Unify all the versions of extra.h into a single multipurpose header

There was previously a huge amount of shared code that had to be
copied back and forth. This should reduce the maintenance burden
by containing all future changes to a single file.

New unified library is fully backwards-compatible but also
introduces and the easy-to-use `for_each_job` macro which
replaces the specific `for(...) START_LOOP ... STOP_LOOP`
format requirement and is generally much harder to abuse.

New unified library also automatically cleans up its shared memory
and semaphores, so this commit also removes the separate
`cleanupSemaphores` binary.

I also found a precursor of `extra.h` written by Sims in
`litmusStuff.h`. This code is only interesting for historical
purposes, so it is also removed in this commit.

This commit also adds debug options to all the Makefiles and
silences rm's complaints about non-existent files in make clean.

25 files changed, 23 insertions, 453 deletions

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/extra.h b/baseline/source/extra.h
deleted file mode 100644
index e8f3d18..0000000
--- a/baseline/source/extra.h
+++ /dev/null
@@ -1,350 +0,0 @@
-/**
- * Copyright 2019 Sims Hill Osborne and Joshua Bakita
- *
- * This header provides facilities by which to separably run and time TACLeBench
- **/
-#define _GNU_SOURCE
-#include <time.h>
-#include <sys/mman.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <signal.h>
-#include <limits.h>
-#include <fcntl.h>
-#include <stdint.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();
-
-// These constants correspond to the imx6q-sabredb platform
-#define LINE_SIZE 32
-#define L2_SIZE 16*2048*32
-
-#if __arm__
-#include <unistd.h>
-#include <sys/syscall.h>
-#endif
-
-#define LITMUS 0
-#define MC2 0
-#define MMDC_PROF 0
-
-#if LITMUS
-#include <litmus.h>
-#endif
-
-#if MMDC_PROF
-#include  "/media/speedy/litmus/tools/mmdc/mmdc.h"
-#endif
-
-#if LITMUS
-#define SET_UP LOAD_PARAMS SETUP_LITMUS
-#else
-#define SET_UP LOAD_PARAMS
-#endif
-
-#if MMDC_PROF
-#define LOAD_PARAMS LOAD_PARAMS_ITRL SETUP_MMDC
-#else
-#define LOAD_PARAMS LOAD_PARAMS_ITRL
-#endif
-
-// Store state globally so that the job can be outside main()
-// Arrays use float as a comprimise between overflow and size
-float *_rt_exec_time;
-#if MMDC_PERF
-float *_rt_mmdc_read;
-float *_rt_mmdc_write;
-#endif
-long _rt_jobs_complete;
-long _rt_max_jobs;
-int _rt_core;
-int _rt_will_output;
-struct timespec _rt_start, _rt_end;
-
-char *_rt_run_id;
-char *_rt_our_prog_name;
-#define _RT_FILENAME_LEN 64
-
-#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;\
-    mlockall(MCL_CURRENT || MCL_FUTURE);
-
-#define SETUP_MMDC \
-    _rt_mmdc_read = calloc(_rt_max_jobs * _rt_will_output, sizeof(float));\
-    _rt_mmdc_write = calloc(_rt_max_jobs * _rt_will_output, sizeof(float));\
-    if (!_rt_mmdc_read || !_rt_mmdc_write) {\
-        perror("Unable to allocate buffer for MMDC data");\
-        exit(1);\
-    }\
-    MMDC_PROFILE_RES_t mmdc_res;\
-    memset(&mmdc_res, 0, sizeof(MMDC_PROFILE_RES_t));\
-    int fd = open("/dev/mem", O_RDWR, 0);\
-    if (fd < 0) {\
-        perror("Unable to open /dev/mem");\
-        exit(1);\
-    }\
-    pMMDC_t mmdc = mmap(NULL, 0x4000, PROT_READ | PROT_WRITE, MAP_SHARED, fd, MMDC_P0_IPS_BASE_ADDR);\
-    if (mmdc == MAP_FAILED) {\
-        perror("Unable to map MMDC address space");\
-        exit(1);\
-    }\
-    mmdc->madpcr1 = axi_arm1;\
-    msync(&(mmdc->madpcr1),4,MS_SYNC);
-
-#define SETUP_LITMUS \
-    unsigned int wait = 0; \
-    if (be_migrate_to_domain(_rt_core) < 0) { \
-        perror("Unable to migrate to specified CPU"); \
-        exit(1); \
-    } \
-    struct reservation_config res; \
-    res.id = gettid(); \
-    res.cpu = cpu; \
-    res.priority = LITMUS_HIGHEST_PRIORITY; \
-    /* we take over half the CPU time (these are ns) */ \
-    res.polling_params.budget = ms2ns(3000); \
-    res.polling_params.period = ms2ns(3000); \
-    res.polling_params.offset = 0; \
-    res.polling_params.relative_deadline = ms2ns(3000); \
-    /* Not 100% sure that we should use periodic polling */ \
-    if (reservation_create(PERIODIC_POLLING, &res) < 0) { \
-        perror("Unable to create reservation"); \
-        exit(1); \
-    } \
-    struct rt_task rt_param; \
-    init_rt_task_param(&rt_param); \
-    /* Supposedly the next two parameters are irrelevant when reservations are enabled, but I'm leaving them anyway... */ \
-    rt_param.exec_cost = ms2ns(999); \
-    rt_param.period = ms2ns(1000); \
-    rt_param.priority = LITMUS_HIGHEST_PRIORITY; \
-    rt_param.cls = RT_CLASS_HARD; \
-    rt_param.release_policy = TASK_PERIODIC; \
-    rt_param.budget_policy = NO_ENFORCEMENT; \
-    rt_param.cpu = cpu; \
-    if (set_rt_task_param(gettid(), &rt_param) < 0) { \
-        perror("Unable to set real-time parameters"); \
-        exit(1); \
-    } \
-    if (init_litmus() != 0) { \
-        perror("init_litmus failed"); \
-        exit(1); \
-    } \
-    MC2_SETUP \
-    if (task_mode(LITMUS_RT_TASK) != 0) { \
-        perror("Unable to become real-time task"); \
-        exit(1); \
-    } \
-    if (wait && wait_for_ts_release() != 0) { \
-        perror("Unable to wait for taskset release"); \
-        exit(1); \
-    }
-
-#if MC2
-#define MC2_SETUP \
-    struct mc2_task mc2_param; \
-    mc2_param.res_id = gettid(); \
-    mc2_param.crit = CRIT_LEVEL_A; \
-    if (set_mc2_task_param(gettid(), &mc2_param) < 0) { \
-        perror("Unable to set MC^2 task params"); \
-        exit(1); \
-    } \
-    set_page_color(rt_param.cpu);
-#else
-#define MC2_SETUP
-#endif
-
-#define CLEANUP_LITMUS \
-    if (task_mode(BACKGROUND_TASK) != 0) { \
-        perror("Unable to become a real-time task"); \
-        exit(1); \
-    } \
-    reservation_destroy(gettid(), rt_param.cpu);
-
-#if __arm__
-// On ARM, manually flush the cache
-#define FLUSH_CACHES \
-    volatile uint8_t buffer[L2_SIZE * 4]; \
-    for (uint32_t j = 0; j < 4; j++) \
-        for (uint32_t i = 0; i < L2_SIZE * 4; i += LINE_SIZE) \
-            buffer[i]++;
-#else
-// On x86 call the wbinvld instruction (it's in a kernel module due to it being ring-0)
-#define FLUSH_CACHES \
-    FILE *fp = fopen("/proc/wbinvd", "r");\
-    if (fp == NULL) {\
-        perror("Cache flush module interface cannot be opened");\
-        exit(1);\
-    }\
-    char dummy;\
-    if (fread(&dummy, 1, 1, fp) == 0) {\
-        perror("Unable to access cache flush module interface");\
-        exit(1);\
-    }\
-    fclose(fp);
-#endif
-
-// Buffer timing result from a single job
-static void _rt_save_job_result() {
-    if (_rt_jobs_complete >= _rt_max_jobs) {
-        fprintf(stderr, "Max jobs setting too small! Trying to record job #%ld when we only have space for %ld jobs. Exiting...\n", _rt_jobs_complete, _rt_max_jobs);
-        exit(1);
-    }
-    if (_rt_jobs_complete > -1 && _rt_will_output) {
-        _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] += _rt_end.tv_nsec - _rt_start.tv_nsec;
-#if MMDC_PROF
-        _rt_mmdc_read[_rt_jobs_complete] = mmdc_res.read_bytes;
-        _rt_mmdc_write[_rt_jobs_complete] = mmdc_res.write_bytes;
-#endif
-    }
-}
-
-// Save all buffered timing results to disk
-static void _rt_write_to_file() {
-    char fileName[_RT_FILENAME_LEN];
-    FILE *fp;
-    if (!_rt_will_output)
-        return;
-    munlockall();
-    strcpy(fileName, _rt_run_id);
-    strcat(fileName, ".txt");
-    fp = fopen(fileName, "a");
-    if (fp == NULL) {
-        perror("Unable to open _rt_will_output file");
-        exit(1);
-    }
-    // Same format as the paired results 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,
-#if MMDC_PROF
-        _rt_mmdc_read[i], _rt_mmdc_write[i]);
-#else
-        0.0, 0.0);
-#endif
-    }
-    fclose(fp);
-#if LITMUS
-    CLEANUP_LITMUS
-#endif
-}
-
-// Start a job
-static void _rt_start_loop() {
-#if LITMUS
-    if (sleep_next_period() != 0) {
-        perror("Unable to sleep for next period");
-    }
-#else
-    sched_yield();
-#endif
-    FLUSH_CACHES
-#if MMDC_PROF
-    /* This disables profiling, resets the counters, clears the overflow bit, and enables profiling */
-    start_mmdc_profiling(mmdc);
-#endif
-    clock_gettime(CLOCK_MONOTONIC, &_rt_start);
-}
-
-// Complete a job
-static void _rt_stop_loop() {
-    clock_gettime(CLOCK_MONOTONIC, &_rt_end);
-#if MMDC_PROF
-    /* This freezes the profiling and makes results available */
-    pause_mmdc_profiling(mmdc);
-    get_mmdc_profiling_results(mmdc, &mmdc_res);
-#endif
-    _rt_save_job_result();
-    _rt_jobs_complete++;
-}
-
-/****** New API ******
- * Intended structure:
- *
- * |int main(int argc, char **argv) {
- * |  SET_UP
- * |  ...
- * |  for_each_job {
- * |    tacleInit();
- * |    tacleMain();
- * |  }
- * |  WRITE_TO_FILE
- * |}
- *
- * The main() function must call its parameters argc and argv for SET_UP to be
- * able to read them.
- * Only SET_UP necessarily has to be in main().
- *
- * We use some niche C features, here's a quick explaination:
- * 1. The && operator doesn't evaluate the right-hand side of the expression
- *    unless the left side evaluated to true. We use this to only execute 
- *    _rt_start_loop() when the loop will actually run.
- * 2. The comma operator executes the first expression and then throws away the
- *    result. We use this to call our void function from inside a comparison.
- */
-#define for_each_job \
-    for (; _rt_jobs_complete < _rt_max_jobs && (_rt_start_loop(),1); \
-         _rt_stop_loop())
-
-/****** Legacy API ******
- * Intended structure:
- *
- * |int main(int argc, char **argv) {
- * |  SET_UP
- * |  for (jobsComplete=0; jobsComplete<maxJobs; jobsComplete++){
- * |    START_LOOP
- * |    tacleInit();
- * |    tacleMain();
- * |    STOP_LOOP
- * |  }
- * |  WRITE_TO_FILE
- * |  tacleReturn
- * |}
- *
- * The main() function must call its parameters argc and argv for SET_UP to be
- * able to read them.
- */
-static int jobsComplete = 0;
-#define START_LOOP _rt_start_loop();
-#define STOP_LOOP _rt_stop_loop();
-#define WRITE_TO_FILE _rt_write_to_file();
-#define maxJobs _rt_max_jobs
-// Has been part of STOP_LOOP for quite some time
-#define SAVE_RESULTS \
-    #warning "The SAVE_RESULTS macro is deprecated and will soon be removed!";
-// Unclear if SLEEP is used anywhere.
-#define SLEEP \
-    #warning "The SLEEP macro is deprecated and may be removed!" \
-    nanosleep((const struct timespec[]){{0, 1000000}}, NULL);
diff --git a/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"