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Commit 5a5fbd6a authored by Thomas Purcell's avatar Thomas Purcell
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set up node value arrays for OMP 

Modify CMakeLists.txt files to incldue open MP
Add a thread count for centeral storage arrays
parent 597dc961
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CMakeLists.txt
View file @ 5a5fbd6a
......@@ -43,6 +43,14 @@ else(EXTERNAL_BOOST)
set(EXTERNAL_BOOST FALSE)
endif()
# Check for FindOpenMP
find_package(OpenMP REQUIRED)
if (OPENMP_FOUND)
# include_directories("${OPENMP_INCLUDES}")
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif(OPENMP_FOUND)
if(USE_PYTHON)
# Check python settings
find_package(PythonInterp 3 REQUIRED)
......
src/CMakeLists.txt
View file @ 5a5fbd6a
......@@ -31,7 +31,7 @@ set_target_properties(sisso++
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
)
target_link_libraries(sisso++ ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} -Wl,--rpath=${Boost_LIB_DIR} -Wl,--rpath=${LAPACK_DIR} ${Boost_LIBRARIES} ${COIN_CLP_LIBRARIES})
target_link_libraries(sisso++ ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} -Wl,--rpath=${Boost_LIB_DIR} -Wl,--rpath=${LAPACK_DIR} ${Boost_LIBRARIES} ${COIN_CLP_LIBRARIES} ${OPENMP_LIBRARIES})
install(TARGETS sisso++ DESTINATION ${CMAKE_CURRENT_LIST_DIR}/../bin/)
if(USE_PYTHON)
......@@ -59,7 +59,7 @@ if(USE_PYTHON)
PREFIX ""
SUFFIX ".so"
)
target_link_libraries(_sisso ${MPI_LIBRARIES} -Wl,--rpath=${PYTHON_PREFIX}/lib/ ${LAPACK_LIBRARIES} ${PYTHON_LIBRARIES} -Wl,--rpath=${Boost_LIB_DIR} ${Boost_LIBRARIES} ${Boost_PYTHON_LIBRARIES} ${COIN_CLP_LIBRARIES})
target_link_libraries(_sisso ${MPI_LIBRARIES} -Wl,--rpath=${PYTHON_PREFIX}/lib/ ${LAPACK_LIBRARIES} ${PYTHON_LIBRARIES} -Wl,--rpath=${Boost_LIB_DIR} ${Boost_LIBRARIES} ${Boost_PYTHON_LIBRARIES} ${COIN_CLP_LIBRARIES} ${OPENMP_LIBRARIES})
install(TARGETS _sisso DESTINATION "${PYTHON_INSTDIR}/cpp_sisso")
install(
DIRECTORY ${CMAKE_CURRENT_LIST_DIR}/python/ DESTINATION ${PYTHON_INSTDIR}/cpp_sisso
......
src/feature_creation/node/value_storage/nodes_value_containers.cpp
View file @ 5a5fbd6a
......@@ -5,6 +5,7 @@ int node_value_arrs::N_SAMPLES = 0;
int node_value_arrs::N_STORE_FEATURES = 0;
int node_value_arrs::N_RUNGS_STORED = 0;
int node_value_arrs::N_SAMPLES_TEST = 0;
int node_value_arrs::MAX_N_THREADS = omp_get_max_threads();
std::vector<int> node_value_arrs::TEMP_STORAGE_REG;
std::vector<int> node_value_arrs::TEMP_STORAGE_TEST_REG;
......@@ -25,11 +26,11 @@ void node_value_arrs::initialize_values_arr(int n_samples, int n_samples_test, i
VALUES_ARR = std::vector<double>(N_STORE_FEATURES * N_SAMPLES);
TEST_VALUES_ARR = std::vector<double>(N_STORE_FEATURES * N_SAMPLES_TEST);
TEMP_STORAGE_ARR = std::vector<double>(3 * N_STORE_FEATURES * N_SAMPLES);
TEMP_STORAGE_REG = std::vector<int>(3 * N_STORE_FEATURES, -1);
TEMP_STORAGE_ARR = std::vector<double>(MAX_N_THREADS * 3 * N_STORE_FEATURES * N_SAMPLES);
TEMP_STORAGE_REG = std::vector<int>(MAX_N_THREADS * 3 * N_STORE_FEATURES, -1);
TEMP_STORAGE_TEST_ARR = std::vector<double>(3 * N_STORE_FEATURES * N_SAMPLES_TEST);
TEMP_STORAGE_TEST_REG = std::vector<int>(3 * N_STORE_FEATURES, -1);
TEMP_STORAGE_TEST_ARR = std::vector<double>(MAX_N_THREADS * 3 * N_STORE_FEATURES * N_SAMPLES_TEST);
TEMP_STORAGE_TEST_REG = std::vector<int>(MAX_N_THREADS * 3 * N_STORE_FEATURES, -1);
}
void node_value_arrs::resize_values_arr(int n_dims, int n_feat, bool use_temp)
......@@ -47,16 +48,16 @@ void node_value_arrs::resize_values_arr(int n_dims, int n_feat, bool use_temp)
if(use_temp)
{
TEMP_STORAGE_ARR.resize(3 * N_STORE_FEATURES * N_SAMPLES);
TEMP_STORAGE_ARR.resize(MAX_N_THREADS * 3 * N_STORE_FEATURES * N_SAMPLES);
TEMP_STORAGE_ARR.shrink_to_fit();
TEMP_STORAGE_REG.resize(3 * N_STORE_FEATURES, - 1);
TEMP_STORAGE_REG.resize(MAX_N_THREADS * 3 * N_STORE_FEATURES, - 1);
TEMP_STORAGE_REG.shrink_to_fit();
TEMP_STORAGE_TEST_ARR.resize(3 * N_STORE_FEATURES * N_SAMPLES_TEST);
TEMP_STORAGE_TEST_ARR.resize(MAX_N_THREADS * 3 * N_STORE_FEATURES * N_SAMPLES_TEST);
TEMP_STORAGE_TEST_ARR.shrink_to_fit();
TEMP_STORAGE_TEST_REG.resize(3 * N_STORE_FEATURES, - 1);
TEMP_STORAGE_TEST_REG.resize(MAX_N_THREADS * 3 * N_STORE_FEATURES, - 1);
TEMP_STORAGE_TEST_REG.shrink_to_fit();
}
else
......@@ -66,22 +67,22 @@ void node_value_arrs::resize_values_arr(int n_dims, int n_feat, bool use_temp)
}
}
double* node_value_arrs::get_value_ptr(int arr_ind, int feat_ind, int offset)
double* node_value_arrs::get_value_ptr(int arr_ind, int feat_ind, int offset, int thread)
{
if(arr_ind < N_STORE_FEATURES)
return access_value_arr(arr_ind);
temp_storage_reg(arr_ind, offset) = feat_ind;
return access_temp_storage((arr_ind % N_STORE_FEATURES) + (offset % 3) * N_STORE_FEATURES);
return access_temp_storage((arr_ind % N_STORE_FEATURES) + (offset % 3) * N_STORE_FEATURES) + thread * N_STORE_FEATURES * 3;
}
double* node_value_arrs::get_test_value_ptr(int arr_ind, int feat_ind, int offset)
double* node_value_arrs::get_test_value_ptr(int arr_ind, int feat_ind, int offset, int thread)
{
if(arr_ind < N_STORE_FEATURES)
return access_test_value_arr(arr_ind);
temp_storage_test_reg(arr_ind, offset) = feat_ind;
return access_temp_storage_test((arr_ind % N_STORE_FEATURES) + (offset % 3) * N_STORE_FEATURES);
return access_temp_storage_test((arr_ind % N_STORE_FEATURES) + (offset % 3) * N_STORE_FEATURES) + thread * N_STORE_FEATURES * 3;
}
void node_value_arrs::initialize_d_matrix_arr()
......
src/feature_creation/node/value_storage/nodes_value_containers.hpp
View file @ 5a5fbd6a
......@@ -14,6 +14,8 @@
#include <memory>
#include <vector>
#include <omp.h>
#include<utils/enum.hpp>
namespace node_value_arrs
......@@ -31,7 +33,7 @@ namespace node_value_arrs
extern int N_SAMPLES_TEST; //!< Number of test samples for each feature
extern int N_STORE_FEATURES; //!< Number of features with stored values
extern int N_RUNGS_STORED; //!< Number of rungs with values stored
extern int MAX_N_THREADS; //!< Get the maximum number of threads possible
/**
* @brief Initialize the node value arrays
* @details Using the size of the initial feature space constructor the storage arrays
......@@ -75,7 +77,7 @@ namespace node_value_arrs
*
* @return The register element for a given feature index and offset
*/
inline int& temp_storage_reg(int ind, int offset = 0){return TEMP_STORAGE_REG[(ind % N_STORE_FEATURES) + (offset % 3) * N_STORE_FEATURES];}
inline int& temp_storage_reg(int ind, int offset = 0, int thread = omp_get_thread_num()){return TEMP_STORAGE_REG[(ind % N_STORE_FEATURES) + (offset % 3) * N_STORE_FEATURES + thread * N_STORE_FEATURES * 3];}
/**
* @brief Get a reference slot/feature register of the test data
......@@ -85,7 +87,7 @@ namespace node_value_arrs
*
* @return The register element for a given feature index and offset
*/
inline int& temp_storage_test_reg(int ind, int offset = 0){return TEMP_STORAGE_TEST_REG[(ind % N_STORE_FEATURES) + (offset % 3) * N_STORE_FEATURES];}
inline int& temp_storage_test_reg(int ind, int offset = 0, int thread = omp_get_thread_num()){return TEMP_STORAGE_TEST_REG[(ind % N_STORE_FEATURES) + (offset % 3) * N_STORE_FEATURES + thread * N_STORE_FEATURES * 3];}
/**
* @brief Access element of the permanent training data storage array
......@@ -132,7 +134,7 @@ namespace node_value_arrs
*
* @return The value pointer
*/
double* get_value_ptr(int arr_ind, int feat_ind, int offset = 0);
double* get_value_ptr(int arr_ind, int feat_ind, int offset = 0, int thread = omp_get_thread_num());
/**
* @brief Get a Node's test_value_ptr
......@@ -143,7 +145,7 @@ namespace node_value_arrs
*
* @return The value pointer
*/
double* get_test_value_ptr(int arr_ind, int feat_ind, int offset = 0);
double* get_test_value_ptr(int arr_ind, int feat_ind, int offset = 0, int thread = omp_get_thread_num());
/**
* @brief Get the pointer to a particular selected Node from sis
......
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