PrIM -- first commit

3 files changed, 191 insertions, 0 deletions

diff --git a/NW/support/common.h b/NW/support/common.h
new file mode 100755
index 0000000..69069e7
--- /dev/null
+++ b/NW/support/common.h
@@ -0,0 +1,76 @@
+#ifndef _COMMON_H_
+#define _COMMON_H_
+
+// Structures used by both the host and the dpu to communicate information 
+typedef struct {
+    uint32_t nblocks;
+    uint32_t active_blocks;
+    uint32_t penalty;
+    uint32_t dummy;
+} dpu_arguments_t;
+
+#ifndef BL
+#define BL 16 
+#endif
+
+// Data type
+#define T int32_t
+
+// MAX
+int32_t maximum(int32_t a, int32_t b, int32_t c) {
+
+    int32_t k;
+    if (a <= b)
+        k = b;
+    else
+        k = a;
+
+    if (k <= c)
+        return c;
+    else
+        return k;
+        
+}
+
+#define DPU_CAPACITY (64 << 20) // A DPU's capacity is 64 MiB
+
+#define ANSI_COLOR_RED     "\x1b[31m"
+#define ANSI_COLOR_GREEN   "\x1b[32m"
+#define ANSI_COLOR_RESET   "\x1b[0m"
+
+#define LIMIT -999
+
+int blosum62[24][24] = {
+    { 4, -1, -2, -2,  0, -1, -1,  0, -2, -1, -1, -1, -1, -2, -1,  1,  0, -3, -2,  0, -2, -1,  0, -4},
+    {-1,  5,  0, -2, -3,  1,  0, -2,  0, -3, -2,  2, -1, -3, -2, -1, -1, -3, -2, -3, -1,  0, -1, -4},
+    {-2,  0,  6,  1, -3,  0,  0,  0,  1, -3, -3,  0, -2, -3, -2,  1,  0, -4, -2, -3,  3,  0, -1, -4},
+    {-2, -2,  1,  6, -3,  0,  2, -1, -1, -3, -4, -1, -3, -3, -1,  0, -1, -4, -3, -3,  4,  1, -1, -4},
+    { 0, -3, -3, -3,  9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4},
+    {-1,  1,  0,  0, -3,  5,  2, -2,  0, -3, -2,  1,  0, -3, -1,  0, -1, -2, -1, -2,  0,  3, -1, -4},
+    {-1,  0,  0,  2, -4,  2,  5, -2,  0, -3, -3,  1, -2, -3, -1,  0, -1, -3, -2, -2,  1,  4, -1, -4},
+    { 0, -2,  0, -1, -3, -2, -2,  6, -2, -4, -4, -2, -3, -3, -2,  0, -2, -2, -3, -3, -1, -2, -1, -4},
+    {-2,  0,  1, -1, -3,  0,  0, -2,  8, -3, -3, -1, -2, -1, -2, -1, -2, -2,  2, -3,  0,  0, -1, -4},
+    {-1, -3, -3, -3, -1, -3, -3, -4, -3,  4,  2, -3,  1,  0, -3, -2, -1, -3, -1,  3, -3, -3, -1, -4},
+    {-1, -2, -3, -4, -1, -2, -3, -4, -3,  2,  4, -2,  2,  0, -3, -2, -1, -2, -1,  1, -4, -3, -1, -4},
+    {-1,  2,  0, -1, -3,  1,  1, -2, -1, -3, -2,  5, -1, -3, -1,  0, -1, -3, -2, -2,  0,  1, -1, -4},
+    {-1, -1, -2, -3, -1,  0, -2, -3, -2,  1,  2, -1,  5,  0, -2, -1, -1, -1, -1,  1, -3, -1, -1, -4},
+    {-2, -3, -3, -3, -2, -3, -3, -3, -1,  0,  0, -3,  0,  6, -4, -2, -2,  1,  3, -1, -3, -3, -1, -4},
+    {-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4,  7, -1, -1, -4, -3, -2, -2, -1, -2, -4},
+    { 1, -1,  1,  0, -1,  0,  0,  0, -1, -2, -2,  0, -1, -2, -1,  4,  1, -3, -2, -2,  0,  0,  0, -4},
+    { 0, -1,  0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1,  1,  5, -2, -2,  0, -1, -1,  0, -4},
+    {-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1,  1, -4, -3, -2, 11,  2, -3, -4, -3, -2, -4},
+    {-2, -2, -2, -3, -2, -1, -2, -3,  2, -1, -1, -2, -1,  3, -3, -2, -2,  2,  7, -1, -3, -2, -1, -4},
+    { 0, -3, -3, -3, -1, -2, -2, -3, -3,  3,  1, -2,  1, -1, -2, -2,  0, -3, -1,  4, -3, -2, -1, -4},
+    {-2, -1,  3,  4, -3,  0,  1, -1,  0, -3, -4,  0, -3, -3, -2,  0, -1, -4, -3, -3,  4,  1, -1, -4},
+    {-1,  0,  0,  1, -3,  3,  4, -2,  0, -3, -3,  1, -1, -3, -1,  0, -1, -3, -2, -2,  1,  4, -1, -4},
+    { 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2,  0,  0, -2, -1, -1, -1, -1, -1, -4},
+    {-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,  1}
+};
+
+#define DYNAMIC 1
+#define PRINT 0
+#define PRINT_FILE 0
+#ifndef ENERGY
+#define ENERGY 0
+#endif
+#endif
diff --git a/NW/support/params.h b/NW/support/params.h
new file mode 100644
index 0000000..8874248
--- /dev/null
+++ b/NW/support/params.h
@@ -0,0 +1,56 @@
+#ifndef _PARAMS_H_
+#define _PARAMS_H_
+
+#include "common.h"
+
+typedef struct Params {
+    unsigned int   max_rows;
+    unsigned int   penalty;
+    unsigned int   n_warmup;
+    unsigned int   n_reps;
+} Params;
+
+static void usage() {
+    fprintf(stderr,
+            "\nUsage:  ./program [options]"
+            "\n"
+            "\nGeneral options:"
+            "\n    -h        help"
+            "\n    -w <W>    # of untimed warmup iterations (default=1)"
+            "\n    -e <E>    # of timed repetition iterations (default=3)"
+            "\n"
+            "\nBenchmark-specific options:"
+            "\n    -n <N>    size of sequence: length of the sequence"
+            "\n    -p <P>    penalty: a positive integer"
+            "\n");
+}
+
+struct Params input_params(int argc, char **argv) {
+    struct Params p;
+    p.n_warmup      = 1;
+    p.n_reps        = 3;
+    p.max_rows      = 256;
+    p.penalty       = 1;
+
+    int opt;
+    while((opt = getopt(argc, argv, "hw:e:n:p:")) >= 0) {
+        switch(opt) {
+            case 'h':
+                usage();
+                exit(0);
+                break;
+            case 'w': p.n_warmup      = atoi(optarg); break;
+            case 'e': p.n_reps        = atoi(optarg); break;
+            case 'n': p.max_rows      = atoi(optarg); break;
+            case 'p': p.penalty       = atoi(optarg); break;
+            default:
+                      fprintf(stderr, "\nUnrecognized option!\n");
+                      usage();
+                      exit(0);
+        }
+    }
+    assert(NR_DPUS > 0 && "Invalid # of dpus!");
+
+    return p;
+}
+#endif
diff --git a/NW/support/timer.h b/NW/support/timer.h
new file mode 100755
index 0000000..efaefcd
--- /dev/null
+++ b/NW/support/timer.h
@@ -0,0 +1,59 @@
+/*

+ * Copyright (c) 2016 University of Cordoba and University of Illinois

+ * All rights reserved.

+ *

+ * Developed by:    IMPACT Research Group

+ *                  University of Cordoba and University of Illinois

+ *                  http://impact.crhc.illinois.edu/

+ *

+ * Permission is hereby granted, free of charge, to any person obtaining a copy

+ * of this software and associated documentation files (the "Software"), to deal

+ * with 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:

+ *

+ *      > Redistributions of source code must retain the above copyright notice,

+ *        this list of conditions and the following disclaimers.

+ *      > Redistributions in binary form must reproduce the above copyright

+ *        notice, this list of conditions and the following disclaimers in the

+ *        documentation and/or other materials provided with the distribution.

+ *      > Neither the names of IMPACT Research Group, University of Cordoba, 

+ *        University of Illinois nor the names of its contributors may be used 

+ *        to endorse or promote products derived from this Software without 

+ *        specific prior written permission.

+ *

+ * 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 

+ * CONTRIBUTORS 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 WITH

+ * THE SOFTWARE.

+ *

+ */

+

+#include <sys/time.h>

+

+typedef struct Timer{

+

+    struct timeval startTime[5];

+    struct timeval stopTime[5];

+    double         time[5];

+

+}Timer;

+

+void start(Timer *timer, int i, int rep) {

+    if(rep == 0) {

+        timer->time[i] = 0.0;

+    }

+    gettimeofday(&timer->startTime[i], NULL);

+}

+

+void stop(Timer *timer, int i) {

+    gettimeofday(&timer->stopTime[i], NULL);

+    timer->time[i] += (timer->stopTime[i].tv_sec - timer->startTime[i].tv_sec) * 1000000.0 +

+                      (timer->stopTime[i].tv_usec - timer->startTime[i].tv_usec); 

+}

+

+void print(Timer *timer, int i, int REP) { printf("Time (ms): %f\t", timer->time[i] / (1000 * REP)); }