Initial checkin

BeefySysLib/perf_tests/fannkuchredux.cpp

@@ -0,0 +1,81 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include "Common.h"
+
+static void fannkuch(int n, int& sumOut, int& maxflipsOut)
+{
+	int sum = 0;
+	int maxflips = 0;
+	
+	/*int* p = (int*)alloca(sizeof(int)*n);
+	int* q = (int*)alloca(sizeof(int)*n);
+	int* s = (int*)alloca(sizeof(int)*n);*/
+    
+    int* p = new int[n];
+     int* q = new int[n];
+     int* s = new int[n];
+
+	int sign = 1, m = n - 1;
+	for (int i = 0; i < n; i++) { p[i] = i; q[i] = i; s[i] = i; }
+	do
+	{
+		// Copy and flip.
+		int q0 = p[0];                                     // Cache 0th element.
+		if (q0 != 0)
+		{
+			for (int i = 1; i < n; i++) q[i] = p[i];             // Work on a copy.
+			int flips = 1;
+			do
+			{
+				int qq = q[q0];
+				if (qq == 0)
+				{                                // ... until 0th element is 0.
+					sum += sign * flips;
+					if (flips > maxflips) maxflips = flips;   // New maximum?
+					break;
+				}
+				q[q0] = q0;
+				if (q0 >= 3)
+				{
+					int i = 1, j = q0 - 1, t;
+					do { t = q[i]; q[i] = q[j]; q[j] = t; i++; j--; } while (i < j);
+				}
+				q0 = qq; flips++;
+			} while (true);
+		}
+		// Permute.
+		if (sign == 1)
+		{
+			int t = p[1]; p[1] = p[0]; p[0] = t; sign = -1; // Rotate 0<-1.
+		}
+		else
+		{
+			int t = p[1]; p[1] = p[2]; p[2] = t; sign = 1;  // Rotate 0<-1 and 0<-1<-2.
+			for (int i = 2; i < n; i++)
+			{
+				int sx = s[i];
+				if (sx != 0) { s[i] = sx - 1; break; }
+				if (i == m) 
+				{					
+					sumOut = sum;
+					maxflipsOut = maxflips;
+					return;  // Out of permutations.
+				}
+				s[i] = i;
+				// Rotate 0<-...<-i+1.
+				t = p[0]; for (int j = 0; j <= i; j++) { p[j] = p[j + 1]; } p[i + 1] = t;
+			}
+		}
+	} while (true);
+}
+
+
+void FannkuchRedux(int n)
+{	
+	int sum;
+	int maxflips;
+	fannkuch(n, sum, maxflips);
+	Beefy::OutputDebugStrF("%d\nPfannkuchenC(%d) = %d\n", sum, n, maxflips);
+}
+

BeefySysLib/perf_tests/fastaredux.cpp

@@ -0,0 +1,140 @@
+#pragma warning(disable:4838)
+#pragma warning(disable:4305)
+
+#define _GNU_SOURCE
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+
+#define MIN(x, y) ((x < y) ? x : y)
+#define LINELEN 60
+#define SLOTS 4095
+
+struct aminoacid {
+	char c;
+	float p;
+};
+
+static struct aminoacid *lu[SLOTS + 1];
+
+static void repeat_fasta(const char *alu, size_t n)
+{
+	const size_t alulen = strlen(alu);
+	assert(alulen < 1024);
+	char buf[1024 + LINELEN];
+	size_t pos = 0, bytes;
+
+	memcpy(buf, alu, alulen);
+	memcpy(buf + alulen, alu, LINELEN);
+	while (n) {
+		bytes = MIN(LINELEN, n);
+		//fwrite_unlocked(buf + pos, bytes, 1, stdout);
+		//putchar_unlocked('\n');
+		pos += bytes;
+		if (pos > alulen)
+			pos -= alulen;
+		n -= bytes;
+	}
+}
+
+static void acc_probs(struct aminoacid *table)
+{
+	struct aminoacid *iter = table;
+
+	while ((++iter)->c) {
+		iter->p += (iter - 1)->p;
+	}
+	for (int i = 0; i <= SLOTS; ++i) {
+		while (i > (table->p * SLOTS))
+			++table;
+		lu[i] = table;
+	}
+}
+
+static float rng(float max)
+{
+	const unsigned int IM = 139968, IA = 3877, IC = 29573;
+	static unsigned int seed = 42;
+
+	seed = (seed * IA + IC) % IM;
+	return max * seed / IM;
+}
+
+static char nextc()
+{
+	float r;
+	struct aminoacid *iter;
+
+	r = rng(1.0f);
+	iter = lu[(int) (r * SLOTS)];
+	while (iter->p < r)
+		++iter;
+	return iter->c;
+}
+
+static void random_fasta(struct aminoacid *table, size_t n)
+{
+	size_t i, lines = n / LINELEN;
+	const size_t chars_left = n % LINELEN;
+	char buf[LINELEN + 1];
+
+	while (lines--) {
+		for (i = 0; i < LINELEN; ++i) {
+			buf[i] = nextc();
+		}
+		buf[i] = '\n';
+		//fwrite_unlocked(buf, i + 1, 1, stdout);
+	}
+	for (i = 0; i < chars_left; ++i)
+		buf[i] = nextc();
+	//fwrite_unlocked(buf, i, 1, stdout);
+}
+
+void FastaRedux(int n)
+{
+	//const size_t n = (argc > 1) ? atoi(argv[1]) : 1000;
+	const char alu [] =
+		"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTG"
+		"GGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGA"
+		"GACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAA"
+		"AATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAAT"
+		"CCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAAC"
+		"CCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTG"
+		"CACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
+	struct aminoacid iub [] = {
+		{ 'a', 0.27 },
+		{ 'c', 0.12 },
+		{ 'g', 0.12 },
+		{ 't', 0.27 },
+		{ 'B', 0.02 },
+		{ 'D', 0.02 },
+		{ 'H', 0.02 },
+		{ 'K', 0.02 },
+		{ 'M', 0.02 },
+		{ 'N', 0.02 },
+		{ 'R', 0.02 },
+		{ 'S', 0.02 },
+		{ 'V', 0.02 },
+		{ 'W', 0.02 },
+		{ 'Y', 0.02 },
+		{ 0, 0 }
+	};
+	struct aminoacid homosapiens [] = {
+		{ 'a', 0.3029549426680 },
+		{ 'c', 0.1979883004921 },
+		{ 'g', 0.1975473066391 },
+		{ 't', 0.3015094502008 },
+		{ 0, 0 }
+	};
+
+	//fputs_unlocked(">ONE Homo sapiens alu\n", stdout);
+	repeat_fasta(alu, n * 2);
+	//fputs_unlocked(">TWO IUB ambiguity codes\n", stdout);
+	acc_probs(iub);
+	random_fasta(iub, n * 3);
+	//fputs_unlocked(">THREE Homo sapiens frequency\n", stdout);
+	acc_probs(homosapiens);
+	random_fasta(homosapiens, n * 5);
+	//putchar_unlocked('\n');
+}

BeefySysLib/perf_tests/nbody.cpp

@@ -0,0 +1,136 @@
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include "Common.h"
+
+#define pi 3.141592653589793
+#define solar_mass (4 * pi * pi)
+#define days_per_year 365.24
+
+struct planet {
+	double x, y, z;
+	double vx, vy, vz;
+	double mass;
+};
+
+void advance(int nbodies, struct planet * bodies, double dt)
+{
+	int i, j;
+
+	for (i = 0; i < nbodies; i++) {
+		struct planet * b = &(bodies[i]);
+		for (j = i + 1; j < nbodies; j++) {
+			struct planet * b2 = &(bodies[j]);
+			double dx = b->x - b2->x;
+			double dy = b->y - b2->y;
+			double dz = b->z - b2->z;
+			double distance = sqrt(dx * dx + dy * dy + dz * dz);
+			double mag = dt / (distance * distance * distance);
+			b->vx -= dx * b2->mass * mag;
+			b->vy -= dy * b2->mass * mag;
+			b->vz -= dz * b2->mass * mag;
+			b2->vx += dx * b->mass * mag;
+			b2->vy += dy * b->mass * mag;
+			b2->vz += dz * b->mass * mag;
+		}
+	}
+	for (i = 0; i < nbodies; i++) {
+		struct planet * b = &(bodies[i]);
+		b->x += dt * b->vx;
+		b->y += dt * b->vy;
+		b->z += dt * b->vz;
+	}
+}
+
+double energy(int nbodies, struct planet * bodies)
+{
+	double e;
+	int i, j;
+
+	e = 0.0;
+	for (i = 0; i < nbodies; i++) {
+		struct planet * b = &(bodies[i]);
+		e += 0.5 * b->mass * (b->vx * b->vx + b->vy * b->vy + b->vz * b->vz);
+		for (j = i + 1; j < nbodies; j++) {
+			struct planet * b2 = &(bodies[j]);
+			double dx = b->x - b2->x;
+			double dy = b->y - b2->y;
+			double dz = b->z - b2->z;
+			double distance = sqrt(dx * dx + dy * dy + dz * dz);
+			e -= (b->mass * b2->mass) / distance;
+		}
+	}
+	return e;
+}
+
+void offset_momentum(int nbodies, struct planet * bodies)
+{
+	double px = 0.0, py = 0.0, pz = 0.0;
+	int i;
+	for (i = 0; i < nbodies; i++) {
+		px += bodies[i].vx * bodies[i].mass;
+		py += bodies[i].vy * bodies[i].mass;
+		pz += bodies[i].vz * bodies[i].mass;
+	}
+	bodies[0].vx = -px / solar_mass;
+	bodies[0].vy = -py / solar_mass;
+	bodies[0].vz = -pz / solar_mass;
+}
+
+#define NBODIES 5
+struct planet orig_bodies[NBODIES] = {
+	{                               /* sun */
+		0, 0, 0, 0, 0, 0, solar_mass
+	},
+	{                               /* jupiter */
+		4.84143144246472090e+00,
+		-1.16032004402742839e+00,
+		-1.03622044471123109e-01,
+		1.66007664274403694e-03 * days_per_year,
+		7.69901118419740425e-03 * days_per_year,
+		-6.90460016972063023e-05 * days_per_year,
+		9.54791938424326609e-04 * solar_mass
+	},
+	{                               /* saturn */
+		8.34336671824457987e+00,
+		4.12479856412430479e+00,
+		-4.03523417114321381e-01,
+		-2.76742510726862411e-03 * days_per_year,
+		4.99852801234917238e-03 * days_per_year,
+		2.30417297573763929e-05 * days_per_year,
+		2.85885980666130812e-04 * solar_mass
+	},
+	{                               /* uranus */
+		1.28943695621391310e+01,
+		-1.51111514016986312e+01,
+		-2.23307578892655734e-01,
+		2.96460137564761618e-03 * days_per_year,
+		2.37847173959480950e-03 * days_per_year,
+		-2.96589568540237556e-05 * days_per_year,
+		4.36624404335156298e-05 * solar_mass
+	},
+	{                               /* neptune */
+		1.53796971148509165e+01,
+		-2.59193146099879641e+01,
+		1.79258772950371181e-01,
+		2.68067772490389322e-03 * days_per_year,
+		1.62824170038242295e-03 * days_per_year,
+		-9.51592254519715870e-05 * days_per_year,
+		5.15138902046611451e-05 * solar_mass
+	}
+};
+
+struct planet bodies[NBODIES];
+
+void NBody(int n)
+{	
+	int i;
+
+	memcpy(bodies, orig_bodies, sizeof(orig_bodies));
+
+	offset_momentum(NBODIES, bodies);
+	printf("%.9f\n", energy(NBODIES, bodies));
+	for (i = 1; i <= n; i++)
+		advance(NBODIES, bodies, 0.01);
+	printf("%.9f\n", energy(NBODIES, bodies));
+}