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#ifndef COMBINATORICS_HPP |
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#define COMBINATORICS_HPP |
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/** Use STL, and vector. */ |
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#include <stdlib.h> |
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#include <stdio.h> |
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#include <vector> |
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#include <random> |
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#include <algorithm> |
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/** Use MPI support. */ |
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#include <hmlp_mpi.hpp> |
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using namespace std; |
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using namespace hmlp; |
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namespace hmlp |
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{ |
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namespace combinatorics |
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{ |
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template<typename T> |
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vector<T> SampleWithoutReplacement( int l, vector<T> v ) |
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{ |
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if ( l >= v.size() ) return v; |
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random_device rd; |
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std::mt19937 generator( rd() ); |
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shuffle( v.begin(), v.end(), generator ); |
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vector<T> ret( l ); |
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for ( int i = 0; i < l; i ++ ) ret[ i ] = v[ i ]; |
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return ret; |
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}; /** end SampleWithoutReplacement() */ |
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#ifdef HMLP_MIC_AVX512 |
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/** use hbw::allocator for Intel Xeon Phi */ |
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template<class T, class Allocator = hbw::allocator<T> > |
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#elif HMLP_USE_CUDA |
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/** use pinned (page-lock) memory for NVIDIA GPUs */ |
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template<class T, class Allocator = thrust::system::cuda::experimental::pinned_allocator<T> > |
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#else |
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/** use default stl allocator */ |
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template<class T, class Allocator = std::allocator<T> > |
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#endif |
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vector<T> Sum( size_t d, size_t n, vector<T, Allocator> &X, vector<size_t> &gids ) |
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{ |
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bool do_general_stride = ( gids.size() == n ); |
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/** assertion */ |
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if ( !do_general_stride ) assert( X.size() == d * n ); |
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/** declaration */ |
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int n_split = omp_get_max_threads(); |
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std::vector<T> sum( d, 0.0 ); |
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std::vector<T> temp( d * n_split, 0.0 ); |
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/** compute partial sum on each thread */ |
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#pragma omp parallel for num_threads( n_split ) |
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for ( int j = 0; j < n_split; j ++ ) |
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for ( int i = j; i < n; i += n_split ) |
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for ( int p = 0; p < d; p ++ ) |
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if ( do_general_stride ) |
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temp[ j * d + p ] += X[ gids[ i ] * d + p ]; |
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else |
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temp[ j * d + p ] += X[ i * d + p ]; |
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/** reduce all temporary buffers */ |
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for ( int j = 0; j < n_split; j ++ ) |
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for ( int p = 0; p < d; p ++ ) |
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sum[ p ] += temp[ j * d + p ]; |
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return sum; |
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}; /** end Sum() */ |
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/** TODO */ |
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#ifdef HMLP_MIC_AVX512 |
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/** use hbw::allocator for Intel Xeon Phi */ |
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template<class T, class Allocator = hbw::allocator<T> > |
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#elif HMLP_USE_CUDA |
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/** use pinned (page-lock) memory for NVIDIA GPUs */ |
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template<class T, class Allocator = thrust::system::cuda::experimental::pinned_allocator<T> > |
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#else |
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/** use default stl allocator */ |
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template<class T, class Allocator = std::allocator<T> > |
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#endif |
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vector<T> Sum( size_t d, size_t n, vector<T, Allocator> &X, mpi::Comm comm ) |
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{ |
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size_t num_points_owned = X.size() / d; |
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/** gids */ |
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vector<size_t> dummy_gids; |
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/** local sum */ |
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auto local_sum = Sum( d, num_points_owned, X, dummy_gids ); |
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/** total sum */ |
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vector<T> total_sum( d, 0 ); |
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/** Allreduce */ |
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hmlp::mpi::Allreduce( |
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local_sum.data(), total_sum.data(), d, MPI_SUM, comm ); |
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return total_sum; |
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}; /** end Sum() */ |
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#ifdef HMLP_MIC_AVX512 |
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/** use hbw::allocator for Intel Xeon Phi */ |
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template<class T, class Allocator = hbw::allocator<T> > |
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#elif HMLP_USE_CUDA |
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/** use pinned (page-lock) memory for NVIDIA GPUs */ |
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template<class T, class Allocator = thrust::system::cuda::experimental::pinned_allocator<T> > |
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#else |
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/** use default stl allocator */ |
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template<class T, class Allocator = std::allocator<T> > |
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#endif |
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std::vector<T> Mean( size_t d, size_t n, std::vector<T, Allocator> &X, std::vector<size_t> &gids ) |
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{ |
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/** sum over n points in d dimensions */ |
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auto mean = Sum( d, n, X, gids ); |
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/** compute average */ |
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for ( int p = 0; p < d; p ++ ) mean[ p ] /= n; |
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return mean; |
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}; /** end Mean() */ |
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/** |
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* @brief Compute the mean values. (alternative interface) |
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* |
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*/ |
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template<typename T> |
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std::vector<T> Mean( size_t d, size_t n, std::vector<T> &X ) |
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{ |
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/** assertion */ |
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assert( X.size() == d * n ); |
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/** gids */ |
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std::vector<std::size_t> dummy_gids; |
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return Mean( d, n, X, dummy_gids ); |
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}; /** end Mean() */ |
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/** TODO */ |
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/** |
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* @biref distributed mean values over d dimensions |
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*/ |
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template<typename T> |
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std::vector<T> Mean( size_t d, size_t n, std::vector<T> &X, |
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hmlp::mpi::Comm comm ) |
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{ |
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/** sum over n points in d dimensions */ |
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auto mean = Sum( d, n, X, comm ); |
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/** compute average */ |
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for ( int p = 0; p < d; p ++ ) mean[ p ] /= n; |
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return mean; |
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}; /** end Mean() */ |
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/** |
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* @brief Parallel prefix scan |
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*/ |
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template<typename TA, typename TB> |
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void Scan( std::vector<TA> &A, std::vector<TB> &B ) |
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{ |
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assert( A.size() == B.size() - 1 ); |
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/** number of threads */ |
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size_t p = omp_get_max_threads(); |
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/** problem size */ |
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size_t n = B.size(); |
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/** step size */ |
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size_t nb = n / p; |
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/** private temporary buffer for each thread */ |
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std::vector<TB> sum( p, (TB)0 ); |
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/** B[ 0 ] = (TB)0 */ |
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B[ 0 ] = (TB)0; |
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/** small problem size: sequential */ |
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if ( n < 100 * p ) |
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{ |
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size_t beg = 0; |
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size_t end = n; |
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for ( size_t j = beg + 1; j < end; j ++ ) |
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B[ j ] = B[ j - 1 ] + A[ j - 1 ]; |
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return; |
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} |
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/** parallel local scan */ |
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#pragma omp parallel for schedule( static ) |
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for ( size_t i = 0; i < p; i ++ ) |
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{ |
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size_t beg = i * nb; |
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size_t end = beg + nb; |
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/** deal with the edge case */ |
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if ( i == p - 1 ) end = n; |
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if ( i != 0 ) B[ beg ] = (TB)0; |
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for ( size_t j = beg + 1; j < end; j ++ ) |
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{ |
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B[ j ] = B[ j - 1 ] + A[ j - 1 ]; |
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} |
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} |
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/** sequential scan on local sum */ |
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for ( size_t i = 1; i < p; i ++ ) |
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{ |
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sum[ i ] = sum[ i - 1 ] + B[ i * nb - 1 ] + A[ i * nb - 1 ]; |
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} |
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#pragma omp parallel for schedule( static ) |
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for ( size_t i = 1; i < p; i ++ ) |
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{ |
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size_t beg = i * nb; |
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size_t end = beg + nb; |
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/** deal with the edge case */ |
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if ( i == p - 1 ) end = n; |
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TB sum_ = sum[ i ]; |
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for ( size_t j = beg; j < end; j ++ ) |
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{ |
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B[ j ] += sum_; |
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} |
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} |
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}; /** end Scan() */ |
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/** |
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* @brief Select the kth element in x in the increasing order. |
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* |
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* @para |
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* |
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* @TODO The mean function is parallel, but the splitter is not. |
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* I need something like a parallel scan. |
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*/ |
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template<typename T> |
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T Select( size_t n, size_t k, std::vector<T> &x ) |
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{ |
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/** assertion */ |
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assert( k <= n && x.size() == n ); |
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/** early return */ |
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if ( n == 1 ) return x[ 0 ]; |
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std::vector<T> mean = Mean( (size_t)1, n, x ); |
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std::vector<T> lhs, rhs; |
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std::vector<size_t> lflag( n, 0 ); |
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std::vector<size_t> rflag( n, 0 ); |
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std::vector<size_t> pscan( n + 1, 0 ); |
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/** mark flags */ |
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#pragma omp parallel for |
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for ( size_t i = 0; i < n; i ++ ) |
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{ |
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if ( x[ i ] > mean[ 0 ] ) rflag[ i ] = 1; |
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else lflag[ i ] = 1; |
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} |
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/** |
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* prefix sum on flags of left hand side |
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* input: flags |
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* output: zero-base index |
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**/ |
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Scan( lflag, pscan ); |
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/** resize left hand side */ |
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lhs.resize( pscan[ n ] ); |
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#pragma omp parallel for |
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for ( size_t i = 0; i < n; i ++ ) |
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{ |
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if ( lflag[ i ] ) |
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lhs[ pscan[ i ] ] = x[ i ]; |
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} |
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/** |
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* prefix sum on flags of right hand side |
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* input: flags |
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* output: zero-base index |
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**/ |
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Scan( rflag, pscan ); |
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/** resize right hand side */ |
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rhs.resize( pscan[ n ] ); |
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#pragma omp parallel for |
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for ( size_t i = 0; i < n; i ++ ) |
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{ |
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if ( rflag[ i ] ) |
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rhs[ pscan[ i ] ] = x[ i ]; |
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} |
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int nlhs = lhs.size(); |
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int nrhs = rhs.size(); |
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if ( nlhs == k || nlhs == n || nrhs == n ) |
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{ |
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return mean[ 0 ]; |
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} |
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else if ( nlhs > k ) |
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{ |
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rhs.clear(); |
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return Select( nlhs, k, lhs ); |
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} |
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else |
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{ |
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lhs.clear(); |
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return Select( nrhs, k - nlhs, rhs ); |
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} |
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}; /** end Select() */ |
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template<typename T> |
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T Select( size_t k, std::vector<T> &x, hmlp::mpi::Comm comm ) |
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{ |
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/** declaration */ |
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std::vector<T> lhs, rhs; |
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lhs.reserve( x.size() ); |
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rhs.reserve( x.size() ); |
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int n = 0; |
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int num_points_owned = x.size(); |
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/** reduce to get the total problem size */ |
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hmlp::mpi::Allreduce( &num_points_owned, &n, 1, MPI_SUM, comm ); |
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/** TODO: mean value */ |
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std::vector<T> mean = Mean( (size_t)1, n, x, comm ); |
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for ( size_t i = 0; i < x.size(); i ++ ) |
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{ |
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if ( x[ i ] < mean[ 0 ] ) lhs.push_back( x[ i ] ); |
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else rhs.push_back( x[ i ] ); |
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} |
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/** reduce nlhs and nrhs */ |
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int nlhs = 0; |
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int nrhs = 0; |
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int num_lhs_owned = lhs.size(); |
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int num_rhs_owned = rhs.size(); |
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hmlp::mpi::Allreduce( &num_lhs_owned, &nlhs, 1, MPI_SUM, comm ); |
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hmlp::mpi::Allreduce( &num_rhs_owned, &nrhs, 1, MPI_SUM, comm ); |
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if ( nlhs == k || n == 1 || n == nlhs || n == nrhs ) |
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{ |
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return mean[ 0 ]; |
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} |
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else if ( nlhs > k ) |
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{ |
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rhs.clear(); |
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return Select( k, lhs, comm ); |
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} |
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else |
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{ |
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lhs.clear(); |
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return Select( k - nlhs, rhs, comm ); |
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} |
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}; /** end Select() */ |
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template<typename T> |
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vector<vector<size_t>> MedianThreeWaySplit( vector<T> &v, T tol ) |
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{ |
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size_t n = v.size(); |
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auto median = Select( n, n / 2, v ); |
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/** Split indices of v into 3-way: lhs, rhs, and mid. */ |
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vector<vector<size_t>> three_ways( 3 ); |
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auto & lhs = three_ways[ 0 ]; |
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auto & rhs = three_ways[ 1 ]; |
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auto & mid = three_ways[ 2 ]; |
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for ( size_t i = 0; i < v.size(); i ++ ) |
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{ |
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if ( std::fabs( v[ i ] - median ) < tol ) mid.push_back( i ); |
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else if ( v[ i ] < median ) lhs.push_back( i ); |
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else rhs.push_back( i ); |
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} |
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return three_ways; |
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}; /** end MedianTreeWaySplit() */ |
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/** @brief Split values into two halfs accroding to the median. */ |
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template<typename T> |
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vector<vector<size_t>> MedianSplit( vector<T> &v ) |
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{ |
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auto three_ways = MedianThreeWaySplit( v, (T)1E-6 ); |
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vector<vector<size_t>> two_ways( 2 ); |
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two_ways[ 0 ] = three_ways[ 0 ]; |
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two_ways[ 1 ] = three_ways[ 1 ]; |
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auto & lhs = two_ways[ 0 ]; |
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auto & rhs = two_ways[ 1 ]; |
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auto & mid = three_ways[ 2 ]; |
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for ( auto it : mid ) |
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{ |
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if ( lhs.size() < rhs.size() ) lhs.push_back( it ); |
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else rhs.push_back( it ); |
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} |
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return two_ways; |
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}; /** end MedianSplit() */ |
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|
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}; /** end namespace combinatorics */ |
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}; /** end namespace hmlp */ |
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#endif /** define COMBINATORICS_HPP */ |