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Added state definition in SPHSmooth. Fixed cmake LINK_FLAGS problem

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This commit is contained in:
Guilhem Lavaux 2014-05-05 12:07:55 +02:00
parent b80734bf07
commit cc769b2b1d
5 changed files with 106 additions and 77 deletions
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12
CMakeLists.txt
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@ -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(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) 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}) set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})

2
sample/CMakeLists.txt
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@ -62,7 +62,7 @@ if (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
include_directories(${SHARP_INCLUDE_PATH}) include_directories(${SHARP_INCLUDE_PATH})
add_executable(test_healpix_calls test_healpix_calls.cpp) add_executable(test_healpix_calls test_healpix_calls.cpp)
target_link_libraries(test_healpix_calls ${tolink} ${SHARP_LIBRARIES}) 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) add_dependencies(test_healpix_calls sharp)
endif (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND) endif (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)

6
sample/testSmooth.cpp
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@ -85,14 +85,16 @@ int main()
uint32_t dims[] = { NX, NX }; uint32_t dims[] = { NX, NX };
ProgressiveOutput<ComputePrecision> out = ProgressiveOutput<ComputePrecision> out =
ProgressiveOutput<ComputePrecision>::saveArrayProgressive("out.nc", dims, 2); ProgressiveOutput<ComputePrecision>::saveArrayProgressive("out.nc", dims, 2);
//#pragma omp parallel for schedule(static)
for (uint32_t iy = 0; iy < NX; iy++) for (uint32_t iy = 0; iy < NX; iy++)
{ {
MySmooth::SPHState state;
cout << "iy=" << iy << endl; cout << "iy=" << iy << endl;
for (uint32_t ix = 0; ix < NX; ix++) for (uint32_t ix = 0; ix < NX; ix++)
{ {
MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX }; MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX };
smooth.fetchNeighbours(c); smooth.fetchNeighbours(c, &state);
out.put(smooth.computeSmoothedValue(c, unit_fun)); out.put(smooth.computeSmoothedValue(c, unit_fun, &state));
} }

43
src/sphSmooth.hpp
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@ -35,7 +35,7 @@ knowledge of the CeCILL license and that you accept its terms.
#ifndef __COSMOTOOL_SPH_SMOOTH_HPP #ifndef __COSMOTOOL_SPH_SMOOTH_HPP
#define __COSMOTOOL_SPH_SMOOTH_HPP #define __COSMOTOOL_SPH_SMOOTH_HPP
#include <boost/shared_ptr.hpp>
#include "config.hpp" #include "config.hpp"
#include "mykdtree.hpp" #include "mykdtree.hpp"
@ -60,37 +60,48 @@ namespace CosmoTool
typedef void (*runParticleValue)(ValType& t); typedef void (*runParticleValue)(ValType& t);
public: public:
struct SPHState
{
boost::shared_ptr<SPHCell *[]> ngb;
boost::shared_ptr<CoordType[]> distances;
typename SPHTree::coords currentCenter;
int currentNgb;
ComputePrecision smoothRadius;
};
SPHSmooth(SPHTree *tree, uint32_t Nsph); SPHSmooth(SPHTree *tree, uint32_t Nsph);
virtual ~SPHSmooth(); 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 fetchNeighbours(const typename SPHTree::coords& c, uint32_t newNsph);
void fetchNeighboursOnVolume(const typename SPHTree::coords& c, ComputePrecision radius); void fetchNeighboursOnVolume(const typename SPHTree::coords& c, ComputePrecision radius);
const typename SPHTree::coords& getCurrentCenter() const const typename SPHTree::coords& getCurrentCenter() const
{ {
return currentCenter; return internal.currentCenter;
} }
ComputePrecision computeSmoothedValue(const typename SPHTree::coords& c, ComputePrecision computeSmoothedValue(const typename SPHTree::coords& c,
computeParticleValue fun); computeParticleValue fun, SPHState *state = 0);
ComputePrecision computeInterpolatedValue(const typename SPHTree::coords& c, ComputePrecision computeInterpolatedValue(const typename SPHTree::coords& c,
computeParticleValue fun); computeParticleValue fun, SPHState *state = 0);
ComputePrecision getMaxDistance(const typename SPHTree::coords& c, ComputePrecision getMaxDistance(const typename SPHTree::coords& c,
SPHNode *node) const; SPHNode *node) const;
ComputePrecision getSmoothingLen() const ComputePrecision getSmoothingLen() const
{ {
return smoothRadius; return internal.smoothRadius;
} }
// TO USE WITH EXTREME CARE ! // TO USE WITH EXTREME CARE !
void setSmoothingLen(ComputePrecision len) void setSmoothingLen(ComputePrecision len)
{ {
smoothRadius = len; internal.smoothRadius = len;
} }
// END // END
void runForEachNeighbour(runParticleValue fun); void runForEachNeighbour(runParticleValue fun, SPHState *state = 0);
void addGridSite(const typename SPHTree::coords& c); void addGridSite(const typename SPHTree::coords& c);
bool hasNeighbours() const; bool hasNeighbours() const;
@ -100,32 +111,26 @@ namespace CosmoTool
SPHTree *getTree() { return tree; } SPHTree *getTree() { return tree; }
void changeNgb(uint32_t newMax) { void changeNgb(uint32_t newMax) {
delete[] ngb; internal.ngb = boost::shared_ptr<SPHCell *>(new SPHCell *[newMax]);
delete[] distances; internal.distances = boost::shared_ptr<CoordType>(new CoordType[newMax]);
ngb = new SPHCell *[newMax];
distances = new CoordType[newMax];
maxNgb = newMax; maxNgb = newMax;
} }
uint32_t getCurrent() const { return currentNgb; } uint32_t getCurrent() const { return internal.currentNgb; }
uint32_t getNgb() const { return maxNgb; } uint32_t getNgb() const { return maxNgb; }
protected: protected:
SPHCell **ngb; SPHState internal;
CoordType *distances;
uint32_t Nsph; uint32_t Nsph;
uint32_t deltaNsph; uint32_t deltaNsph;
uint32_t maxNgb; uint32_t maxNgb;
uint32_t currentNgb;
SPHTree *tree; SPHTree *tree;
ComputePrecision smoothRadius;
typename SPHTree::coords currentCenter;
ComputePrecision computeWValue(const typename SPHTree::coords & c, ComputePrecision computeWValue(const typename SPHTree::coords & c,
SPHCell& cell, SPHCell& cell,
CoordType d, CoordType d,
computeParticleValue fun); computeParticleValue fun, SPHState *state);
void runUnrollNode(SPHNode *node, void runUnrollNode(SPHNode *node,
runParticleValue fun); runParticleValue fun);
}; };

112
src/sphSmooth.tcc
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@ -1,4 +1,5 @@
#include <cmath> #include <cmath>
#include "algo.hpp"
namespace CosmoTool { namespace CosmoTool {
@ -7,29 +8,27 @@ SPHSmooth<ValType,Ndims>::SPHSmooth(SPHTree *tree, uint32_t Nsph)
{ {
this->Nsph = Nsph; this->Nsph = Nsph;
this->tree = tree; this->tree = tree;
this->currentNgb = 0; internal.currentNgb = 0;
this->maxNgb = Nsph; this->maxNgb = Nsph;
ngb = new SPHCell *[maxNgb]; internal.ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[maxNgb]);
distances = new CoordType[maxNgb]; internal.distances = boost::shared_ptr<CoordType[]>(new CoordType[maxNgb]);
} }
template<typename ValType, int Ndims> template<typename ValType, int Ndims>
SPHSmooth<ValType,Ndims>::~SPHSmooth() SPHSmooth<ValType,Ndims>::~SPHSmooth()
{ {
delete[] ngb;
delete[] distances;
} }
template<typename ValType, int Ndims> template<typename ValType, int Ndims>
ComputePrecision SPHSmooth<ValType,Ndims>::computeWValue(const typename SPHTree::coords& c, ComputePrecision SPHSmooth<ValType,Ndims>::computeWValue(const typename SPHTree::coords& c,
SPHCell& cell, SPHCell& cell,
CoordType d, CoordType d,
computeParticleValue fun) computeParticleValue fun, SPHState *state)
{ {
CoordType weight; CoordType weight;
d /= smoothRadius; d /= state->smoothRadius;
weight = getKernel(d); weight = getKernel(d);
if (cell.val.weight != 0) if (cell.val.weight != 0)
@ -47,51 +46,54 @@ SPHSmooth<ValType,Ndims>::fetchNeighbours(const typename SPHTree::coords& c, uin
if (requested > maxNgb) if (requested > maxNgb)
{ {
delete[] ngb;
delete[] distances;
maxNgb = requested; maxNgb = requested;
ngb = new SPHCell *[maxNgb]; internal.ngb = new SPHCell *[maxNgb];
distances = new CoordType[maxNgb]; internal.distances = new CoordType[maxNgb];
} }
memcpy(currentCenter, c, sizeof(c)); memcpy(internal.currentCenter, c, sizeof(c));
tree->getNearestNeighbours(c, requested, ngb, distances); tree->getNearestNeighbours(c, requested, internal.ngb, internal.distances);
currentNgb = 0; internal.currentNgb = 0;
for (uint32_t i = 0; i < requested && ngb[i] != 0; i++,currentNgb++) for (uint32_t i = 0; i < requested && internal.ngb[i] != 0; i++,internal.currentNgb++)
{ {
distances[i] = sqrt(distances[i]); internal.distances[i] = sqrt(internal.distances[i]);
d2 = distances[i]; d2 = internal.distances[i];
if (d2 > max_dist) if (d2 > max_dist)
max_dist = d2; max_dist = d2;
} }
smoothRadius = max_dist / 2; internal.smoothRadius = max_dist / 2;
} }
template<typename ValType, int Ndims> template<typename ValType, int Ndims>
void void SPHSmooth<ValType,Ndims>::fetchNeighbours(const typename SPHTree::coords& c, SPHState *state)
SPHSmooth<ValType,Ndims>::fetchNeighbours(const typename SPHTree::coords& c)
{ {
ComputePrecision d2, max_dist = 0; ComputePrecision d2, max_dist = 0;
uint32_t requested = Nsph; uint32_t requested = Nsph;
memcpy(currentCenter, c, sizeof(c)); if (state != 0) {
tree->getNearestNeighbours(c, requested, ngb, distances); state->distances = boost::shared_ptr<CoordType[]>(new CoordType[Nsph]);
state->ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[Nsph]);
} else
state = &internal;
currentNgb = 0; memcpy(state->currentCenter, c, sizeof(c));
for (uint32_t i = 0; i < requested && ngb[i] != 0; i++,currentNgb++)
tree->getNearestNeighbours(c, requested, state->ngb.get(), state->distances.get());
state->currentNgb = 0;
for (uint32_t i = 0; i < requested && state->ngb[i] != 0; i++,state->currentNgb++)
{ {
distances[i] = sqrt(distances[i]); d2 = internal.distances[i] = sqrt(internal.distances[i]);
d2 = distances[i];
if (d2 > max_dist) if (d2 > max_dist)
max_dist = d2; max_dist = d2;
} }
smoothRadius = max_dist / 2; state->smoothRadius = max_dist / 2;
} }
template<typename ValType, int Ndims> template<typename ValType, int Ndims>
void void
SPHSmooth<ValType,Ndims>::fetchNeighboursOnVolume(const typename SPHTree::coords& c, SPHSmooth<ValType,Ndims>::fetchNeighboursOnVolume(const typename SPHTree::coords& c,
@ -100,33 +102,35 @@ SPHSmooth<ValType,Ndims>::fetchNeighboursOnVolume(const typename SPHTree::coords
uint32_t numPart; uint32_t numPart;
ComputePrecision d2, max_dist = 0; 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); maxNgb);
for (uint32_t i = 0; i < currentNgb; i++) for (uint32_t i = 0; i < internal.currentNgb; i++)
{ {
distances[i] = sqrt(distances[i]); d2 = internal.distances[i] = sqrt(internal.distances[i]);
d2 = distances[i];
if (d2 > max_dist) if (d2 > max_dist)
max_dist = d2; max_dist = d2;
} }
smoothRadius = max_dist / 2; internal.smoothRadius = max_dist / 2;
} }
template<typename ValType, int Ndims> template<typename ValType, int Ndims>
ComputePrecision ComputePrecision
SPHSmooth<ValType,Ndims>::computeSmoothedValue(const typename SPHTree::coords& c, SPHSmooth<ValType,Ndims>::computeSmoothedValue(const typename SPHTree::coords& c,
computeParticleValue fun) computeParticleValue fun, SPHState *state)
{ {
if (state == 0)
state = &internal;
ComputePrecision outputValue = 0; ComputePrecision outputValue = 0;
ComputePrecision max_dist = 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; return outputValue / r3;
@ -141,27 +145,33 @@ ComputePrecision interpolateOne(const ValType& t)
// WARNING ! Cell's weight must be 1 !!! // WARNING ! Cell's weight must be 1 !!!
template<typename ValType, int Ndims> template<typename ValType, int Ndims>
ComputePrecision SPHSmooth<ValType,Ndims>::computeInterpolatedValue(const typename SPHTree::coords& c, ComputePrecision SPHSmooth<ValType,Ndims>::computeInterpolatedValue(const typename SPHTree::coords& c,
computeParticleValue fun) computeParticleValue fun, SPHState *state)
{ {
if (state == 0)
state = &internal;
ComputePrecision outputValue = 0; ComputePrecision outputValue = 0;
ComputePrecision max_dist = 0; ComputePrecision max_dist = 0;
ComputePrecision weight = 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); outputValue += computeWValue(c, *state->ngb[i], state->distances[i], fun);
weight += computeWValue(c, *ngb[i], distances[i], interpolateOne); weight += computeWValue(c, *state->ngb[i], state->distances[i], interpolateOne);
} }
return (outputValue == 0) ? 0 : (outputValue / weight); return (outputValue == 0) ? 0 : (outputValue / weight);
} }
template<typename ValType, int Ndims> template<typename ValType, int Ndims>
void SPHSmooth<ValType,Ndims>::runForEachNeighbour(runParticleValue fun) void SPHSmooth<ValType,Ndims>::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<ValType,Ndims>::addGridSite(const typename SPHTree::coords& c)
ComputePrecision outputValue = 0; ComputePrecision outputValue = 0;
ComputePrecision max_dist = 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]; ComputePrecision d = internal.distances[i];
SPHCell& cell = *ngb[i]; SPHCell& cell = *internal.ngb[i];
cell.val.weight += getKernel(d/smoothRadius) / r3; cell.val.weight += getKernel(d/internal.smoothRadius) / r3;
} }
} }
@ -202,7 +212,7 @@ SPHSmooth<ValType,Ndims>::getKernel(ComputePrecision x) const
template<typename ValType, int Ndims> template<typename ValType, int Ndims>
bool SPHSmooth<ValType,Ndims>::hasNeighbours() const bool SPHSmooth<ValType,Ndims>::hasNeighbours() const
{ {
return (currentNgb != 0); return (internal.currentNgb != 0);
} }
template<class ValType1, class ValType2, int Ndims> template<class ValType1, class ValType2, int Ndims>