From a2373d8919f5dea4c571824cf3e59ce9d3b9d1d6 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Mon, 3 Mar 2014 19:06:31 +0100 Subject: [PATCH 1/6] Fixed types --- src/fourier/details/euclidian_maps.hpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/fourier/details/euclidian_maps.hpp b/src/fourier/details/euclidian_maps.hpp index 5673565..4cbf6a3 100644 --- a/src/fourier/details/euclidian_maps.hpp +++ b/src/fourier/details/euclidian_maps.hpp @@ -36,6 +36,7 @@ knowledge of the CeCILL license and that you accept its terms. #ifndef __DETAILS_EUCLIDIAN_MAPS #define __DETAILS_EUCLIDIAN_MAPS +#include namespace CosmoTool { @@ -246,7 +247,7 @@ namespace CosmoTool { long idx = q0+dims[0]*p; assert(idx < this->size()); - result += 2*(conj(d1[idx]) * d2[idx]).real(); + result += T(2)*(std::conj(d1[idx]) * d2[idx]).real(); } } if (even0) @@ -254,8 +255,8 @@ namespace CosmoTool for (long p = 0; p < plane_size; p++) { long q0 = N0*p, q1 = (p+1)*N0-1; - result += 2*conj(d1[q0]) * d2[q0]; - result += 2*conj(d1[q1]) * d2[q1]; + result += T(2)*std::conj(d1[q0]) * d2[q0]; + result += T(2)*std::conj(d1[q1]) * d2[q1]; } } return result; From 9ae42a2442f0dccf89422e77baf0725749645a43 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Wed, 2 Apr 2014 09:52:06 +0200 Subject: [PATCH 2/6] Fixed unit_vel in Ramses. Added a new type alias in FourierMap --- src/fourier/base_types.hpp | 3 +++ src/loadRamses.cpp | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/src/fourier/base_types.hpp b/src/fourier/base_types.hpp index ff092ef..42b579a 100644 --- a/src/fourier/base_types.hpp +++ b/src/fourier/base_types.hpp @@ -55,6 +55,7 @@ namespace CosmoTool protected: SpectrumFunction() {} public: + typedef T type; typedef Eigen::Array VecType; typedef Eigen::Map MapType; typedef Eigen::Map ConstMapType; @@ -88,6 +89,7 @@ namespace CosmoTool FourierMap() {} public: + typedef T type; typedef Eigen::Array VecType; typedef Eigen::Map MapType; typedef Eigen::Map ConstMapType; @@ -190,6 +192,7 @@ namespace CosmoTool class MapUtilityFunction { public: + typedef T type; typedef SpectrumFunction Spectrum; typedef boost::shared_ptr Spectrum_ptr; typedef FourierMap > FMap; diff --git a/src/loadRamses.cpp b/src/loadRamses.cpp index 3eb909c..5154921 100644 --- a/src/loadRamses.cpp +++ b/src/loadRamses.cpp @@ -309,7 +309,7 @@ CosmoTool::SimuData *CosmoTool::loadRamsesSimu(const char *basename, int outputI double hubble = info.aexp*info.aexp/info.unit_t / (1e5/CM_IN_MPC); double L0 = info.boxSize*info.unitLength*hubble/100/CM_IN_MPC/info.aexp; - double unit_vel = L0*hubble/info.aexp; + double unit_vel = L0*100/info.aexp; while (1) { From bba009ef42489c6d4fa71b5aa19108545716ca16 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Wed, 2 Apr 2014 16:53:14 +0200 Subject: [PATCH 3/6] Export correctly the const-ness of saveArray --- src/yorick.hpp | 2 +- src/yorick_nc3.cpp | 8 ++++---- src/yorick_nc4.cpp | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/yorick.hpp b/src/yorick.hpp index 39fd20d..59d4656 100644 --- a/src/yorick.hpp +++ b/src/yorick.hpp @@ -218,7 +218,7 @@ namespace CosmoTool template void saveArray(const std::string& fname, - T *array, uint32_t *dimList, uint32_t rank); + const T *array, uint32_t *dimList, uint32_t rank); template void loadArray(const std::string& fname, diff --git a/src/yorick_nc3.cpp b/src/yorick_nc3.cpp index d80781e..8a69d9b 100644 --- a/src/yorick_nc3.cpp +++ b/src/yorick_nc3.cpp @@ -235,7 +235,7 @@ namespace CosmoTool { template void saveArray(const std::string& fname, - T *array, uint32_t *dimList, uint32_t rank) + const T *array, uint32_t *dimList, uint32_t rank) { NcFile f(fname.c_str(), NcFile::Replace, 0, 0, NcFile::Netcdf4); @@ -300,10 +300,10 @@ namespace CosmoTool { double*& array, uint32_t *&dimList, uint32_t& rank); template void saveArray(const std::string& fname, - int *array, uint32_t *dimList, uint32_t rank); + const int *array, uint32_t *dimList, uint32_t rank); template void saveArray(const std::string& fname, - float *array, uint32_t *dimList, uint32_t rank); + const float *array, uint32_t *dimList, uint32_t rank); template void saveArray(const std::string& fname, - double *array, uint32_t *dimList, uint32_t rank); + const double *array, uint32_t *dimList, uint32_t rank); } diff --git a/src/yorick_nc4.cpp b/src/yorick_nc4.cpp index ed4cd9e..49ae5b5 100644 --- a/src/yorick_nc4.cpp +++ b/src/yorick_nc4.cpp @@ -203,7 +203,7 @@ namespace CosmoTool { template void saveArray(const std::string& fname, - T *array, uint32_t *dimList, uint32_t rank) + const T *array, uint32_t *dimList, uint32_t rank) { NcFile f(fname.c_str(), NcFile::replace); @@ -263,10 +263,10 @@ namespace CosmoTool { double*& array, uint32_t *&dimList, uint32_t& rank); template void saveArray(const std::string& fname, - int *array, uint32_t *dimList, uint32_t rank); + const int *array, uint32_t *dimList, uint32_t rank); template void saveArray(const std::string& fname, - float *array, uint32_t *dimList, uint32_t rank); + const float *array, uint32_t *dimList, uint32_t rank); template void saveArray(const std::string& fname, - double *array, uint32_t *dimList, uint32_t rank); + const double *array, uint32_t *dimList, uint32_t rank); } From e3ff41e30ae1de71bb42d09c60f5a5228de6f4d8 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Wed, 2 Apr 2014 17:56:09 +0200 Subject: [PATCH 4/6] Added new calls specific to EuclidianTransform --- src/fourier/details/euclidian_transform.hpp | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/fourier/details/euclidian_transform.hpp b/src/fourier/details/euclidian_transform.hpp index eaab4fd..e5ef34a 100644 --- a/src/fourier/details/euclidian_transform.hpp +++ b/src/fourier/details/euclidian_transform.hpp @@ -122,12 +122,22 @@ namespace CosmoTool calls::execute(m_synthesis); realMap->scale(1/volume); } + + void synthesis_unnormed() + { + calls::execute(m_synthesis); + } void analysis() { calls::execute(m_analysis); fourierMap->scale(volume/N); } + + void analysis_unnormed() + { + calls::execute(m_analysis); + } void synthesis_conjugate() { From b80734bf07ad698b1daed93f42c461d20418c928 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Thu, 10 Apr 2014 09:12:01 +0200 Subject: [PATCH 5/6] Enforce C compiler as given by CMake --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 858dbaa..9d69ebe 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -37,7 +37,7 @@ if (ENABLE_SHARP) ExternalProject_Add(sharp SOURCE_DIR ${SHARP_SOURCE} BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND ${SHARP_SOURCE}/configure --prefix=${DEP_BUILD} + CONFIGURE_COMMAND ${SHARP_SOURCE}/configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} BUILD_COMMAND ${CMAKE_MAKE_PROGRAM} INSTALL_COMMAND echo "No install" ) From cc769b2b1d525347edcfebe3394a76b0a6631a68 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Mon, 5 May 2014 12:07:55 +0200 Subject: [PATCH 6/6] Added state definition in SPHSmooth. Fixed cmake LINK_FLAGS problem --- CMakeLists.txt | 12 +++++ sample/CMakeLists.txt | 2 +- sample/testSmooth.cpp | 6 ++- src/sphSmooth.hpp | 43 ++++++++------- src/sphSmooth.tcc | 120 +++++++++++++++++++++++------------------- 5 files changed, 106 insertions(+), 77 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 9d69ebe..e2e45f6 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -71,6 +71,18 @@ set(GSL_FIND_REQUIRED TRUE) FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH) FIND_PACKAGE_HANDLE_STANDARD_ARGS(GSL DEFAULT_MSG GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH) +IF(ENABLE_OPENMP) + + IF (NOT OPENMP_FOUND) + MESSAGE(ERROR "No known compiler option for enabling OpenMP") + ENDIF(NOT OPENMP_FOUND) + + SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKED_FLAGS} ${OpenMP_C_FLAGS}") +ENDIF(ENABLE_OPENMP) + + set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY}) diff --git a/sample/CMakeLists.txt b/sample/CMakeLists.txt index 64bb51f..5b58290 100644 --- a/sample/CMakeLists.txt +++ b/sample/CMakeLists.txt @@ -62,7 +62,7 @@ if (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND) include_directories(${SHARP_INCLUDE_PATH}) add_executable(test_healpix_calls test_healpix_calls.cpp) target_link_libraries(test_healpix_calls ${tolink} ${SHARP_LIBRARIES}) - set_target_properties(test_healpix_calls PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS}) + set_target_properties(test_healpix_calls PROPERTIES COMPILE_FLAGS "${OpenMP_CXX_FLAGS}" LINK_FLAGS "${OpenMP_CXX_FLAGS}") add_dependencies(test_healpix_calls sharp) endif (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND) diff --git a/sample/testSmooth.cpp b/sample/testSmooth.cpp index 4f3011d..ddb8c3e 100644 --- a/sample/testSmooth.cpp +++ b/sample/testSmooth.cpp @@ -85,14 +85,16 @@ int main() uint32_t dims[] = { NX, NX }; ProgressiveOutput out = ProgressiveOutput::saveArrayProgressive("out.nc", dims, 2); +//#pragma omp parallel for schedule(static) for (uint32_t iy = 0; iy < NX; iy++) { + MySmooth::SPHState state; cout << "iy=" << iy << endl; for (uint32_t ix = 0; ix < NX; ix++) { MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX }; - smooth.fetchNeighbours(c); - out.put(smooth.computeSmoothedValue(c, unit_fun)); + smooth.fetchNeighbours(c, &state); + out.put(smooth.computeSmoothedValue(c, unit_fun, &state)); } diff --git a/src/sphSmooth.hpp b/src/sphSmooth.hpp index f6fe582..b347178 100644 --- a/src/sphSmooth.hpp +++ b/src/sphSmooth.hpp @@ -35,7 +35,7 @@ knowledge of the CeCILL license and that you accept its terms. #ifndef __COSMOTOOL_SPH_SMOOTH_HPP #define __COSMOTOOL_SPH_SMOOTH_HPP - +#include #include "config.hpp" #include "mykdtree.hpp" @@ -60,37 +60,48 @@ namespace CosmoTool typedef void (*runParticleValue)(ValType& t); public: + struct SPHState + { + boost::shared_ptr ngb; + boost::shared_ptr distances; + typename SPHTree::coords currentCenter; + int currentNgb; + ComputePrecision smoothRadius; + }; + + SPHSmooth(SPHTree *tree, uint32_t Nsph); virtual ~SPHSmooth(); - void fetchNeighbours(const typename SPHTree::coords& c); + void fetchNeighbours(const typename SPHTree::coords& c, SPHState *state = 0); + void fetchNeighbours(const typename SPHTree::coords& c, uint32_t newNsph); void fetchNeighboursOnVolume(const typename SPHTree::coords& c, ComputePrecision radius); const typename SPHTree::coords& getCurrentCenter() const { - return currentCenter; + return internal.currentCenter; } ComputePrecision computeSmoothedValue(const typename SPHTree::coords& c, - computeParticleValue fun); + computeParticleValue fun, SPHState *state = 0); ComputePrecision computeInterpolatedValue(const typename SPHTree::coords& c, - computeParticleValue fun); + computeParticleValue fun, SPHState *state = 0); ComputePrecision getMaxDistance(const typename SPHTree::coords& c, SPHNode *node) const; ComputePrecision getSmoothingLen() const { - return smoothRadius; + return internal.smoothRadius; } // TO USE WITH EXTREME CARE ! void setSmoothingLen(ComputePrecision len) { - smoothRadius = len; + internal.smoothRadius = len; } // END - void runForEachNeighbour(runParticleValue fun); + void runForEachNeighbour(runParticleValue fun, SPHState *state = 0); void addGridSite(const typename SPHTree::coords& c); bool hasNeighbours() const; @@ -100,32 +111,26 @@ namespace CosmoTool SPHTree *getTree() { return tree; } void changeNgb(uint32_t newMax) { - delete[] ngb; - delete[] distances; - ngb = new SPHCell *[newMax]; - distances = new CoordType[newMax]; + internal.ngb = boost::shared_ptr(new SPHCell *[newMax]); + internal.distances = boost::shared_ptr(new CoordType[newMax]); maxNgb = newMax; } - uint32_t getCurrent() const { return currentNgb; } + uint32_t getCurrent() const { return internal.currentNgb; } uint32_t getNgb() const { return maxNgb; } protected: - SPHCell **ngb; - CoordType *distances; + SPHState internal; uint32_t Nsph; uint32_t deltaNsph; uint32_t maxNgb; - uint32_t currentNgb; SPHTree *tree; - ComputePrecision smoothRadius; - typename SPHTree::coords currentCenter; ComputePrecision computeWValue(const typename SPHTree::coords & c, SPHCell& cell, CoordType d, - computeParticleValue fun); + computeParticleValue fun, SPHState *state); void runUnrollNode(SPHNode *node, runParticleValue fun); }; diff --git a/src/sphSmooth.tcc b/src/sphSmooth.tcc index 0cf7de8..b9c9d2e 100644 --- a/src/sphSmooth.tcc +++ b/src/sphSmooth.tcc @@ -1,4 +1,5 @@ #include +#include "algo.hpp" namespace CosmoTool { @@ -7,29 +8,27 @@ SPHSmooth::SPHSmooth(SPHTree *tree, uint32_t Nsph) { this->Nsph = Nsph; this->tree = tree; - this->currentNgb = 0; + internal.currentNgb = 0; this->maxNgb = Nsph; - ngb = new SPHCell *[maxNgb]; - distances = new CoordType[maxNgb]; + internal.ngb = boost::shared_ptr(new SPHCell *[maxNgb]); + internal.distances = boost::shared_ptr(new CoordType[maxNgb]); } template SPHSmooth::~SPHSmooth() { - delete[] ngb; - delete[] distances; } template ComputePrecision SPHSmooth::computeWValue(const typename SPHTree::coords& c, SPHCell& cell, CoordType d, - computeParticleValue fun) + computeParticleValue fun, SPHState *state) { CoordType weight; - d /= smoothRadius; + d /= state->smoothRadius; weight = getKernel(d); if (cell.val.weight != 0) @@ -47,86 +46,91 @@ SPHSmooth::fetchNeighbours(const typename SPHTree::coords& c, uin if (requested > maxNgb) { - delete[] ngb; - delete[] distances; - maxNgb = requested; - ngb = new SPHCell *[maxNgb]; - distances = new CoordType[maxNgb]; + internal.ngb = new SPHCell *[maxNgb]; + internal.distances = new CoordType[maxNgb]; } - memcpy(currentCenter, c, sizeof(c)); - tree->getNearestNeighbours(c, requested, ngb, distances); + memcpy(internal.currentCenter, c, sizeof(c)); + tree->getNearestNeighbours(c, requested, internal.ngb, internal.distances); - currentNgb = 0; - for (uint32_t i = 0; i < requested && ngb[i] != 0; i++,currentNgb++) + internal.currentNgb = 0; + for (uint32_t i = 0; i < requested && internal.ngb[i] != 0; i++,internal.currentNgb++) { - distances[i] = sqrt(distances[i]); - d2 = distances[i]; + internal.distances[i] = sqrt(internal.distances[i]); + d2 = internal.distances[i]; if (d2 > max_dist) max_dist = d2; } - smoothRadius = max_dist / 2; + internal.smoothRadius = max_dist / 2; } template -void -SPHSmooth::fetchNeighbours(const typename SPHTree::coords& c) +void SPHSmooth::fetchNeighbours(const typename SPHTree::coords& c, SPHState *state) { ComputePrecision d2, max_dist = 0; uint32_t requested = Nsph; - memcpy(currentCenter, c, sizeof(c)); - tree->getNearestNeighbours(c, requested, ngb, distances); + if (state != 0) { + state->distances = boost::shared_ptr(new CoordType[Nsph]); + state->ngb = boost::shared_ptr(new SPHCell *[Nsph]); + } else + state = &internal; + + memcpy(state->currentCenter, c, sizeof(c)); + + tree->getNearestNeighbours(c, requested, state->ngb.get(), state->distances.get()); - currentNgb = 0; - for (uint32_t i = 0; i < requested && ngb[i] != 0; i++,currentNgb++) + state->currentNgb = 0; + for (uint32_t i = 0; i < requested && state->ngb[i] != 0; i++,state->currentNgb++) { - distances[i] = sqrt(distances[i]); - d2 = distances[i]; + d2 = internal.distances[i] = sqrt(internal.distances[i]); if (d2 > max_dist) - max_dist = d2; + max_dist = d2; } - smoothRadius = max_dist / 2; -} + state->smoothRadius = max_dist / 2; +} + template void SPHSmooth::fetchNeighboursOnVolume(const typename SPHTree::coords& c, - ComputePrecision radius) + ComputePrecision radius) { uint32_t numPart; ComputePrecision d2, max_dist = 0; - memcpy(currentCenter, c, sizeof(c)); + memcpy(internal.currentCenter, c, sizeof(c)); - currentNgb = tree->getIntersection(c, radius, ngb, distances, + internal.currentNgb = tree->getIntersection(c, radius, internal.ngb, internal.distances, maxNgb); - for (uint32_t i = 0; i < currentNgb; i++) + for (uint32_t i = 0; i < internal.currentNgb; i++) { - distances[i] = sqrt(distances[i]); - d2 = distances[i]; + d2 = internal.distances[i] = sqrt(internal.distances[i]); if (d2 > max_dist) - max_dist = d2; + max_dist = d2; } - smoothRadius = max_dist / 2; + internal.smoothRadius = max_dist / 2; } template ComputePrecision SPHSmooth::computeSmoothedValue(const typename SPHTree::coords& c, - computeParticleValue fun) + computeParticleValue fun, SPHState *state) { + if (state == 0) + state = &internal; + ComputePrecision outputValue = 0; ComputePrecision max_dist = 0; - ComputePrecision r3 = smoothRadius * smoothRadius * smoothRadius; + ComputePrecision r3 = cube(state->smoothRadius); - for (uint32_t i = 0; i < currentNgb; i++) + for (uint32_t i = 0; i < state->currentNgb; i++) { - outputValue += computeWValue(c, *ngb[i], distances[i], fun); + outputValue += computeWValue(c, *state->ngb[i], state->distances[i], fun, state); } return outputValue / r3; @@ -141,27 +145,33 @@ ComputePrecision interpolateOne(const ValType& t) // WARNING ! Cell's weight must be 1 !!! template ComputePrecision SPHSmooth::computeInterpolatedValue(const typename SPHTree::coords& c, - computeParticleValue fun) + computeParticleValue fun, SPHState *state) { + if (state == 0) + state = &internal; + ComputePrecision outputValue = 0; ComputePrecision max_dist = 0; ComputePrecision weight = 0; - for (uint32_t i = 0; i < currentNgb; i++) + for (uint32_t i = 0; i < state->currentNgb; i++) { - outputValue += computeWValue(c, *ngb[i], distances[i], fun); - weight += computeWValue(c, *ngb[i], distances[i], interpolateOne); + outputValue += computeWValue(c, *state->ngb[i], state->distances[i], fun); + weight += computeWValue(c, *state->ngb[i], state->distances[i], interpolateOne); } return (outputValue == 0) ? 0 : (outputValue / weight); } template -void SPHSmooth::runForEachNeighbour(runParticleValue fun) +void SPHSmooth::runForEachNeighbour(runParticleValue fun, SPHState *state) { - for (uint32_t i = 0; i < currentNgb; i++) + if (state == 0) + state = &internal; + + for (uint32_t i = 0; i < state->currentNgb; i++) { - fun(ngb[i]); + fun(state->ngb[i]); } } @@ -172,13 +182,13 @@ void SPHSmooth::addGridSite(const typename SPHTree::coords& c) ComputePrecision outputValue = 0; ComputePrecision max_dist = 0; - ComputePrecision r3 = smoothRadius * smoothRadius * smoothRadius; + ComputePrecision r3 = cube(internal.smoothRadius); - for (uint32_t i = 0; i < currentNgb; i++) + for (uint32_t i = 0; i < internal.currentNgb; i++) { - ComputePrecision d = distances[i]; - SPHCell& cell = *ngb[i]; - cell.val.weight += getKernel(d/smoothRadius) / r3; + ComputePrecision d = internal.distances[i]; + SPHCell& cell = *internal.ngb[i]; + cell.val.weight += getKernel(d/internal.smoothRadius) / r3; } } @@ -202,7 +212,7 @@ SPHSmooth::getKernel(ComputePrecision x) const template bool SPHSmooth::hasNeighbours() const { - return (currentNgb != 0); + return (internal.currentNgb != 0); } template