From 1b3e0d6d5792a3950e392fbcd5997b7c6341fade Mon Sep 17 00:00:00 2001 From: Pim Kunis Date: Sat, 3 Jul 2021 17:59:32 +0200 Subject: [PATCH] Publish --- .gitignore | 23 + LICENSE | 674 ++++++++++++++++++ README.md | 27 + code/.gitignore | 6 + code/Makefile | 31 + code/benchmark.c | 79 ++ code/benchmark_cpu.py | 64 ++ code/construct.c | 30 + code/cpu_results/dblp.xml.10MB.cpu4.result | 5 + code/cpu_results/dblp.xml.10MB.cpu6.result | 5 + code/cpu_results/dblp.xml.10MB.cpu8.result | 5 + code/cpu_results/dblp.xml.15MB.cpu4.result | 5 + code/cpu_results/dblp.xml.15MB.cpu6.result | 5 + code/cpu_results/dblp.xml.15MB.cpu8.result | 5 + code/cpu_results/dblp.xml.20MB.cpu4.result | 5 + code/cpu_results/dblp.xml.20MB.cpu6.result | 5 + code/cpu_results/dblp.xml.20MB.cpu8.result | 5 + code/cpu_results/dna.10MB.cpu4.result | 5 + code/cpu_results/dna.10MB.cpu6.result | 5 + code/cpu_results/dna.10MB.cpu8.result | 5 + code/cpu_results/dna.15MB.cpu4.result | 5 + code/cpu_results/dna.15MB.cpu6.result | 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + 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 +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..5993010 --- /dev/null +++ b/README.md @@ -0,0 +1,27 @@ +# 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. diff --git a/code/.gitignore b/code/.gitignore new file mode 100644 index 0000000..9d7ab1c --- /dev/null +++ b/code/.gitignore @@ -0,0 +1,6 @@ +program +repl +construct +experiment_data +generate_test_data +benchmark diff --git a/code/Makefile b/code/Makefile new file mode 100644 index 0000000..075612e --- /dev/null +++ b/code/Makefile @@ -0,0 +1,31 @@ +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) diff --git a/code/benchmark.c b/code/benchmark.c new file mode 100644 index 0000000..4d4dce5 --- /dev/null +++ b/code/benchmark.c @@ -0,0 +1,79 @@ +#define _GNU_SOURCE + +#include "fmindex.h" +#include "rapl.h" +#include "util.h" + +#include +#include +#include +#include +#include + +// 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 \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; +} diff --git a/code/benchmark_cpu.py b/code/benchmark_cpu.py new file mode 100644 index 0000000..b58a691 --- /dev/null +++ b/code/benchmark_cpu.py @@ -0,0 +1,64 @@ +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) diff --git a/code/construct.c b/code/construct.c new file mode 100644 index 0000000..e1c31a0 --- /dev/null +++ b/code/construct.c @@ -0,0 +1,30 @@ +#include "fmindex.h" +#include "util.h" + +#include + +int main(int argc, char *argv[]) { + if (argc < 3) { + printf("Usage: $ %s \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; +} diff --git a/code/cpu_results/dblp.xml.10MB.cpu4.result b/code/cpu_results/dblp.xml.10MB.cpu4.result new file mode 100644 index 0000000..2c431f9 --- /dev/null +++ b/code/cpu_results/dblp.xml.10MB.cpu4.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dblp.xml.10MB.cpu6.result b/code/cpu_results/dblp.xml.10MB.cpu6.result new file mode 100644 index 0000000..39d7cdf --- /dev/null +++ b/code/cpu_results/dblp.xml.10MB.cpu6.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dblp.xml.10MB.cpu8.result b/code/cpu_results/dblp.xml.10MB.cpu8.result new file mode 100644 index 0000000..946a9b7 --- /dev/null +++ b/code/cpu_results/dblp.xml.10MB.cpu8.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dblp.xml.15MB.cpu4.result b/code/cpu_results/dblp.xml.15MB.cpu4.result new file mode 100644 index 0000000..045a7a4 --- /dev/null +++ b/code/cpu_results/dblp.xml.15MB.cpu4.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dblp.xml.15MB.cpu6.result b/code/cpu_results/dblp.xml.15MB.cpu6.result new file mode 100644 index 0000000..271de45 --- /dev/null +++ b/code/cpu_results/dblp.xml.15MB.cpu6.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dblp.xml.15MB.cpu8.result b/code/cpu_results/dblp.xml.15MB.cpu8.result new file mode 100644 index 0000000..05cd1e3 --- /dev/null +++ b/code/cpu_results/dblp.xml.15MB.cpu8.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dblp.xml.20MB.cpu4.result b/code/cpu_results/dblp.xml.20MB.cpu4.result new file mode 100644 index 0000000..0e81f19 --- /dev/null +++ b/code/cpu_results/dblp.xml.20MB.cpu4.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dblp.xml.20MB.cpu6.result b/code/cpu_results/dblp.xml.20MB.cpu6.result new file mode 100644 index 0000000..2fa51df --- /dev/null +++ b/code/cpu_results/dblp.xml.20MB.cpu6.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dblp.xml.20MB.cpu8.result b/code/cpu_results/dblp.xml.20MB.cpu8.result new file mode 100644 index 0000000..6818c65 --- /dev/null +++ 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/dev/null +++ b/code/cpu_results/dna.15MB.cpu6.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dna.15MB.cpu8.result b/code/cpu_results/dna.15MB.cpu8.result new file mode 100644 index 0000000..86b943b --- /dev/null +++ b/code/cpu_results/dna.15MB.cpu8.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/dna.20MB.cpu4.result b/code/cpu_results/dna.20MB.cpu4.result new file mode 100644 index 0000000..864a892 --- /dev/null +++ b/code/cpu_results/dna.20MB.cpu4.result @@ -0,0 +1,5 @@ +0x1.6d8ecp+0 0x1.2f4f214p+27 746010747 +0x1.71c79cp+0 0x1.2f301bp+27 749721648 +0x1.6ec31cp+0 0x1.2f3a726p+27 747612561 +0x1.70d87p+0 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b/code/cpu_results/proteins.15MB.cpu8.result new file mode 100644 index 0000000..dc4a342 --- /dev/null +++ b/code/cpu_results/proteins.15MB.cpu8.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/proteins.20MB.cpu4.result b/code/cpu_results/proteins.20MB.cpu4.result new file mode 100644 index 0000000..fdf9f63 --- /dev/null +++ b/code/cpu_results/proteins.20MB.cpu4.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/proteins.20MB.cpu6.result b/code/cpu_results/proteins.20MB.cpu6.result new file mode 100644 index 0000000..e71062e --- /dev/null +++ b/code/cpu_results/proteins.20MB.cpu6.result @@ -0,0 +1,5 @@ +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 diff --git a/code/cpu_results/proteins.20MB.cpu8.result b/code/cpu_results/proteins.20MB.cpu8.result new file mode 100644 index 0000000..657e098 --- /dev/null +++ b/code/cpu_results/proteins.20MB.cpu8.result @@ -0,0 +1,5 @@ +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 diff --git a/code/fmindex.c b/code/fmindex.c new file mode 100644 index 0000000..0904a1c --- /dev/null +++ b/code/fmindex.c @@ -0,0 +1,345 @@ +#define _GNU_SOURCE + +#include "fmindex.h" +#include "util.h" + +#include +#include +#include +#include + +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; +} diff --git a/code/fmindex.h b/code/fmindex.h new file mode 100644 index 0000000..b54a8bb --- /dev/null +++ b/code/fmindex.h @@ -0,0 +1,35 @@ +#pragma once + +#ifdef __cplusplus +extern "C" { +#endif + +#include + +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 diff --git a/code/fpga/.gitignore b/code/fpga/.gitignore new file mode 100644 index 0000000..5a3f56a --- /dev/null +++ b/code/fpga/.gitignore @@ -0,0 +1,13 @@ +verify +sw_emu +hw_emu +hw +.Xil +.run +emconfig.json +vitis_env.sh +.ipcache +example_output +test.txt +*.jou +*.str diff --git a/code/fpga/Makefile b/code/fpga/Makefile new file mode 100644 index 0000000..abb7744 --- /dev/null +++ b/code/fpga/Makefile @@ -0,0 +1,106 @@ +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) diff --git a/code/fpga/benchmark.cpp b/code/fpga/benchmark.cpp new file mode 100644 index 0000000..c40d430 --- /dev/null +++ b/code/fpga/benchmark.cpp @@ -0,0 +1,171 @@ +#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 +#include +#include +#include +#include +#include +#include +#include + +#include "../fmindex.h" +#include "../util.h" + +std::vector 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 \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 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 get_xilinx_devices() { + size_t i; + cl_int err; + std::vector platforms; + err = cl::Platform::get(&platforms); + cl::Platform platform; + for (i = 0; i < platforms.size(); i++) { + platform = platforms[i]; + std::string platformName = platform.getInfo(&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 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; +} diff --git a/code/fpga/benchmark_fpga.py b/code/fpga/benchmark_fpga.py new file mode 100644 index 0000000..3f0dd07 --- /dev/null +++ b/code/fpga/benchmark_fpga.py @@ -0,0 +1,232 @@ +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) diff --git a/code/fpga/final.cl b/code/fpga/final.cl new file mode 100644 index 0000000..078b596 --- /dev/null +++ b/code/fpga/final.cl @@ -0,0 +1,72 @@ +#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]; + } +} diff --git a/code/fpga/final_results/dblp.xml.10MB.len4/run0.json b/code/fpga/final_results/dblp.xml.10MB.len4/run0.json new file mode 100644 index 0000000..53e7d1a --- /dev/null +++ b/code/fpga/final_results/dblp.xml.10MB.len4/run0.json @@ -0,0 +1 @@ +{"power": [{"timestamp": 43.5334, "power": 35.656904999999995}, {"timestamp": 64.3313, "power": 35.656904999999995}, {"timestamp": 84.8616, "power": 35.656904999999995}, {"timestamp": 105.428, "power": 35.656904999999995}, {"timestamp": 126.008, "power": 35.656904999999995}, {"timestamp": 146.545, "power": 35.656904999999995}, {"timestamp": 167.07, "power": 35.656904999999995}, {"timestamp": 187.587, "power": 35.656904999999995}, {"timestamp": 208.111, "power": 35.656904999999995}, {"timestamp": 228.63, "power": 35.656904999999995}, {"timestamp": 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(s[i] == c) + return i; + ++i; + } +} + +kernel +__attribute__((reqd_work_group_size(1, 1, 1))) +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) { + __private char _alphabet[MAX_ALPHABET_SZ]; + __attribute__((xcl_pipeline_loop(1))) + for (unsigned j = 0; j < alphabet_sz; ++j) + _alphabet[j] = alphabet[j]; + + __private unsigned _ranges[MAX_RANGES_SZ]; + __attribute__((xcl_pipeline_loop(1))) + for (unsigned j = 0; j < 2 * alphabet_sz; ++j) + _ranges[j] = ranges[j]; + + for (unsigned i = 0; i < pattern_count; ++i) { + __private char pattern[MAX_PATTERN_SZ]; + __attribute__((xcl_pipeline_loop(1))) + for (unsigned j = 0; j < pattern_sz; ++j) + pattern[j] = patterns[i * pattern_sz + j]; + + int p_idx = pattern_sz - 1; + char c = pattern[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 = pattern[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[i * out_sz] = match_count; + + __attribute__((xcl_pipeline_loop(1))) + for (unsigned j = 0; j < match_count; ++j) + out[i * out_sz + j + 1] = sa[start + j]; + } +} diff --git a/code/fpga/memory_results/dblp.xml.10MB.len4/run0.json b/code/fpga/memory_results/dblp.xml.10MB.len4/run0.json new file mode 100644 index 0000000..a47d775 --- /dev/null +++ b/code/fpga/memory_results/dblp.xml.10MB.len4/run0.json @@ -0,0 +1 @@ +{"power": [{"timestamp": 34.8655, 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1.78741, "size": 0.0080001}, {"interface": "DDR[1:3]", "type": "WRITE", "transfers": 128545, "speed": 450.843, "utilization": 3.91357, "size": 0.114938}]} \ No newline at end of file diff --git a/code/fpga/ndrange.cfg b/code/fpga/ndrange.cfg new file mode 100644 index 0000000..840c29c --- /dev/null +++ b/code/fpga/ndrange.cfg @@ -0,0 +1,39 @@ +platform=xilinx_u250_gen3x16_xdma_3_1_202020_1 +debug=1 +save-temps=1 + +[connectivity] +nk=fmindex:5 +sp=fmindex_1.bwt:DDR[1] +sp=fmindex_1.alphabet:DDR[2] +sp=fmindex_1.ranks:DDR[3] +sp=fmindex_1.sa:DDR[2] +sp=fmindex_1.ranges:DDR[2] +sp=fmindex_1.out:DDR[1] +sp=fmindex_2.bwt:DDR[1] +sp=fmindex_2.alphabet:DDR[2] +sp=fmindex_2.ranks:DDR[3] +sp=fmindex_2.sa:DDR[2] +sp=fmindex_2.ranges:DDR[2] +sp=fmindex_2.out:DDR[1] +sp=fmindex_3.bwt:DDR[1] +sp=fmindex_3.alphabet:DDR[2] +sp=fmindex_3.ranks:DDR[3] +sp=fmindex_3.sa:DDR[2] +sp=fmindex_3.ranges:DDR[2] +sp=fmindex_3.out:DDR[1] +sp=fmindex_4.bwt:DDR[1] +sp=fmindex_4.alphabet:DDR[2] +sp=fmindex_4.ranks:DDR[3] +sp=fmindex_4.sa:DDR[2] +sp=fmindex_4.ranges:DDR[2] +sp=fmindex_4.out:DDR[1] +sp=fmindex_5.bwt:DDR[1] +sp=fmindex_5.alphabet:DDR[2] +sp=fmindex_5.ranks:DDR[3] +sp=fmindex_5.sa:DDR[2] +sp=fmindex_5.ranges:DDR[2] +sp=fmindex_5.out:DDR[1] + +[profile] +data=all:all:all diff --git a/code/fpga/ndrange.cl b/code/fpga/ndrange.cl new file mode 100644 index 0000000..8e2d395 --- /dev/null +++ b/code/fpga/ndrange.cl @@ -0,0 +1,47 @@ +#define LOCAL_SIZE 300 + +inline static int string_index(__global 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) { + __attribute__((xcl_pipeline_workitems)) { + int i = get_global_id(0); + int p_idx = pattern_sz - 1; + char c = patterns[i * 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[i * 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[i * out_sz] = match_count; + for (unsigned j = 0; j < match_count; ++j) + out[i * out_sz + j + 1] = sa[start + j]; + } +} diff --git a/code/fpga/ndrange_results/dblp.xml.10MB.len4/run0.json b/code/fpga/ndrange_results/dblp.xml.10MB.len4/run0.json new file mode 100644 index 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gridspec +import matplotlib.pyplot as plt +import numpy as np +import json +import glob +from scipy.integrate import simps + + +kernel_name_map = { + "unopt": "reference FPGA kernel", + "memory": "memory optimized kernel", + "ndrange": "NDRange optimized kernel", + "final": "fully optimized kernel" +} +cmap = plt.get_cmap('cividis') +colors = [cmap(i) for i in np.linspace(0, 1, 6)] + + +def main(corpora, sizes, lengths, fpgadir, cpudir, save, count, kernel): + plt.style.use('seaborn') + + fpgaresults = parse_fpga_results(corpora, sizes, lengths, fpgadir) + cpuresults = parse_cpu_results(corpora, sizes, lengths, cpudir) + plot_speedup(fpgaresults, cpuresults, corpora, sizes, lengths, save, count, kernel) + plot_speedup_cycles(fpgaresults, cpuresults, corpora, sizes, lengths, save, kernel) + print_energy_table(fpgaresults, cpuresults, corpora, sizes, lengths) + + +def parse_fpga_results(corpora, sizes, lengths, dir): + results = dict() + + for corpus in corpora: + results[corpus] = dict() + for size in sizes: + results[corpus][size] = dict() + for length in lengths: + results[corpus][size][length] = parse_fpga_result(corpus, size, length, dir) + + return results + + +def parse_fpga_result(corpus, size, length, dir): + resultdir = f"{dir}/{corpus}.{size}MB.len{length}" + result = [] + for filepath in glob.iglob(f"{resultdir}/*"): + with open(filepath, "r") as f: + data = json.load(f) + time = data['Kernel Execution'][0]['time'] + energy = get_energy_usage(data) + result.append((time/1000, energy)) + + return result + + +def get_energy_usage(data): + xs = list(map(lambda x: x["timestamp"], data["power"])) + ys = list(map(lambda y: y["power"], data["power"])) + + # Get start and end timestamp of kernel execution. + start = float(data["timeline"]["START"]) + end = float(data["timeline"]["END"]) + + # Find nearest power data points. + nearest_start = min(range(len(xs)), key=lambda i: abs(xs[i] - start)) + nearest_end = min(range(len(xs)), key=lambda i: abs(xs[i] - end)) + + # Find power data points within kernel execution + kernel_xs = np.array(xs)[nearest_start:nearest_end+1] / 1000 + kernel_ys = np.array(ys)[nearest_start:nearest_end+1] + + # Use Simpson's Rule to integrate and find energy usage. + return simps(y=kernel_ys, x=kernel_xs) + + +def parse_cpu_results(corpora, sizes, lengths, dir): + results = dict() + + for corpus in corpora: + results[corpus] = dict() + for size in sizes: + results[corpus][size] = dict() + for length in lengths: + results[corpus][size][length] = parse_cpu_result(corpus, size, length, dir) + + return results + + +def parse_cpu_result(corpus, size, length, dir): + def parse_line(line): + [range_time, index_time, total_matches] = line.split(" ") + return (float.fromhex(range_time), float.fromhex(index_time), int(total_matches)) + + filename = f"{dir}/{corpus}.{size}MB.cpu{length}.result" + + with open(filename, "r") as f: + data = list(map(parse_line, f.read().splitlines())) + + return data + + +def plot_speedup(fpgaresults, cpuresults, corpora, sizes, lengths, save, count, kernel): + def calculate_speedup(corpus, size, length): + result = [] + for (fpgaresult, cpuresult) in zip(fpgaresults[corpus][size][length], cpuresults[corpus][size][length]): + fpgatime = count / fpgaresult[0] + cputime = count / cpuresult[0] + result.append(cputime / fpgatime) + return result + + width = .1 + labels = [f"{size}MB" for size in sizes] + xs = np.arange(len(labels)) + gs = gridspec.GridSpec(2, 4) + gs.update(wspace=1.0, hspace=0.5) + + axes = [plt.subplot(gs[0, 1:3], ), plt.subplot(gs[1, :2]), plt.subplot(gs[1, 2:])] + for axi, ax in enumerate(axes): + corpus = corpora[axi] + ax.sharey(axes[0]) + + means = np.array([[np.mean(calculate_speedup(corpus, size, length)) for size in sizes] for length in lengths]) + stds = np.array([[np.std(calculate_speedup(corpus, size, length)) for size in sizes] for length in lengths]) + for i in range(len(lengths)): + ax.bar(xs - (width*len(lengths))/2 + i * width + width/2, means[i], width, label=f"{lengths[i]} characters", yerr=stds[i], color=colors[i]) + + if axi in [0, 1]: + ax.set_ylabel("Throughput CPU / FPGA") + ax.set_xlabel("Corpus size (MB)") + ax.set_title(f"\"{corpus}\" corpus"); + ax.set_xticks(xs) + ax.set_xticklabels(labels) + if axi == 0: + ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left', borderaxespad=0., title="Pattern length") + + plt.suptitle(f"Throughput comparison of the {kernel_name_map[kernel]} and reference CPU application") + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 7) + plt.savefig(f"speedup_{kernel}.png", format="png", dpi=100) + else: + plt.show() + + +def plot_speedup_cycles(fpgaresults, cpuresults, corpora, sizes, lengths, save, kernel): + fpga_clockspeed = 0.3 + cpu_clockspeed = 3.4 + def calculate_speedup(corpus, size, length): + result = [] + for (fpgaresult, cpuresult) in zip(fpgaresults[corpus][size][length], cpuresults[corpus][size][length]): + fpgacycles = fpgaresult[0] * fpga_clockspeed + cpucycles = cpuresult[0] * cpu_clockspeed + result.append(cpucycles / fpgacycles) + return result + + width = .1 + labels = [f"{size}MB" for size in sizes] + xs = np.arange(len(labels)) + gs = gridspec.GridSpec(2, 4) + gs.update(wspace=1.0, hspace=0.5) + + axes = [plt.subplot(gs[0, 1:3], ), plt.subplot(gs[1, :2]), plt.subplot(gs[1, 2:])] + for axi, ax in enumerate(axes): + corpus = corpora[axi] + ax.sharey(axes[0]) + + means = np.array([[np.mean(calculate_speedup(corpus, size, length)) for size in sizes] for length in lengths]) + stds = np.array([[np.std(calculate_speedup(corpus, size, length)) for size in sizes] for length in lengths]) + for i in range(len(lengths)): + ax.bar(xs - (width*len(lengths))/2 + i * width + width/2, means[i], width, label=f"{lengths[i]} characters", yerr=stds[i], color=colors[i+3]) + + if axi in [0, 1]: + ax.set_ylabel("Cycles CPU / FPGA") + ax.set_xlabel("Corpus size (MB)") + ax.set_title(f"\"{corpus}\" corpus"); + ax.set_xticks(xs) + ax.set_xticklabels(labels) + if axi == 0: + ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left', borderaxespad=0., title="Pattern length") + + plt.suptitle(f"Clock cycle comparison of the {kernel_name_map[kernel]} and the reference CPU application") + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 7) + plt.savefig(f"speedup_cycles_{kernel}.png", format="png", dpi=100) + else: + plt.show() + + +def print_energy_table(fpgaresults, cpuresults, corpora, sizes, lengths): + for length in lengths: + print(f"{length}", end="") + for corpus in corpora: + for size in sizes: + cpumean = np.mean([result[1] for result in cpuresults[corpus][size][length]]) + fpgamean = np.mean([result[1] for result in fpgaresults[corpus][size][length]]) + comp = fpgamean / (cpumean / 1000000) + print(" & ${:.1f}\\times$".format(comp), end="") + print(" \\\\") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("-c", "--count", help="number of patterns", type=int, required=True) + parser.add_argument("-l", "--lengths", help="length of the patterns", type=int, nargs="+", default=[], required=True) + parser.add_argument("-f", "--fpgadir", help="directory containing FPGA results", required=True) + parser.add_argument("-d", "--cpudir", help="directory containing CPU results", required=True) + parser.add_argument("-t", "--corpora", help="text corpora (without file size)", nargs="+", default=[], required=True) + parser.add_argument("-s", "--sizes", help="file sizes", type=int, nargs="+", default=[], required=True) + parser.add_argument("-k", "--kernel", help="kernel", required=True) + parser.add_argument("-o", "--save", help="save as PNG", action="store_true", required=False) + args = parser.parse_args() + + main(args.corpora, args.sizes, args.lengths, args.fpgadir, args.cpudir, args.save, args.count, args.kernel) diff --git a/code/fpga/plot_fpga.py b/code/fpga/plot_fpga.py new file mode 100644 index 0000000..7a456fa --- /dev/null +++ b/code/fpga/plot_fpga.py @@ -0,0 +1,170 @@ +import argparse +import matplotlib as mpl +mpl.use('TkAgg') +import matplotlib.gridspec as gridspec +import matplotlib.pyplot as plt +import numpy as np +import json +import glob +from scipy.integrate import simps + + +kernel_name_map = { + "unopt": "reference FPGA kernel", + "memory": "memory optimized kernel", + "ndrange": "NDRange optimized kernel", + "final": "memory and NDRAnge optimized kernel" +} +cmap = plt.get_cmap('viridis') +colors = [cmap(i) for i in np.linspace(0, 1, 6)] + + +def main(corpora, sizes, lengths, dir, count, save, kernel): + plt.style.use('seaborn') + + results = parse_results(corpora, sizes, lengths, dir) + plot_throughput(results, corpora, sizes, lengths, count, save, kernel) + plot_energy(results, corpora, sizes, lengths, save, kernel) + print_memory_transfers(results, corpora, sizes, lengths) + + +def parse_results(corpora, sizes, lengths, dir): + results = dict() + + for corpus in corpora: + results[corpus] = dict() + for size in sizes: + results[corpus][size] = dict() + for length in lengths: + results[corpus][size][length] = parse_result(corpus, size, length, dir) + + return results + + +def parse_result(corpus, size, length, dir): + resultdir = f"{dir}/{corpus}.{size}MB.len{length}" + result = [] + for filepath in glob.iglob(f"{resultdir}/*"): + with open(filepath, "r") as f: + data = json.load(f) + time = data['Kernel Execution'][0]['time'] + transfer_time = sum(map(lambda x: x['time'], data['Data Transfer: Host to Global Memory'])) + energy = get_energy_usage(data) + result.append((time/1000, energy, transfer_time)) + + return result + + +def get_energy_usage(data): + xs = list(map(lambda x: x["timestamp"], data["power"])) + ys = list(map(lambda y: y["power"], data["power"])) + + # Get start and end timestamp of kernel execution. + start = float(data["timeline"]["START"]) + end = float(data["timeline"]["END"]) + + # Find nearest power data points. + nearest_start = min(range(len(xs)), key=lambda i: abs(xs[i] - start)) + nearest_end = min(range(len(xs)), key=lambda i: abs(xs[i] - end)) + + # Find power data points within kernel execution + kernel_xs = np.array(xs)[nearest_start:nearest_end+1] / 1000 + kernel_ys = np.array(ys)[nearest_start:nearest_end+1] + + # Use Simpson's Rule to integrate and find energy usage. + return simps(y=kernel_ys, x=kernel_xs) + + +def plot_throughput(results, corpora, sizes, lengths, count, save, kernel): + width = .1 + labels = [f"{size}MB" for size in sizes] + xs = np.arange(len(labels)) + gs = gridspec.GridSpec(2, 4) + gs.update(wspace=1.0, hspace=0.5) + + axes = [plt.subplot(gs[0, 1:3], ), plt.subplot(gs[1, :2]), plt.subplot(gs[1, 2:])] + for axi, ax in enumerate(axes): + corpus = corpora[axi] + ax.sharey(axes[0]) + + means = np.array([[int(np.mean([count / result[0] for result in results[corpus][size][length]])) for size in sizes] for length in lengths]) + stds = np.array([[np.std([count / result[0] for result in results[corpus][size][length]]) for size in sizes] for length in lengths]) + for i in range(len(lengths)): + ax.bar(xs - (width*len(lengths))/2 + i * width + width/2, means[i], width, label=f"{lengths[i]} characters", yerr=stds[i], color=colors[i]) + + if axi in [0, 1]: + ax.set_ylabel("Throughput (patterns matched/s)") + ax.set_xlabel("Corpus size (MB)") + ax.set_title(f"\"{corpus}\" corpus"); + ax.set_xticks(xs) + ax.set_xticklabels(labels) + if axi == 0: + ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left', borderaxespad=0., title="Pattern length") + + plt.suptitle(f"Average throughput for the {kernel_name_map[kernel]}") + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 7) + plt.savefig(f"throughput_{kernel}.png", format="png", dpi=100) + else: + plt.show() + + +def plot_energy(results, corpora, sizes, lengths, save, kernel): + width = .1 + labels = [f"{size}MB" for size in sizes] + xs = np.arange(len(labels)) + gs = gridspec.GridSpec(2, 4) + gs.update(wspace=1.0, hspace=0.5) + + axes = [plt.subplot(gs[0, 1:3], ), plt.subplot(gs[1, :2]), plt.subplot(gs[1, 2:])] + for axi, ax in enumerate(axes): + corpus = corpora[axi] + + means = np.array([[int(np.mean([result[1] for result in results[corpus][size][length]])) for size in sizes] for length in lengths]) + stds = np.array([[np.std([result[1] for result in results[corpus][size][length]]) for size in sizes] for length in lengths]) + for i in range(len(lengths)): + ax.bar(xs - (width*len(lengths))/2 + i * width + width/2, means[i], width, label=f"{lengths[i]} characters", yerr=stds[i], color=colors[i+3]) + + if axi in [0, 1]: + ax.set_ylabel("Energy consumption (J)") + ax.set_xlabel("Corpus size (MB)") + ax.set_title(f"\"{corpus}\" corpus"); + ax.set_xticks(xs) + ax.set_xticklabels(labels) + if axi == 0: + ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left', borderaxespad=0., title="Pattern length") + + plt.suptitle(f"Average energy consumption for the {kernel_name_map[kernel]}") + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 7) + plt.savefig(f"energy_{kernel}.png", format="png", dpi=100) + else: + plt.show() + + +def print_memory_transfers(results, corpora, sizes, lengths): + for length in lengths: + print(f"{length}", end="") + for corpus in corpora: + for size in sizes: + mean = np.mean([result[2] / 1000 for result in results[corpus][size][length]]) + print(" & \\SI{{{:.2f}}}{{s}}".format(mean), end="") + print(" \\\\") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("-c", "--count", help="number of patterns", 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 results", required=True) + parser.add_argument("-t", "--corpora", help="text corpora (without file size)", nargs="+", default=[], required=True) + parser.add_argument("-s", "--sizes", help="file sizes", type=int, nargs="+", default=[], required=True) + parser.add_argument("-k", "--kernel", help="kernel", required=True) + parser.add_argument("-o", "--save", help="save as SVG", action="store_true", required=False) + args = parser.parse_args() + + main(args.corpora, args.sizes, args.lengths, args.dir, args.count, args.save, args.kernel) diff --git a/code/fpga/plot_opt_comparison.py b/code/fpga/plot_opt_comparison.py new file mode 100644 index 0000000..e1e4a36 --- /dev/null +++ b/code/fpga/plot_opt_comparison.py @@ -0,0 +1,147 @@ +import argparse +import matplotlib as mpl +mpl.use('TkAgg') +import matplotlib.pyplot as plt +import numpy as np +import json +import glob +from scipy.integrate import simps + + +kernel_name_map = { + "cpu": "reference CPU application", + "unopt": "reference FPGA kernel", + "memory": "memory optimized kernel", + "ndrange": "NDRange optimized kernel", + "final": "fully optimized kernel" +} +cmap = plt.get_cmap('viridis') +colors = [cmap(i) for i in np.linspace(0, 1, 3)] + + +def main(corpora, sizes, lengths, optdir, unoptdir, cpudir, save, count, kernel): + plt.style.use('seaborn') + + optresults = parse_fpga_results(corpora, sizes, lengths, optdir) + unoptresults = parse_fpga_results(corpora, sizes, lengths, unoptdir) + cpuresults = parse_cpu_results(corpora, sizes, lengths, cpudir) + plot_throughput(optresults, unoptresults, cpuresults, corpora, lengths, save, count, kernel) + + +def parse_fpga_results(corpora, sizes, lengths, dir): + results = dict() + + for corpus in corpora: + results[corpus] = dict() + for size in sizes: + results[corpus][size] = dict() + for length in lengths: + results[corpus][size][length] = parse_fpga_result(corpus, size, length, dir) + + return results + + +def parse_fpga_result(corpus, size, length, dir): + resultdir = f"{dir}/{corpus}.{size}MB.len{length}" + result = [] + for filepath in glob.iglob(f"{resultdir}/*"): + with open(filepath, "r") as f: + data = json.load(f) + time = data['Kernel Execution'][0]['time'] + energy = get_energy_usage(data) + result.append((time/1000, energy)) + + return result + + +def get_energy_usage(data): + xs = list(map(lambda x: x["timestamp"], data["power"])) + ys = list(map(lambda y: y["power"], data["power"])) + + # Get start and end timestamp of kernel execution. + start = float(data["timeline"]["START"]) + end = float(data["timeline"]["END"]) + + # Find nearest power data points. + nearest_start = min(range(len(xs)), key=lambda i: abs(xs[i] - start)) + nearest_end = min(range(len(xs)), key=lambda i: abs(xs[i] - end)) + + # Find power data points within kernel execution + kernel_xs = np.array(xs)[nearest_start:nearest_end+1] / 1000 + kernel_ys = np.array(ys)[nearest_start:nearest_end+1] + + # Use Simpson's Rule to integrate and find energy usage. + return simps(y=kernel_ys, x=kernel_xs) + + +def parse_cpu_results(corpora, sizes, lengths, dir): + results = dict() + + for corpus in corpora: + results[corpus] = dict() + for size in sizes: + results[corpus][size] = dict() + for length in lengths: + results[corpus][size][length] = parse_cpu_result(corpus, size, length, dir) + + return results + + +def parse_cpu_result(corpus, size, length, dir): + def parse_line(line): + [range_time, index_time, total_matches] = line.split(" ") + return (float.fromhex(range_time), float.fromhex(index_time), int(total_matches)) + + filename = f"{dir}/{corpus}.{size}MB.cpu{length}.result" + + with open(filename, "r") as f: + data = list(map(parse_line, f.read().splitlines())) + + return data + + +def plot_throughput(optresults, unoptresults, cpuresults, corpora, lengths, save, count, kernel): + width = .2 + keys = np.array([[(corpus, length) for length in lengths] for corpus in corpora]).reshape(len(corpora) * len(lengths), 2) + labels = [f"({corpus}, {length})" for (corpus, length) in keys] + xs = np.arange(len(labels)) + size = 20 + _, ax = plt.subplots() + + for i, (results, name) in enumerate([(cpuresults, "cpu"), (unoptresults, "unopt"), (optresults, kernel)]): + means = [np.mean(count / np.array(results[corpus][size][int(length)])[:, 0]) for (corpus, length) in keys] + stds = [np.std(count / np.array(results[corpus][size][int(length)])[:, 0]) for (corpus, length) in keys] + ax.bar(xs - (width*len(lengths))/2 + i * width + width/2, means, width, label=kernel_name_map[name].capitalize(), yerr=stds, color=colors[i]) + + ax.set_ylabel("Throughput (patterns matched/s)") + ax.set_xlabel("Corpus and pattern length") + ax.set_xticks(xs) + ax.tick_params(axis="x", rotation=25) + ax.set_xticklabels(labels) + ax.legend() + ax.set_title(f"Throughput comparison between reference applications and {kernel_name_map[kernel]}") + + plt.subplots_adjust(bottom=0.16) + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 5) + plt.savefig(f"throughput_comparison_{kernel}.png", format="png", dpi=100) + else: + plt.show() + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("-c", "--count", help="number of patterns", type=int, required=True) + parser.add_argument("-l", "--lengths", help="length of the patterns", type=int, nargs="+", default=[], required=True) + parser.add_argument("-f", "--optdir", help="directory containing optimized FPGA results", required=True) + parser.add_argument("-u", "--unoptdir", help="directory containing unoptimized FPGA results", required=True) + parser.add_argument("-d", "--cpudir", help="directory containing CPU results", required=True) + parser.add_argument("-t", "--corpora", help="text corpora (without file size)", nargs="+", default=[], required=True) + parser.add_argument("-s", "--sizes", help="file sizes", type=int, nargs="+", default=[], required=True) + parser.add_argument("-k", "--kernel", help="kernel", required=True) + parser.add_argument("-o", "--save", help="save as PNG", action="store_true", required=False) + args = parser.parse_args() + + main(args.corpora, args.sizes, args.lengths, args.optdir, args.unoptdir, args.cpudir, args.save, args.count, args.kernel) diff --git a/code/fpga/plot_opts.py b/code/fpga/plot_opts.py new file mode 100644 index 0000000..629b202 --- /dev/null +++ b/code/fpga/plot_opts.py @@ -0,0 +1,261 @@ +import argparse +import matplotlib as mpl +mpl.use('TkAgg') +import matplotlib.pyplot as plt +import numpy as np +import json +import glob +from scipy.integrate import simps + + +kernel_name_map = { + "cpu": "reference CPU application", + "unopt": "reference FPGA kernel", + "memory": "memory optimized kernel", + "ndrange": "NDRange optimized kernel", + "final": "fully optimized kernel" +} +cmap = plt.get_cmap('cividis') +colors = [cmap(i) for i in np.linspace(0, 1, 5)] + + +def main(corpora, sizes, lengths,save, count, unoptdir, memorydir, ndrangedir, finaldir, cpudir): + plt.style.use('seaborn') + + unoptresults = parse_fpga_results(corpora, sizes, lengths, unoptdir) + memoryresults = parse_fpga_results(corpora, sizes, lengths, memorydir) + ndrangeresults = parse_fpga_results(corpora, sizes, lengths, ndrangedir) + finalresults = parse_fpga_results(corpora, sizes, lengths, finaldir) + cpuresults = parse_cpu_results(corpora, sizes, lengths, cpudir) + # plot_throughput(cpuresults, unoptresults, memoryresults, ndrangeresults, finalresults, corpora, lengths, save, count) + # plot_throughput(cpuresults, unoptresults, memoryresults, ndrangeresults, finalresults, corpora, lengths, save, count, log=True) + # plot_cycles(cpuresults, unoptresults, memoryresults, ndrangeresults, finalresults, corpora, lengths, save, count) + # print_energy_table(cpuresults, memoryresults, ndrangeresults, finalresults, corpora, sizes, lengths) + plot_time_energy(cpuresults, finalresults, corpora, lengths, save) + + +def parse_fpga_results(corpora, sizes, lengths, dir): + results = dict() + + for corpus in corpora: + results[corpus] = dict() + for size in sizes: + results[corpus][size] = dict() + for length in lengths: + results[corpus][size][length] = parse_fpga_result(corpus, size, length, dir) + + return results + + +def parse_fpga_result(corpus, size, length, dir): + resultdir = f"{dir}/{corpus}.{size}MB.len{length}" + result = [] + for filepath in glob.iglob(f"{resultdir}/*"): + with open(filepath, "r") as f: + data = json.load(f) + time = data['Kernel Execution'][0]['time'] + energy = get_energy_usage(data) + result.append((time/1000, energy)) + + return result + + +def parse_cpu_results(corpora, sizes, lengths, dir): + results = dict() + + for corpus in corpora: + results[corpus] = dict() + for size in sizes: + results[corpus][size] = dict() + for length in lengths: + results[corpus][size][length] = parse_cpu_result(corpus, size, length, dir) + + return results + + +def parse_cpu_result(corpus, size, length, dir): + def parse_line(line): + [range_time, index_time, total_matches] = line.split(" ") + return (float.fromhex(range_time), float.fromhex(index_time), int(total_matches)) + + filename = f"{dir}/{corpus}.{size}MB.cpu{length}.result" + + with open(filename, "r") as f: + data = list(map(parse_line, f.read().splitlines())) + + return data + + +def get_energy_usage(data): + xs = list(map(lambda x: x["timestamp"], data["power"])) + ys = list(map(lambda y: y["power"], data["power"])) + + # Get start and end timestamp of kernel execution. + start = float(data["timeline"]["START"]) + end = float(data["timeline"]["END"]) + + # Find nearest power data points. + nearest_start = min(range(len(xs)), key=lambda i: abs(xs[i] - start)) + nearest_end = min(range(len(xs)), key=lambda i: abs(xs[i] - end)) + + # Find power data points within kernel execution + kernel_xs = np.array(xs)[nearest_start:nearest_end+1] / 1000 + kernel_ys = np.array(ys)[nearest_start:nearest_end+1] + + # Use Simpson's Rule to integrate and find energy usage. + return simps(y=kernel_ys, x=kernel_xs) + + +def plot_throughput(cpuresults, unoptresults, memoryresults, ndrangeresults, finalresults, corpora, lengths, save, count, log=False): + width = .15 + keys = np.array([[(corpus, length) for length in lengths] for corpus in corpora]).reshape(len(corpora) * len(lengths), 2) + labels = [f"({corpus}, {length})" for (corpus, length) in keys] + xs = np.arange(len(labels)) + size = 20 + _, ax = plt.subplots() + + for i, (results, name) in enumerate([(cpuresults, "cpu"), (unoptresults, "unopt"), (memoryresults, "memory"), (ndrangeresults, "ndrange"), (finalresults, "final")]): + means = [np.mean(count / np.array(results[corpus][size][int(length)])[:, 0]) for (corpus, length) in keys] + stds = [np.std(count / np.array(results[corpus][size][int(length)])[:, 0]) for (corpus, length) in keys] + ax.bar(xs - (width*len(lengths))/2 + i * width + width/2, means, width, label=kernel_name_map[name].capitalize(), yerr=stds, color=colors[i]) + + ax.set_ylabel("Throughput (patterns matched/s)") + ax.set_xlabel("Corpus and pattern length") + ax.set_xticks(xs) + ax.tick_params(axis="x", rotation=25) + ax.set_xticklabels(labels) + ax.legend() + ax.set_title(f"Throughput of the reference applications and the optimized kernels") + if log: + ax.set_yscale('log') + + plt.subplots_adjust(bottom=0.16) + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 5) + plt.savefig(f"throughput_opts{'_log' if log else ''}.png", format="png", dpi=100) + else: + plt.show() + + +def plot_cycles(cpuresults, unoptresults, memoryresults, ndrangeresults, finalresults, corpora, lengths, save, count): + size = 20 + fpga_clockspeed = 0.3 + cpu_clockspeed = 3.4 + def calculate_cycles(fpgaresults, corpus, length): + result = [] + length = int(length) + for (fpgaresult, cpuresult) in zip(fpgaresults[corpus][size][length], cpuresults[corpus][size][length]): + fpgacycles = fpgaresult[0] * fpga_clockspeed + cpucycles = cpuresult[0] * cpu_clockspeed + result.append(cpucycles / fpgacycles) + return result + width = .15 + keys = np.array([[(corpus, length) for length in lengths] for corpus in corpora]).reshape(len(corpora) * len(lengths), 2) + labels = [f"({corpus}, {length})" for (corpus, length) in keys] + xs = np.arange(len(labels)) + _, ax = plt.subplots() + + for i, (results, name) in enumerate([(unoptresults, "unopt"), (memoryresults, "memory"), (ndrangeresults, "ndrange"), (finalresults, "final")]): + means = [np.mean(calculate_cycles(results, corpus, length)) for (corpus, length) in keys] + stds = [np.std(calculate_cycles(results, corpus, length)) for (corpus, length) in keys] + ax.bar(xs - (width*len(lengths))/2 + i * width + width/2, means, width, label=kernel_name_map[name].capitalize(), yerr=stds, color=colors[i]) + + ax.set_ylabel("Cycles CPU / FPGA") + ax.set_xlabel("Corpus and pattern length") + ax.set_xticks(xs) + ax.tick_params(axis="x", rotation=25) + ax.set_xticklabels(labels) + ax.legend() + ax.set_title(f"Clock cycle comparison of the FPGA kernels and the reference CPU application") + + plt.subplots_adjust(bottom=0.16) + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 5) + plt.savefig("cycles_opts.png", format="png", dpi=100) + else: + plt.show() + + +def print_energy_table(cpuresults, memoryresults, ndrangeresults, finalresults, corpora, sizes, lengths): + size = 20 + for (results, kernel) in [(memoryresults, "memory"), (ndrangeresults, "NDRange"), (finalresults, "full")]: + print(f"\\textit{{{kernel}}}", end="") + for corpus in corpora: + for length in lengths: + cpumean = np.mean([result[1] for result in cpuresults[corpus][size][length]]) + fpgamean = np.mean([result[1] for result in results[corpus][size][length]]) + comp = fpgamean / (cpumean / 1000000) + print(" & ${:.1f}\\times$".format(comp), end="") + print(" \\\\") + + +def plot_time_energy(cpuresults, fpgaresults, corpora, lengths, save): + cmap = plt.get_cmap('viridis') + colors = [cmap(i) for i in np.linspace(0, 1, 3)] + size = 20 + + def calculate_time(fpgaresults, corpus, length): + result = [] + length = int(length) + for (fpgaresult, cpuresult) in zip(fpgaresults[corpus][size][length], cpuresults[corpus][size][length]): + result.append(fpgaresult[0] / cpuresult[0]) + return result + + def calculate_energy(fpgaresults, corpus, length): + result = [] + length = int(length) + for (fpgaresult, cpuresult) in zip(fpgaresults[corpus][size][length], cpuresults[corpus][size][length]): + result.append(fpgaresult[1] / (cpuresult[1]/1000000)) + return result + + width = .25 + keys = np.array([[(corpus, length) for length in lengths] for corpus in corpora]).reshape(len(corpora) * len(lengths), 2) + labels = [f"({corpus}, {length})" for (corpus, length) in keys] + xs = np.arange(len(labels)) + _, ax = plt.subplots() + + means = [np.mean(calculate_time(fpgaresults, corpus, length)) for (corpus, length) in keys] + stds = [np.std(calculate_time(fpgaresults, corpus, length)) for (corpus, length) in keys] + ax.bar(xs - width/2, means, width, label=r"time$_{FPGA}$ / time$_{CPU}$", yerr=stds, color=colors[1]) + + means = [np.mean(calculate_energy(fpgaresults, corpus, length)) for (corpus, length) in keys] + stds = [np.std(calculate_energy(fpgaresults, corpus, length)) for (corpus, length) in keys] + ax.bar(xs + width/2, means, width, label=r"energy$_{FPGA}$ / energy$_{CPU}$", yerr=stds, color=colors[2]) + + ax.set_ylabel("Fraction") + ax.set_xlabel("Corpus and pattern length") + ax.set_xticks(xs) + ax.tick_params(axis="x", rotation=25) + ax.set_xticklabels(labels) + ax.legend() + ax.set_title(f"Comparison of time and energy between the reference CPU application and fully optimized FPGA kernel") + + plt.subplots_adjust(bottom=0.16) + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 5) + plt.savefig("final_time_energy.png", format="png", dpi=100) + else: + plt.show() + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("-c", "--count", help="number of patterns", type=int, required=True) + parser.add_argument("-l", "--lengths", help="length of the patterns", type=int, nargs="+", default=[], required=True) + parser.add_argument("-t", "--corpora", help="text corpora (without file size)", nargs="+", default=[], required=True) + parser.add_argument("-s", "--sizes", help="file sizes", type=int, nargs="+", default=[], required=True) + parser.add_argument("-o", "--save", help="save as PNG", action="store_true", required=False) + parser.add_argument("-u", "--unoptdir", help="directory containing unoptimized FPGA results", required=True) + parser.add_argument("-m", "--memorydir", help="directory containing memory-optimized FPGA results", required=True) + parser.add_argument("-n", "--ndrangedir", help="directory containing NDRange-optimized FPGA results", required=True) + parser.add_argument("-f", "--finaldir", help="directory containing final FPGA results", required=True) + parser.add_argument("-p", "--cpudir", help="directory containing CPU results", required=True) + args = parser.parse_args() + + main(args.corpora, args.sizes, args.lengths, args.save, args.count, args.unoptdir, args.memorydir, args.ndrangedir, args.finaldir, args.cpudir) diff --git a/code/fpga/unopt.cl b/code/fpga/unopt.cl new file mode 100644 index 0000000..0a5265e --- /dev/null +++ b/code/fpga/unopt.cl @@ -0,0 +1,41 @@ +inline static int string_index(__global char *s, char c) { + int i = 0; + while (1) { + if (s[i] == c) + return i; + ++i; + } +} + +kernel __attribute__((reqd_work_group_size(1, 1, 1))) +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) { + for (unsigned i = 0; i < pattern_count; ++i) { + int p_idx = pattern_sz - 1; + char c = patterns[i * pattern_sz + p_idx]; + unsigned start = ranges[2 * string_index(alphabet, c)]; + unsigned end = ranges[2 * string_index(alphabet, c) + 1]; + + p_idx -= 1; + while (p_idx >= 0 && end > 1) { + c = patterns[i * pattern_sz + p_idx]; + unsigned range_start = ranges[2 * string_index(alphabet, c)]; + int alphabet_idx = string_index(alphabet, c); + 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[i * out_sz] = match_count; + for (unsigned j = 0; j < match_count; ++j) + out[i * out_sz + j + 1] = sa[start + j]; + } +} diff --git a/code/fpga/unopt_results/dblp.xml.10MB.len4/run0.json b/code/fpga/unopt_results/dblp.xml.10MB.len4/run0.json new file mode 100644 index 0000000..9050876 --- /dev/null +++ b/code/fpga/unopt_results/dblp.xml.10MB.len4/run0.json @@ -0,0 +1 @@ +{"power": [{"timestamp": 39.1185, "power": 32.75726}, {"timestamp": 59.7271, "power": 32.75726}, {"timestamp": 80.3011, "power": 32.75726}, {"timestamp": 100.867, "power": 32.75726}, {"timestamp": 121.545, "power": 32.75726}, {"timestamp": 142.187, "power": 32.75726}, {"timestamp": 162.67, "power": 32.75726}, {"timestamp": 183.204, 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0.11511}]} \ No newline at end of file diff --git a/code/fpga/verify.cpp b/code/fpga/verify.cpp new file mode 100644 index 0000000..606850d --- /dev/null +++ b/code/fpga/verify.cpp @@ -0,0 +1,202 @@ +#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 +#include +#include +#include +#include +#include +#include + +#include "../fmindex.h" +#include "../util.h" + +std::vector get_xilinx_devices(); +char *read_binary_file(const std::string &xclbin_file_name, unsigned &nb); + +int main(int argc, char **argv) { + if (argc < 6) { + printf( + "Usage: %s \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) { + printf("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))) { + printf("Could not read test data file.\n"); + return 1; + } + + // Initialize OpenCL. + cl_int err; + unsigned fileBufSize; + std::vector 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 host pointers. + size_t *out = (size_t *)q.enqueueMapBuffer( + out_buf, CL_TRUE, CL_MAP_READ, 0, + sizeof(unsigned long) * pattern_count * max_match_count); + + // 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(); + + // Verify whether kernel calculations are correct. + for (unsigned i = 0; i < pattern_count; ++i) { + char *pattern = &patterns[i * pattern_sz]; + ranges_t start, end; + FMIndexFindMatchRange(index, pattern, pattern_sz, &start, &end); + unsigned long match_count = end - start; + unsigned long *match_indices = + (unsigned long *)calloc(match_count, sizeof(unsigned long)); + FMIndexFindRangeIndices(index, start, end, &match_indices); + + printf("Verifying pattern \"%.*s\": ", pattern_sz, pattern); + unsigned long *results = &out[i * (max_match_count + 1)]; + if (results[0] != match_count) { + printf("INCORRECT (match count %lu != %lu)\n", results[0], match_count); + continue; + } + int success = 1; + for (unsigned j = 0; j < match_count; j++) + if (results[j + 1] != match_indices[j]) { + printf("INCORRECT (index %lu != %lu)\n", results[j + 1], + match_indices[j]); + success = 0; + break; + } + if (success) + printf("CORRECT\n"); + } + + // Release resources. + delete[] fileBuf; + FMIndexFree(index); + return EXIT_SUCCESS; +} + +// ------------------------------------------------------------------------------------ +// Utility functions +// ------------------------------------------------------------------------------------ +std::vector get_xilinx_devices() { + size_t i; + cl_int err; + std::vector platforms; + err = cl::Platform::get(&platforms); + cl::Platform platform; + for (i = 0; i < platforms.size(); i++) { + platform = platforms[i]; + std::string platformName = platform.getInfo(&err); + if (platformName == "Xilinx") { + std::cout << "INFO: Found Xilinx Platform" << std::endl; + break; + } + } + if (i == platforms.size()) { + std::cout << "ERROR: Failed to find Xilinx platform" << std::endl; + exit(EXIT_FAILURE); + } + + // Getting ACCELERATOR Devices and selecting 1st such device + std::vector 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::cout << "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; +} diff --git a/code/fpga/xrt.ini b/code/fpga/xrt.ini new file mode 100644 index 0000000..256c30b --- /dev/null +++ b/code/fpga/xrt.ini @@ -0,0 +1,8 @@ +[Debug] +profile=true +power_profile=true +timeline_trace=true +data_transfer_trace=coarse +stall_trace=all +[Profile] +exec=all:all diff --git a/code/generate_test_data.cpp b/code/generate_test_data.cpp new file mode 100644 index 0000000..a23c789 --- /dev/null +++ b/code/generate_test_data.cpp @@ -0,0 +1,99 @@ +#include +#include +#include + +#include "fmindex.h" +#include "util.h" + +int main(int argc, char **argv) { + if (argc < 7) { + printf("Usage: $ %s " + " \n", + argv[0]); + return 1; + } + + int count = atoi(argv[4]); + int length = atoi(argv[5]); + + char *s = ReadFile(argv[1]); + if (!s) + return 1; + + fm_index *index = FMIndexReadFromFile(argv[2], 0); + if (!index) { + fprintf(stderr, "Error reading FM-index from file\n"); + return 1; + } + + size_t sz = strlen(s); + + unsigned long seed = time(NULL); + fprintf(stderr, "Seed: %lu\n", seed); + + std::random_device rand_dev; + std::mt19937 generator(seed); + std::uniform_int_distribution distr(0, sz - length); + + unsigned long indices[count]; + unsigned max_match_count = 1; + char pattern[length + 1]; + pattern[length] = '\0'; + + unsigned long match_total = 0; + for (int i = 0; i < count; ++i) { + // Find the average match count. + unsigned long idx = distr(generator); + memcpy(pattern, &s[idx], length); + ranges_t start, end; + FMIndexFindMatchRange(index, pattern, length, &start, &end); + match_total += end - start; + } + + fprintf(stderr, "Average match count: %lu\n", match_total / count); + + unsigned max_allowed_matches = atoi(argv[6]); + for (int i = 0; i < count; ++i) { + // Make sure the pattern does not contain newlines as it would + // mess with the formatting of the file. + // Skews the distributivity a bit, but shouldn't matter really. + unsigned long idx; + int valid; + ranges_t start, end; + + do { + idx = distr(generator); + valid = 1; + for (int i = 0; i < length; ++i) + if (s[idx + i] == '\n') + valid = 0; + if (valid) { + memcpy(pattern, &s[idx], length); + FMIndexFindMatchRange(index, pattern, length, &start, &end); + if (end - start > max_allowed_matches) + valid = 0; + } + } while (!valid); + + indices[i] = idx; + if (end - start > max_match_count) + max_match_count = end - start; + } + + FILE *f = fopen(argv[3], "w"); + if (!f) { + fprintf(stderr, "Failed to open output file.\n"); + return 1; + } + + fprintf(f, "%i\n", max_match_count); + fprintf(f, "%i\n", count); + fprintf(f, "%i\n", length); + for (int i = 0; i < count; ++i) { + fprintf(f, "%.*s\n", length, &s[indices[i]]); + } + + FMIndexFree(index); + + return 0; +} diff --git a/code/plot_cpu.py b/code/plot_cpu.py new file mode 100644 index 0000000..3e353ac --- /dev/null +++ b/code/plot_cpu.py @@ -0,0 +1,142 @@ +import argparse +import matplotlib as mpl +mpl.use('TkAgg') +import matplotlib.gridspec as gridspec +from matplotlib import ticker +import matplotlib.pyplot as plt +import numpy as np + + +cmap = plt.get_cmap('viridis') +colors = [cmap(i) for i in np.linspace(0, 1, 6)] + + +def main(corpora, sizes, lengths, dir, count, save): + plt.style.use('seaborn') + + results = parse_results(corpora, sizes, lengths, dir) + plot_throughput(results, corpora, sizes, lengths, count, save) + plot_energy(results, corpora, sizes, lengths, save) + print_match_count_table(results, corpora, sizes, lengths, count) + + +def parse_results(corpora, sizes, lengths, dir): + results = dict() + + for corpus in corpora: + results[corpus] = dict() + for size in sizes: + results[corpus][size] = dict() + for length in lengths: + results[corpus][size][length] = parse_result(corpus, size, length, dir) + + return results + + +def parse_result(corpus, size, length, dir): + def parse_line(line): + [range_time, index_time, total_matches] = line.split(" ") + return (float.fromhex(range_time), float.fromhex(index_time), int(total_matches)) + + filename = f"{dir}/{corpus}.{size}MB.cpu{length}.result" + + with open(filename, "r") as f: + data = list(map(parse_line, f.read().splitlines())) + + return data + + +def plot_throughput(results, corpora, sizes, lengths, count, save): + width = .1 + labels = [f"{size}MB" for size in sizes] + xs = np.arange(len(labels)) + gs = gridspec.GridSpec(2, 4) + gs.update(wspace=0.5, hspace=0.5) + + axes = [plt.subplot(gs[0, 1:3], ), plt.subplot(gs[1, :2]), plt.subplot(gs[1, 2:])] + for axi, ax in enumerate(axes): + corpus = corpora[axi] + ax.sharey(axes[0]) + + means = np.array([[int(np.mean([count / result[0] for result in results[corpus][size][length]])) for size in sizes] for length in lengths]) + stds = np.array([[np.std([count / result[0] for result in results[corpus][size][length]]) for size in sizes] for length in lengths]) + for i in range(len(lengths)): + ax.bar(xs - (width*len(lengths))/2 + i * width + width/2, means[i], width, label=f"{lengths[i]} characters", yerr=stds[i], color=colors[i]) + + if axi in [0, 1]: + ax.set_ylabel("Throughput (patterns matched/s)") + ax.set_xlabel("Corpus size (MB)") + ax.set_title(f"\"{corpus}\" corpus"); + ax.set_xticks(xs) + ax.set_xticklabels(labels) + if axi == 0: + ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left', borderaxespad=0., title="Pattern length") + ax.yaxis.set_major_formatter(ticker.FuncFormatter(lambda y, _: str(int(y/1000)) + ("K" if y != 0 else ""))) + + plt.suptitle("Average throughput for the reference CPU application") + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 7) + plt.savefig("throughput_cpu.png", format="png", dpi=100) + else: + plt.show() + + +def plot_energy(results, corpora, sizes, lengths, save): + width = .1 + labels = [f"{size}MB" for size in sizes] + xs = np.arange(len(labels)) + gs = gridspec.GridSpec(2, 4) + gs.update(wspace=0.5, hspace=0.5) + + + axes = [plt.subplot(gs[0, 1:3], ), plt.subplot(gs[1, :2]), plt.subplot(gs[1, 2:])] + for axi, ax in enumerate(axes): + corpus = corpora[axi] + + means = np.array([[np.mean([result[1]/1000000 for result in results[corpus][size][length]]) for size in sizes] for length in lengths]) + stds = np.array([[np.std([result[1]/1000000 for result in results[corpus][size][length]]) for size in sizes] for length in lengths]) + for i in range(len(lengths)): + ax.bar(xs - (width*len(lengths))/2 + i * width + width/2, means[i], width, label=f"{lengths[i]} characters", yerr=stds[i], color=colors[i+3]) + + if axi in [0, 1]: + ax.set_ylabel("Energy consumption (J)") + ax.set_xlabel("Corpus size (MB)") + ax.set_title(f"\"{corpus}\" corpus"); + ax.set_xticks(xs) + ax.set_xticklabels(labels) + if axi == 0: + ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left', borderaxespad=0., title="Pattern length") + + plt.suptitle("Average energy consumption for the reference CPU application") + + if save: + figure = plt.gcf() + figure.set_size_inches(9, 7) + plt.savefig("energy_cpu.png", format="png", dpi=100) + else: + plt.show() + + +def print_match_count_table(results, corpora, sizes, lengths, count): + for length in lengths: + print(f"{length}", end="") + for corpus in corpora: + for size in sizes: + mean = np.mean([result[2] / count for result in results[corpus][size][length]]) + print(f" & {round(mean)}", end="") + print(" \\\\") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("-c", "--count", help="number of patterns", 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 results", required=True) + parser.add_argument("-t", "--corpora", help="text corpora (without file size)", nargs="+", default=[], required=True) + parser.add_argument("-s", "--sizes", help="file sizes", type=int, nargs="+", default=[], required=True) + parser.add_argument("-o", "--save", help="save as SVG", action="store_true", required=False) + args = parser.parse_args() + + main(args.corpora, args.sizes, args.lengths, args.dir, args.count, args.save) diff --git a/code/program.c b/code/program.c new file mode 100644 index 0000000..ea85dfe --- /dev/null +++ b/code/program.c @@ -0,0 +1,46 @@ +#include "fmindex.h" +#include +#include +#include + +int main() { + char *s = "ALALA"; + char *pattern = "AL"; + + printf("> Constructing FM-index...\n"); + fm_index *index = FMIndexConstruct(s); + if (!index) { + printf("Failed to allocate memory for index...\n"); + return 1; + } + + printf("> FM-index constructed.\n"); + + printf("BWT: \"%s\"\n", index->bwt); + + ranges_t start, end; + FMIndexFindMatchRange(index, pattern, strlen(pattern), &start, &end); + unsigned long match_count = end - start; + unsigned long *match_indices = calloc(match_count, sizeof(unsigned long)); + FMIndexFindRangeIndices(index, start, end, &match_indices); + + printf("\nPattern \"%s\" occurs: %lu times\nIndices: ", pattern, match_count); + for (unsigned long i = 0; i < match_count; ++i) + printf("%lu ", match_indices[i]); + printf("\n"); + if (match_count) + printf("%s\n", s); + for (unsigned long i = 0; i < index->bwt_sz - 1; ++i) { + int found = 0; + for (unsigned long j = 0; j < match_count; ++j) + if (match_indices[j] == i) + found = 1; + + printf("%c", (found) ? '^' : ' '); + } + printf("\n"); + + free(match_indices); + FMIndexFree(index); + return 0; +} diff --git a/code/rapl.c b/code/rapl.c new file mode 100644 index 0000000..3a7ae8c --- /dev/null +++ b/code/rapl.c @@ -0,0 +1,187 @@ +/* Read the RAPL registers on recent (>sandybridge) Intel processors */ +/* */ +/* There are currently three ways to do this: */ +/* 1. Read the MSRs directly with /dev/cpu/??/msr */ +/* 2. Use the perf_event_open() interface */ +/* 3. Read the values from the sysfs powercap interface */ +/* */ +/* MSR Code originally based on a (never made it upstream) linux-kernel */ +/* RAPL driver by Zhang Rui */ +/* https://lkml.org/lkml/2011/5/26/93 */ +/* Additional contributions by: */ +/* Romain Dolbeau -- romain @ dolbeau.org */ +/* */ +/* For raw MSR access the /dev/cpu/??/msr driver must be enabled and */ +/* permissions set to allow read access. */ +/* You might need to "modprobe msr" before it will work. */ +/* */ +/* perf_event_open() support requires at least Linux 3.14 and to have */ +/* /proc/sys/kernel/perf_event_paranoid < 1 */ +/* */ +/* the sysfs powercap interface got into the kernel in */ +/* 2d281d8196e38dd (3.13) */ +/* */ +/* Compile with: gcc -O2 -Wall -o rapl-read rapl-read.c -lm */ +/* */ +/* Vince Weaver -- vincent.weaver @ maine.edu -- 11 September 2015 */ +/* */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#define MAX_CPUS 1024 +#define MAX_PACKAGES 16 + +static int package_map[MAX_PACKAGES]; + +static void detect_packages(int *total_cores, int *total_packages) { + + char filename[BUFSIZ]; + FILE *fff; + int package; + int i; + + *total_packages = 0; + + for (i = 0; i < MAX_PACKAGES; i++) + package_map[i] = -1; + + fprintf(stderr, "\t"); + for (i = 0; i < MAX_CPUS; i++) { + sprintf(filename, + "/sys/devices/system/cpu/cpu%d/topology/physical_package_id", i); + fff = fopen(filename, "r"); + if (fff == NULL) + break; + fscanf(fff, "%d", &package); + fprintf(stderr, "%d (%d)", i, package); + if (i % 8 == 7) + fprintf(stderr, "\n\t"); + else + fprintf(stderr, ", "); + fclose(fff); + + if (package_map[package] == -1) { + (*total_packages)++; + package_map[package] = i; + } + } + + fprintf(stderr, "\n"); + + *total_cores = i; + + fprintf(stderr, "\tDetected %d cores in %d packages\n\n", *total_cores, + *total_packages); +} + +#define NUM_RAPL_DOMAINS 5 + +int rapl_sysfs(void (*func)(void), double *result) { + + char event_names[MAX_PACKAGES][NUM_RAPL_DOMAINS][256]; + char filenames[MAX_PACKAGES][NUM_RAPL_DOMAINS][256]; + char basename[MAX_PACKAGES][256]; + char tempfile[256]; + long long before[MAX_PACKAGES][NUM_RAPL_DOMAINS]; + long long after[MAX_PACKAGES][NUM_RAPL_DOMAINS]; + int valid[MAX_PACKAGES][NUM_RAPL_DOMAINS]; + int i, j; + FILE *fff; + + int total_cores, total_packages; + detect_packages(&total_cores, &total_packages); + + fprintf(stderr, "\nTrying sysfs powercap interface to gather results\n\n"); + + for (j = 0; j < total_packages; j++) { + i = 0; + sprintf(basename[j], "/sys/class/powercap/intel-rapl/intel-rapl:%d", j); + sprintf(tempfile, "%s/name", basename[j]); + fff = fopen(tempfile, "r"); + if (fff == NULL) { + fprintf(stderr, "\tCould not open %s\n", tempfile); + return -1; + } + fscanf(fff, "%s", event_names[j][i]); + valid[j][i] = 1; + fclose(fff); + sprintf(filenames[j][i], "%s/energy_uj", basename[j]); + + /* Handle subdomains */ + for (i = 1; i < NUM_RAPL_DOMAINS; i++) { + sprintf(tempfile, "%s/intel-rapl:%d:%d/name", basename[j], j, i - 1); + fff = fopen(tempfile, "r"); + if (fff == NULL) { + valid[j][i] = 0; + continue; + } + valid[j][i] = 1; + fscanf(fff, "%s", event_names[j][i]); + fclose(fff); + sprintf(filenames[j][i], "%s/intel-rapl:%d:%d/energy_uj", basename[j], j, + i - 1); + } + } + + /* Gather before values */ + for (j = 0; j < total_packages; j++) { + for (i = 0; i < NUM_RAPL_DOMAINS; i++) { + if (valid[j][i]) { + fff = fopen(filenames[j][i], "r"); + if (fff == NULL) { + fprintf(stderr, "\tError opening %s!\n", filenames[j][i]); + } else { + fscanf(fff, "%lld", &before[j][i]); + fclose(fff); + } + } + } + } + + func(); + + /* Gather after values */ + for (j = 0; j < total_packages; j++) { + for (i = 0; i < NUM_RAPL_DOMAINS; i++) { + if (valid[j][i]) { + fff = fopen(filenames[j][i], "r"); + if (fff == NULL) { + fprintf(stderr, "\tError opening %s!\n", filenames[j][i]); + } else { + fscanf(fff, "%lld", &after[j][i]); + fclose(fff); + } + } + } + } + + const char *package_prefix = "package-"; + double total_joules = 0.; + + for (j = 0; j < total_packages; j++) { + for (i = 0; i < NUM_RAPL_DOMAINS; i++) { + if (valid[j][i]) { + if (strncmp(event_names[j][i], package_prefix, + strlen(package_prefix)) == 0) { + total_joules += (double)after[j][i] - (double)before[j][i]; + } + } + } + } + + *result = total_joules; + + return 0; +} diff --git a/code/rapl.h b/code/rapl.h new file mode 100644 index 0000000..d5a4632 --- /dev/null +++ b/code/rapl.h @@ -0,0 +1,3 @@ +#pragma once + +int rapl_sysfs(void (*func)(void), double *result); diff --git a/code/repl.c b/code/repl.c new file mode 100644 index 0000000..02a88f9 --- /dev/null +++ b/code/repl.c @@ -0,0 +1,46 @@ +#include "fmindex.h" + +#include +#include +#include +#include + +int main(int argc, char *argv[]) { + if (argc < 2) { + printf("Usage: $ %s \n", argv[0]); + return 1; + } + + fm_index *index = FMIndexReadFromFile(argv[1], 0); + if (!index) { + printf("Could not read FM-index from file.\n"); + return 1; + } + + int input_len = 256; + char input[input_len]; + do { + printf("Type your query: "); + fgets(input, input_len, stdin); + if (!strlen(input)) + break; + input[strlen(input) - 1] = '\0'; + + ranges_t start, end; + FMIndexFindMatchRange(index, input, strlen(input), &start, &end); + unsigned long match_count = end - start; + unsigned long *match_indices = calloc(match_count, sizeof(unsigned long)); + FMIndexFindRangeIndices(index, start, end, &match_indices); + + printf("Indices: "); + for (unsigned long i = 0; i < match_count; ++i) { + printf("%lu ", match_indices[i]); + } + printf("\n"); + printf("Found %lu matches.\n", match_count); + free(match_indices); + } while (1); + + FMIndexFree(index); + return 0; +} diff --git a/code/util.c b/code/util.c new file mode 100644 index 0000000..fc7ddcc --- /dev/null +++ b/code/util.c @@ -0,0 +1,98 @@ +#include "util.h" + +#include +#include +#include + +// https://stackoverflow.com/questions/2029103/#2029227 +char *ReadFile(char *filename) { + char *source = NULL; + FILE *fp = fopen(filename, "r"); + if (!fp) { + printf("Failed to open file.\n"); + return NULL; + } + + if (fseek(fp, 0L, SEEK_END) == 0) { + long bufsize = ftell(fp); + if (bufsize == -1) { + printf("Failed to determine file size.\n"); + return NULL; + } + source = malloc(sizeof(char) * (bufsize + 1)); + if (!source) { + printf("Failed to allocate space for file contents.\n"); + return NULL; + } + + if (fseek(fp, 0L, SEEK_SET) != 0) { + printf("Failed to move to the start of the file.\n"); + return NULL; + } + + size_t newLen = fread(source, sizeof(char), bufsize, fp); + if (ferror(fp) != 0) { + printf("Error reading from file.\n"); + return NULL; + } + + source[newLen++] = '\0'; + } + + fclose(fp); + return source; +} + +// https://stackoverflow.com/questions/1202687/18386648#18386648 +int randomrange(int min, int max) { + return min + rand() / (RAND_MAX / (max - min + 1) + 1); +} + +int LoadTestData(char *filename, char **tests, unsigned *pattern_count, + unsigned *pattern_sz, unsigned *max_match_count, int aligned) { + FILE *fp; + char *line = NULL; + size_t len = 0; + ssize_t read; + + if (!(fp = fopen(filename, "r"))) + return 0; + + // Read max match count. + if ((read = getline(&line, &len, fp)) == -1) + return 0; + *max_match_count = atoi(line); + + // Read test count. + if ((read = getline(&line, &len, fp)) == -1) + return 0; + *pattern_count = atoi(line); + + // Read test length. + if ((read = getline(&line, &len, fp)) == -1) + return 0; + *pattern_sz = atoi(line); + + if (!MaybeMallocAligned((void **)tests, + *pattern_count * *pattern_sz * sizeof(char), aligned)) + return 0; + + // Read each test on a seperate line. + for (unsigned i = 0; i < *pattern_count; ++i) { + if ((read = getline(&line, &len, fp)) == -1) + return 0; + memcpy(&(*tests)[i * *pattern_sz], line, *pattern_sz); + } + + fclose(fp); + free(line); + + return 1; +} + +int MaybeMallocAligned(void **mem, size_t sz, int aligned) { + if (aligned) + return posix_memalign(mem, 4096, sz) == 0; + else + return (*mem = malloc(sz)) != NULL; +} diff --git a/code/util.h b/code/util.h new file mode 100644 index 0000000..a5d5ce6 --- /dev/null +++ b/code/util.h @@ -0,0 +1,17 @@ +#pragma once + +#ifdef __cplusplus +extern "C" { +#endif + +#include + +char *ReadFile(char *filename); +int randomrange(int min, int max); +int LoadTestData(char *filename, char **tests, unsigned *pattern_count, + unsigned *pattern_sz, unsigned *max_match_count, int aligned); +int MaybeMallocAligned(void **mem, size_t sz, int aligned); + +#ifdef __cplusplus +} +#endif diff --git a/hls_performance_thesis.pdf b/hls_performance_thesis.pdf new file mode 100644 index 0000000000000000000000000000000000000000..e6f901c39966fe4d53bd6838d9709e9ebc0e1d2c GIT binary patch literal 1145621 zcmce-bBr%tw=LXu_pfd4cK61b?ENGoEg?`SM!Y-nR-48y|% zgS#{UP@{$4O4-}0@4jxYyrFb|$p`j5LNU5L}Z?~zt 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