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Made CDistance use openmp
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@lisitsyn
lisitsyn committed Jul 8, 2012
1 parent c23a3c1 commit 4e109e3
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Showing 2 changed files with 32 additions and 121 deletions.
150 changes: 32 additions & 118 deletions src/shogun/distance/Distance.cpp
View file
Expand Up @@ -22,43 +22,15 @@

#include <string.h>
#include <unistd.h>

#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif
#include <omp.h>

using namespace shogun;

#ifndef DOXYGEN_SHOULD_SKIP_THIS
struct DISTANCE_THREAD_PARAM
{
// CDistance instance used by thread to compute distance
CDistance* distance;
// distance matrix to store computed distances
float64_t* distance_matrix;
// starting index of the main loop
int32_t idx_start;
// end index of the main loop
int32_t idx_stop;
// step of the main loop
int32_t idx_step;
// number of lhs vectors
int32_t lhs_vectors_number;
// number of rhs vectors
int32_t rhs_vectors_number;
// whether matrix distance is symmetric
bool symmetric;
// chunking method
bool chunk_by_lhs;
};
#endif /* DOXYGEN_SHOULD_SKIP_THIS */

CDistance::CDistance() : CSGObject()
{
init();
}


CDistance::CDistance(CFeatures* p_lhs, CFeatures* p_rhs) : CSGObject()
{
init();
Expand Down Expand Up @@ -318,92 +290,16 @@ float64_t* CDistance::get_distance_matrix_real(
// select chunking method according to greatest dimension
bool chunk_by_lhs = (lhs_vectors_number >= rhs_vectors_number);

#ifdef HAVE_PTHREAD
// init parallel to work
int32_t num_threads = parallel->get_num_threads();
ASSERT(num_threads>0);
pthread_t* threads = SG_MALLOC(pthread_t, num_threads);
DISTANCE_THREAD_PARAM* parameters = SG_MALLOC(DISTANCE_THREAD_PARAM,num_threads);
pthread_attr_t attr;
pthread_attr_init(&attr);
pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
// run threads
for (int32_t t=0; t<num_threads; t++)
{
parameters[t].idx_start = t;
parameters[t].idx_stop = chunk_by_lhs ? lhs_vectors_number : rhs_vectors_number;
parameters[t].idx_step = num_threads;
parameters[t].distance_matrix = distance_matrix;
parameters[t].symmetric = symmetric;
parameters[t].lhs_vectors_number = lhs_vectors_number;
parameters[t].rhs_vectors_number = rhs_vectors_number;
parameters[t].chunk_by_lhs = chunk_by_lhs;
parameters[t].distance = this;
pthread_create(&threads[t], &attr, run_distance_thread, (void*)&parameters[t]);
}
// join, i.e. wait threads for finish
for (int32_t t=0; t<num_threads; t++)
{
pthread_join(threads[t], NULL);
}
// cleanup
pthread_attr_destroy(&attr);
SG_FREE(parameters);
SG_FREE(threads);
#else
// init one-threaded parameters
DISTANCE_THREAD_PARAM single_thread_param;
single_thread_param.idx_start = 0;
single_thread_param.idx_stop = chunk_by_lhs ? lhs_vectors_number : rhs_vectors_number;
single_thread_param.idx_step = 1;
single_thread_param.distance_matrix = distance_matrix;
single_thread_param.symmetric = symmetric;
single_thread_param.lhs_vectors_number = lhs_vectors_number;
single_thread_param.rhs_vectors_number = rhs_vectors_number;
single_thread_param.chunk_by_lhs = chunk_by_lhs;
single_thread_param.distance = this;
// run thread
run_distance_thread((void*)&single_thread_param);
#endif

return distance_matrix;
}

void CDistance::init()
{
precomputed_matrix = NULL;
precompute_matrix = false;
lhs = NULL;
rhs = NULL;
num_lhs=0;
num_rhs=0;

m_parameters->add((CSGObject**) &lhs, "lhs",
"Feature vectors to occur on left hand side.");
m_parameters->add((CSGObject**) &rhs, "rhs",
"Feature vectors to occur on right hand side.");
}

void* CDistance::run_distance_thread(void* p)
{
DISTANCE_THREAD_PARAM* parameters = (DISTANCE_THREAD_PARAM*)p;
float64_t* distance_matrix = parameters->distance_matrix;
CDistance* distance = parameters->distance;
int32_t idx_start = parameters->idx_start;
int32_t idx_stop = parameters->idx_stop;
int32_t idx_step = parameters->idx_step;
int32_t lhs_vectors_number = parameters->lhs_vectors_number;
int32_t rhs_vectors_number = parameters->rhs_vectors_number;
bool symmetric = parameters->symmetric;
bool chunk_by_lhs = parameters->chunk_by_lhs;

int32_t i,j;
if (symmetric)
{
for (int32_t i=idx_start; i<idx_stop; i+=idx_step)
#pragma omp parallel private(i,j)
#pragma omp for schedule(dynamic) nowait
for (i=0; i<lhs_vectors_number; i++)
{
for (int32_t j=i; j<rhs_vectors_number; j++)
for (j=i; j<rhs_vectors_number; j++)
{
float64_t ij_distance = distance->compute(i,j);
float64_t ij_distance = compute(i,j);
distance_matrix[i*rhs_vectors_number+j] = ij_distance;
distance_matrix[j*rhs_vectors_number+i] = ij_distance;
}
Expand All @@ -413,25 +309,43 @@ void* CDistance::run_distance_thread(void* p)
{
if (chunk_by_lhs)
{
for (int32_t i=idx_start; i<idx_stop; i+=idx_step)
#pragma omp parallel private(i,j)
#pragma omp for schedule(dynamic) nowait
for (i=0; i<lhs_vectors_number; i++)
{
for (int32_t j=0; j<rhs_vectors_number; j++)
for (j=0; j<rhs_vectors_number; j++)
{
distance_matrix[j*lhs_vectors_number+i] = distance->compute(i,j);
distance_matrix[j*lhs_vectors_number+i] = compute(i,j);
}
}
}
else
{
for (int32_t j=idx_start; j<idx_stop; j+=idx_step)
#pragma omp parallel private(i,j)
#pragma omp for schedule(dynamic) nowait
for (j=0; j<rhs_vectors_number; j++)
{
for (int32_t i=0; i<lhs_vectors_number; i++)
for (i=0; i<lhs_vectors_number; i++)
{
distance_matrix[j*lhs_vectors_number+i] = distance->compute(i,j);
distance_matrix[j*lhs_vectors_number+i] = compute(i,j);
}
}
}
}
return distance_matrix;
}

void CDistance::init()
{
precomputed_matrix = NULL;
precompute_matrix = false;
lhs = NULL;
rhs = NULL;
num_lhs=0;
num_rhs=0;

return NULL;
m_parameters->add((CSGObject**) &lhs, "lhs",
"Feature vectors to occur on left hand side.");
m_parameters->add((CSGObject**) &rhs, "rhs",
"Feature vectors to occur on right hand side.");
}
3 changes: 0 additions & 3 deletions src/shogun/distance/Distance.h
View file
Expand Up @@ -334,9 +334,6 @@ class CDistance : public CSGObject

protected:

/// run distance thread
static void* run_distance_thread(void* p);

/// compute distance function for features a and b
/// idx_{a,b} denote the index of the feature vectors
/// in the corresponding feature object
Expand Down

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