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For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.

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# A Performance Analysis of High-Level Synthesis for FPGAs
This repository stores the code and latex of my bachelor's thesis. The full thesis PDF can be found in [hls_performance_thesis.pdf](hls_performance_thesis.pdf).
## Abstract
It is becoming increasingly popular to use Field-Programmable Gate Arrays (FPGAs)
as hardware accelerators in order to speed up certain parts of an algorithm. FPGAs
promise more energy efficiency and increased performance compared to CPUs. They are,
however, traditionally programmed with Hardware Description Languages (HDLs), which
are notoriously hard to use.
To accelerate their adoption in different contexts and domains, FPGAs can nowadays
also be programmed with high-level languages, such as C/C++ or OpenCL, in a process
called High-Level Synthesis (HLS). However, it can be a challenge to efficiently accelerate
algorithms using HLS.
In this thesis, we investigate the performance of HLS for a non-trivial case-study. To
this end, we devise a performance comparison between a sequential CPU algorithm and its
FPGA version, programmed with OpenCL for the Xilinx Vitis platform. Our case study is a
string-searching algorithm using the FM-index method, which is able to efficiently locate
substrings in arbitrarily long texts.
Our naive reference implementation is a simple port from CPU to OpenCL. In search
for more performance, on top of this naive OpenCL implementation, we also propose and
evaluate two FPGA-specific optimizations, suggested by literature.
Our empirical analysis shows that optimizations can greatly improve the performance of
algorithms programmed with HLS for FPGAs. However, the performance of our HLS-based
FPGA version for our case study could not match the performance of the CPU, despite
being more work efficient.

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program
repl
construct
experiment_data
generate_test_data
benchmark

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CC=gcc
CPPC=g++
CFLAGS=-I. -Wextra -Wall -g
DEPS = fmindex.h util.h
OBJ = fmindex.o util.o rapl.o
EXES = program repl construct generate_test_data benchmark
%.o: %.c $(DEPS)
$(CC) -c -o $@ $< $(CFLAGS)
all: $(EXES)
program: $(OBJ) program.o
$(CC) -o $@ $^ $(CFLAGS)
repl: $(OBJ) repl.o
$(CC) -o $@ $^ $(CFLAGS)
construct: $(OBJ) construct.o
$(CC) -o $@ $^ $(CFLAGS)
generate_test_data: $(OBJ) generate_test_data.o
$(CPPC) -o $@ $^ $(CFLAGS)
benchmark: $(OBJ) benchmark.o
$(CPPC) -o $@ $^ $(CFLAGS)
.PHONY: clean all
clean:
rm -f *.o *~ core $(EXES)

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#define _GNU_SOURCE
#include "fmindex.h"
#include "rapl.h"
#include "util.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <unistd.h>
// Global variables which can be accessed in function reference.
unsigned pattern_count, pattern_sz, max_match_count;
char *patterns;
fm_index *fm;
float total_time;
unsigned long total_matches = 0;
unsigned long *match_indices;
static void benchmark(void) {
float time1 = 0., time2 = 0.;
float start_time, end_time;
for (unsigned i = 0; i < pattern_count; ++i) {
ranges_t start, end;
start_time = (float)clock() / CLOCKS_PER_SEC;
FMIndexFindMatchRange(fm, &patterns[i * pattern_sz], pattern_sz, &start,
&end);
end_time = (float)clock() / CLOCKS_PER_SEC;
time1 += end_time - start_time;
start_time = (float)clock() / CLOCKS_PER_SEC;
FMIndexFindRangeIndices(fm, start, end, &match_indices);
end_time = (float)clock() / CLOCKS_PER_SEC;
time2 += end_time - start_time;
total_matches += end - start;
}
total_time = time1 + time2;
}
int main(int argc, char **argv) {
if (argc < 3) {
fprintf(stderr, "Usage: $ %s <FMFILE> <TESTFILE>\n", argv[0]);
return 1;
}
fm = FMIndexReadFromFile(argv[1], 0);
if (!fm) {
fprintf(stderr, "Failed to read FM-index from file.\n");
return 1;
}
if (!(LoadTestData(argv[2], &patterns, &pattern_count, &pattern_sz,
&max_match_count, 0))) {
fprintf(stderr, "Could not read test data file.\n");
return 1;
}
match_indices = calloc(max_match_count, sizeof(unsigned long));
if (!match_indices) {
fprintf(stderr, "Failed to allocate memory for match indices.\n");
return 1;
}
double total_joules;
if (rapl_sysfs(benchmark, &total_joules) != 0) {
fprintf(stderr, "Failed to get energy consumption\n");
return 1;
}
printf("%a %a %lu\n", total_time, total_joules, total_matches);
free(match_indices);
free(patterns);
FMIndexFree(fm);
return 0;
}

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import argparse
import subprocess
import os
def main(repeats, count, maxmatches, lengths, dir, filenames):
for filename in filenames:
for length in lengths:
benchmark(repeats, count, maxmatches, length, dir, filename)
def benchmark(repeats, count, maxmatches, length, dir, filename):
testfilename = f"{dir}/{filename}.cpu{length}.test"
fmfilename = f"{dir}/{filename}.fm"
textfilename = f"{dir}/{filename}"
resultfilename = f"{dir}/{filename}.cpu{length}.result"
gentestargs = ["./generate_test_data", textfilename, fmfilename, testfilename, str(count), str(length), str(maxmatches)]
benchmarkargs = ["./benchmark", fmfilename, testfilename]
print(" ".join(gentestargs))
print(" ".join(benchmarkargs))
# Remove result file if it already exists.
try:
os.remove(resultfilename)
except OSError:
pass
for n in range(repeats):
print(f"{n+1}/{repeats}")
# Create test file.
gentestproc = subprocess.Popen(gentestargs, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = gentestproc.communicate()
if stderr:
print(f">{stderr.strip()}")
ret = gentestproc.poll()
if ret != 0:
print(f"Error creating test data: {stdout.strip()}")
exit(1)
# Create result file.
with open(resultfilename, "a") as resultfile:
benchmarkproc = subprocess.Popen(benchmarkargs, stdout=resultfile, universal_newlines=True, stderr=subprocess.PIPE)
_, stderr = benchmarkproc.communicate()
if stderr:
print(f">{stderr.strip()}")
ret = benchmarkproc.poll()
if ret != 0:
print("Error benchmarking test data")
exit(1)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("-n", "--repeats", help="number of times to repeat each experiment", type=int, required=True)
parser.add_argument("-c", "--count", help="number of patterns", type=int, required=True)
parser.add_argument("-m", "--maxmatches", help="maximum number of matches per pattern", type=int, required=True)
parser.add_argument("-l", "--lengths", help="length of the patterns", type=int, nargs="+", default=[], required=True)
parser.add_argument("-d", "--dir", help="directory containing FM-indices and original texts (with the same name)", required=True)
parser.add_argument("-f", "--files", help="FM-index files to benchmark", nargs="+", default=[], required=True)
args = parser.parse_args()
main(args.repeats, args.count, args.maxmatches, args.lengths, args.dir, args.files)

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#include "fmindex.h"
#include "util.h"
#include <stdio.h>
int main(int argc, char *argv[]) {
if (argc < 3) {
printf("Usage: $ %s <INPUTFILE> <OUTPUTFILE>\n", argv[0]);
return 1;
}
char *s = ReadFile(argv[1]);
if (!s)
return 1;
fm_index *index = FMIndexConstruct(s);
if (!index) {
printf("Failed to construct index.\n");
return 1;
}
if (!FMIndexDumpToFile(index, argv[2])) {
printf("Failed to write FM-index to file.\n");
return 1;
}
FMIndexFree(index);
free(s);
return 0;
}

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0x1.6477fp-2 0x1.22abebp+25 171360982
0x1.5b44c8p-2 0x1.2b59f9p+25 174285929
0x1.66d8p-2 0x1.28d3dcp+25 172040584
0x1.59b5ep-2 0x1.29edabp+25 174000838
0x1.5f7ep-2 0x1.1f099cp+25 168176711

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0x1.dc032p-3 0x1.885c8ap+24 108982070
0x1.e32bp-3 0x1.8e6becp+24 110444451
0x1.e262ap-3 0x1.8d2bf8p+24 110958122
0x1.f334p-3 0x1.9b5deep+24 115123603
0x1.ce874p-3 0x1.81151p+24 113346544

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0x1.d3c5p-4 0x1.903b2ap+23 53234288
0x1.c491cp-4 0x1.86f7dcp+23 51182855
0x1.cfe28p-4 0x1.8f3564p+23 52348451
0x1.c04p-4 0x1.800afep+23 50877186
0x1.f90c8p-4 0x1.b10df8p+23 50214738

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0x1.fb7a8p-2 0x1.a2b59e8p+25 256535338
0x1.f103ap-2 0x1.9a685cp+25 250410896
0x1.f7b0fp-2 0x1.a13b028p+25 248846051
0x1.f6ec6p-2 0x1.a16cb88p+25 253974661
0x1.ff299p-2 0x1.a58ed2p+25 258322531

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0x1.4d16ap-2 0x1.1620e78p+25 165252248
0x1.53f52p-2 0x1.1b1bb98p+25 168443910
0x1.438b4p-2 0x1.0d4fcd8p+25 160215390
0x1.4b71ep-2 0x1.12ba34p+25 163605068
0x1.4fafcp-2 0x1.1698d4p+25 166128629

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0x1.41d8ap-3 0x1.11bfap+24 74552832
0x1.3eefep-3 0x1.0daaa3p+24 74737159
0x1.3c48ap-3 0x1.0aea5ap+24 74006790
0x1.4209ap-3 0x1.12066fp+24 75652221
0x1.3e1a2p-3 0x1.0f36e4p+24 74332277

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0x1.4045dp-1 0x1.09ff364p+26 319604955
0x1.45e9cp-1 0x1.0e48e38p+26 325973389
0x1.4ec6cp-1 0x1.167383cp+26 334037324
0x1.44e6cp-1 0x1.0b42dd4p+26 324111950
0x1.494b4p-1 0x1.0ec5e1p+26 329018290

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0x1.ba04ep-2 0x1.6f1d43p+25 215259281
0x1.b1094p-2 0x1.67563b8p+25 211398266
0x1.a9b66p-2 0x1.63b7078p+25 211580469
0x1.a923ap-2 0x1.62cc108p+25 211496190
0x1.a2bd4p-2 0x1.5db353p+25 209139670

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0x1.9d7fcp-3 0x1.5d2c61p+24 97664968
0x1.a1b28p-3 0x1.61a48cp+24 99282005
0x1.8a2ecp-3 0x1.4df333p+24 92818122
0x1.8d93p-3 0x1.4f55f7p+24 94123638
0x1.9f80cp-3 0x1.5ca19ep+24 99177125

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0x1.845828p-1 0x1.35f82dp+26 398786955
0x1.83880cp-1 0x1.3729878p+26 398482564
0x1.80a4aap-1 0x1.3b15634p+26 394461926
0x1.82cccep-1 0x1.3dccf9p+26 395082462
0x1.7d2d2p-1 0x1.3768a68p+26 389967743

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0x1.125d58p-4 0x1.e6b25cp+22 30743684
0x1.1521ecp-4 0x1.ea8d6cp+22 30733306
0x1.11be7p-4 0x1.e61bbp+22 30733306
0x1.13663p-4 0x1.eda22p+22 30733306
0x1.11cec8p-4 0x1.ee1d24p+22 30417546

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0x1.117a6p-6 0x1.3a3a3p+21 2970948
0x1.17e02p-6 0x1.3a5c88p+21 3124607
0x1.18c4cp-6 0x1.3b61ep+21 3124607
0x1.11e68p-6 0x1.344a18p+21 2892252
0x1.0cb7p-6 0x1.37acp+21 2892252

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0x1.220476p+0 0x1.dccf43cp+26 593315165
0x1.22aa62p+0 0x1.dcfa4c8p+26 592263458
0x1.22da9p+0 0x1.dd50e78p+26 593423513
0x1.1ff9cp+0 0x1.d815f2cp+26 590120821
0x1.23b0fcp+0 0x1.ddc499p+26 596923038

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0x1.8e7eep-4 0x1.5d36a2p+23 45834923
0x1.90183p-4 0x1.5d6cfep+23 46403238
0x1.8ed448p-4 0x1.5d5062p+23 46403238
0x1.8d61c8p-4 0x1.5b89p+23 46113391
0x1.8d3038p-4 0x1.5b6894p+23 46485028

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0x1.6c464p-6 0x1.82f5b8p+21 4495841
0x1.4d9eep-6 0x1.6b5b4p+21 4544987
0x1.4460ep-6 0x1.63f73p+21 4407471
0x1.4afa4p-6 0x1.69936p+21 4407471
0x1.4609ep-6 0x1.64212p+21 4295384

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0x1.6d8ecp+0 0x1.2f4f214p+27 746010747
0x1.71c79cp+0 0x1.2f301bp+27 749721648
0x1.6ec31cp+0 0x1.2f3a726p+27 747612561
0x1.70d87p+0 0x1.2edfc9ep+27 750618917
0x1.6ec052p+0 0x1.2f4e6a2p+27 748739834

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0x1.00d65p-3 0x1.b9f4c6p+23 61287159
0x1.05935p-3 0x1.c33dccp+23 62472530
0x1.065c2p-3 0x1.bc9bc8p+23 62363451
0x1.045de8p-3 0x1.b96f42p+23 61764726

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0x1.86b58p-6 0x1.928bd8p+21 6072658
0x1.9694p-6 0x1.9fdc58p+21 6469630
0x1.8e7ccp-6 0x1.998cdp+21 6232401
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0x1.39b24p-6 0x1.5654cp+21 4815936
0x1.371e4p-6 0x1.556278p+21 4696974
0x1.3561p-6 0x1.50c5d8p+21 4712326
0x1.3b6ccp-6 0x1.5829e8p+21 4915309
0x1.3af18p-6 0x1.503c8p+21 4856245

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0x1.15a98p-6 0x1.31103p+21 2748401
0x1.15968p-6 0x1.33adbp+21 2761448
0x1.18ca8p-6 0x1.364d08p+21 2771358
0x1.19dbcp-6 0x1.361f5p+21 2807302

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0x1.248ccp-6 0x1.309438p+21 2028498
0x1.1ba54p-6 0x1.3654bp+21 1966015
0x1.2766p-6 0x1.43da8p+21 2049837
0x1.238fcp-6 0x1.4395d8p+21 2008116
0x1.25804p-6 0x1.36f11p+21 2061600

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0x1.5bc68p-6 0x1.711bcp+21 5783326
0x1.6099p-6 0x1.7d223p+21 5898449
0x1.66854p-6 0x1.7739ap+21 6078789
0x1.6189cp-6 0x1.787828p+21 6050872
0x1.6b70cp-6 0x1.7dd76p+21 6253011

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0x1.263dp-6 0x1.490a08p+21 2963082
0x1.2396p-6 0x1.4304e8p+21 2984599
0x1.298f8p-6 0x1.4e9adp+21 3180703
0x1.27a28p-6 0x1.4a6158p+21 3016497
0x1.1fd18p-6 0x1.3c4108p+21 2913659

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0x1.36784p-6 0x1.635e9p+21 2393193
0x1.3a3a4p-6 0x1.51c57p+21 2397301
0x1.38688p-6 0x1.572878p+21 2449818
0x1.35684p-6 0x1.44aa68p+21 2267396
0x1.3395cp-6 0x1.53db88p+21 2294787

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0x1.6376p-6 0x1.79c41p+21 5720934
0x1.620cp-6 0x1.748edp+21 5745857
0x1.9e548p-6 0x1.a69888p+21 6040126
0x1.6031p-6 0x1.7a4d68p+21 5780235
0x1.6ee28p-6 0x1.888e2p+21 6174243

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0x1.1d6a8p-6 0x1.378d78p+21 2639463
0x1.16ddp-6 0x1.37a828p+21 2403897
0x1.1bec8p-6 0x1.379518p+21 2522317
0x1.1828p-6 0x1.37952p+21 2494930
0x1.1b8dp-6 0x1.3dbc9p+21 2490305

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0x1.2e9d8p-6 0x1.4bb4dp+21 1915812
0x1.2c43p-6 0x1.442aap+21 1825102
0x1.2931p-6 0x1.440ffp+21 1824534
0x1.31928p-6 0x1.440ep+21 1962021
0x1.2cef8p-6 0x1.483648p+21 1863384

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#define _GNU_SOURCE
#include "fmindex.h"
#include "util.h"
#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
inline static int string_index(char *s, char c) { return strchr(s, c) - s; }
static int CompareChar(const void *a, const void *b) {
char i = *(char *)a;
char j = *(char *)b;
// Dollar sign is always sorted first.
if (i == '$')
return -1;
if (j == '$')
return 1;
return i > j;
}
/* Converts the given string to a newly allocated string
* of all distinct characters, sorted in lexicographical order.
* The dollar sign is always sorted first.
* Return NULL on memory allocation error.
*/
char *TextToAlphabet(char *text, size_t sz) {
char *alphabet = calloc(2, sizeof(char));
if (!alphabet)
return NULL;
alphabet[0] = '$';
alphabet[1] = '\0';
int len = 2;
for (size_t i = 0; i < sz; ++i) {
if (!strchr(alphabet, text[i])) {
len += 1;
alphabet = realloc(alphabet, len);
alphabet[len - 2] = text[i];
alphabet[len - 1] = '\0';
}
}
qsort(alphabet, len - 1, sizeof(char), &CompareChar);
return alphabet;
}
static int CompareSuffixArray(const void *a, const void *b, void *arg) {
sa_t i = *(sa_t *)a;
sa_t j = *(sa_t *)b;
char *s = arg;
while (s[i] != '\0' && s[j] != '\0' && s[i] == s[j]) {
++i;
++j;
}
if (s[i] == '\0')
return -1;
if (s[j] == '\0')
return 1;
return s[i] > s[j];
}
/* Construct a newly allocated suffix array for the given string.
* The suffix array holds the index for each suffix in the given string.
* Then the indices are sorted by the lexicographical ordering of the suffices.
* Return NULL on memory allocation error.
*/
sa_t *ConstructSuffixArray(char *s, size_t sz) {
sa_t *suffix_array = calloc(sz + 1, sizeof(sa_t));
if (!suffix_array)
return NULL;
for (size_t i = 0; i < sz + 1; ++i)
suffix_array[i] = i;
qsort_r(suffix_array, sz + 1, sizeof(sa_t), &CompareSuffixArray, s);
return suffix_array;
}
/* Construct the Burrows-Wheeler transform of the given string,
* using the corresponding suffix array.
* Return NULL on memory allocation error.
*/
char *ConstructBWT(char *s, size_t sz, sa_t *suffix_array) {
char *bwt = calloc(sz + 2, sizeof(char));
if (!bwt)
return NULL;
for (size_t i = 0; i < sz + 1; ++i) {
sa_t n = suffix_array[i];
// Index 0 is always the dollar sign.
bwt[i] = (n) ? s[suffix_array[i] - 1] : '$';
}
bwt[sz + 1] = '\0';
return bwt;
}
/* Construct the rank matrix for the given Burrows-Wheeler transformed string.
* The rank matrix is an (alphabet X bwt) sized array that holds the accumulated
* counts of encountered characters in the BWT.
* A newly allocated rank matrix is returned, or NULL on memory error.
*/
ranks_t *ConstructRankMatrix(char *bwt, size_t sz, char *alphabet) {
size_t alphabet_sz = strlen(alphabet);
ranks_t *rank_matrix = calloc(sz * alphabet_sz, sizeof(ranks_t));
if (!rank_matrix) {
printf("Failed to allocate %lu bytes.\n", sz * alphabet_sz);
return NULL;
}
ranks_t acc[alphabet_sz];
// Initialize counts with zero.
for (size_t i = 0; i < alphabet_sz; ++i)
acc[i] = 0;
for (size_t i = 0; i < sz; ++i) {
char c = bwt[i];
// Update accumulator.
for (unsigned j = 0; j < alphabet_sz; ++j)
if (c == alphabet[j]) {
++acc[j];
break;
}
for (unsigned j = 0; j < alphabet_sz; ++j)
rank_matrix[i * alphabet_sz + j] = acc[j];
}
return rank_matrix;
}
/* Calculate the ranges in the "F column" where each character
* in the alphabet appears.
* Return a (2 X alphabet) matrix where each row means the starting
* and ending range for a character.
* Return NULL on memory error.
*/
ranges_t *ConstructCharacterRanges(char *bwt, size_t sz, char *alphabet) {
size_t alphabet_sz = strlen(alphabet);
unsigned long counts[alphabet_sz];
// Set counts to zero.
for (size_t i = 0; i < alphabet_sz; ++i)
counts[i] = 0;
// Count total amounts of characters.
for (size_t i = 0; i < sz; ++i)
counts[string_index(alphabet, bwt[i])]++;
// Accumulate counts.
size_t acc = 0;
for (size_t i = 0; i < alphabet_sz; ++i) {
counts[i] += acc;
acc = counts[i];
}
// Calculate ranges.
ranges_t *ranges = calloc(2 * alphabet_sz, sizeof(ranges_t));
if (!ranges)
return NULL;
unsigned long cur_idx = 0;
for (size_t i = 0; i < alphabet_sz; ++i) {
ranges[2 * i] = cur_idx;
ranges[2 * i + 1] = counts[i];
cur_idx = counts[i];
}
return ranges;
}
/* Find the range of matches for the given pattern in the F column of the
* given FM-index.
*/
void FMIndexFindMatchRange(fm_index *fm, char *pattern, size_t pattern_sz,
ranges_t *start, ranges_t *end) {
int p_idx = pattern_sz - 1;
char c = pattern[p_idx];
// Initial range is all instances of the last character in pattern.
*start = fm->ranges[2 * string_index(fm->alphabet, c)];
*end = fm->ranges[2 * string_index(fm->alphabet, c) + 1];
p_idx -= 1;
while (p_idx >= 0 && *end > 1) {
c = pattern[p_idx];
ranges_t range_start = fm->ranges[2 * string_index(fm->alphabet, c)];
int alphabet_idx = string_index(fm->alphabet, c);
*start =
range_start + fm->ranks[fm->alphabet_sz * (*start - 1) + alphabet_idx];
*end = range_start + fm->ranks[fm->alphabet_sz * (*end - 1) + alphabet_idx];
p_idx -= 1;
}
}
/* Find the matching indices in the original text for the given
* range in the "F column" of the Burrows-Wheeler matrix.
*/
void FMIndexFindRangeIndices(fm_index *fm, ranges_t start, ranges_t end,
unsigned long **match_indices) {
for (unsigned long i = 0; i < end - start; ++i)
(*match_indices)[i] = fm->sa[start + i];
}
fm_index *FMIndexConstruct(char *s) {
fm_index *index = malloc(sizeof(fm_index));
if (!index)
return NULL;
memset(index, 0, sizeof(fm_index));
size_t sz = strlen(s);
if (!(index->alphabet = TextToAlphabet(s, sz)))
goto error;
index->alphabet_sz = strlen(index->alphabet);
if (!(index->sa = ConstructSuffixArray(s, sz)))
goto error;
if (!(index->bwt = ConstructBWT(s, sz, index->sa)))
goto error;
++sz; // Because of the added dollar sign.
index->bwt_sz = sz;
if (!(index->ranks = ConstructRankMatrix(index->bwt, sz, index->alphabet)))
goto error;
if (!(index->ranges =
ConstructCharacterRanges(index->bwt, sz, index->alphabet)))
goto error;
return index;
error:
if (index->alphabet)
free(index->alphabet);
if (index->sa)
free(index->sa);
if (index->bwt)
free(index->bwt);
if (index->ranks)
free(index->ranks);
if (index->ranges)
free(index->ranges);
free(index);
return NULL;
}
void FMIndexFree(fm_index *index) {
free(index->alphabet);
free(index->sa);
free(index->bwt);
free(index->ranks);
free(index->ranges);
free(index);
}
int FMIndexDumpToFile(fm_index *index, char *filename) {
FILE *f = fopen(filename, "w");
if (!f)
return 0;
fwrite(&index->bwt_sz, sizeof(index->bwt_sz), 1, f);
fwrite(index->bwt, sizeof(char), index->bwt_sz, f);
fwrite(&index->alphabet_sz, sizeof(index->alphabet_sz), 1, f);
fwrite(index->alphabet, sizeof(char), index->alphabet_sz, f);
fwrite(index->ranges, sizeof(ranges_t), 2 * index->alphabet_sz, f);
fwrite(index->ranks, sizeof(ranks_t), index->bwt_sz * index->alphabet_sz, f);
fwrite(index->sa, sizeof(sa_t), index->bwt_sz, f);
fclose(f);
return 1;
}
fm_index *FMIndexReadFromFile(char *filename, int aligned) {
FILE *f = fopen(filename, "r");
if (!f)
return NULL;
fm_index *index;
if (!(index = calloc(1, sizeof(fm_index))))
goto error;
fread(&index->bwt_sz, sizeof(index->bwt_sz), 1, f);
if (!MaybeMallocAligned((void **)&index->bwt,
(index->bwt_sz + 1) * sizeof(char), aligned))
goto error;
fread(index->bwt, sizeof(char), index->bwt_sz, f);
index->bwt[index->bwt_sz] = '\0';
fread(&index->alphabet_sz, sizeof(index->alphabet_sz), 1, f);
if (!MaybeMallocAligned((void **)&index->alphabet,
(index->alphabet_sz + 1) * sizeof(char), aligned))
goto error;
fread(index->alphabet, sizeof(char), index->alphabet_sz, f);
index->alphabet[index->alphabet_sz] = '\0';
if (!MaybeMallocAligned((void **)&index->ranges,
2 * index->alphabet_sz * sizeof(ranges_t), aligned))
goto error;
fread(index->ranges, sizeof(ranges_t), 2 * index->alphabet_sz, f);
if (!MaybeMallocAligned((void **)&index->ranks,
index->bwt_sz * index->alphabet_sz * sizeof(ranks_t),
aligned))
goto error;
fread(index->ranks, sizeof(ranks_t), index->bwt_sz * index->alphabet_sz, f);
if (!MaybeMallocAligned((void **)&index->sa, index->bwt_sz * sizeof(sa_t),
aligned))
goto error;
fread(index->sa, sizeof(sa_t), index->bwt_sz, f);
fclose(f);
return index;
error:
if (index) {
if (index->bwt)
free(index->bwt);
if (index->alphabet)
free(index->alphabet);
if (index->ranges)
free(index->ranges);
if (index->ranks)
free(index->ranks);
if (index->sa)
free(index->sa);
free(index);
}
fclose(f);
return NULL;
}

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#pragma once
#ifdef __cplusplus
extern "C" {
#endif
#include <stdlib.h>
typedef unsigned ranges_t;
typedef unsigned ranks_t;
typedef unsigned sa_t;
typedef struct fm_index {
char *bwt;
size_t bwt_sz;
char *alphabet;
size_t alphabet_sz;
ranks_t *ranks;
sa_t *sa;
ranges_t *ranges;
} fm_index;
fm_index *FMIndexConstruct(char *s);
void FMIndexFree(fm_index *index);
fm_index *FMIndexReadFromFile(char *filename, int aligned);
int FMIndexDumpToFile(fm_index *index, char *filename);
void FMIndexFindMatchRange(fm_index *fm, char *pattern, size_t pattern_sz,
ranges_t *start, ranges_t *end);
void FMIndexFindRangeIndices(fm_index *fm, ranges_t start, ranges_t end,
unsigned long **match_indices);
#ifdef __cplusplus
}
#endif

13
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verify
sw_emu
hw_emu
hw
.Xil
.run
emconfig.json
vitis_env.sh
.ipcache
example_output
test.txt
*.jou
*.str

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ifndef PLATFORM
$(error PLATFORM is not set.)
endif
ifndef TARGET
$(info TARGET is not set; using sw_emu.)
endif
TARGET ?= sw_emu
TARGETS := sw_emu hw_emu hw
ifeq ($(filter $(TARGET),$(TARGETS)),)
$(error TARGET can only be one of: "$(TARGETS)")
endif
VXXFLAGS := -t ${TARGET} --log_dir $(TARGET) --report_dir $(TARGET) --temp_dir $(TARGET) -I/usr/include/x86_64-linux-gnu -Wno-unused-label
GXXFLAGS := -Wall -g -std=c++11 -I${XILINX_XRT}/include/ -L${XILINX_XRT}/lib/ -lOpenCL -lpthread -lrt -lstdc++ -I..
PROJ_HEADERS := ../fmindex.h ../util.h
PROJ_OBJS := ../fmindex.o ../util.o
ifeq ($(TARGET), hw)
EMULATION_FLAG :=
else
EMULATION_FLAG := XCL_EMULATION_MODE=$(TARGET)
endif
.PHONY: all run-verify clean cleanall unopt opt
all: $(TARGET) verify benchmark unopt opt
unopt: $(TARGET)/unopt.xclbin
ndrange: $(TARGET)/ndrange.xclbin
ndrange2: $(TARGET)/ndrange2.xclbin
memory: $(TARGET)/memory.xclbin
final: $(TARGET)/final.xclbin
run-verify: verify $(TARGET)/$(KERNEL).xclbin
@test -n "$(FMFILE)" || (echo "FMFILE undefined" ; exit 1)
@test -n "$(TESTFILE)" || (echo "TESTFILE undefined" ; exit 1)
@test -n "$(KERNEL)" || (echo "KERNEL undefined" ; exit 1)
@test -n "$(NDRANGE)" || (echo "NDRANGE undefined" ; exit 1)
@test -n "$(LOCALSIZE)" || (echo "LOCALSIZE undefined" ; exit 1)
cd $(TARGET) && $(EMULATION_FLAG) ../verify ../$(FMFILE) ../$(TARGET)/$(KERNEL).xclbin ../$(TESTFILE) $(NDRANGE) $(LOCALSIZE)
$(TARGET):
mkdir $(TARGET)
%.o: %.cpp $(PROJ_HEADERS)
g++ -c -o $@ $< $(GXXFLAGS)
verify: verify.o
g++ -o $@ $(PROJ_OBJS) $< $(GXXFLAGS)
benchmark: benchmark.o
g++ -o $@ $(PROJ_OBJS) $< $(GXXFLAGS)
$(TARGET)/unopt.xo: unopt.cl no_ndrange.cfg
v++ -c -k fmindex $< $(VXXFLAGS) --config no_ndrange.cfg -o $@
$(TARGET)/unopt.xclbin: $(TARGET)/unopt.xo emconfig.json
v++ -l $< $(VXXFLAGS) --config no_ndrange.cfg -o $@
mv -t $(TARGET) xrc.log xcd.log
$(TARGET)/memory.xo: memory.cl no_ndrange.cfg
v++ -c -k fmindex $< $(VXXFLAGS) --config no_ndrange.cfg -o $@
$(TARGET)/memory.xclbin: $(TARGET)/memory.xo emconfig.json
v++ -l $< $(VXXFLAGS) --config no_ndrange.cfg -o $@
mv -t $(TARGET) xrc.log xcd.log
$(TARGET)/ndrange.xo: ndrange.cl ndrange.cfg
v++ -c -k fmindex $< $(VXXFLAGS) --config ndrange.cfg -o $@
$(TARGET)/ndrange.xclbin: $(TARGET)/ndrange.xo emconfig.json
v++ -l $< $(VXXFLAGS) --config ndrange.cfg -o $@
mv -t $(TARGET) xrc.log xcd.log
$(TARGET)/ndrange2.xo: ndrange2.cl ndrange2.cfg
v++ -c -k fmindex $< $(VXXFLAGS) --config ndrange2.cfg -o $@
$(TARGET)/ndrange2.xclbin: $(TARGET)/ndrange2.xo emconfig.json
v++ -l $< $(VXXFLAGS) --config ndrange2.cfg -o $@
mv -t $(TARGET) xrc.log xcd.log
$(TARGET)/final.xo: final.cl ndrange.cfg
v++ -c -k fmindex $< $(VXXFLAGS) --config ndrange.cfg -o $@
$(TARGET)/final.xclbin: $(TARGET)/final.xo emconfig.json
v++ -l $< $(VXXFLAGS) --config ndrange.cfg -o $@
mv -t $(TARGET) xrc.log xcd.log
emconfig.json:
emconfigutil --platform $(PLATFORM) --nd 1
clean:
rm -rf emconfig.json *.info *.link_summary *.compile_summary \
*.xclbin *.xo *.log _x $(TARGET) verify TempConfig *.csv *.run_summary \
*.o .Xil .run .ipcache
cleanall: clean
rm -rf $(TARGETS)

171
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#define CL_HPP_CL_1_2_DEFAULT_BUILD
#define CL_HPP_TARGET_OPENCL_VERSION 120
#define CL_HPP_MINIMUM_OPENCL_VERSION 120
#define CL_HPP_ENABLE_PROGRAM_CONSTRUCTION_FROM_ARRAY_COMPATIBILITY 1
#define CL_USE_DEPRECATED_OPENCL_1_2_APIS
#include <CL/cl2.hpp>
#include <fstream>
#include <iostream>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <unistd.h>
#include <vector>
#include "../fmindex.h"
#include "../util.h"
std::vector<cl::Device> get_xilinx_devices();
char *read_binary_file(const std::string &xclbin_file_name, unsigned &nb);
int main(int argc, char **argv) {
if (argc < 6) {
fprintf(
stderr,
"Usage: %s <FMINDEXFILE> <XCLBIN> <TESTFILE> <NDRANGE> <LOCALSIZE>\n",
argv[0]);
return 1;
}
int use_ndrange = atoi(argv[4]);
int local_size = atoi(argv[5]);
// Load FM-index.
fm_index *index = FMIndexReadFromFile(argv[1], 1);
if (!index) {
fprintf(stderr, "Could not read FM-index from file.\n");
return 1;
}
// Load test file.
unsigned pattern_count, pattern_sz, max_match_count;
char *patterns;
if (!(LoadTestData(argv[3], &patterns, &pattern_count, &pattern_sz,
&max_match_count, 1))) {
fprintf(stderr, "Could not read test data file.\n");
return 1;
}
// Initialize OpenCL.
cl_int err;
unsigned fileBufSize;
std::vector<cl::Device> devices = get_xilinx_devices();
devices.resize(1);
cl::Device device = devices[0];
cl::Context context(device, NULL, NULL, NULL, &err);
char *fileBuf = read_binary_file(argv[2], fileBufSize);
cl::Program::Binaries bins{{fileBuf, fileBufSize}};
cl::Program program(context, devices, bins, NULL, &err);
cl::CommandQueue q(context, device, CL_QUEUE_PROFILING_ENABLE, &err);
cl::Kernel kernel(program, "fmindex", &err);
// Create OpenCL buffers for host data.
cl::Buffer bwt_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR,
sizeof(char) * index->bwt_sz, index->bwt, &err);
cl::Buffer alphabet_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR,
sizeof(char) * index->alphabet_sz, index->alphabet,
&err);
cl::Buffer ranks_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR,
sizeof(ranks_t) * index->bwt_sz * index->alphabet_sz,
index->ranks, &err);
cl::Buffer sa_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR,
sizeof(sa_t) * index->bwt_sz, index->sa, &err);
cl::Buffer ranges_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR,
sizeof(ranges_t) * 2 * index->alphabet_sz,
index->ranges, &err);
cl::Buffer patterns_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR,
sizeof(char) * pattern_count * pattern_sz, patterns,
&err);
cl::Buffer out_buf(context, CL_MEM_WRITE_ONLY,
sizeof(unsigned long) *
(pattern_count * (max_match_count + 1)),
NULL, &err);
// Map OpenCL buffers to kernel arguments.
kernel.setArg(0, bwt_buf);
kernel.setArg(1, alphabet_buf);
kernel.setArg(2, ranks_buf);
kernel.setArg(3, sa_buf);
kernel.setArg(4, ranges_buf);
kernel.setArg(5, patterns_buf);
kernel.setArg(6, out_buf);
// Map OpenCL buffers to kernel arguments including scalars.
kernel.setArg(0, bwt_buf);
kernel.setArg(1, alphabet_buf);
kernel.setArg(2, ranks_buf);
kernel.setArg(3, sa_buf);
kernel.setArg(4, ranges_buf);
kernel.setArg(5, patterns_buf);
kernel.setArg(6, out_buf);
kernel.setArg(7, index->bwt_sz);
kernel.setArg(8, index->alphabet_sz);
kernel.setArg(9, pattern_count);
kernel.setArg(10, pattern_sz);
kernel.setArg(11, max_match_count + 1);
// Schedule transfer of inputs and output.
q.enqueueMigrateMemObjects(
{bwt_buf, alphabet_buf, ranks_buf, sa_buf, ranges_buf, patterns_buf}, 0);
if (use_ndrange)
q.enqueueNDRangeKernel(kernel, 0, pattern_count, local_size);
else
q.enqueueTask(kernel);
q.enqueueMigrateMemObjects({out_buf}, CL_MIGRATE_MEM_OBJECT_HOST);
q.finish();
// Release resources.
delete[] fileBuf;
FMIndexFree(index);
return EXIT_SUCCESS;
}
// ------------------------------------------------------------------------------------
// Utility functions
// ------------------------------------------------------------------------------------
std::vector<cl::Device> get_xilinx_devices() {
size_t i;
cl_int err;
std::vector<cl::Platform> platforms;
err = cl::Platform::get(&platforms);
cl::Platform platform;
for (i = 0; i < platforms.size(); i++) {
platform = platforms[i];
std::string platformName = platform.getInfo<CL_PLATFORM_NAME>(&err);
if (platformName == "Xilinx") {
std::cerr << "INFO: Found Xilinx Platform" << std::endl;
break;
}
}
if (i == platforms.size()) {
std::cerr << "ERROR: Failed to find Xilinx platform" << std::endl;
exit(EXIT_FAILURE);
}
// Getting ACCELERATOR Devices and selecting 1st such device
std::vector<cl::Device> devices;
err = platform.getDevices(CL_DEVICE_TYPE_ACCELERATOR, &devices);
return devices;
}
char *read_binary_file(const std::string &xclbin_file_name, unsigned &nb) {
if (access(xclbin_file_name.c_str(), R_OK) != 0) {
printf("ERROR: %s xclbin not available please build\n",
xclbin_file_name.c_str());
exit(EXIT_FAILURE);
}
// Loading XCL Bin into char buffer
std::cerr << "INFO: Loading '" << xclbin_file_name << "'\n";
std::ifstream bin_file(xclbin_file_name.c_str(), std::ifstream::binary);
bin_file.seekg(0, bin_file.end);
nb = bin_file.tellg();
bin_file.seekg(0, bin_file.beg);
char *buf = new char[nb];
bin_file.read(buf, nb);
return buf;
}

232
code/fpga/benchmark_fpga.py Normal file
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import argparse
import subprocess
import os
import shutil
import json
from pathlib import Path
# Thanks Tristan Laan for data extraction functions.
def _calculate_wattage(data: list) -> float:
return (int(data[1]) / 1000) * (int(data[2]) / 1000) \
+ (int(data[3]) / 1000) * (int(data[4]) / 1000)
def _get_power_profile_data(directory: Path) -> list:
file = next(directory.glob('power_profile_*.csv'))
data = []
with file.open() as f:
for i, line in enumerate(f):
if i < 2:
continue
csv_data = line.split(',')
data.append({'timestamp': float(csv_data[0]),
'power': _calculate_wattage(csv_data)})
return data
def _get_timeline_data(directory: Path) -> dict:
file = next(directory.glob('timeline_trace.csv'))
data = {}
with file.open() as f:
for i, line in enumerate(f):
cells = line.split(',')
if i < 13:
continue
if cells[0] == 'Footer':
break
if cells[1].startswith("KERNEL") and cells[1].endswith("all") and cells[2] in ["START", "END"]:
data[cells[2]] = cells[0]
return data
def _is_mode(line: str):
if line == 'OpenCL API Calls':
return True
if line == 'Kernel Execution':
return True
if line == 'Compute Unit Utilization':
return True
if line == 'Data Transfer: Host to Global Memory':
return True
if line == 'Data Transfer: Kernels to Global Memory':
return True
def _get_profile_summary_data(file: Path) -> dict:
data = dict()
mode = None
skip_line = False
with file.open() as f:
for line in f:
line = line.strip()
if skip_line:
skip_line = False
continue
if _is_mode(line):
mode = line
data[mode] = []
skip_line = True
continue
if line == '':
mode = None
if not mode:
continue
csv_data = line.split(',')
if mode == 'OpenCL API Calls':
data[mode].append({
'name': csv_data[0],
'calls': int(csv_data[1]),
'time': float(csv_data[2])
})
if mode == 'Kernel Execution':
data[mode].append({
'kernel': csv_data[0],
'enqueues': int(csv_data[1]),
'time': float(csv_data[2])
})
if mode == 'Compute Unit Utilization':
data[mode].append({
'cu': csv_data[1],
'kernel': csv_data[2],
'time': float(csv_data[9])
})
if mode == 'Data Transfer: Host to Global Memory':
data[mode].append({
'type': csv_data[1],
'transfers': int(csv_data[2]),
'speed': float(csv_data[3]),
'utilization': float(csv_data[4]),
'size': float(csv_data[5]),
'time': float(csv_data[6])
})
if mode == 'Data Transfer: Kernels to Global Memory':
data[mode].append({
'interface': csv_data[3],
'type': csv_data[4],
'transfers': int(csv_data[5]),
'speed': float(csv_data[6]),
'utilization': float(csv_data[7]),
'size': float(csv_data[8])
})
return data
def read_data(directory: Path) -> dict:
data = dict()
profile = directory / 'profile_summary.csv'
try:
data['power'] = _get_power_profile_data(directory)
data['timeline'] = _get_timeline_data(directory)
except StopIteration:
pass
if profile.exists():
data.update(_get_profile_summary_data(profile))
return data
def write_data(data: dict, file: Path):
with file.open('w') as f:
json.dump(data, f)
class cd:
"""Context manager for changing the current working directory"""
def __init__(self, newPath):
self.newPath = os.path.expanduser(newPath)
def __enter__(self):
self.savedPath = os.getcwd()
os.chdir(self.newPath)
def __exit__(self, etype, value, traceback):
os.chdir(self.savedPath)
def main(repeats, count, maxmatches, lengths, dir, filenames, kernel, target, localsize, ndrange):
for filename in filenames:
for length in lengths:
benchmark(repeats, count, maxmatches, length, dir, filename, kernel, target, localsize, ndrange)
def benchmark(repeats, count, maxmatches, length, dir, filename, kernel, target, localsize, ndrange):
textfilename = f"../{dir}/{filename}"
fmfilename = f"{textfilename}.fm"
resultdir = f"../{kernel}_results/{filename}.len{length}"
testfilename = f"{resultdir}/test.txt"
if target != "hw":
env = dict(os.environ, XCL_EMULATION_MODE=target)
else:
env = os.environ
gentestargs = ["../../generate_test_data", textfilename, fmfilename, testfilename, str(count), str(length), str(maxmatches)]
benchmarkargs = ["../benchmark", fmfilename, f"{kernel}.xclbin", testfilename, str(ndrange), str(localsize)]
print(" ".join(gentestargs))
print(" ".join(benchmarkargs))
with cd(target):
shutil.rmtree(resultdir, ignore_errors=True)
Path(resultdir).mkdir(parents=True, exist_ok=True)
for n in range(repeats):
print(f"{n+1}/{repeats}")
# Create test file.
gentestproc = subprocess.Popen(gentestargs, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = gentestproc.communicate()
if stderr:
print(f">{stderr.strip()}")
ret = gentestproc.poll()
if ret != 0:
print(f"Error creating test data: {stdout.strip()}")
exit(1)
# Execute kernel
benchmarkproc = subprocess.Popen(benchmarkargs, stdout=subprocess.PIPE, universal_newlines=True, stderr=subprocess.PIPE, env=env)
_, stderr = benchmarkproc.communicate()
if stderr:
print(f">{stderr.strip()}")
ret = benchmarkproc.poll()
if ret != 0:
print("Error benchmarking test data")
exit(1)
# Move data to result directory.
data = read_data(Path("."))
write_data(data, Path(resultdir) / f"run{n}.json")
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("-n", "--repeats", help="number of times to repeat each experiment", type=int, required=True)
parser.add_argument("-c", "--count", help="number of patterns", type=int, required=True)
parser.add_argument("-m", "--maxmatches", help="maximum number of matches per pattern", type=int, required=True)
parser.add_argument("-l", "--lengths", help="length of the patterns", type=int, nargs="+", default=[], required=True)
parser.add_argument("-d", "--dir", help="directory containing FM-indices and original texts (with the same name)", required=True)
parser.add_argument("-f", "--files", help="FM-index files to benchmark", nargs="+", default=[], required=True)
parser.add_argument("-k", "--kernel", help="FPGA kernel", required=True)
parser.add_argument("-t", "--target", help="compilation target", default="sw_emu", required=False)
parser.add_argument("-s", "--localsize", help="NDRange local size", type=int, required=True)
parser.add_argument("-r", "--ndrange", help="use NDRange", type=int, required=True)
args = parser.parse_args()
main(args.repeats, args.count, args.maxmatches, args.lengths, args.dir, args.files, args.kernel, args.target, args.localsize, args.ndrange)

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#define LOCAL_SIZE 300
#define MAX_PATTERN_SZ 8
#define MAX_ALPHABET_SZ 97
#define MAX_RANGES_SZ (2 * MAX_ALPHABET_SZ)
#define PATTERNS_SZ (MAX_PATTERN_SZ * LOCAL_SIZE)
inline static int string_index(__private char *s, char c) {
int i = 0;
while (1) {
if (s[i] == c)
return i;
++i;
}
}
kernel
__attribute__((reqd_work_group_size(LOCAL_SIZE, 1, 1)))
__attribute__((xcl_zero_global_work_offset))
void fmindex(__global char *bwt,
__global char *alphabet,
__global unsigned *ranks,
__global unsigned *sa,
__global unsigned *ranges,
__global char *patterns,
__global unsigned long *out,
size_t bwt_sz, size_t alphabet_sz, unsigned pattern_count,
unsigned pattern_sz, unsigned out_sz) {
int group_id = get_group_id(0);
__local char _patterns[PATTERNS_SZ];
__attribute__((xcl_pipeline_loop(1)))
for (unsigned i = 0; i < PATTERNS_SZ; ++i)
_patterns[i] = patterns[group_id * LOCAL_SIZE * pattern_sz + i];
__attribute__((xcl_pipeline_workitems)) {
int work_id = get_global_id(0);
int local_id = get_local_id(0);
__private char _alphabet[MAX_ALPHABET_SZ];
__attribute__((xcl_pipeline_loop(1)))
for (unsigned i = 0; i < alphabet_sz; ++i)
_alphabet[i] = alphabet[i];
__private unsigned _ranges[MAX_RANGES_SZ];
__attribute__((xcl_pipeline_loop(1)))
for (unsigned i = 0; i < 2 * alphabet_sz; ++i)
_ranges[i] = ranges[i];
int p_idx = pattern_sz - 1;
char c = _patterns[local_id * pattern_sz + p_idx];
int alphabet_idx = string_index(_alphabet, c);
unsigned start = _ranges[2 * alphabet_idx];
unsigned end = _ranges[2 * alphabet_idx + 1];
p_idx -= 1;
while (p_idx >= 0 && end > 1) {
c = _patterns[local_id * pattern_sz + p_idx];
alphabet_idx = string_index(_alphabet, c);
unsigned range_start = _ranges[2 * alphabet_idx];
start = range_start + ranks[alphabet_sz * (start - 1) + alphabet_idx];
end = range_start + ranks[alphabet_sz * (end - 1) + alphabet_idx];
p_idx -= 1;
}
unsigned long match_count = end - start;
out[work_id * out_sz] = match_count;
__attribute__((xcl_pipeline_loop(1)))
for (unsigned i = 0; i < match_count; ++i)
out[work_id * out_sz + i + 1] = sa[start + i];
}
}

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{"power": [{"timestamp": 37.8581, "power": 35.3288}, {"timestamp": 58.5703, "power": 35.3288}, {"timestamp": 79.0738, "power": 35.3288}, {"timestamp": 99.609, "power": 35.3288}, {"timestamp": 120.151, "power": 35.3288}, {"timestamp": 140.789, "power": 35.3288}, {"timestamp": 161.382, "power": 35.3288}, {"timestamp": 181.94, "power": 35.3288}, {"timestamp": 202.498, "power": 35.3288}, {"timestamp": 223.0, "power": 35.3288}, {"timestamp": 243.546, "power": 35.3288}, {"timestamp": 264.094, "power": 35.3288}, {"timestamp": 284.638, "power": 35.3288}, {"timestamp": 305.188, "power": 35.3288}, {"timestamp": 325.74, "power": 35.3288}, {"timestamp": 346.294, "power": 35.3288}, {"timestamp": 366.809, "power": 35.3288}, {"timestamp": 387.352, "power": 35.3288}, {"timestamp": 407.899, "power": 35.3288}, {"timestamp": 428.445, "power": 35.3288}, {"timestamp": 449.024, "power": 35.3288}, {"timestamp": 469.623, "power": 35.3288}, {"timestamp": 490.116, "power": 35.3288}, {"timestamp": 510.633, "power": 35.3288}, {"timestamp": 531.131, "power": 35.3288}, {"timestamp": 551.647, "power": 35.3288}, {"timestamp": 572.344, "power": 35.3288}, {"timestamp": 592.961, "power": 35.3288}, {"timestamp": 613.414, "power": 35.3288}, {"timestamp": 633.856, "power": 35.3288}, {"timestamp": 654.298, "power": 35.3288}, {"timestamp": 674.764, "power": 35.3288}, {"timestamp": 695.258, "power": 35.3288}, {"timestamp": 715.801, "power": 35.3288}, {"timestamp": 736.339, "power": 35.3288}, {"timestamp": 756.873, "power": 35.3288}, {"timestamp": 777.787, "power": 35.3288}, {"timestamp": 798.354, "power": 35.3288}], "timeline": {"START": "470.05948", "END": "523.05116"}, "OpenCL API Calls": [{"name": "clSetKernelArg", "calls": 19, "time": 284.273}, {"name": "clFinish", "calls": 1, "time": 229.365}, {"name": "clReleaseKernel", "calls": 1, "time": 86.4594}, {"name": "clCreateProgramWithBinary", "calls": 1, "time": 63.9265}, {"name": "clReleaseContext", "calls": 1, "time": 51.3423}, {"name": "clCreateContext", "calls": 1, "time": 35.5788}, {"name": "clReleaseProgram", "calls": 1, "time": 11.7884}, {"name": "clEnqueueMigrateMemObjects", "calls": 2, "time": 0.367593}, {"name": "clCreateKernel", "calls": 1, "time": 0.34037}, {"name": "clEnqueueNDRangeKernel", "calls": 1, "time": 0.146976}, {"name": "clReleaseMemObject", "calls": 21, "time": 0.077769}, {"name": "clRetainMemObject", "calls": 14, "time": 0.037016}, {"name": "clGetExtensionFunctionAddress", "calls": 1, "time": 0.025618}, {"name": "clCreateBuffer", "calls": 7, "time": 0.024742}, {"name": "clReleaseDevice", "calls": 2, "time": 0.023307}, {"name": "clGetPlatformInfo", "calls": 4, "time": 0.010228}, {"name": "clGetExtensionFunctionAddressForPlatform", "calls": 1, "time": 0.009001}, {"name": "clReleaseCommandQueue", "calls": 1, "time": 0.0084}, {"name": "clCreateCommandQueue", "calls": 1, "time": 0.007222}, {"name": "clGetDeviceIDs", "calls": 2, "time": 0.006521}, {"name": "clRetainDevice", "calls": 2, "time": 0.004685}], "Kernel Execution": [{"kernel": "fmindex", "enqueues": 1, "time": 52.9917}], "Compute Unit Utilization": [{"cu": "fmindex_1", "kernel": "fmindex", "time": 47.4359}, {"cu": "fmindex_2", "kernel": "fmindex", "time": 49.6304}, {"cu": "fmindex_3", "kernel": "fmindex", "time": 48.7461}, {"cu": "fmindex_4", "kernel": "fmindex", "time": 52.5406}, {"cu": "fmindex_5", "kernel": "fmindex", "time": 52.4821}], "Data Transfer: Host to Global Memory": [{"type": "READ", "transfers": 1, "speed": 7632.600307, "utilization": 79.506253, "size": 969240.0, "time": 126.986867}, {"type": "WRITE", "transfers": 1, "speed": 7027.815445, "utilization": 73.206411, "size": 346090.0, "time": 49.245769}], "Data Transfer: Kernels to Global Memory": [{"interface": "DDR[1:3]", "type": "READ", "transfers": 564951, "speed": 102.623, "utilization": 0.890823, "size": 0.00812744}, {"interface": "DDR[1:3]", "type": "WRITE", "transfers": 35684, "speed": 371.67, "utilization": 3.2263, "size": 0.118922}, {"interface": "DDR[1:3]", "type": "READ", "transfers": 604431, "speed": 104.444, "utilization": 0.906631, "size": 0.00811912}, {"interface": "DDR[1:3]", "type": "WRITE", "transfers": 38166, "speed": 372.547, "utilization": 3.23391, "size": 0.119464}, {"interface": "DDR[1:3]", "type": "READ", "transfers": 587746, "speed": 103.73, "utilization": 0.900437, "size": 0.0081225}, {"interface": "DDR[1:3]", "type": "WRITE", "transfers": 37061, "speed": 372.351, "utilization": 3.23221, "size": 0.119424}, {"interface": "DDR[1:3]", "type": "READ", "transfers": 670506, "speed": 109.093, "utilization": 0.946991, "size": 0.00810738}, {"interface": "DDR[1:3]", "type": "WRITE", "transfers": 42277, "speed": 376.434, "utilization": 3.26766, "size": 0.12035}, {"interface": "DDR[1:3]", "type": "READ", "transfers": 669545, "speed": 108.988, "utilization": 0.946073, "size": 0.00810754}, {"interface": "DDR[1:3]", "type": "WRITE", "transfers": 42234, "speed": 376.111, "utilization": 3.26485, "size": 0.120291}]}

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