54 files changed, 317 insertions, 446 deletions

diff --git a/all_pairs/Makefile b/all_pairs/Makefile
index 36cf55a..0042372 100644
--- a/all_pairs/Makefile
+++ b/all_pairs/Makefile
@@ -1,57 +1,73 @@
-CC = gcc
-CFLAGS = -pthread -O2
+LIBLITMUS ?= /media/speedy/litmus/liblitmus
+CC ?= gcc
+CFLAGS = -pthread -O2 -I.. -DPAIRED
 LDFLAGS = -lrt
-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 bin/cleanupSemaphores
+COMMON = ../extra.h
+
+# Handle cases where we're also profiling with the MMDC on the i.MX6Q
+ifneq ($(shell grep "define MMDC 1" ../extra.h),)
+        COMMON += /media/speedy/litmus/tools/mmdc/mmdc.c
+endif
+
+# Include all the LITMUS^RT headers if we're using it
+ifneq ($(shell grep "define LITMUS 1" ../extra.h),)
+        CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
+        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
+
+debug: all
+debug: CFLAGS += -ggdb3
 
 .PHONY: clean
 clean:
-        rm 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 bin/cleanupSemaphores
+        rm -f 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
 
-bin/cleanupSemaphores: ./source/extra.h  ./source/cleanupSemaphores.c
-        $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/cjpeg_wrbmp: ./source/extra.h  ./source/cjpeg_wrbmp/cjpeg_wrbmp.c ./source/cjpeg_wrbmp/input.c
+bin/cjpeg_wrbmp: ${COMMON} ./source/cjpeg_wrbmp/cjpeg_wrbmp.c ./source/cjpeg_wrbmp/input.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/huff_enc: ./source/extra.h  ./source/huff_enc/huff_enc.c
+bin/huff_enc: ${COMMON} ./source/huff_enc/huff_enc.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/gsm_enc: ./source/extra.h  ./source/gsm_enc/gsm_enc.c
+bin/gsm_enc: ${COMMON} ./source/gsm_enc/gsm_enc.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/dijkstra: ./source/extra.h  ./source/dijkstra/dijkstra.c ./source/dijkstra/input.c
+bin/dijkstra: ${COMMON} ./source/dijkstra/dijkstra.c ./source/dijkstra/input.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/h264_dec: ./source/extra.h  ./source/h264_dec/h264_dec.c ./source/h264_dec/h264_decinput.c
+bin/h264_dec: ${COMMON} ./source/h264_dec/h264_dec.c ./source/h264_dec/h264_decinput.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/susan: ./source/extra.h  ./source/susan/input.c ./source/susan/susan.c ./source/susan/wccfile.c ./source/susan/wcclibm.c ./source/susan/wccmalloc.c
+bin/susan: ${COMMON} ./source/susan/input.c ./source/susan/susan.c ./source/susan/wccfile.c ./source/susan/wcclibm.c ./source/susan/wccmalloc.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/adpcm_enc: ./source/extra.h  ./source/adpcm_enc/adpcm_enc.c
+bin/adpcm_enc: ${COMMON} ./source/adpcm_enc/adpcm_enc.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/rijndael_dec: ./source/extra.h  ./source/rijndael_dec/aes.c ./source/rijndael_dec/input_small_enc.c ./source/rijndael_dec/rijndael_dec.c ./source/rijndael_dec/rijndael_dec_libc.c
+bin/rijndael_dec: ${COMMON} ./source/rijndael_dec/aes.c ./source/rijndael_dec/input_small_enc.c ./source/rijndael_dec/rijndael_dec.c ./source/rijndael_dec/rijndael_dec_libc.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/huff_dec: ./source/extra.h  ./source/huff_dec/huff_dec.c
+bin/huff_dec: ${COMMON} ./source/huff_dec/huff_dec.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/rijndael_enc: ./source/extra.h  ./source/rijndael_enc/aes.c ./source/rijndael_enc/input_small.c ./source/rijndael_enc/rijndael_enc.c ./source/rijndael_enc/rijndael_enc_libc.c
+bin/rijndael_enc: ${COMMON} ./source/rijndael_enc/aes.c ./source/rijndael_enc/input_small.c ./source/rijndael_enc/rijndael_enc.c ./source/rijndael_enc/rijndael_enc_libc.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/gsm_dec: ./source/extra.h  ./source/gsm_dec/gsm_dec.c
+bin/gsm_dec: ${COMMON} ./source/gsm_dec/gsm_dec.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/anagram: ./source/extra.h  ./source/anagram/anagram.c ./source/anagram/anagram_input.c ./source/anagram/anagram_stdlib.c
+bin/anagram: ${COMMON} ./source/anagram/anagram.c ./source/anagram/anagram_input.c ./source/anagram/anagram_stdlib.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/epic: ./source/extra.h  ./source/epic/epic.c
+bin/epic: ${COMMON} ./source/epic/epic.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/ammunition: ./source/extra.h  ./source/ammunition/ammunition.c ./source/ammunition/ammunition_libc.c ./source/ammunition/arithm.c ./source/ammunition/bits.c
+bin/ammunition: ${COMMON} ./source/ammunition/ammunition.c ./source/ammunition/ammunition_libc.c ./source/ammunition/arithm.c ./source/ammunition/bits.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/g723_enc: ./source/extra.h  ./source/g723_enc/g723_enc.c
+bin/g723_enc: ${COMMON} ./source/g723_enc/g723_enc.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/ndes: ./source/extra.h  ./source/ndes/ndes.c
+bin/ndes: ${COMMON} ./source/ndes/ndes.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/petrinet: ./source/extra.h  ./source/petrinet/petrinet.c
+bin/petrinet: ${COMMON} ./source/petrinet/petrinet.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/statemate: ./source/extra.h  ./source/statemate/statemate.c
+bin/statemate: ${COMMON} ./source/statemate/statemate.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/cjpeg_transupp: ./source/extra.h  ./source/cjpeg_transupp/cjpeg_transupp.c
+bin/cjpeg_transupp: ${COMMON} ./source/cjpeg_transupp/cjpeg_transupp.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/mpeg2: ./source/extra.h  ./source/mpeg2/mpeg2.c
+bin/mpeg2: ${COMMON} ./source/mpeg2/mpeg2.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/fmref: ./source/extra.h  ./source/fmref/fmref.c ./source/fmref/wcclibm.c
+bin/fmref: ${COMMON} ./source/fmref/fmref.c ./source/fmref/wcclibm.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/audiobeam: ./source/extra.h  ./source/audiobeam/audiobeam.c ./source/audiobeam/audiobeaminput.c ./source/audiobeam/audiobeamlibmalloc.c ./source/audiobeam/audiobeamlibm.c
+bin/audiobeam: ${COMMON} ./source/audiobeam/audiobeam.c ./source/audiobeam/audiobeaminput.c ./source/audiobeam/audiobeamlibmalloc.c ./source/audiobeam/audiobeamlibm.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
-bin/adpcm_dec: ./source/extra.h  ./source/adpcm_dec/adpcm_dec.c
+bin/adpcm_dec: ${COMMON} ./source/adpcm_dec/adpcm_dec.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
+
diff --git a/all_pairs/source/adpcm_dec/adpcm_dec.c b/all_pairs/source/adpcm_dec/adpcm_dec.c
index 04a5746..368e98d 100644
--- a/all_pairs/source/adpcm_dec/adpcm_dec.c
+++ b/all_pairs/source/adpcm_dec/adpcm_dec.c
@@ -35,7 +35,7 @@
   Forward declaration of functions
 */
 
-#include "../extra.h"
+#include "extra.h"
 
 void adpcm_dec_decode( int );
 int adpcm_dec_filtez( int *bpl, int *dlt );
diff --git a/all_pairs/source/adpcm_enc/adpcm_enc.c b/all_pairs/source/adpcm_enc/adpcm_enc.c
index 464768f..777aaf5 100644
--- a/all_pairs/source/adpcm_enc/adpcm_enc.c
+++ b/all_pairs/source/adpcm_enc/adpcm_enc.c
@@ -29,7 +29,7 @@
 
 /* common sampling rate for sound cards on IBM/PC */
 
-#include "../extra.h"
+#include "extra.h"
 #define SAMPLE_RATE 11025
 
 #define PI 3141
diff --git a/all_pairs/source/ammunition/ammunition.c b/all_pairs/source/ammunition/ammunition.c
index 269f4c0..052520e 100644
--- a/all_pairs/source/ammunition/ammunition.c
+++ b/all_pairs/source/ammunition/ammunition.c
@@ -24,7 +24,7 @@
 
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "bits.h"
 #include "arithm.h"
 #include "ammunition_stdlib.h"
diff --git a/all_pairs/source/anagram/anagram.c b/all_pairs/source/anagram/anagram.c
index b458fd2..5c1f29a 100644
--- a/all_pairs/source/anagram/anagram.c
+++ b/all_pairs/source/anagram/anagram.c
@@ -157,7 +157,7 @@
    steps to FindAnagram.
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "anagram_ctype.h"
 #include "anagram_stdlib.h"
 #include "anagram_strings.h"
diff --git a/all_pairs/source/audiobeam/audiobeam.c b/all_pairs/source/audiobeam/audiobeam.c
index 208de80..50ebfff 100644
--- a/all_pairs/source/audiobeam/audiobeam.c
+++ b/all_pairs/source/audiobeam/audiobeam.c
@@ -23,7 +23,7 @@
   Include section
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "audiobeamlibm.h"
 #include "audiobeamlibmalloc.h"
 #include "audiobeam.h"
diff --git a/all_pairs/source/cjpeg_transupp/cjpeg_transupp.c b/all_pairs/source/cjpeg_transupp/cjpeg_transupp.c
index 3f48539..5ec7e5e 100644
--- a/all_pairs/source/cjpeg_transupp/cjpeg_transupp.c
+++ b/all_pairs/source/cjpeg_transupp/cjpeg_transupp.c
@@ -29,7 +29,7 @@
   Include section
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "jpeglib.h"
 
 
diff --git a/all_pairs/source/cjpeg_wrbmp/cjpeg_wrbmp.c b/all_pairs/source/cjpeg_wrbmp/cjpeg_wrbmp.c
index 278725c..3c8d7ec 100644
--- a/all_pairs/source/cjpeg_wrbmp/cjpeg_wrbmp.c
+++ b/all_pairs/source/cjpeg_wrbmp/cjpeg_wrbmp.c
@@ -24,7 +24,7 @@
 
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "cdjpeg.h"
 
 #ifdef CJPEG_WRBMP_BMP_SUPPORTED
diff --git a/all_pairs/source/cleanupSemaphores.c b/all_pairs/source/cleanupSemaphores.c
deleted file mode 100644
index dde2bb3..0000000
--- a/all_pairs/source/cleanupSemaphores.c
+++ /dev/null
@@ -1,6 +0,0 @@
-#include <semaphore.h>
-
-int main(){
-        sem_unlink("/firstTacleSem");
-        sem_unlink("/secondTacleSem");
-}
diff --git a/all_pairs/source/dijkstra/dijkstra.c b/all_pairs/source/dijkstra/dijkstra.c
index 1b6a52f..333fd43 100644
--- a/all_pairs/source/dijkstra/dijkstra.c
+++ b/all_pairs/source/dijkstra/dijkstra.c
@@ -17,7 +17,7 @@
 
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "input.h"
 
 /*
diff --git a/all_pairs/source/empty.c b/all_pairs/source/empty.c
index c7c5f5d..6681ba7 100644
--- a/all_pairs/source/empty.c
+++ b/all_pairs/source/empty.c
@@ -1,4 +1,4 @@
-#include "../extra.h"
+#include "extra.h"
 
 int main(int argc, char **argv)
 {
diff --git a/all_pairs/source/epic/epic.c b/all_pairs/source/epic/epic.c
index e258a4a..a1e344c 100644
--- a/all_pairs/source/epic/epic.c
+++ b/all_pairs/source/epic/epic.c
@@ -35,7 +35,7 @@
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 #include "epic.h"
 
 #define X_SIZE  64
diff --git a/all_pairs/source/extra.h b/all_pairs/source/extra.h
deleted file mode 100644
index 0681250..0000000
--- a/all_pairs/source/extra.h
+++ /dev/null
@@ -1,211 +0,0 @@
-/**
- * Copyright 2019 Sims Hill Osborne and Joshua Bakita
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- **/
-#define _GNU_SOURCE
-#include <fcntl.h>
-#include <limits.h>
-#include <semaphore.h>
-#include <signal.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <sys/mman.h>
-#include <sys/stat.h>
-#include <time.h>
-#include <unistd.h>
-#include <sched.h>
-
-// This is only visible if _GNU_SOURCE is defined, and that define does not
-// come along to places where this file is included. Address this by manually
-// forcing it into the global namespace.
-extern int sched_getcpu();
-
-// Benchmarks use SET_UP, START_LOOP, STOP_LOOP, and WRITE_TO_FILE
-// These are macros so that we can declare and maintain additional state inside
-// the benchmark.
-#define SET_UP if (argc != 8) {\
-        printf("Usage: %s <name> <runs> <my core> <other core> <other program> <runID> <lockID>", argv[0]);\
-        exit(1);\
-    }\
-    char * thisProgram = argv[1];\
-    int maxJobs = atoi(argv[2]);\
-    unsigned int thisCore = atoi(argv[3]);\
-    unsigned int otherCore = atoi(argv[4]);\
-    thisCore = sched_getcpu();\
-    char * otherProgram = argv[5];\
-    char * runID = argv[6];\
-    int lockID = atoi(argv[7]);\
-    struct timespec _start, _end;\
-    int jobsComplete;\
-    int jobs_complete = -1;\
-    long * startS = malloc(sizeof(long) *maxJobs);\
-    long * startN = malloc(sizeof(long) *maxJobs);\
-    long * endS = malloc(sizeof(long) *maxJobs);\
-    long * endN = malloc(sizeof(long) *maxJobs);\
-    char * bigArray;\
-    char fileName[strlen(runID) + 5];\
-    strcpy(fileName, runID);\
-    strcat(fileName, ".txt");\
-    mlockall(MCL_CURRENT || MCL_FUTURE);\
-    sem_t *firstSem=sem_open("/firstTacleSem", O_CREAT, 644, 0);\
-    if (firstSem == SEM_FAILED) {\
-        perror("Error opening/creating first semaphore");\
-        exit(1);\
-    }\
-    sem_t *secondSem=sem_open("/secondTacleSem", O_CREAT, 644, 0);\
-    if (secondSem == SEM_FAILED) {\
-        perror("Error opening/creating second semaphore");\
-        exit(1);\
-    }\
-    int barrier_file = shm_open("/TacleBarrier", O_CREAT | O_RDWR, 644);\
-    if (barrier_file == -1) {\
-        perror("Error creating shared memory");\
-        exit(1);\
-    }\
-    /* This sets our shared file to be one byte of '\0'*/ \
-    if (ftruncate(barrier_file, 1) == -1) {\
-        perror("Error setting size of shared memory");\
-        exit(1);\
-    }\
-    char * barrier = mmap(NULL, 1, PROT_WRITE, MAP_SHARED, barrier_file, 0);\
-    if (barrier == MAP_FAILED) {\
-        perror("Error mapping shared memory");\
-        exit(1);\
-    }\
-    int val;
-
-#define SAVE_RESULTS \
-     if(jobs_complete >= maxJobs) {\
-        fprintf(stderr, "Max jobs setting too small! Trying to record job #%d when we only have space for %d jobs. Exiting...\n", jobs_complete, maxJobs);\
-        exit(1);\
-    }\
-    if (jobs_complete > -1){\
-        startS[jobs_complete]=_start.tv_sec;\
-        startN[jobs_complete]=_start.tv_nsec;\
-        endS[jobs_complete]=_end.tv_sec;\
-        endN[jobs_complete]=_end.tv_nsec;\
-    }
-
-#define WRITE_TO_FILE {\
-    munlockall();\
-    FILE *fp = fopen(fileName, "a");\
-    if (fp == NULL) {\
-        perror("Error opening file. \n");\
-        exit(1);\
-    }\
-    for(int i = 0; i <= jobs_complete; i++){\
-        fprintf(fp, "%s %s %u %u %d %ld %ld %ld %ld %s %d \n",\
-        thisProgram, otherProgram, thisCore, otherCore, maxJobs,\
-        startS[i], startN[i], endS[i], endN[i],\
-        runID, i);\
-    }\
-    fclose(fp);\
-    /* Clean up the barrier synchronization shared memory */\
-    munmap(barrier, 1);\
-    shm_unlink("/TacleBarrier");\
-    free(startS);\
-    free(startN);\
-    free(endS);\
-    free(endN);\
-}
-
-// Call the wbinvld instruction (it's in a kernel module due to it being ring-0)
-#define FLUSH_CACHES FILE *fp = fopen("/proc/wbinvd", "r");\
-    if (fp == NULL) {\
-        perror("Cache flush module interface cannot be opened");\
-        exit(1);\
-    }\
-    char dummy;\
-    if (fread(&dummy, 1, 1, fp) == 0) {\
-        perror("Unable to access cache flush module interface");\
-        exit(1);\
-    }\
-    fclose(fp);
-
-// These timers should just be aliases to the hardware counters w/ some small adjustments
-#define START_TIMER clock_gettime(CLOCK_MONOTONIC, &_start);
-#define STOP_TIMER clock_gettime(CLOCK_MONOTONIC, &_end);
-
-//check value of sem
-//if sem=0, unlock
-//if sem=1, spin
-
-#define SLEEP nanosleep((const struct timespec[]){{0, 1000000}}, NULL);
-
-#define FIRST_UNLOCK if (lockID == 1) {\
-        if (sem_post(secondSem) != 0) {\
-            perror("Unable to unlock second semaphore");\
-            exit(1);\
-        }\
-    } \
-    else {\
-        if (sem_post(firstSem) != 0) {\
-            perror("Unable to unlock first semaphore");\
-            exit(1);\
-        }\
-    } \
-
-#define FIRST_LOCK if (lockID == 1) {\
-        if (sem_wait(firstSem) != 0) {\
-            perror("Unable to wait on first semaphore");\
-            exit(1);\
-        }\
-    }\
-    else {\
-        if (sem_wait(secondSem) != 0) {\
-            perror("Unable to wait on second semaphore");\
-            exit(1);\
-        }\
-    }
-
-
-#define SECOND_UNLOCK   if (lockID==1){sem_post(fourthSem) ; }\
-            else {sem_post(thirdSem) ; }
-
-#define SECOND_LOCK if (lockID==1){sem_wait(thirdSem); }\
-            else {sem_wait(fourthSem); }
-
-#define BARRIER_SYNC if (__sync_bool_compare_and_swap(barrier, 0, 1)) {\
-        while (!__sync_bool_compare_and_swap(barrier, 0, 0)) {};\
-    }\
-    else {\
-        __sync_bool_compare_and_swap(barrier, 1, 0);\
-    }
-
-#define START_LOOP FIRST_UNLOCK FIRST_LOCK sched_yield(); FLUSH_CACHES BARRIER_SYNC START_TIMER
-#define STOP_LOOP STOP_TIMER jobs_complete++; SAVE_RESULTS
-
-
-/*
-Intended structure
-
-main
-SET_UP
-notice that STOP LOOP negates the ++ if outout=0
-for (jobsComplete=0; jobsComplete<maxJobs; jobsComplete++){
-        START_LOOP
-        tacleInit();
-        tacleMain();
-        STOP_LOOP
-}
-WRITE_TO_FILE
-tacleReturn 
-*/
diff --git a/all_pairs/source/fmref/fmref.c b/all_pairs/source/fmref/fmref.c
index bcc7ce6..e4c9aaa 100644
--- a/all_pairs/source/fmref/fmref.c
+++ b/all_pairs/source/fmref/fmref.c
@@ -5,7 +5,7 @@
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 #include "wcclibm.h"
 #ifndef M_PI
 #define M_PI        3.1415926535897932384626433832795
diff --git a/all_pairs/source/g723_enc/g723_enc.c b/all_pairs/source/g723_enc/g723_enc.c
index 331c821..209e3ce 100644
--- a/all_pairs/source/g723_enc/g723_enc.c
+++ b/all_pairs/source/g723_enc/g723_enc.c
@@ -31,7 +31,7 @@
    included in this Recommendation.
 */
 
-#include "../extra.h"
+#include "extra.h"
 struct g723_enc_state_t {
   long yl;  /* Locked or steady state step size multiplier. */
   short yu; /* Unlocked or non-steady state step size multiplier. */
diff --git a/all_pairs/source/gsm_dec/gsm_dec.c b/all_pairs/source/gsm_dec/gsm_dec.c
index 06d24d5..ba9a9e9 100644
--- a/all_pairs/source/gsm_dec/gsm_dec.c
+++ b/all_pairs/source/gsm_dec/gsm_dec.c
@@ -21,7 +21,7 @@
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 #include "gsm.h"
 #include "add.h"
 #include "data.h"
diff --git a/all_pairs/source/gsm_enc/gsm_enc.c b/all_pairs/source/gsm_enc/gsm_enc.c
index 3f051ec..e8154bb 100644
--- a/all_pairs/source/gsm_enc/gsm_enc.c
+++ b/all_pairs/source/gsm_enc/gsm_enc.c
@@ -5,7 +5,7 @@
  * details.  THERE IS ABSOLUTELY NO WARRANTY FOR THIS SOFTWARE.
  */
 
-#include "../extra.h"
+#include "extra.h"
 #include "private.h"
 
 /*
diff --git a/all_pairs/source/h264_dec/h264_dec.c b/all_pairs/source/h264_dec/h264_dec.c
index 1fed68b..e74bec9 100644
--- a/all_pairs/source/h264_dec/h264_dec.c
+++ b/all_pairs/source/h264_dec/h264_dec.c
@@ -25,7 +25,7 @@
   Include section
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "h264_dec.h"
 
 
diff --git a/all_pairs/source/huff_dec/huff_dec.c b/all_pairs/source/huff_dec/huff_dec.c
index b83b99d..58b40d3 100644
--- a/all_pairs/source/huff_dec/huff_dec.c
+++ b/all_pairs/source/huff_dec/huff_dec.c
@@ -49,7 +49,7 @@ new schemes (this item is not a must)
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 typedef struct s_tree {
   unsigned int byte; /* A byte has to be coded as an unsigned integer to
                         allow a node to have a value over 255 */
diff --git a/all_pairs/source/huff_enc/huff_enc.c b/all_pairs/source/huff_enc/huff_enc.c
index 133fe95..0d74916 100644
--- a/all_pairs/source/huff_enc/huff_enc.c
+++ b/all_pairs/source/huff_enc/huff_enc.c
@@ -50,7 +50,7 @@ new schemes (this item is not a must)
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 typedef struct huff_enc_s_tree {
   unsigned int byte; /* A byte has to be coded as an unsigned integer to
                         allow a node to have a value over 255 */
diff --git a/all_pairs/source/mpeg2/mpeg2.c b/all_pairs/source/mpeg2/mpeg2.c
index a810744..0567225 100644
--- a/all_pairs/source/mpeg2/mpeg2.c
+++ b/all_pairs/source/mpeg2/mpeg2.c
@@ -48,7 +48,7 @@
 /*
   Forward declaration of data types
 */
-#include "../extra.h"
+#include "extra.h"
 struct mbinfo;
 
 
diff --git a/all_pairs/source/ndes/ndes.c b/all_pairs/source/ndes/ndes.c
index b0f494c..f169c62 100644
--- a/all_pairs/source/ndes/ndes.c
+++ b/all_pairs/source/ndes/ndes.c
@@ -17,7 +17,7 @@
 */
 
 /* A read from this address will result in an known value of 1 */
-#include "../extra.h"
+#include "extra.h"
 #define KNOWN_VALUE 1
 #define NDES_WORSTCASE 1
 /*
diff --git a/all_pairs/source/petrinet/petrinet.c b/all_pairs/source/petrinet/petrinet.c
index cabb40d..6ef3392 100644
--- a/all_pairs/source/petrinet/petrinet.c
+++ b/all_pairs/source/petrinet/petrinet.c
@@ -25,7 +25,7 @@
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 
 #ifdef PROFILING
 #include <stdio.h>
diff --git a/all_pairs/source/rijndael_dec/rijndael_dec.c b/all_pairs/source/rijndael_dec/rijndael_dec.c
index 93bb424..61db767 100644
--- a/all_pairs/source/rijndael_dec/rijndael_dec.c
+++ b/all_pairs/source/rijndael_dec/rijndael_dec.c
@@ -38,7 +38,7 @@
   -----------------------------------------------------------------------
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "aes.h"
 #include "rijndael_dec_libc.h"
 
diff --git a/all_pairs/source/rijndael_enc/rijndael_enc.c b/all_pairs/source/rijndael_enc/rijndael_enc.c
index 0c10353..6c85eee 100644
--- a/all_pairs/source/rijndael_enc/rijndael_enc.c
+++ b/all_pairs/source/rijndael_enc/rijndael_enc.c
@@ -38,7 +38,7 @@
   -----------------------------------------------------------------------
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "aes.h"
 #include "rijndael_enc_libc.h"
 
diff --git a/all_pairs/source/statemate/statemate.c b/all_pairs/source/statemate/statemate.c
index 00491e5..888d0fa 100644
--- a/all_pairs/source/statemate/statemate.c
+++ b/all_pairs/source/statemate/statemate.c
@@ -27,7 +27,7 @@
   Macro definitions
 */
 
-#include "../extra.h"
+#include "extra.h"
 
 #define SYS_bit_get(a,b) (a)[(b)]
 #define SYS_bit_clr(a,b) (a)[(b)] = 0
diff --git a/all_pairs/source/susan/susan.c b/all_pairs/source/susan/susan.c
index 4bc4cb8..dc27fb1 100644
--- a/all_pairs/source/susan/susan.c
+++ b/all_pairs/source/susan/susan.c
@@ -269,7 +269,7 @@
 
 \**********************************************************************/
 
-#include "../extra.h"
+#include "extra.h"
 #include "wcclibm.h"
 #include "wccfile.h"
 #include "wccmalloc.h"
diff --git a/baseline/Makefile b/baseline/Makefile
index ef39b7d..40b57f4 100644
--- a/baseline/Makefile
+++ b/baseline/Makefile
@@ -1,25 +1,28 @@
 LIBLITMUS ?= /media/speedy/litmus/liblitmus
 CC ?= gcc
-CFLAGS = -pthread -O2
+CFLAGS = -pthread -O2 -I..
 LDFLAGS = -lrt
-COMMON = ./source/extra.h
+COMMON = ../extra.h
 
 # Handle cases where we're also profiling with the MMDC on the i.MX6Q
-ifneq ($(shell grep "define MMDC 1" source/extra.h),)
+ifneq ($(shell grep "define MMDC 1" ../extra.h),)
         COMMON += /media/speedy/litmus/tools/mmdc/mmdc.c
 endif
 
 # Include all the LITMUS^RT headers if we're using it
-ifneq ($(shell grep "define LITMUS 1" source/extra.h),)
+ifneq ($(shell grep "define LITMUS 1" ../extra.h),)
         CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
         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
 
+debug: all
+debug: CFLAGS += -ggdb3
+
 .PHONY: clean
 clean:
-        rm 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
+        rm -f 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
 
 bin/cjpeg_wrbmp: ${COMMON} ./source/cjpeg_wrbmp/cjpeg_wrbmp.c ./source/cjpeg_wrbmp/input.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
diff --git a/baseline/source/adpcm_dec/adpcm_dec.c b/baseline/source/adpcm_dec/adpcm_dec.c
index 04a5746..368e98d 100644
--- a/baseline/source/adpcm_dec/adpcm_dec.c
+++ b/baseline/source/adpcm_dec/adpcm_dec.c
@@ -35,7 +35,7 @@
   Forward declaration of functions
 */
 
-#include "../extra.h"
+#include "extra.h"
 
 void adpcm_dec_decode( int );
 int adpcm_dec_filtez( int *bpl, int *dlt );
diff --git a/baseline/source/adpcm_enc/adpcm_enc.c b/baseline/source/adpcm_enc/adpcm_enc.c
index 464768f..777aaf5 100644
--- a/baseline/source/adpcm_enc/adpcm_enc.c
+++ b/baseline/source/adpcm_enc/adpcm_enc.c
@@ -29,7 +29,7 @@
 
 /* common sampling rate for sound cards on IBM/PC */
 
-#include "../extra.h"
+#include "extra.h"
 #define SAMPLE_RATE 11025
 
 #define PI 3141
diff --git a/baseline/source/ammunition/ammunition.c b/baseline/source/ammunition/ammunition.c
index 269f4c0..052520e 100644
--- a/baseline/source/ammunition/ammunition.c
+++ b/baseline/source/ammunition/ammunition.c
@@ -24,7 +24,7 @@
 
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "bits.h"
 #include "arithm.h"
 #include "ammunition_stdlib.h"
diff --git a/baseline/source/anagram/anagram.c b/baseline/source/anagram/anagram.c
index b458fd2..5c1f29a 100644
--- a/baseline/source/anagram/anagram.c
+++ b/baseline/source/anagram/anagram.c
@@ -157,7 +157,7 @@
    steps to FindAnagram.
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "anagram_ctype.h"
 #include "anagram_stdlib.h"
 #include "anagram_strings.h"
diff --git a/baseline/source/audiobeam/audiobeam.c b/baseline/source/audiobeam/audiobeam.c
index 208de80..50ebfff 100644
--- a/baseline/source/audiobeam/audiobeam.c
+++ b/baseline/source/audiobeam/audiobeam.c
@@ -23,7 +23,7 @@
   Include section
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "audiobeamlibm.h"
 #include "audiobeamlibmalloc.h"
 #include "audiobeam.h"
diff --git a/baseline/source/cjpeg_transupp/cjpeg_transupp.c b/baseline/source/cjpeg_transupp/cjpeg_transupp.c
index 3f48539..5ec7e5e 100644
--- a/baseline/source/cjpeg_transupp/cjpeg_transupp.c
+++ b/baseline/source/cjpeg_transupp/cjpeg_transupp.c
@@ -29,7 +29,7 @@
   Include section
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "jpeglib.h"
 
 
diff --git a/baseline/source/cjpeg_wrbmp/cjpeg_wrbmp.c b/baseline/source/cjpeg_wrbmp/cjpeg_wrbmp.c
index 278725c..3c8d7ec 100644
--- a/baseline/source/cjpeg_wrbmp/cjpeg_wrbmp.c
+++ b/baseline/source/cjpeg_wrbmp/cjpeg_wrbmp.c
@@ -24,7 +24,7 @@
 
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "cdjpeg.h"
 
 #ifdef CJPEG_WRBMP_BMP_SUPPORTED
diff --git a/baseline/source/dijkstra/dijkstra.c b/baseline/source/dijkstra/dijkstra.c
index 1b6a52f..333fd43 100644
--- a/baseline/source/dijkstra/dijkstra.c
+++ b/baseline/source/dijkstra/dijkstra.c
@@ -17,7 +17,7 @@
 
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "input.h"
 
 /*
diff --git a/baseline/source/epic/epic.c b/baseline/source/epic/epic.c
index e258a4a..a1e344c 100644
--- a/baseline/source/epic/epic.c
+++ b/baseline/source/epic/epic.c
@@ -35,7 +35,7 @@
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 #include "epic.h"
 
 #define X_SIZE  64
diff --git a/baseline/source/fmref/fmref.c b/baseline/source/fmref/fmref.c
index bcc7ce6..e4c9aaa 100644
--- a/baseline/source/fmref/fmref.c
+++ b/baseline/source/fmref/fmref.c
@@ -5,7 +5,7 @@
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 #include "wcclibm.h"
 #ifndef M_PI
 #define M_PI        3.1415926535897932384626433832795
diff --git a/baseline/source/g723_enc/g723_enc.c b/baseline/source/g723_enc/g723_enc.c
index 331c821..209e3ce 100644
--- a/baseline/source/g723_enc/g723_enc.c
+++ b/baseline/source/g723_enc/g723_enc.c
@@ -31,7 +31,7 @@
    included in this Recommendation.
 */
 
-#include "../extra.h"
+#include "extra.h"
 struct g723_enc_state_t {
   long yl;  /* Locked or steady state step size multiplier. */
   short yu; /* Unlocked or non-steady state step size multiplier. */
diff --git a/baseline/source/gsm_dec/gsm_dec.c b/baseline/source/gsm_dec/gsm_dec.c
index 06d24d5..ba9a9e9 100644
--- a/baseline/source/gsm_dec/gsm_dec.c
+++ b/baseline/source/gsm_dec/gsm_dec.c
@@ -21,7 +21,7 @@
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 #include "gsm.h"
 #include "add.h"
 #include "data.h"
diff --git a/baseline/source/gsm_enc/gsm_enc.c b/baseline/source/gsm_enc/gsm_enc.c
index 3f051ec..e8154bb 100644
--- a/baseline/source/gsm_enc/gsm_enc.c
+++ b/baseline/source/gsm_enc/gsm_enc.c
@@ -5,7 +5,7 @@
  * details.  THERE IS ABSOLUTELY NO WARRANTY FOR THIS SOFTWARE.
  */
 
-#include "../extra.h"
+#include "extra.h"
 #include "private.h"
 
 /*
diff --git a/baseline/source/h264_dec/h264_dec.c b/baseline/source/h264_dec/h264_dec.c
index 1fed68b..e74bec9 100644
--- a/baseline/source/h264_dec/h264_dec.c
+++ b/baseline/source/h264_dec/h264_dec.c
@@ -25,7 +25,7 @@
   Include section
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "h264_dec.h"
 
 
diff --git a/baseline/source/huff_dec/huff_dec.c b/baseline/source/huff_dec/huff_dec.c
index b83b99d..58b40d3 100644
--- a/baseline/source/huff_dec/huff_dec.c
+++ b/baseline/source/huff_dec/huff_dec.c
@@ -49,7 +49,7 @@ new schemes (this item is not a must)
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 typedef struct s_tree {
   unsigned int byte; /* A byte has to be coded as an unsigned integer to
                         allow a node to have a value over 255 */
diff --git a/baseline/source/huff_enc/huff_enc.c b/baseline/source/huff_enc/huff_enc.c
index 133fe95..0d74916 100644
--- a/baseline/source/huff_enc/huff_enc.c
+++ b/baseline/source/huff_enc/huff_enc.c
@@ -50,7 +50,7 @@ new schemes (this item is not a must)
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 typedef struct huff_enc_s_tree {
   unsigned int byte; /* A byte has to be coded as an unsigned integer to
                         allow a node to have a value over 255 */
diff --git a/baseline/source/litmusStuff.h b/baseline/source/litmusStuff.h
deleted file mode 100644
index dca2360..0000000
--- a/baseline/source/litmusStuff.h
+++ /dev/null
@@ -1,80 +0,0 @@
-#include <time.h>
-#include <sys/mman.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <signal.h>
-#include <limits.h>
-#include <../litmus.h>
-
-#define L3_CACHE_SIZE (11264*1024)
-
-#define SAVE_RESULTS if(jobsComplete>-1) progTime[jobsComplete]=(end.tv_nsec-start.tv_nsec)+(1000000000*(end.tv_sec-start.tv_sec));
-
-
-#define SET_UP char *thisProgram=argv[1];\
-        int maxJobs=atoi(argv[2]);\
-        char *thisCore=argv[3];\
-        char *otherCore=argv[4];\
-        char *otherProgram=argv[5];\
-        char *runID=argv[6];\
-        int output=atoi(argv[7]);\
-        struct timespec start, end;\
-        int jobsComplete;\
-        long progTime[maxJobs*output];\
-        char fileName[50];\
-        char *bigArray;\
-        strcpy(fileName, runID);\
-        strcat(fileName, ".txt");\
-        mlockall(MCL_CURRENT || MCL_FUTURE);
-
-#define WRITE_TO_FILE if (output){\
-        munlockall();\
-        FILE *fp=fopen(fileName, "a");\
-        for(jobsComplete=0; jobsComplete<maxJobs; jobsComplete++){\
-                fprintf(fp, "%s %s %s %s %d %ld %s %d \n",\
-                thisProgram, otherProgram, thisCore, otherCore, maxJobs,\
-                progTime[jobsComplete], runID, jobsComplete);\
-        }\
-        fclose(fp);\
-        }
-
-#define KILL_CACHE bigArray=(char *)malloc(L3_CACHE_SIZE);\
-if (bigArray==NULL) perror("Malloc failed.\n");\
-memset(bigArray, 1, L3_CACHE_SIZE);\
-munlock(bigArray, L3_CACHE_SIZE);\
-free(bigArray);\
-bigArray=NULL;
-
-
-
-//invoke start timer twice, stop timer to make sure timer and vars are in cache
-#define START_TIMER clock_gettime(CLOCK_MONOTONIC, &start);\
-        clock_gettime(CLOCK_MONOTONIC, &end);\
-        clock_gettime(CLOCK_MONOTONIC, &start);\
-                
-#define STOP_TIMER clock_gettime(CLOCK_MONOTONIC, &end);
-
-
-#define START_LOOP START_TIMER
-
-#define STOP_LOOP if (output) {STOP_TIMER SAVE_RESULTS} sleep_next_period();
-
-
-/*
-Intended structure
-
-main
-SET_UP
-notice that STOP LOOP negates the ++ if outout=0
-for (jobsComplete=-1; jobsComplete<maxJobs; jobsComplete++){
-                KILL_CACHE
-                START_TIMER
-                tacleInit();
-                tacleMain();
-                STOP_TIMER
-                SAVE_RESULTS
-}
-WRITE_TO_FILE
-tacleReturn     
-*/
diff --git a/baseline/source/mpeg2/mpeg2.c b/baseline/source/mpeg2/mpeg2.c
index a810744..0567225 100644
--- a/baseline/source/mpeg2/mpeg2.c
+++ b/baseline/source/mpeg2/mpeg2.c
@@ -48,7 +48,7 @@
 /*
   Forward declaration of data types
 */
-#include "../extra.h"
+#include "extra.h"
 struct mbinfo;
 
 
diff --git a/baseline/source/ndes/ndes.c b/baseline/source/ndes/ndes.c
index b0f494c..f169c62 100644
--- a/baseline/source/ndes/ndes.c
+++ b/baseline/source/ndes/ndes.c
@@ -17,7 +17,7 @@
 */
 
 /* A read from this address will result in an known value of 1 */
-#include "../extra.h"
+#include "extra.h"
 #define KNOWN_VALUE 1
 #define NDES_WORSTCASE 1
 /*
diff --git a/baseline/source/petrinet/petrinet.c b/baseline/source/petrinet/petrinet.c
index cabb40d..6ef3392 100644
--- a/baseline/source/petrinet/petrinet.c
+++ b/baseline/source/petrinet/petrinet.c
@@ -25,7 +25,7 @@
 */
 
 
-#include "../extra.h"
+#include "extra.h"
 
 #ifdef PROFILING
 #include <stdio.h>
diff --git a/baseline/source/rijndael_dec/rijndael_dec.c b/baseline/source/rijndael_dec/rijndael_dec.c
index 93bb424..61db767 100644
--- a/baseline/source/rijndael_dec/rijndael_dec.c
+++ b/baseline/source/rijndael_dec/rijndael_dec.c
@@ -38,7 +38,7 @@
   -----------------------------------------------------------------------
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "aes.h"
 #include "rijndael_dec_libc.h"
 
diff --git a/baseline/source/rijndael_enc/rijndael_enc.c b/baseline/source/rijndael_enc/rijndael_enc.c
index 0c10353..6c85eee 100644
--- a/baseline/source/rijndael_enc/rijndael_enc.c
+++ b/baseline/source/rijndael_enc/rijndael_enc.c
@@ -38,7 +38,7 @@
   -----------------------------------------------------------------------
 */
 
-#include "../extra.h"
+#include "extra.h"
 #include "aes.h"
 #include "rijndael_enc_libc.h"
 
diff --git a/baseline/source/statemate/statemate.c b/baseline/source/statemate/statemate.c
index 00491e5..888d0fa 100644
--- a/baseline/source/statemate/statemate.c
+++ b/baseline/source/statemate/statemate.c
@@ -27,7 +27,7 @@
   Macro definitions
 */
 
-#include "../extra.h"
+#include "extra.h"
 
 #define SYS_bit_get(a,b) (a)[(b)]
 #define SYS_bit_clr(a,b) (a)[(b)] = 0
diff --git a/baseline/source/susan/susan.c b/baseline/source/susan/susan.c
index 4bc4cb8..dc27fb1 100644
--- a/baseline/source/susan/susan.c
+++ b/baseline/source/susan/susan.c
@@ -269,7 +269,7 @@
 
 \**********************************************************************/
 
-#include "../extra.h"
+#include "extra.h"
 #include "wcclibm.h"
 #include "wccfile.h"
 #include "wccmalloc.h"
diff --git a/dis/Makefile b/dis/Makefile
index 2c1ff89..df93116 100755
--- a/dis/Makefile
+++ b/dis/Makefile
@@ -4,34 +4,33 @@
 # that a good Makefile should follow. Sorry - at least I have one.)
 LIBLITMUS ?= /media/speedy/litmus/liblitmus
 CC ?= gcc
-override CFLAGS += -pthread -O2
+CFLAGS += -pthread -O2 -I..
 LDFLAGS = -lrt -lm
-
-# We need a different include path depending on the target, so use a
-# target-specific variable
-field matrix neighborhood pointer transitive update random_walk: override CFLAGS += -I../baseline/source
-field matrix neighborhood pointer transitive update random_walk: COMMON = ../baseline/source/extra.h
-field_all matrix_all neighborhood_all pointer_all transitive_all update_all: override CFLAGS += -I../all_pairs/source
-field_all matrix_all neighborhood_all pointer_all transitive_all update_all: COMMON = ../all_pairs/source/extra.h
+COMMON = ../extra.h
 
 # Handle cases where we're also profiling with the MMDC on the i.MX6Q
-ifneq ($(shell grep "define MMDC 1" ../baseline/source/extra.h),)
+ifneq ($(shell grep "define MMDC 1" ../extra.h),)
         COMMON += /media/speedy/litmus/tools/mmdc/mmdc.c
 endif
 
 # Include all the LITMUS^RT headers if we're using it
-ifneq ($(shell grep "define LITMUS 1" ../baseline/source/extra.h),)
+ifneq ($(shell grep "define LITMUS 1" ../extra.h),)
         CFLAGS += -I${LIBLITMUS}/include -I${LIBLITMUS}/arch/arm/include
         LDFLAGS += -L${LIBLITMUS} -llitmus
 endif
 
 all: baseline
+debug: baseline
+debug_pairs: pairs
+debug debug_pairs: CFLAGS += -ggdb3
 baseline: field matrix neighborhood pointer transitive update random_walk
 pairs: field_all matrix_all neighborhood_all pointer_all transitive_all update_all
 
 .PHONY: clean
 clean:
-        rm field_all matrix_all neighborhood_all pointer_all transitive_all update_all field matrix neighborhood pointer transitive update random_walk
+        rm -f field_all matrix_all neighborhood_all pointer_all \
+      transitive_all update_all field matrix neighborhood \
+      pointer transitive update random_walk
 
 field: ${COMMON} ./Field/field.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
@@ -49,14 +48,14 @@ random_walk: ${COMMON} random_walk.c
         $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
 
 field_all: ${COMMON} ./Field/field.c
-        $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
+        $(CC) $(CFLAGS) -DPAIRED $^ -o $@ $(LDFLAGS)
 matrix_all: ${COMMON} ./Matrix/ver2/matrix.c
-        $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
+        $(CC) $(CFLAGS) -DPAIRED $^ -o $@ $(LDFLAGS)
 neighborhood_all: ${COMMON} ./Neighborhood/neighborhood.c
-        $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
+        $(CC) $(CFLAGS) -DPAIRED $^ -o $@ $(LDFLAGS)
 pointer_all: ${COMMON} ./Pointer/pointer.c
-        $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
+        $(CC) $(CFLAGS) -DPAIRED $^ -o $@ $(LDFLAGS)
 transitive_all: ${COMMON} ./Transitive/transitive.c
-        $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
+        $(CC) $(CFLAGS) -DPAIRED $^ -o $@ $(LDFLAGS)
 update_all: ${COMMON} ./Update/update.c
-        $(CC) $(CFLAGS) $^ -o $@ $(LDFLAGS)
+        $(CC) $(CFLAGS) -DPAIRED $^ -o $@ $(LDFLAGS)
diff --git a/baseline/source/extra.h b/extra.h
index e8f3d18..3215951 100644
--- a/baseline/source/extra.h
+++ b/extra.h
@@ -2,18 +2,18 @@
  * Copyright 2019 Sims Hill Osborne and Joshua Bakita
  *
  * This header provides facilities by which to separably run and time TACLeBench
+ * To use this for paired task timing, define PAIRED (pass CFLAGS=-DPAIRED to make)
  **/
 #define _GNU_SOURCE
-#include <time.h>
-#include <sys/mman.h>
-#include <stdlib.h>
+#include <fcntl.h>     // For O_CREAT and O_RDWR
+#include <sched.h>     // For sched_yield()
+#include <semaphore.h> // For sem_{open, post, wait}()
 #include <stdio.h>
-#include <string.h>
-#include <signal.h>
-#include <limits.h>
-#include <fcntl.h>
-#include <stdint.h>
-#include <sched.h>
+#include <stdlib.h>    // For exit()
+#include <string.h>    // For strlen()
+#include <sys/mman.h>  // For mlockall()
+#include <unistd.h>    // For ftruncate()
+#include <time.h>
 
 // This is only visible if _GNU_SOURCE is defined, and that define does not
 // come along to places where this file is included. Address this by manually
@@ -55,7 +55,13 @@ extern int sched_getcpu();
 
 // Store state globally so that the job can be outside main()
 // Arrays use float as a comprimise between overflow and size
+// Paired arrays use long longs as precision is more important for those times
+#ifdef PAIRED
+long long *_rt_start_time;
+long long *_rt_end_time;
+#else
 float *_rt_exec_time;
+#endif
 #if MMDC_PERF
 float *_rt_mmdc_read;
 float *_rt_mmdc_write;
@@ -68,36 +74,103 @@ struct timespec _rt_start, _rt_end;
 
 char *_rt_run_id;
 char *_rt_our_prog_name;
+char *_rt_other_prog_name;
+char *_rt_other_core;
 #define _RT_FILENAME_LEN 64
+#define _BILLION (1000*1000*1000)
+#ifdef PAIRED
+char *_rt_barrier;
+sem_t *_rt_first_sem, *_rt_second_sem;
+int _rt_lock_id;
+#endif
 
-#define LOAD_PARAMS_ITRL \
-    if (argc != 6) { \
-        fprintf(stderr, "Usage: %s <name> <loops> <my core> <runID> <save results?>\n", argv[0]);\
-        fprintf(stderr, " <loops> integer number of iterations. -1 for infitite.\n");\
-        fprintf(stderr, " <save results?> 1 to save results, 0 to discard.\n");\
-        fprintf(stderr, " <my core> UNUSED. Core is now auto-detected.\n");\
-        exit(1);\
-    }\
-    _rt_our_prog_name = argv[1];\
-    _rt_max_jobs = atol(argv[2]);\
-    _rt_core = sched_getcpu();\
-    _rt_run_id = argv[4];\
-    _rt_will_output = atoi(argv[5]);\
-    if (_rt_max_jobs < 0 && _rt_will_output != 0) {\
-        fprintf(stderr, "Infinite loops only supported when _rt_will_output is disabled!\n");\
-        exit(1);\
-    }\
-    if (strlen(_rt_run_id) + 5 > _RT_FILENAME_LEN) {\
-        fprintf(stderr, "Run ID is too large! Keep it to less than %d characters.\n", _RT_FILENAME_LEN);\
-        exit(1);\
-    }\
-    _rt_exec_time = calloc(_rt_max_jobs * _rt_will_output, sizeof(float));\
-    if (!_rt_exec_time) {\
-        perror("Unable to allocate buffer for execution times");\
-        exit(1);\
-    }\
-    _rt_jobs_complete = 0;\
+static void _rt_load_params_itrl(int argc, char **argv) {
+#ifdef PAIRED
+    if (argc != 8) {
+        fprintf(stderr, "Usage: %s <name> <loops> <my core> <other core> <other name> <runID> <lockID>", argv[0]);
+        fprintf(stderr, " <name> string for logging. Name of this task.\n");
+        fprintf(stderr, " <loops> integer number of iterations. -1 for infinite.\n");
+        fprintf(stderr, " <my core> UNUSED. Core is now auto-detected.\n");
+        fprintf(stderr, " <other core> integer for logging. Core of paired task.\n");
+        fprintf(stderr, " <other name> string for logging. Name of paired task.\n");
+        fprintf(stderr, " <runID> string to append with .txt to yield output file name.\n");
+        fprintf(stderr, " <lockID> 1 to indicate this is pair member 1, otherwise pair member 2.\n");
+        exit(1);
+    }
+#else
+    if (argc != 6) {
+        fprintf(stderr, "Usage: %s <name> <loops> <my core> <runID> <save results?>\n", argv[0]);
+        fprintf(stderr, " <name> string for logging. Name of this task.\n");
+        fprintf(stderr, " <loops> integer number of iterations. -1 for infinite.\n");
+        fprintf(stderr, " <my core> UNUSED. Core is now auto-detected.\n");
+        fprintf(stderr, " <runID> string to append with .txt to yield output file name.\n");
+        fprintf(stderr, " <save results?> 1 to save results, 0 to discard.\n");
+        exit(1);
+    }
+#endif
+    _rt_our_prog_name = argv[1];
+    _rt_max_jobs = atol(argv[2]);
+    _rt_core = sched_getcpu();
+#ifdef PAIRED
+    _rt_other_core = argv[4];
+    _rt_other_prog_name = argv[5];
+    _rt_run_id = argv[6];
+    _rt_lock_id = atoi(argv[7]);
+    // The paired version doesn't support disabling output (legacy compatibility)
+    _rt_will_output = 1;
+#else
+    _rt_other_core = "none";
+    _rt_other_prog_name = "none";
+    _rt_run_id = argv[4];
+    _rt_will_output = atoi(argv[5]);
+#endif /* PAIRED */
+    if (_rt_max_jobs < 0 && _rt_will_output != 0) {
+        fprintf(stderr, "Infinite loops only supported when _rt_will_output is disabled!\n");
+        exit(1);
+    }
+    if (strlen(_rt_run_id) + 5 > _RT_FILENAME_LEN) {
+        fprintf(stderr, "Run ID is too large! Keep it to less than %d characters.\n", _RT_FILENAME_LEN);
+        exit(1);
+    }
+#ifdef PAIRED
+    _rt_start_time = calloc(_rt_max_jobs * _rt_will_output, sizeof(long long));
+    _rt_end_time = calloc(_rt_max_jobs * _rt_will_output, sizeof(long long));
+    if (!_rt_end_time || !_rt_start_time) {
+        perror("Unable to allocate buffers for execution times");
+        exit(1);
+    }
+    _rt_first_sem = sem_open("/_libextra_first_sem", O_CREAT, 644, 0);
+    _rt_second_sem = sem_open("/_libextra_second_sem", O_CREAT, 644, 0);
+    if (_rt_first_sem == SEM_FAILED || _rt_second_sem == SEM_FAILED) {
+        perror("Error while creating semaphores");
+        exit(1);
+    }
+    int barrier_file = shm_open("/_libextra_barrier", O_CREAT | O_RDWR, 644);
+    if (barrier_file == -1) {
+        perror("Error while creating shared memory for barrier synchronization");
+        exit(1);
+    }
+    if (ftruncate(barrier_file, 1) == -1) {
+        perror("Error while setting size of shared memory for barrier synchronization");
+        exit(1);
+    }
+    _rt_barrier = mmap(NULL, 1, PROT_WRITE, MAP_SHARED, barrier_file, 0);
+    if (_rt_barrier == MAP_FAILED) {
+        perror("Error while mapping shared memory for barrier synchronization");
+        exit(1);
+    }
+    *_rt_barrier = 0;
+#else
+    _rt_exec_time = calloc(_rt_max_jobs * _rt_will_output, sizeof(float));
+    if (!_rt_exec_time) {
+        perror("Unable to allocate buffer for execution times");
+        exit(1);
+    }
+#endif /* PAIRED */
+    _rt_jobs_complete = 0;
     mlockall(MCL_CURRENT || MCL_FUTURE);
+}
+#define LOAD_PARAMS_ITRL _rt_load_params_itrl(argc, argv);
 
 #define SETUP_MMDC \
     _rt_mmdc_read = calloc(_rt_max_jobs * _rt_will_output, sizeof(float));\
@@ -213,6 +286,44 @@ char *_rt_our_prog_name;
     fclose(fp);
 #endif
 
+// This semaphore-based synchronization is from Sims
+#define FIRST_UNLOCK \
+    if (_rt_lock_id == 1) {\
+        if (sem_post(_rt_second_sem) != 0) {\
+            perror("Unable to unlock second semaphore");\
+            exit(1);\
+        }\
+    } \
+    else {\
+        if (sem_post(_rt_first_sem) != 0) {\
+            perror("Unable to unlock first semaphore");\
+            exit(1);\
+        }\
+    } \
+
+#define FIRST_LOCK \
+    if (_rt_lock_id == 1) {\
+        if (sem_wait(_rt_first_sem) != 0) {\
+            perror("Unable to wait on first semaphore");\
+            exit(1);\
+        }\
+    }\
+    else {\
+        if (sem_wait(_rt_second_sem) != 0) {\
+            perror("Unable to wait on second semaphore");\
+            exit(1);\
+        }\
+    }
+
+// This ensures a very low difference between pair member start times
+#define BARRIER_SYNC \
+    if (__sync_bool_compare_and_swap(_rt_barrier, 0, 1)) {\
+        while (!__sync_bool_compare_and_swap(_rt_barrier, 0, 0)) {};\
+    }\
+    else {\
+        __sync_bool_compare_and_swap(_rt_barrier, 1, 0);\
+    }
+
 // Buffer timing result from a single job
 static void _rt_save_job_result() {
     if (_rt_jobs_complete >= _rt_max_jobs) {
@@ -220,9 +331,18 @@ static void _rt_save_job_result() {
         exit(1);
     }
     if (_rt_jobs_complete > -1 && _rt_will_output) {
+#ifdef PAIRED
+        _rt_start_time[_rt_jobs_complete] = _rt_start.tv_sec;
+        _rt_start_time[_rt_jobs_complete] *= _BILLION;
+        _rt_start_time[_rt_jobs_complete] += _rt_start.tv_nsec;
+        _rt_end_time[_rt_jobs_complete] = _rt_end.tv_sec;
+        _rt_end_time[_rt_jobs_complete] *= _BILLION;
+        _rt_end_time[_rt_jobs_complete] += _rt_end.tv_nsec;
+#else
         _rt_exec_time[_rt_jobs_complete] = _rt_end.tv_sec - _rt_start.tv_sec;
-        _rt_exec_time[_rt_jobs_complete] *= 1e9;
+        _rt_exec_time[_rt_jobs_complete] *= _BILLION;
         _rt_exec_time[_rt_jobs_complete] += _rt_end.tv_nsec - _rt_start.tv_nsec;
+#endif /* PAIRED */
 #if MMDC_PROF
         _rt_mmdc_read[_rt_jobs_complete] = mmdc_res.read_bytes;
         _rt_mmdc_write[_rt_jobs_complete] = mmdc_res.write_bytes;
@@ -234,31 +354,54 @@ static void _rt_save_job_result() {
 static void _rt_write_to_file() {
     char fileName[_RT_FILENAME_LEN];
     FILE *fp;
-    if (!_rt_will_output)
-        return;
     munlockall();
+    if (!_rt_will_output)
+        goto out;
     strcpy(fileName, _rt_run_id);
     strcat(fileName, ".txt");
     fp = fopen(fileName, "a");
     if (fp == NULL) {
-        perror("Unable to open _rt_will_output file");
+        perror("Unable to open output file");
         exit(1);
     }
-    // Same format as the paired results with "none" for unused fields
+    // Baseline output uses a similar format with "none" for unused fields
     for (int i = 0; i < _rt_jobs_complete; i++){
-        fprintf(fp, "%s none %u none %ld %.f %s %d %.f %.f \n",
-        _rt_our_prog_name, _rt_core, _rt_max_jobs,
-        _rt_exec_time[i], _rt_run_id, i,
+        fprintf(fp, "%s %s %u %s %ld", _rt_our_prog_name, _rt_other_prog_name,
+            _rt_core, _rt_other_core, _rt_max_jobs);
+#ifdef PAIRED
+        // For unclear legacy reasons, paired tasks emit sec and ns separately
+        fprintf(fp, " %lld %lld %lld %lld",
+            _rt_start_time[i] / _BILLION, _rt_start_time[i] % _BILLION,
+            _rt_end_time[i] / _BILLION, _rt_end_time[i] % _BILLION);
+#else
+        fprintf(fp, " %.f", _rt_exec_time[i]);
+#endif /* PAIRED */
+        fprintf(fp, " %s %d %.f %.f\n",  _rt_run_id, i,
 #if MMDC_PROF
-        _rt_mmdc_read[i], _rt_mmdc_write[i]);
+            _rt_mmdc_read[i], _rt_mmdc_write[i]);
 #else
-        0.0, 0.0);
-#endif
+            0.0, 0.0);
+#endif /* MMDC_PROF */
     }
     fclose(fp);
+out:
 #if LITMUS
     CLEANUP_LITMUS
-#endif
+#endif /* LITMUS */
+#ifdef PAIRED
+    munmap(_rt_barrier, 1);
+    shm_unlink("/_libextra_barrier");
+    sem_unlink("/_libextra_first_sem");
+    sem_unlink("/_libextra_second_sem");
+    free(_rt_start_time);
+    free(_rt_end_time);
+#else
+    free(_rt_exec_time);
+#endif /* PAIRED */
+#if MMDC_PROF
+    free(_rt_mmdc_read);
+    free(_rt_mmdc_write);
+#endif /* MMDC_PROF */
 }
 
 // Start a job
@@ -269,12 +412,19 @@ static void _rt_start_loop() {
     }
 #else
     sched_yield();
-#endif
+#endif /* LITMUS */
+#ifdef PAIRED
+    FIRST_UNLOCK
+    FIRST_LOCK
+#endif /* PAIRED */
     FLUSH_CACHES
+#ifdef PAIRED
+    BARRIER_SYNC
+#endif /* PAIRED */
 #if MMDC_PROF
     /* This disables profiling, resets the counters, clears the overflow bit, and enables profiling */
     start_mmdc_profiling(mmdc);
-#endif
+#endif /* MMDC_PROF */
     clock_gettime(CLOCK_MONOTONIC, &_rt_start);
 }
 
@@ -285,7 +435,7 @@ static void _rt_stop_loop() {
     /* This freezes the profiling and makes results available */
     pause_mmdc_profiling(mmdc);
     get_mmdc_profiling_results(mmdc, &mmdc_res);
-#endif
+#endif /* MMDC_PROF */
     _rt_save_job_result();
     _rt_jobs_complete++;
 }