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BenBrockBenBrock
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Add C++ examples, C++ CI (#10)
* Add C++ examples, C++ CI * Remove extraneous entry from CMake * Use g++-14 for C++ CI * Minor fix * Verbose build for debugging * Use gcc 13 * GCC 12
1 parent 705f775 commit 122cce8

16 files changed

+1009
-3
lines changed

Diff for: ‎.github/workflows/ci.yml

+3-3
Original file line numberDiff line numberDiff line change
@@ -33,9 +33,9 @@ jobs:
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- name: CMake
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run: |
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sudo apt-get update
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sudo apt-get install libhdf5-dev
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cmake -B build
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sudo apt-get install libhdf5-dev g++-12
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CXX=g++-12 cmake -B build
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- name: Build
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run: make -C build -j `nproc`
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run: VERBOSE=true make -C build -j `nproc`
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- name: Test
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run: ctest --test-dir ./build/test/bash

Diff for: ‎CMakeLists.txt

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@@ -5,6 +5,8 @@ cmake_policy(SET CMP0079 NEW)
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set(CMAKE_C_STANDARD 11)
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set(CMAKE_CXX_STANDARD 20)
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set(CMAKE_C_FLAGS "-O3 -march=native")
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add_subdirectory(include)

Diff for: ‎examples/CMakeLists.txt

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Original file line numberDiff line numberDiff line change
@@ -14,3 +14,5 @@ add_example(bsp-ls)
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add_example(benchmark_read)
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add_example(benchmark_read_parallel)
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add_example(benchmark_write)
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add_subdirectory(cpp)

Diff for: ‎examples/cpp/CMakeLists.txt

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@@ -0,0 +1,15 @@
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function(add_example example_name)
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add_executable(${example_name}-cpp ${example_name}.cpp)
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target_link_libraries(${example_name}-cpp binsparse-rc)
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endfunction()
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add_example(simple_matrix_write)
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add_example(simple_matrix_read)
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add_example(simple_read)
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add_example(simple_write)
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add_example(mtx2bsp)
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add_example(bsp2mtx)
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add_example(check_equivalence)
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add_example(bsp-ls)
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add_example(benchmark_read)
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add_example(benchmark_write)

Diff for: ‎examples/cpp/benchmark_read.cpp

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@@ -0,0 +1,123 @@
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#include <binsparse/binsparse.h>
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#include <stdlib.h>
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#include <time.h>
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double gettime() {
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struct timespec time;
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clock_gettime(CLOCK_MONOTONIC, &time);
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return ((double) time.tv_sec) + ((double) 1e-9) * time.tv_nsec;
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}
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int compar(const void* a, const void* b) {
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double x = *((const double*) a);
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double y = *((const double*) b);
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double diff = x - y;
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if (diff > 0) {
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return 1;
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} else if (diff < 0) {
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return -1;
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} else {
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return 0;
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}
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}
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double compute_variance(double* x, size_t n) {
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double sum = 0;
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for (size_t i = 0; i < n; i++) {
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sum += x[i];
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}
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double mean = sum / n;
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double sum_of_squares = 0;
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for (size_t i = 0; i < n; i++) {
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sum_of_squares += (x[i] - mean) * (x[i] - mean);
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}
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return sum_of_squares / (n - 1);
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}
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void flush_cache() {
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#ifdef __APPLE__
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system("bash -c \"sync && sudo purge\"");
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#elif __linux__
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system("bash -c \"sync\" && sudo echo 3 > /proc/sys/vm/drop_caches");
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#else
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static_assert(false);
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#endif
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}
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int main(int argc, char** argv) {
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if (argc < 2) {
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fprintf(stderr, "usage: ./benchmark_read [file_name.h5]\n");
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return 1;
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}
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char* file_name = argv[1];
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printf("Opening %s\n", file_name);
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const int num_trials = 1;
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double durations[num_trials];
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size_t nbytes = 0;
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// To flush the filesystem cache before each trial, change to `true`.
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bool cold_cache = false;
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for (size_t i = 0; i < num_trials; i++) {
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if (cold_cache) {
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flush_cache();
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}
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double begin = gettime();
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bsp_matrix_t mat = bsp_read_matrix(file_name, NULL);
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double end = gettime();
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durations[i] = end - begin;
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nbytes = bsp_matrix_nbytes(mat);
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bsp_destroy_matrix_t(mat);
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}
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printf("[");
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for (size_t i = 0; i < num_trials; i++) {
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printf("%lf", durations[i]);
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if (i + 1 < num_trials) {
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printf(", ");
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}
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}
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printf("]\n");
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qsort(durations, num_trials, sizeof(double), compar);
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double variance = compute_variance(durations, num_trials);
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double median_time = durations[num_trials / 2];
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printf("Read file in %lf seconds\n", median_time);
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if (num_trials > 1) {
102+
printf("Variance is %lf seconds, standard devication is %lf seconds\n",
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variance, sqrt(variance));
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}
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double gbytes = ((double) nbytes) / 1024 / 1024 / 1024;
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double gbytes_s = gbytes / median_time;
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printf("Achieved %lf GiB/s\n", gbytes_s);
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printf("[");
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for (size_t i = 0; i < num_trials; i++) {
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printf("%lf", durations[i]);
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if (i + 1 < num_trials) {
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printf(", ");
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}
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}
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printf("]\n");
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printf("FORPARSER: %s,%lf,%lf\n", file_name, median_time, gbytes_s);
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return 0;
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}

Diff for: ‎examples/cpp/benchmark_write.cpp

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@@ -0,0 +1,170 @@
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#include <binsparse/binsparse.h>
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#include <stdlib.h>
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#include <time.h>
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double gettime() {
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struct timespec time;
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clock_gettime(CLOCK_MONOTONIC, &time);
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return ((double) time.tv_sec) + ((double) 1e-9) * time.tv_nsec;
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}
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11+
int compar(const void* a, const void* b) {
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double x = *((const double*) a);
13+
double y = *((const double*) b);
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double diff = x - y;
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17+
if (diff > 0) {
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return 1;
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} else if (diff < 0) {
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return -1;
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} else {
22+
return 0;
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}
24+
}
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26+
double compute_variance(double* x, size_t n) {
27+
double sum = 0;
28+
29+
for (size_t i = 0; i < n; i++) {
30+
sum += x[i];
31+
}
32+
33+
double mean = sum / n;
34+
35+
double sum_of_squares = 0;
36+
for (size_t i = 0; i < n; i++) {
37+
sum_of_squares += (x[i] - mean) * (x[i] - mean);
38+
}
39+
40+
return sum_of_squares / (n - 1);
41+
}
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43+
void flush_cache() {
44+
#ifdef __APPLE__
45+
system("bash -c \"sync && sudo purge\"");
46+
#elif __linux__
47+
system("bash -c \"sync\" && sudo echo 3 > /proc/sys/vm/drop_caches");
48+
#else
49+
static_assert(false);
50+
#endif
51+
}
52+
53+
void flush_writes() {
54+
#ifdef __APPLE__
55+
system("bash -c \"sync\"");
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#elif __linux__
57+
system("bash -c \"sync\"");
58+
#else
59+
static_assert(false);
60+
#endif
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}
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void delete_file(const char* file_name) {
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char command[2048];
65+
snprintf(command, 2047, "rm %s", file_name);
66+
system(command);
67+
}
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int main(int argc, char** argv) {
70+
if (argc < 2) {
71+
fprintf(stderr,
72+
"usage: ./benchmark_read [file_name.h5] [scratch_space] [optional: "
73+
"compression_level]\n");
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return 1;
75+
}
76+
77+
char* file_name = argv[1];
78+
char* scratch_space = argv[2];
79+
80+
int compression_level = 0;
81+
82+
if (argc >= 4) {
83+
compression_level = atoi(argv[3]);
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}
85+
86+
printf("Opening %s\n", file_name);
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const int num_trials = 1;
89+
90+
double durations[num_trials];
91+
92+
bsp_matrix_t mat = bsp_read_matrix(file_name, NULL);
93+
size_t nbytes = bsp_matrix_nbytes(mat);
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char output_filename[2048];
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strncpy(output_filename, scratch_space, 2047);
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strncpy(output_filename + strlen(scratch_space), "/benchmark_write_file_n.h5",
98+
2047 - strlen(scratch_space));
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// Current output name logic does not do much.
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assert(num_trials <= 10);
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// To flush the filesystem cache before each trial, change to `true`.
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bool cold_cache = false;
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// To flush each write to the filesystem and include this in the timing,
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// change to `true`.
108+
bool flush_each_write = true;
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for (size_t i = 0; i < num_trials; i++) {
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if (cold_cache) {
112+
flush_cache();
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}
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output_filename[strlen(scratch_space) + 21] = '0' + i;
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printf("Writing to file %s\n", output_filename);
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double begin = gettime();
119+
bsp_write_matrix(output_filename, mat, NULL, NULL, compression_level);
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if (flush_each_write) {
122+
flush_writes();
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}
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double end = gettime();
126+
durations[i] = end - begin;
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128+
delete_file(output_filename);
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}
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printf("[");
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for (size_t i = 0; i < num_trials; i++) {
133+
printf("%lf", durations[i]);
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if (i + 1 < num_trials) {
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printf(", ");
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}
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}
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printf("]\n");
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qsort(durations, num_trials, sizeof(double), compar);
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double variance = compute_variance(durations, num_trials);
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double median_time = durations[num_trials / 2];
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146+
printf("Wrote file in %lf seconds\n", median_time);
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if (num_trials > 1) {
149+
printf("Variance is %lf seconds, standard devication is %lf seconds\n",
150+
variance, sqrt(variance));
151+
}
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double gbytes = ((double) nbytes) / 1024 / 1024 / 1024;
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double gbytes_s = gbytes / median_time;
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printf("Achieved %lf GiB/s\n", gbytes_s);
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printf("[");
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for (size_t i = 0; i < num_trials; i++) {
160+
printf("%lf", durations[i]);
161+
if (i + 1 < num_trials) {
162+
printf(", ");
163+
}
164+
}
165+
printf("]\n");
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167+
printf("FORPARSER: %s,%lf,%lf\n", file_name, median_time, gbytes_s);
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return 0;
170+
}

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