27 files changed, 69 insertions, 270 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"