commit 2a39a04c690e8854bde55432e1374dcf7710a80d
parent 2a9d3bf13585c5378e5b1bddb77106ee86719d29
Author: NunoSempere <nuno.sempere@protonmail.com>
Date: Sat, 18 Nov 2023 20:10:29 +0000
add desiderata split_array_refactor
Diffstat:
5 files changed, 404 insertions(+), 0 deletions(-)
diff --git a/C/alt/04-factor-out-paralellization/why.md b/C/alt/04-factor-out-paralellization/why.md
@@ -0,0 +1 @@
+So that the mixture distribution could be composable with other functions in squiggle.c
diff --git a/C/alt/05-refactor-split-array/desiderata.md b/C/alt/05-refactor-split-array/desiderata.md
@@ -0,0 +1,37 @@
+Instead of
+
+```C
+#pragma omp parallel private(i, sample_index, split_array_length)
+{
+ #pragma omp for
+ for (i = 0; i < n_threads; i++) {
+ split_array_length = split_array_get_length(i, N, n_threads);
+ for (int j = 0; j < split_array_length; j++) {
+ results[i][j] = sampler(seeds[i]);
+ }
+ }
+}
+
+```
+
+Algo como
+
+```C
+#pragma omp parallel private(i, sample_index, bounds)
+{
+ #pragma omp for
+ for (i = 0; i < n_threads; i++) {
+ int bounds[2] = split_array_get_bounds(i, N, n_threads);
+ for (int j = bound[0]; j < bounds[1] + 1; j++) {
+ // o j < bounds[1], no se si el +1 va a ser más elegante
+ // dentro o fuera, aunque algo me dice que dentro
+ results[j] = sampler(seeds[i]);
+ }
+ }
+}
+
+```
+
+Por qué? Porque esto hace que la estructura subyacente sea un solo array,
+lo cual implica que no *tengo* que utilizar split_array_functions especializadas
+si no quiero
diff --git a/C/alt/05-refactor-split-array/makefile b/C/alt/05-refactor-split-array/makefile
@@ -0,0 +1,106 @@
+# Interface:
+# make
+# make build
+# make format
+# make run
+
+# Compiler
+CC=gcc
+# CC=tcc # <= faster compilation
+
+# Main file
+SRC=samples.c
+OUTPUT=out/samples
+
+SRC_ONE_THREAD=./samples-one-thread.c
+OUTPUT_ONE_THREAD=out/samples-one-thread
+
+## Dependencies
+# Has no dependencies
+MATH=-lm
+
+## Flags
+DEBUG= #'-g'
+STANDARD=-std=c99
+WARNINGS=-Wall
+OPTIMIZED=-O3 #-O3 actually gives better performance than -Ofast, at least for this version
+OPENMP=-fopenmp
+
+## Formatter
+STYLE_BLUEPRINT=webkit
+FORMATTER=clang-format -i -style=$(STYLE_BLUEPRINT)
+
+## make build
+build: $(SRC)
+ $(CC) $(OPTIMIZED) $(DEBUG) $(SRC) $(OPENMP) $(MATH) -o $(OUTPUT)
+
+static:
+ $(CC) $(OPTIMIZED) $(DEBUG) $(SRC) $(OPENMP) $(MATH) -o $(OUTPUT)
+
+format: $(SRC)
+ $(FORMATTER) $(SRC)
+
+run: $(SRC) $(OUTPUT)
+ OMP_NUM_THREADS=1 ./$(OUTPUT) && echo
+
+multi:
+ OMP_NUM_THREADS=1 ./$(OUTPUT) && echo
+ OMP_NUM_THREADS=2 ./$(OUTPUT) && echo
+ OMP_NUM_THREADS=4 ./$(OUTPUT) && echo
+ OMP_NUM_THREADS=8 ./$(OUTPUT) && echo
+ OMP_NUM_THREADS=16 ./$(OUTPUT) && echo
+
+## Timing
+
+time-linux:
+ @echo "Requires /bin/time, found on GNU/Linux systems" && echo
+
+ @echo "Running 100x and taking avg time: OMP_NUM_THREADS=1 $(OUTPUT)"
+ @t=$$(/usr/bin/time -f "%e" -p bash -c 'for i in {1..100}; do OMP_NUM_THREADS=1 $(OUTPUT); done' 2>&1 >/dev/null | grep real | awk '{print $$2}' ); echo "scale=2; 1000 * $$t / 100" | bc | sed "s|^|Time using 1 thread: |" | sed 's|$$|ms|' && echo
+
+ @echo "Running 100x and taking avg time: OMP_NUM_THREADS=2 $(OUTPUT)"
+ @t=$$(/usr/bin/time -f "%e" -p bash -c 'for i in {1..100}; do OMP_NUM_THREADS=2 $(OUTPUT); done' 2>&1 >/dev/null | grep real | awk '{print $$2}' ); echo "scale=2; 1000 * $$t / 100" | bc | sed "s|^|Time using 2 threads: |" | sed 's|$$|ms|' && echo
+
+ @echo "Running 100x and taking avg time: OMP_NUM_THREADS=4 $(OUTPUT)"
+ @t=$$(/usr/bin/time -f "%e" -p bash -c 'for i in {1..100}; do OMP_NUM_THREADS=4 $(OUTPUT); done' 2>&1 >/dev/null | grep real | awk '{print $$2}' ); echo "scale=2; 1000 * $$t / 100" | bc | sed "s|^|Time for 4 threads: |" | sed 's|$$|ms|' && echo
+
+ @echo "Running 100x and taking avg time: OMP_NUM_THREADS=8 $(OUTPUT)"
+ @t=$$(/usr/bin/time -f "%e" -p bash -c 'for i in {1..100}; do OMP_NUM_THREADS=8 $(OUTPUT); done' 2>&1 >/dev/null | grep real | awk '{print $$2}' ); echo "scale=2; 1000 * $$t / 100" | bc | sed "s|^|Time using 8 threads: |" | sed 's|$$|ms|' && echo
+
+ @echo "Running 100x and taking avg time: OMP_NUM_THREADS=16 $(OUTPUT)"
+ @t=$$(/usr/bin/time -f "%e" -p bash -c 'for i in {1..100}; do OMP_NUM_THREADS=16 $(OUTPUT); done' 2>&1 >/dev/null | grep real | awk '{print $$2}' ); echo "scale=2; 1000 * $$t / 100" | bc | sed "s|^|Time using 16 threads: |" | sed 's|$$|ms|' && echo
+
+time-linux-fastest:
+ @echo "Running 100x and taking avg time: OMP_NUM_THREADS=16 $(OUTPUT)"
+ @t=$$(/usr/bin/time -f "%e" -p bash -c 'for i in {1..100}; do OMP_NUM_THREADS=16 $(OUTPUT); done' 2>&1 >/dev/null | grep real | awk '{print $$2}' ); echo "scale=2; 1000 * $$t / 100" | bc | sed "s|^|Time using 16 threads: |" | sed 's|$$|ms|' && echo
+
+time-linux-simple:
+ @echo "Requires /bin/time, found on GNU/Linux systems" && echo
+ OMP_NUM_THREADS=1 /bin/time -f "Time: %es" ./$(OUTPUT) && echo
+ OMP_NUM_THREADS=2 /bin/time -f "Time: %es" ./$(OUTPUT) && echo
+ OMP_NUM_THREADS=4 /bin/time -f "Time: %es" ./$(OUTPUT) && echo
+ OMP_NUM_THREADS=8 /bin/time -f "Time: %es" ./$(OUTPUT) && echo
+ OMP_NUM_THREADS=16 /bin/time -f "Time: %es" ./$(OUTPUT) && echo
+
+## Profiling
+
+profile-linux:
+ echo "Requires perf, which depends on the kernel version, and might be in linux-tools package or similar"
+ echo "Must be run as sudo"
+ $(CC) $(SRC) $(OPENMP) $(MATH) -o $(OUTPUT)
+ # ./$(OUTPUT)
+ # gprof:
+ # gprof $(OUTPUT) gmon.out > analysis.txt
+ # rm gmon.out
+ # vim analysis.txt
+ # rm analysis.txt
+ # perf:
+ OMP_NUM_THREADS=16 sudo perf record $(OUTPUT)
+ sudo perf report
+ rm perf.data
+
+
+## Install
+debian-install-dependencies:
+ sudo apt-get install libomp-dev
+
diff --git a/C/alt/05-refactor-split-array/out/samples b/C/alt/05-refactor-split-array/out/samples
Binary files differ.
diff --git a/C/alt/05-refactor-split-array/samples.c b/C/alt/05-refactor-split-array/samples.c
@@ -0,0 +1,260 @@
+#include <math.h>
+#include <omp.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+const float PI = 3.14159265358979323846;
+
+#define N 1000000
+
+//Array helpers
+
+void array_print(float* array, int length)
+{
+ for (int i = 0; i < length; i++) {
+ printf("item[%d] = %f\n", i, array[i]);
+ }
+ printf("\n");
+}
+
+float array_sum(float* array, int length)
+{
+ float output = 0.0;
+ for (int i = 0; i < length; i++) {
+ output += array[i];
+ }
+ return output;
+}
+
+void array_cumsum(float* array_to_sum, float* array_cumsummed, int length)
+{
+ array_cumsummed[0] = array_to_sum[0];
+ for (int i = 1; i < length; i++) {
+ array_cumsummed[i] = array_cumsummed[i - 1] + array_to_sum[i];
+ }
+}
+
+// Split array helpers
+int split_array_get_length(int index, int total_length, int n_threads)
+{
+ return (total_length % n_threads > index ? total_length / n_threads + 1 : total_length / n_threads);
+}
+
+void split_array_allocate(float** meta_array, int length, int divide_into)
+{
+ int split_array_length;
+
+ for (int i = 0; i < divide_into; i++) {
+ split_array_length = split_array_get_length(i, length, divide_into);
+ meta_array[i] = malloc(split_array_length * sizeof(float));
+ }
+}
+
+void split_array_free(float** meta_array, int divided_into)
+{
+ for (int i = 0; i < divided_into; i++) {
+ free(meta_array[i]);
+ }
+ free(meta_array);
+}
+
+float split_array_sum(float** meta_array, int length, int divided_into)
+{
+ int i;
+ float output = 0;
+
+#pragma omp parallel for reduction(+ \
+ : output)
+ for (int i = 0; i < divided_into; i++) {
+ float own_partial_sum = 0;
+ int split_array_length = split_array_get_length(i, length, divided_into);
+ for (int j = 0; j < split_array_length; j++) {
+ own_partial_sum += meta_array[i][j];
+ }
+ output += own_partial_sum;
+ }
+ return output;
+}
+
+// Pseudo Random number generator
+
+uint32_t xorshift32(uint32_t* seed)
+{
+ // Algorithm "xor" from p. 4 of Marsaglia, "Xorshift RNGs"
+ // See <https://stackoverflow.com/questions/53886131/how-does-xorshift32-works>
+ // https://en.wikipedia.org/wiki/Xorshift
+ // Also some drama: <https://www.pcg-random.org/posts/on-vignas-pcg-critique.html>, <https://prng.di.unimi.it/>
+
+ uint32_t x = *seed;
+ x ^= x << 13;
+ x ^= x >> 17;
+ x ^= x << 5;
+ return *seed = x;
+}
+
+// Distribution & sampling functions
+
+float rand_0_to_1(uint32_t* seed)
+{
+ return ((float)xorshift32(seed)) / ((float)UINT32_MAX);
+ /*
+ uint32_t x = *seed;
+ x ^= x << 13;
+ x ^= x >> 17;
+ x ^= x << 5;
+ return ((float)(*seed = x))/((float) UINT32_MAX);
+ */
+ // previously:
+ // ((float)rand_r(seed) / (float)RAND_MAX)
+ // and before that: rand, but it wasn't thread-safe.
+ // See: <https://stackoverflow.com/questions/43151361/how-to-create-thread-safe-random-number-generator-in-c-using-rand-r> for why to use rand_r:
+ // rand() is not thread-safe, as it relies on (shared) hidden seed.
+}
+
+float rand_float(float max, uint32_t* seed)
+{
+ return rand_0_to_1(seed) * max;
+}
+
+float ur_normal(uint32_t* seed)
+{
+ float u1 = rand_0_to_1(seed);
+ float u2 = rand_0_to_1(seed);
+ float z = sqrtf(-2.0 * log(u1)) * sin(2 * PI * u2);
+ return z;
+}
+
+float random_uniform(float from, float to, uint32_t* seed)
+{
+ return rand_0_to_1(seed) * (to - from) + from;
+}
+
+float random_normal(float mean, float sigma, uint32_t* seed)
+{
+ return (mean + sigma * ur_normal(seed));
+}
+
+float random_lognormal(float logmean, float logsigma, uint32_t* seed)
+{
+ return expf(random_normal(logmean, logsigma, seed));
+}
+
+float random_to(float low, float high, uint32_t* seed)
+{
+ const float NORMAL95CONFIDENCE = 1.6448536269514722;
+ float loglow = logf(low);
+ float loghigh = logf(high);
+ float logmean = (loglow + loghigh) / 2;
+ float logsigma = (loghigh - loglow) / (2.0 * NORMAL95CONFIDENCE);
+ return random_lognormal(logmean, logsigma, seed);
+}
+
+// Mixture function
+
+float mixture(float (*samplers[])(uint32_t*), float* weights, int n_dists, uint32_t* seed)
+{
+
+ // You can see a slightly simpler version of this function in the git history
+ // or in alt/C-02-better-algorithm-one-thread/
+ float sum_weights = array_sum(weights, n_dists);
+ float* cumsummed_normalized_weights = malloc(n_dists * sizeof(float));
+ cumsummed_normalized_weights[0] = weights[0] / sum_weights;
+ for (int i = 1; i < n_dists; i++) {
+ cumsummed_normalized_weights[i] = cumsummed_normalized_weights[i - 1] + weights[i] / sum_weights;
+ }
+
+ //create var holders
+ float p1, result;
+ int sample_index, i, own_length;
+ p1 = random_uniform(0, 1, seed);
+ for (int i = 0; i < n_dists; i++) {
+ if (p1 < cumsummed_normalized_weights[i]) {
+ result = samplers[i](seed);
+ break;
+ }
+ }
+ free(cumsummed_normalized_weights);
+ return result;
+}
+
+// Parallization function
+void paralellize(float (*sampler)(uint32_t* seed), float** results, int n_threads){
+
+ int sample_index, i, split_array_length;
+ uint32_t** seeds = malloc(n_threads * sizeof(uint32_t*));
+ for (uint32_t i = 0; i < n_threads; i++) {
+ seeds[i] = malloc(sizeof(uint32_t));
+ *seeds[i] = i + 1; // xorshift can't start with 0
+ }
+
+ #pragma omp parallel private(i, sample_index, split_array_length)
+ {
+ #pragma omp for
+ for (i = 0; i < n_threads; i++) {
+ split_array_length = split_array_get_length(i, N, n_threads);
+ for (int j = 0; j < split_array_length; j++) {
+ results[i][j] = sampler(seeds[i]);
+ }
+ }
+ }
+
+ for (uint32_t i = 0; i < n_threads; i++) {
+ free(seeds[i]);
+ }
+ free(seeds);
+}
+
+// Functions used for the BOTEC.
+// Their type has to be the same, as we will be passing them around.
+
+float sample_0(uint32_t* seed)
+{
+ return 0;
+}
+
+float sample_1(uint32_t* seed)
+{
+ return 1;
+}
+
+float sample_few(uint32_t* seed)
+{
+ return random_to(1, 3, seed);
+}
+
+float sample_many(uint32_t* seed)
+{
+ return random_to(2, 10, seed);
+}
+
+float sample_mixture(uint32_t* seed){
+ float p_a, p_b, p_c;
+
+ // Initialize variables
+ p_a = 0.8;
+ p_b = 0.5;
+ p_c = p_a * p_b;
+
+ // Generate mixture
+ int n_dists = 4;
+ float weights[] = { 1 - p_c, p_c / 2, p_c / 4, p_c / 4 };
+ float (*samplers[])(uint32_t*) = { sample_0, sample_1, sample_few, sample_many };
+
+ return mixture(samplers, weights, n_dists, seed);
+}
+
+int main()
+{
+ int n_threads = omp_get_max_threads();
+ // printf("Max threads: %d\n", n_threads);
+ // omp_set_num_threads(n_threads);
+ float** split_array_results = malloc(n_threads * sizeof(float*));
+ split_array_allocate(split_array_results, N, n_threads);
+
+ paralellize(sample_mixture, split_array_results, n_threads);
+ printf("Sum(split_array_results, N)/N = %f\n", split_array_sum(split_array_results, N, n_threads) / N);
+
+ split_array_free(split_array_results, n_threads);
+ return 0;
+}
