2][:numJobs - 1]
+                    jList=time[b1][b2][:numJobs-1]
+                    # offset, time scatterplot
+                    plt.scatter(oList, jList)
+                    plt.title(benchmarkNames[b1] + " " + benchmarkNames[b2] + " Offsets v. Time")
+                    plt.show()
+                    #time histogram
+                    #plt.hist(jList, bins=10)
+                    #plt.title(benchmarkNames[b1] + benchmarkNames[b2] + "Completion Times")
+                    #plt.show()
+                    #offset histogram
+                    #plt.hist(oList, bins=10)
+                    #plt.title(benchmarkNames[b1] + benchmarkNames[b2] + "Offsets")
+                    #plt.show()
+"""
diff --git a/smt_analysis/libSMT.py b/smt_analysis/libSMT.py
new file mode 100755
index 0000000..cca2fce
--- /dev/null
+++ b/smt_analysis/libSMT.py
@@ -0,0 +1,151 @@
+import numpy as np
+import sys
+import os
+def assert_valid_input_files(names, on_fail):
+    # Check that all input files are valid
+    for f in names:
+        if not os.path.exists(f) or os.path.getsize(f) == 0:
+            print("ERROR: File '{}' does not exist or is empty".format(f), file=sys.stderr);
+            on_fail()
+            exit()
+# This parses the result data from unthreaded timing experiments
+# @param f File name to load
+# @returns res Map of benchmark name to sample count
+# @returns samples Map of benchmark name to list of execution time samples
+# @returns max_res May of benchmark to maximum execution time among all samples for that benchmark
+def load_baseline(f):
+    # constants for columns of baseline data files
+    TOTAL_NS = 5
+    BENCH_NAME = 0
+    SAMPLES = 4
+    # Load baseline data. This logic is based off the summarize programs
+    res = {} # Map of benchmark to list of all execution time samples
+    samples = {} # Map of benchmark name to sample count
+    max_res = {} # Map of benchmark name to maximum execution time
+    with open(f) as fp:
+        for line in fp:
+            s = line.split()
+            if s[BENCH_NAME] not in res:
+                res[s[BENCH_NAME]] = list([int(s[TOTAL_NS])])
+                samples[s[BENCH_NAME]] = int(s[SAMPLES])
+                max_res[s[BENCH_NAME]] = int(s[TOTAL_NS])
+            else:
+                res[s[BENCH_NAME]].append(int(s[TOTAL_NS]))
+                max_res[s[BENCH_NAME]] = max(int(s[TOTAL_NS]), max_res[s[BENCH_NAME]])
+    return res, samples, max_res
+# This parses the result data from paired, threaded timing experiements
+# @param file1 The -A file name
+# @param file2 The -B file name
+# @returns time 2D array of benchmark IDs to list of total container execution times
+# @returns offset 2D array of benchmark IDs to list of differences between the start
+#                 of the first and the start of the second benchmark
+# @returns name_to_idx Map of benchmark names to benchmark IDs
+# @returns idx_to_name List which when indexed with benchmark ID will yield the benchmark name
+def load_paired(file1, file2, benchmarkCount):
+    # constants for columns of paired data files
+    FIRST_PROG = 0
+    SECOND_PROG = 1
+    FIRST_CORE = 2
+    SECOND_CORE = 3
+    TRIALS = 4
+    START_S = 5 # Start seconds
+    START_N = 6 # Start nanoseconds
+    END_S = 7   # End seconds
+    END_N = 8   # End nanoseconds
+    RUN_ID = 9
+    JOB_NUM = 10
+    with open(file1) as f1:
+        numJobs = int(f1.readline().split()[TRIALS])
+    assert numJobs > 0
+    assert benchmarkCount > 0
+    # Total times of each container
+    time=[[[0 for x in range(numJobs)]for y in range(benchmarkCount)]for z in range(benchmarkCount)]
+    # Difference in time between when the first and the second task start in the container
+    offset=[[[0 for x in range(numJobs)]for y in range(benchmarkCount)]for z in range(benchmarkCount)]
+    # Some aggregate counters that we update as we go along
+    avg_off = 0
+    avg_off_samp = 0
+    # Load paired data
+    bench1 = 0 # Index to what's the current first benchmark being examined
+    bench2 = 0 # Index to what's the current second benchmark being examined
+    name_to_idx = {}
+    idx_to_name = [0 for x in range(benchmarkCount)]
+    job_idx = 0
+    with open(file1) as f1, open(file2) as f2:
+        for line1, line2 in zip(f1, f2):
+            lineArr1 = line1.split()
+            lineArr2 = line2.split()
+            start1 = int(lineArr1[START_S]) * 10**9 + int(lineArr1[START_N])
+            start2 = int(lineArr2[START_S]) * 10**9 + int(lineArr2[START_N])
+            minStart = min(start1, start2)
+            end1 = int(lineArr1[END_S]) * 10**9 + int(lineArr1[END_N])
+            end2 = int(lineArr2[END_S]) * 10**9 + int(lineArr2[END_N])
+            maxEnd = max(end1, end2)
+            # Time actually co-scheduled is minEnd - maxStart, but Sims uses a different model
+#            time[bench1][bench2][int(lineArr1[JOB_NUM])] = maxEnd - minStart
+            time[bench1][bench2][job_idx] = maxEnd - minStart
+            if lineArr1[SECOND_PROG] == "h264_dec" and lineArr2[JOB_NUM] == 0:
+                print(maxEnd - minStart)
+            # Compute offset: if first job starts at t=0, when does second start?
+#            offset[bench1][bench2][int(lineArr1[JOB_NUM])] = abs(start2-start1)
+            offset[bench1][bench2][job_idx] = abs(start2-start1)
+            # Compute some running statistics
+            avg_off += abs(start2-start1)
+            avg_off_samp += 1
+            # Increment to the next benchmark, this is weird because of the zip()
+            # This is doubly weird because our results are an upper trianguler matrix
+            if job_idx == numJobs - 1: #int(lineArr1[JOB_NUM]) == numJobs - 1:
+                if bench2 < benchmarkCount-1:
+                    bench2 = bench2 + 1
+                    job_idx = 0
+                else:
+                    name_to_idx[lineArr1[FIRST_PROG]] = bench1
+                    idx_to_name[bench1] = lineArr1[FIRST_PROG]
+                    bench1 = bench1 + 1
+                    bench2 = bench1 # bench1 will never again appear as bench2
+                    job_idx = 0
+            else:
+                job_idx += 1
+    print("Average offset is: " + str(avg_off/avg_off_samp) + "ns")
+    return time, offset, name_to_idx, idx_to_name
+# Paired times use an abuse of the baseline file format
+def load_fake_paired(fake_paired_filename):
+    paired_times_raw, _, _ = load_baseline(fake_paired_filename)
+    benchmarkCount = int(np.sqrt(len(list(paired_times_raw.keys()))))
+    numJobs = len(next(iter(paired_times_raw.values())))
+    paired_times=[[[0 for x in range(numJobs)]for y in range(benchmarkCount)]for z in range(benchmarkCount)]
+    idx_to_name=[]
+    name_to_idx={}
+    bench1 = -1
+    #Generate the indexing approach
+    for pair in sorted(paired_times_raw.keys()):
+        [bench1name, bench2name] = pair.split('+') # Benchmark name is pair concatenated together with a '+' delimiter
+        if bench1 == -1 or bench1name != idx_to_name[-1]:
+            idx_to_name.append(bench1name)
+            name_to_idx[bench1name] = len(idx_to_name) - 1
+            bench1 += 1
+    # Populate the array
+    for bench1 in range(len(idx_to_name)):
+        for bench2 in range(len(idx_to_name)):
+            paired_times[bench1][bench2] = paired_times_raw[idx_to_name[bench1]+"+"+idx_to_name[bench2]]
+    return paired_times, name_to_idx, idx_to_name
+def assert_base_and_pair_keys_match(baseline_times, name_to_idx):
+    if sorted(baseline_times.keys()) != sorted(name_to_idx.keys()):
+        print("ERROR: The baseline and paired experiments were over a different set of benchmarks!", file=sys.stderr)
+        print("Baseline keys:", baseline_times.keys(), file=sys.stderr)
+        print("Paired keys:", name_to_idx.keys(), file=sys.stderr)
+        exit();
diff --git a/smt_analysis/plotille b/smt_analysis/plotille
new file mode 160000
+Subproject 41f50df2f5b499425465f506a9aae5acf1a39c0
diff --git a/smt_analysis_rtss20/run_all_pairs_Level-C_DIS.sh b/smt_analysis_rtss20/run_all_pairs_Level-C_DIS.sh
deleted file mode 100755
index 2ac3fc1..0000000
--- a/smt_analysis_rtss20/run_all_pairs_Level-C_DIS.sh
+++ /dev/null
@@ -1,175 +0,0 @@
-#!/bin/bash
-firstCore=$1
-secondCore=$2
-maxJobs=$3
-userRunID=$4
-tacleNames=tacleNames.txt
-if [ $# -lt 4 ]; then
-    echo "Usage $0 <first core ID> <second core ID> <number of iterations> <run ID> [TACLe names file] [--contend]"
-    exit
-fi
-if [ $# -gt 4 ]; then
-    echo "Using alternate list of TACLe benchmarks from $5"
-    tacleNames=$5
-fi
-if [ "$EUID" -ne 0 ]
-then
-    echo "You need to be root to enable interrupt isolation and real-time execution!"
-    exit
-fi
-echo "Making sure that binaries are up to date..."
-while read i; do
-    make bin/$i
-done < $tacleNames
-echo "Done. Disabling real-time throttling..."
-# Turn off rt throttling
-echo -1 > /proc/sys/kernel/sched_rt_runtime_us
-echo "Done. Redirecting all interrupts to core 0..."
-# Redirect all interrupts to core 0
-i=0
-for IRQ in /proc/irq/*
-do
-    # Skip default_smp_affinity
-    if [ -d $IRQ ]; then
-        irqList[$i]=$(cat $IRQ/smp_affinity_list)
-        echo 0 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
-# Read the names of each benchmark
-j=0
-while read i; do
-    tacleProg[$j]=$i
-    j=$(( $j + 1 ))
-done < $tacleNames
-echo "Done. Checking for wbinvd module..."
-if [[ ! -f "/proc/wbinvd" ]]; then
-    echo "ERROR: wbinvd module not loaded. Exiting..."
-    exit
-fi
-# Enable L3 isolation
-echo "Done. Enabling L3 isolation..."
-mount -t resctrl resctrl /sys/fs/resctrl
-mkdir -p /sys/fs/resctrl/benchmarks
-echo $firstCore > /sys/fs/resctrl/benchmarks/cpus_list
-echo $secondCore > /sys/fs/resctrl/benchmarks/cpus_list
-# Reset global bandwith control and remove L3 from global
-echo "L3:0=ffff;1=ffff;2=ffff;3=0000" > /sys/fs/resctrl/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/schemata
-# Alloc L3 to benchmark
-echo "L3:0=0000;1=0000;2=0000;3=ffff" > /sys/fs/resctrl/benchmarks/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks/schemata
-echo "Done. Verifying configuration with user..."
-# Generate file name string
-# We append to this as we parse the environment settings
-runID=$(date +"%b%d-%H")
-# Confirm configuration with user
-echo "=== Global Config ==="
-cat /sys/fs/resctrl/schemata
-echo "=== Core $firstCore and $secondCore Config ==="
-cat /sys/fs/resctrl/benchmarks/schemata
-if [[ $6 == "--contend" ]]; then
-    if [[ ! -f "/playpen/mc2/imx6q-thrasher/thrasher" ]]; then
-        echo "ERROR: thrasher binary not fonud. Exiting..."
-        exit
-    fi
-    echo "Will run 6 contending tasks"
-    runID=$runID-c
-else
-    runID=$runID-xc
-fi
-if uname -a | grep -q "mc2"; then
-    echo "MC^2 Autodetected. Cache coloring will be DISABLED."
-    runID=$runID-i
-else
-    echo "MC^2 not detected. Cache coloring will be DISABLED."
-    runID=$runID-xi
-fi
-echo "Results will be saved as $runID-$userRunID-LC-DIS.txt"
-echo "Press enter to confirm environment, Ctrl-C to exit..."
-read
-# Start contending tasks
-if [[ $6 == "--contend" ]]; then
-    echo "Done. Starting 6 contending tasks..."
-    # Run two contending tasks on each other CCX
-    taskset -c 1 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 2 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 5 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 6 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 9 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 10 /playpen/mc2/imx6q-thrasher/thrasher &
-fi
-sleep 1 # Wait for contending tasks to start
-echo "Done. Beginning benchmarks..."
-num_tests=$(wc -l < $tacleNames)
-for (( i = 0; i < $num_tests ; i++ ))
-do
-    # For level-C analysis, we must run all vs all
-    for (( j = 0; j < $num_tests ; j++ ))  #loop through programs
-    do
-        # Autodetect MC^2
-        # Get DIS to loop continuously in the background by infinite restarts
-        if uname -a | grep -q "mc2"; then
-            bash -c "while true; do  chrt -r 97 numactl --interleave=all taskset -c $firstCore  ./bin/${tacleProg[$i]} NULL -1 $firstCore NULL 0 &> /dev/null; done" & PID1=$!;
-        else
-            bash -c "while true; do  chrt -r 97 taskset -c $firstCore  ./bin/${tacleProg[$i]} NULL -1 $firstCore NULL 0 &> /dev/null; done" & PID1=$!;
-        fi
-        # Each sample runs in its own process
-        for ((k=0;k<=maxJobs;k++)); do
-            if uname -a | grep -q "mc2"; then
-                chrt -r 97 numactl --interleave=all taskset -c $secondCore ./bin/${tacleProg[$i]} ${tacleProg[$i]}"+"${tacleProg[$j]} $maxJobs $secondCore $runID-$userRunID-LC-DIS 1 & PID2=$!;
-            else
-                chrt -r 97 taskset -c $secondCore ./bin/${tacleProg[$i]} ${tacleProg[$i]}"+"${tacleProg[$j]} $maxJobs $secondCore $runID-$userRunID-LC-DIS 1 & PID2=$!;
-            fi
-        done
-        # The paired task runs continuously in this configuration, so we have
-        # to kill it once the task that we're measuring finishes.
-        wait $PID2
-        kill $PID1
-        # Killing bash will not kill its children by default - work aronud that here
-        killall transitive &> /dev/null
-        killall matrix &> /dev/null
-        killall pointer &> /dev/null
-        killall field &> /dev/null
-        killall neighborhood &> /dev/null
-        killall update &> /dev/null
-        killall gen_input.py &> /dev/null
-        echo ${tacleProg[$i]} ${tacleProg[$j]}
-    done
-    echo COMPLETE: ${tacleProg[$i]}
-done
-# End contending tasks
-if [[ $6 == "--contend" ]]; then
-    killall thrasher
-fi
-# Remove semaphores from system
-# Leaving them won't hurt these tests, but would be messy and is bad practice 
-# TODO: Do this directly in the benchmarks. They should clean up after themselves
-./bin/cleanupSemaphores
-# Put smp_affinty back the way it was
-i=0
-for IRQ in /proc/irq/*
-do
-    if [ -d $IRQ ]; then
-        echo ${irqList[$i]} 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
diff --git a/smt_analysis_rtss20/run_all_pairs_Level-C_TACLe.sh b/smt_analysis_rtss20/run_all_pairs_Level-C_TACLe.sh
deleted file mode 100755
index 923dba0..0000000
--- a/smt_analysis_rtss20/run_all_pairs_Level-C_TACLe.sh
+++ /dev/null
@@ -1,161 +0,0 @@
-#!/bin/bash
-firstCore=$1
-secondCore=$2
-maxJobs=$3
-userRunID=$4
-tacleNames=tacleNames.txt
-if [ $# -lt 4 ]; then
-    echo "Usage $0 <first core ID> <second core ID> <number of iterations> <run ID> [TACLe names file] [--contend]"
-    exit
-fi
-if [ $# -gt 4 ]; then
-    echo "Using alternate list of TACLe benchmarks from $5"
-    tacleNames=$5
-fi
-if [ "$EUID" -ne 0 ]
-then
-    echo "You need to be root to enable interrupt isolation and real-time execution!"
-    exit
-fi
-echo "Making sure that binaries are up to date..."
-while read i; do
-    make bin/$i
-done < $tacleNames
-echo "Done. Disabling real-time throttling..."
-# Turn off rt throttling
-echo -1 > /proc/sys/kernel/sched_rt_runtime_us
-echo "Done. Redirecting all interrupts to core 0..."
-# Redirect all interrupts to core 0
-i=0
-for IRQ in /proc/irq/*
-do
-    # Skip default_smp_affinity
-    if [ -d $IRQ ]; then
-        irqList[$i]=$(cat $IRQ/smp_affinity_list)
-        echo 0 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
-# Read the names of each benchmark
-j=0
-while read i; do
-    tacleProg[$j]=$i
-    j=$(( $j + 1 ))
-done < $tacleNames
-echo "Done. Checking for wbinvd module..."
-if [[ ! -f "/proc/wbinvd" ]]; then
-    echo "ERROR: wbinvd module not loaded. Exiting..."
-    exit
-fi
-# Enable L3 isolation
-echo "Done. Enabling L3 isolation..."
-mount -t resctrl resctrl /sys/fs/resctrl
-mkdir -p /sys/fs/resctrl/benchmarks
-echo $firstCore > /sys/fs/resctrl/benchmarks/cpus_list
-echo $secondCore > /sys/fs/resctrl/benchmarks/cpus_list
-# Reset global bandwith control and remove L3 from global
-echo "L3:0=ffff;1=ffff;2=ffff;3=0000" > /sys/fs/resctrl/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/schemata
-# Alloc L3 to benchmark
-echo "L3:0=0000;1=0000;2=0000;3=ffff" > /sys/fs/resctrl/benchmarks/schemata
-echo "MB:0=2048;1=2048;2=2048;3=2048" > /sys/fs/resctrl/benchmarks/schemata
-echo "Done. Verifying configuration with user..."
-# Generate file name string
-# We append to this as we parse the environment settings
-runID=$(date +"%b%d-%H")
-# Confirm configuration with user
-echo "=== Global Config ==="
-cat /sys/fs/resctrl/schemata
-echo "=== Core $firstCore and $secondCore Config ==="
-cat /sys/fs/resctrl/benchmarks/schemata
-if [[ $6 == "--contend" ]]; then
-    if [[ ! -f "/playpen/mc2/imx6q-thrasher/thrasher" ]]; then
-        echo "ERROR: thrasher binary not fonud. Exiting..."
-        exit
-    fi
-    echo "Will run 6 contending tasks"
-    runID=$runID-c
-else
-    runID=$runID-xc
-fi
-if uname -a | grep -q "mc2"; then
-    echo "MC^2 Autodetected. Cache coloring will be DISABLED."
-    runID=$runID-i
-else
-    echo "MC^2 not detected. Cache coloring will be DISABLED."
-    runID=$runID-xi
-fi
-echo "Results will be saved as $runID-$userRunID-LC-TACLe.txt"
-echo "Press enter to confirm environment, Ctrl-C to exit..."
-read
-# Start contending tasks
-if [[ $6 == "--contend" ]]; then
-    echo "Done. Starting 6 contending tasks..."
-    # Run two contending tasks on each other CCX
-    taskset -c 1 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 2 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 5 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 6 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 9 /playpen/mc2/imx6q-thrasher/thrasher &
-    taskset -c 10 /playpen/mc2/imx6q-thrasher/thrasher &
-fi
-sleep 1 # Wait for contending tasks to start
-echo "Done. Beginning benchmarks..."
-num_tests=$(wc -l < $tacleNames)
-for (( i = 0; i < $num_tests ; i++ ))
-do
-    # For level-C analysis, we must run all vs all
-    for (( j = 0; j < $num_tests ; j++ ))  #loop through programs
-    do
-        # Autodetect MC^2
-        if uname -a | grep -q "mc2"; then
-            # -1 loops means loop forever
-            chrt -r 97 numactl --interleave=all taskset -c $firstCore  ./bin/${tacleProg[$i]} NULL -1 $firstCore NULL 0 & PID1=$!;
-            chrt -r 97 numactl --interleave=all taskset -c $secondCore ./bin/${tacleProg[$i]} ${tacleProg[$i]}"+"${tacleProg[$j]} $maxJobs $secondCore $runID-$userRunID-LC-TACLe 1 & PID2=$!;
-        else
-            chrt -r 97 taskset -c $firstCore  ./bin/${tacleProg[$i]} NULL -1 $firstCore NULL 0 & PID1=$!;
-            chrt -r 97 taskset -c $secondCore ./bin/${tacleProg[$i]} ${tacleProg[$i]}"+"${tacleProg[$j]} $maxJobs $secondCore $runID-$userRunID-LC-TACLe 1 & PID2=$!;
-        fi
-        # The paired task runs continuously in this configuration, so we have
-        # to kill it once the task that we're measuring finishes.
-        wait $PID2
-        kill $PID1
-        echo ${tacleProg[$i]} ${tacleProg[$j]}
-    done
-    echo COMPLETE: ${tacleProg[$i]}
-done
-# End contending tasks
-if [[ $6 == "--contend" ]]; then
-    killall thrasher
-fi
-# Remove semaphores from system
-# Leaving them won't hurt these tests, but would be messy and is bad practice 
-# TODO: Do this directly in the benchmarks. They should clean up after themselves
-./bin/cleanupSemaphores
-# Put smp_affinty back the way it was
-i=0
-for IRQ in /proc/irq/*
-do
-    if [ -d $IRQ ]; then
-        echo ${irqList[$i]} 2> /dev/null > $IRQ/smp_affinity_list
-    fi
-    i=$(( $i + 1 ))
-done
diff --git a/dis/summarize.py b/summarize.py
index 31dcccc..2183c41 100755
--- a/dis/summarize.py
+++ b/summarize.py
@@ -50,19 +50,28 @@ def percentile(N, percent, key=lambda x:x):
    d1 = key(N[int(c)]) * (k-f)
    return d0+d1
 ## end of http://code.activestate.com/recipes/511478/ }}}
+def memstring(memr, memw, samples):
+    if memr or memw:
+        return "\t{:>12.f}\t{:>12.f}".format(memr/samples, memw/samples)
+    else:
+        return ""
 avg_max = 0
 avg_99th = 0
 avg_avg = 0
-print("Name\t\tAverage\t\tMax\t\t99th %\t\tAvg Mem Read\tAvg Mem Write\t")
+# Only include memory info in the header if relevant
+if mem_res[s[0]] == 0:
+    print("Name\t\tAverage\t\tMax\t\t99th %")
+else:
+    print("Name\t\tAverage\t\tMax\t\t99th %\t\tAvg Mem Read\tAvg Mem Write\t")
 for r in sorted(res.keys()):
 #    print(r + "\t\t" + str(res[r]/samples[r]) + "\t\t" + str(max_res[r]))
    avg_avg += sum(res[r])/len(res[r])
    avg_max += max(res[r])
    avg_99th += percentile(sorted(res[r]), 0.99)
    if len(sys.argv) > 2 and sys.argv[2] == "--inf-precision":
-        print("{:12}\t{:>12.0f}\t{:>12.0f}\t{:>12.0f}\t{:>12.0f}\t{:>12.0f}".format(r, sum(res[r])/len(res[r]), max(res[r]), percentile(sorted(res[r]), 0.99), mem_res[r]/samples[r], memw_res[r]/samples[r]))
+        print("{:12}\t{:>12.0f}\t{:>12.0f}\t{:>12.0f}".format(r, sum(res[r])/len(res[r]), max(res[r]), percentile(sorted(res[r]), 0.99)) + memstring(mem_res[r], memw_res[r], samples[r]))
    else:
-        print("{:12.12}\t{:>12.0f}\t{:>12.0f}\t{:>12.0f}\t{:>12.0f}\t{:>12.0f}".format(r, sum(res[r])/len(res[r]), max(res[r]), percentile(sorted(res[r]), 0.99), mem_res[r]/samples[r], memw_res[r]/samples[r]))
+        print("{:12.12}\t{:>12.0f}\t{:>12.0f}\t{:>12.0f}".format(r, sum(res[r])/len(res[r]), max(res[r]), percentile(sorted(res[r]), 0.99)) + memstring(mem_res[r], memw_res[r], samples[r]))
 print("Average average:", avg_avg/len(res.keys()))
 print("Average max:", avg_max/len(res.keys()))
diff --git a/wbinvd b/wbinvd
new file mode 160000
+Subproject 912e9a22c23da6f5b1af13e410ee74d9b27146a