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unifrac_task.cpp
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unifrac_task.cpp
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#include "unifrac_task.hpp"
#include <cstdlib>
void su::_unnormalized_weighted_unifrac_task(std::vector<double*> &__restrict__ dm_stripes,
std::vector<double*> &__restrict__ dm_stripes_total,
double* __restrict__ embedded_proportions,
double length,
const su::task_parameters* task_p) {
double *dm_stripe;
for(unsigned int stripe=task_p->start; stripe < task_p->stop; stripe++) {
dm_stripe = dm_stripes[stripe];
/* intrinsics yield about a 2x reduction in runtime on llvm. they
* were not effective on linux gcc 4.9.1 or 4.9.2. it is unclear
* if they would be effective on other versions of gcc.
*
* one reason they help is that these for loops are not easily
* autovectorizable. using the intrinsics effectively gets around
* this. ...although, it also appears that loop unrolling works.
*
* it may make sense to revisit the inclusion of intriniscs, however
* support must be tested at compile time, so it's rather annoying
* at the moment. basically, we can't assume the presence of avx2.
*/
for(unsigned int j = 0; j < task_p->n_samples / 4; j++) {
int k = j * 4;
double u1 = embedded_proportions[k];
double u2 = embedded_proportions[k + 1];
double u3 = embedded_proportions[k + 2];
double u4 = embedded_proportions[k + 3];
double v1 = embedded_proportions[k + stripe + 1];
double v2 = embedded_proportions[k + stripe + 2];
double v3 = embedded_proportions[k + stripe + 3];
double v4 = embedded_proportions[k + stripe + 4];
dm_stripe[k] += fabs(u1 - v1) * length;
dm_stripe[k + 1] += fabs(u2 - v2) * length;
dm_stripe[k + 2] += fabs(u3 - v3) * length;
dm_stripe[k + 3] += fabs(u4 - v4) * length;
}
if((task_p->n_samples % 4) != 0) {
for(unsigned int k = task_p->n_samples - (task_p->n_samples % 4); k < task_p->n_samples; k++) {
double u = embedded_proportions[k];
double v = embedded_proportions[k + stripe + 1];
dm_stripe[k] += fabs(u - v) * length;
}
}
}
}
void su::_vaw_unnormalized_weighted_unifrac_task(std::vector<double*> &__restrict__ dm_stripes,
std::vector<double*> &__restrict__ dm_stripes_total,
double* __restrict__ embedded_proportions,
double* __restrict__ embedded_counts,
double* __restrict__ sample_total_counts,
double length,
const su::task_parameters* task_p) {
double *dm_stripe;
for(unsigned int stripe=task_p->start; stripe < task_p->stop; stripe++) {
dm_stripe = dm_stripes[stripe];
for(unsigned int j = 0; j < task_p->n_samples; j++) {
double u = embedded_proportions[j];
double v = embedded_proportions[j + stripe + 1];
double m = sample_total_counts[j] + sample_total_counts[j + stripe + 1];
double mi = embedded_counts[j] + embedded_counts[j + stripe + 1];
double vaw = sqrt(mi * (m - mi));
if(vaw > 0)
dm_stripe[j] += (fabs(u - v) * length) / vaw;
}
}
}
void su::_normalized_weighted_unifrac_task(std::vector<double*> &__restrict__ dm_stripes,
std::vector<double*> &__restrict__ dm_stripes_total,
double* __restrict__ embedded_proportions,
double length,
const su::task_parameters* task_p) {
double *dm_stripe;
double *dm_stripe_total;
unsigned int trailing = task_p->n_samples - (task_p->n_samples % 4);
// point of thread
for(unsigned int stripe = task_p->start; stripe < task_p->stop; stripe++) {
dm_stripe = dm_stripes[stripe];
dm_stripe_total = dm_stripes_total[stripe];
for(unsigned int j = 0; j < task_p->n_samples / 4; j++) {
int k = j * 4;
int l = k + stripe;
double u1 = embedded_proportions[k];
double u2 = embedded_proportions[k + 1];
double u3 = embedded_proportions[k + 2];
double u4 = embedded_proportions[k + 3];
double v1 = embedded_proportions[l + 1];
double v2 = embedded_proportions[l + 2];
double v3 = embedded_proportions[l + 3];
double v4 = embedded_proportions[l + 4];
double diff1 = u1 - v1;
double diff2 = u2 - v2;
double diff3 = u3 - v3;
double diff4 = u4 - v4;
double sum1 = u1 + v1;
double sum2 = u2 + v2;
double sum3 = u3 + v3;
double sum4 = u4 + v4;
dm_stripe[k] += fabs(diff1) * length;
dm_stripe[k + 1] += fabs(diff2) * length;
dm_stripe[k + 2] += fabs(diff3) * length;
dm_stripe[k + 3] += fabs(diff4) * length;
dm_stripe_total[k] += sum1 * length;
dm_stripe_total[k + 1] += sum2 * length;
dm_stripe_total[k + 2] += sum3 * length;
dm_stripe_total[k + 3] += sum4 * length;
}
for(unsigned int k = trailing; k < task_p->n_samples; k++) {
double u = embedded_proportions[k];
double v = embedded_proportions[k + stripe + 1];
double diff = u - v;
double sum = u + v;
dm_stripe[k] += fabs(diff) * length;
dm_stripe_total[k] += sum * length;
}
}
}
void su::_vaw_normalized_weighted_unifrac_task(std::vector<double*> &__restrict__ dm_stripes,
std::vector<double*> &__restrict__ dm_stripes_total,
double* __restrict__ embedded_proportions,
double* __restrict__ embedded_counts,
double* __restrict__ sample_total_counts,
double length,
const su::task_parameters* task_p) {
double *dm_stripe;
double *dm_stripe_total;
// point of thread
for(unsigned int stripe = task_p->start; stripe < task_p->stop; stripe++) {
dm_stripe = dm_stripes[stripe];
dm_stripe_total = dm_stripes_total[stripe];
for(unsigned int j = 0; j < task_p->n_samples; j++) {
double u = embedded_proportions[j];
double v = embedded_proportions[j + stripe + 1];
double m = sample_total_counts[j] + sample_total_counts[j + stripe + 1];
double mi = embedded_counts[j] + embedded_counts[j + stripe + 1];
double vaw = sqrt(mi * (m - mi));
if(vaw > 0) {
dm_stripe[j] += (fabs(u - v) * length) / vaw;
dm_stripe_total[j] += ((u + v) * length) / vaw;
}
}
}
}
#define GUNIFRAC(u, v, s, j) if(s != 0.0) { \
double sub1 = fabs(u - v); \
double sum_pow1 = pow(s, task_p->g_unifrac_alpha) * length; \
dm_stripe[j] += sum_pow1 * (sub1 / s); \
dm_stripe_total[j] += sum_pow1; \
}
void su::_generalized_unifrac_task(std::vector<double*> &__restrict__ dm_stripes,
std::vector<double*> &__restrict__ dm_stripes_total,
double* __restrict__ embedded_proportions,
double length,
const su::task_parameters* task_p) {
double *dm_stripe;
double *dm_stripe_total;
unsigned int trailing = task_p->n_samples - (task_p->n_samples % 4);
// point of thread
for(unsigned int stripe = task_p->start; stripe < task_p->stop; stripe++) {
dm_stripe = dm_stripes[stripe];
dm_stripe_total = dm_stripes_total[stripe];
for(unsigned int j = 0; j < task_p->n_samples / 4; j++) {
int k = j * 4;
int l = k + stripe;
double u1 = embedded_proportions[k];
double u2 = embedded_proportions[k + 1];
double u3 = embedded_proportions[k + 2];
double u4 = embedded_proportions[k + 3];
double v1 = embedded_proportions[l + 1];
double v2 = embedded_proportions[l + 2];
double v3 = embedded_proportions[l + 3];
double v4 = embedded_proportions[l + 4];
double sum1 = u1 + v1;
double sum2 = u2 + v2;
double sum3 = u3 + v3;
double sum4 = u4 + v4;
GUNIFRAC(u1, v1, sum1, k)
GUNIFRAC(u2, v2, sum2, k + 1)
GUNIFRAC(u3, v3, sum3, k + 2)
GUNIFRAC(u4, v4, sum4, k + 3)
}
for(unsigned int k = trailing; k < task_p->n_samples; k++) {
double u = embedded_proportions[k];
double v = embedded_proportions[k + stripe + 1];
double s = u + v;
GUNIFRAC(u, v, s, k)
}
}
}
void su::_vaw_generalized_unifrac_task(std::vector<double*> &__restrict__ dm_stripes,
std::vector<double*> &__restrict__ dm_stripes_total,
double* __restrict__ embedded_proportions,
double* __restrict__ embedded_counts,
double* __restrict__ sample_total_counts,
double length,
const su::task_parameters* task_p) {
double *dm_stripe;
double *dm_stripe_total;
// point of thread
for(unsigned int stripe = task_p->start; stripe < task_p->stop; stripe++) {
dm_stripe = dm_stripes[stripe];
dm_stripe_total = dm_stripes_total[stripe];
for(unsigned int j = 0; j < task_p->n_samples; j++) {
double m = sample_total_counts[j] + sample_total_counts[j + stripe + 1];
double mi = embedded_counts[j] + embedded_counts[j + stripe + 1];
double vaw = sqrt(mi * (m - mi));
double u1 = embedded_proportions[j];
double v1 = embedded_proportions[j + stripe + 1];
if(vaw > 0.0) {
double sum1 = (u1 + v1) / vaw;
double sub1 = fabs(u1 - v1) / vaw;
double sum_pow1 = pow(sum1, task_p->g_unifrac_alpha) * length;
dm_stripe[j] += sum_pow1 * (sub1 / sum1);
dm_stripe_total[j] += sum_pow1;
}
}
}
}
void su::_unweighted_unifrac_task(std::vector<double*> &__restrict__ dm_stripes,
std::vector<double*> &__restrict__ dm_stripes_total,
double* __restrict__ embedded_proportions,
double length,
const su::task_parameters* task_p) {
double *dm_stripe;
double *dm_stripe_total;
for(unsigned int stripe = task_p->start; stripe < task_p->stop; stripe++) {
dm_stripe = dm_stripes[stripe];
dm_stripe_total = dm_stripes_total[stripe];
for(unsigned int j = 0; j < task_p->n_samples / 4; j++) {
int k = j * 4;
int32_t u1 = embedded_proportions[k] > 0;
int32_t u2 = embedded_proportions[k + 1] > 0;
int32_t u3 = embedded_proportions[k + 2] > 0;
int32_t u4 = embedded_proportions[k + 3] > 0;
int32_t v1 = embedded_proportions[k + stripe + 1] > 0;
int32_t v2 = embedded_proportions[k + stripe + 2] > 0;
int32_t v3 = embedded_proportions[k + stripe + 3] > 0;
int32_t v4 = embedded_proportions[k + stripe + 4] > 0;
dm_stripe[k] += (u1 ^ v1) * length;
dm_stripe[k + 1] += (u2 ^ v2) * length;
dm_stripe[k + 2] += (u3 ^ v3) * length;
dm_stripe[k + 3] += (u4 ^ v4) * length;
dm_stripe_total[k] += (u1 | v1) * length;
dm_stripe_total[k + 1] += (u2 | v2) * length;
dm_stripe_total[k + 2] += (u3 | v3) * length;
dm_stripe_total[k + 3] += (u4 | v4) * length;
}
if((task_p->n_samples % 4) != 0) {
for(unsigned int k = task_p->n_samples - (task_p->n_samples % 4); k < task_p->n_samples; k++) {
int32_t u = embedded_proportions[k] > 0;
int32_t v = embedded_proportions[k + stripe + 1] > 0;
dm_stripe[k] += (u ^ v) * length;
dm_stripe_total[k] += (u | v) * length;
}
}
}
}
void su::_vaw_unweighted_unifrac_task(std::vector<double*> &__restrict__ dm_stripes,
std::vector<double*> &__restrict__ dm_stripes_total,
double* __restrict__ embedded_proportions,
double* __restrict__ embedded_counts,
double* __restrict__ sample_total_counts,
double length,
const su::task_parameters* task_p) {
double *dm_stripe;
double *dm_stripe_total;
for(unsigned int stripe = task_p->start; stripe < task_p->stop; stripe++) {
dm_stripe = dm_stripes[stripe];
dm_stripe_total = dm_stripes_total[stripe];
for(unsigned int j = 0; j < task_p->n_samples; j++) {
int32_t u = embedded_proportions[j] > 0;
int32_t v = embedded_proportions[j + stripe + 1] > 0;
double m = sample_total_counts[j] + sample_total_counts[j + stripe + 1];
double mi = embedded_counts[j] + embedded_counts[j + stripe + 1];
double vaw = sqrt(mi * (m - mi));
if(vaw > 0) {
dm_stripe[j] += ((u ^ v) * length) / vaw;
dm_stripe_total[j] += ((u | v) * length) / vaw;
}
}
}
}