Changed dependency to libsharp (MPI support, better performance). Added new power spectrum abstraction

This commit is contained in:
Guilhem Lavaux 2012-11-10 09:02:08 -05:00
parent bddd26a5ca
commit 414edbd28a
5 changed files with 390 additions and 46 deletions

View File

@ -27,6 +27,9 @@ find_library(NETCDFCPP_LIBRARY NAMES netcdf_c++ netcdf_c++4)
find_library(GSL_LIBRARY gsl)
find_library(GSLCBLAS_LIBRARY gslcblas)
find_library(SHARP_LIBRARY sharp)
find_path(SHARP_INCLUDE_PATH sharp.h)
set(HDF5_FIND_COMPONENTS HL CXX)
if(HDF5_ROOTDIR)
SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})

View File

@ -1,6 +1,10 @@
SET(tolink ${GSL_LIBRARIES} CosmoTool ${CosmoTool_LIBS})
include_directories(${CMAKE_SOURCE_DIR}/src ${FFTW3_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS} ${NETCDF_INCLUDE_PATH} ${GSL_INCLUDE_PATH})
IF(SHARP_INCLUDE_PATH)
include_directories(BEFORE ${SHARP_INCLUDE_PATH})
ENDIF(SHARP_INCLUDE_PATH)
add_executable(testBQueue testBQueue.cpp)
target_link_libraries(testBQueue ${tolink})
@ -41,6 +45,11 @@ add_executable(testBSP testBSP.cpp)
target_link_libraries(testBSP ${tolink})
if (FFTW3_FOUND AND EIGEN3_FOUND)
add_executable(test_fft_calls test_fft_calls)
add_executable(test_fft_calls test_fft_calls.cpp)
target_link_libraries(test_fft_calls ${tolink} ${FFTW3_LIBRARIES})
endif (FFTW3_FOUND AND EIGEN3_FOUND)
if (SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
add_executable(test_sharp_calls test_sharp_calls.cpp)
target_link_libraries(test_sharp_calls ${tolink} ${SHARP_LIBRARY})
endif (SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)

View File

@ -1,12 +1,37 @@
#ifndef __BASE_FOURIER_TYPES_HPP
#define __BASE_FOURIER_TYPES_HPP
#include <gsl/gsl_rng.h>
#include <boost/shared_ptr.hpp>
#include <string>
#include <Eigen/Dense>
#include <complex>
#include <exception>
namespace CosmoTool
{
class IncompatibleMap: virtual std::exception {};
template<typename T> class FourierMap;
template<typename T>
class SpectrumFunction
{
protected:
SpectrumFunction() {}
public:
typedef Eigen::Array<T, 1, Eigen::Dynamic> VecType;
typedef Eigen::Map<VecType, Eigen::Aligned> MapType;
typedef Eigen::Map<VecType const, Eigen::Aligned> ConstMapType;
typedef FourierMap<std::complex<T> > FourierMapType;
virtual boost::shared_ptr<FourierMapType>
newRandomFourier(gsl_rng *rng, const FourierMapType& like_map) const = 0;
virtual void mul(FourierMap<std::complex<T> >& m) const = 0;
};
template<typename T>
class FourierMap
{
@ -14,7 +39,7 @@ namespace CosmoTool
FourierMap() {}
public:
typedef Eigen::Matrix<T, 1, Eigen::Dynamic> VecType;
typedef Eigen::Array<T, 1, Eigen::Dynamic> VecType;
typedef Eigen::Map<VecType, Eigen::Aligned> MapType;
typedef Eigen::Map<VecType const, Eigen::Aligned> ConstMapType;
@ -35,6 +60,12 @@ namespace CosmoTool
return ConstMapType(data(), size());
}
void sqrt()
{
MapType m = eigen();
m = m.sqrt();
}
void scale(const T& factor)
{
MapType m(data(), size());
@ -71,6 +102,9 @@ namespace CosmoTool
return m;
}
virtual T dot_product(const FourierMap<T>& second) const
throw(std::bad_cast) = 0;
virtual FourierMap<T> *mimick() const = 0;
};

View File

@ -1,23 +1,49 @@
#ifndef __COSMOTOOL_FOURIER_EUCLIDIAN_HPP
#define __COSMOTOOL_FOURIER_EUCLIDIAN_HPP
#include <boost/function.hpp>
#include <vector>
#include <boost/shared_ptr.hpp>
#include <gsl/gsl_randist.h>
#include "base_types.hpp"
#include "fft/fftw_calls.hpp"
#include "../algo.hpp"
namespace CosmoTool
{
template<typename T>
class EuclidianSpectrum_1D: public SpectrumFunction<T>
{
public:
typedef boost::function1<T, T> Function;
protected:
Function f;
public:
typedef typename SpectrumFunction<T>::FourierMapType FourierMapType;
typedef boost::shared_ptr<FourierMapType> ptr_map;
EuclidianSpectrum_1D(Function P)
: f(P)
{
}
ptr_map newRandomFourier(gsl_rng *rng, const FourierMapType& like_map) const;
void mul(FourierMap<std::complex<T> >& m) const;
};
template<typename T>
class EuclidianFourierMap: public FourierMap<T>
class EuclidianFourierMapBase: public FourierMap<T>
{
public:
typedef std::vector<int> DimArray;
private:
boost::shared_ptr<T> m_data;
std::vector<int> m_dims;
DimArray m_dims;
long m_size;
public:
EuclidianFourierMap(boost::shared_ptr<T> indata, std::vector<int> indims)
EuclidianFourierMapBase(boost::shared_ptr<T> indata, const DimArray& indims)
{
m_data = indata;
m_dims = indims;
@ -26,10 +52,12 @@ namespace CosmoTool
m_size *= m_dims[i];
}
virtual ~EuclidianFourierMap()
virtual ~EuclidianFourierMapBase()
{
}
const DimArray& getDims() const { return m_dims; }
virtual const T *data() const { return m_data.get(); }
virtual T *data() { return m_data.get(); }
virtual long size() const { return m_size; }
@ -41,32 +69,149 @@ namespace CosmoTool
return m;
}
};
template<typename T>
class EuclidianFourierMapReal: public EuclidianFourierMapBase<T>
{
public:
typedef typename EuclidianFourierMapBase<T>::DimArray DimArray;
EuclidianFourierMapReal(boost::shared_ptr<T> indata, const DimArray& indims)
: EuclidianFourierMapBase<T>(indata, indims)
{}
virtual FourierMap<T> *mimick() const
{
return new EuclidianFourierMap<T>(
boost::shared_ptr<T>((T *)fftw_malloc(sizeof(T)*m_size),
return new EuclidianFourierMapReal<T>(
boost::shared_ptr<T>((T *)fftw_malloc(sizeof(T)*this->size()),
std::ptr_fun(fftw_free)),
m_dims);
this->getDims());
}
virtual T dot_product(const FourierMap<T>& other) const
throw(std::bad_cast)
{
const EuclidianFourierMapReal<T>& m2 = dynamic_cast<const EuclidianFourierMapReal<T>&>(other);
if (this->size() != m2.size())
throw std::bad_cast();
return (this->eigen()*m2.eigen()).sum();
}
};
template<typename T>
class EuclidianFourierMapComplex: public EuclidianFourierMapBase<std::complex<T> >
{
protected:
typedef boost::shared_ptr<std::complex<T> > ptr_t;
std::vector<double> delta_k;
long plane_size;
public:
typedef typename EuclidianFourierMapBase<std::complex<T> >::DimArray DimArray;
EuclidianFourierMapComplex(ptr_t indata,
const DimArray& indims,
const std::vector<double>& dk)
: EuclidianFourierMapBase<std::complex<T> >(indata, indims), delta_k(dk)
{
assert(dk.size() == indims.size());
plane_size = 1;
for (int q = 1; q < indims.size(); q++)
plane_size *= indims[q];
}
virtual FourierMap<std::complex<T> > *mimick() const
{
return
new EuclidianFourierMapComplex<T>(
ptr_t((std::complex<T> *)
fftw_malloc(sizeof(std::complex<T>)*this->size()),
std::ptr_fun(fftw_free)),
this->getDims(),
this->delta_k);
}
template<typename Array>
double get_K(const Array& ik)
{
const DimArray& dims = this->getDims();
assert(ik.size() == dims.size());
double k2 = 0;
for (int q = 0; q < ik.size(); q++)
{
int dk = ik;
if (dk > dims[q]/2)
dk = dk - dims[q];
k2 += CosmoTool::square(delta_k[q]*dk);
}
return std::sqrt(k2);
}
double get_K(long p)
{
const DimArray& dims = this->getDims();
DimArray d(delta_k.size());
for (int q = 0; q < d.size(); q++)
{
d[q] = p%dims[q];
p = (p-d[q])/dims[q];
}
return get_K(d);
}
virtual std::complex<T> dot_product(const FourierMap<std::complex<T> >& other) const
throw(std::bad_cast)
{
const EuclidianFourierMapComplex<T>& m2 = dynamic_cast<const EuclidianFourierMapComplex<T>&>(other);
if (this->size() != m2.size())
throw std::bad_cast();
const std::complex<T> *d1 = this->data();
const std::complex<T> *d2 = m2.data();
const DimArray& dims = this->getDims();
int N0 = dims[0];
std::complex<T> result = 0;
for (long q0 = 1; q0 < N0-1; q0++)
{
for (long p = 0; p < plane_size; p++)
{
result += 2*(conj(d1[q0+N0*p]) * d2[q0+N0*p]).real();
}
}
for (long p = 0; p < plane_size; p++)
{
long q0 = N0*p, q1 = (p+1)*N0-1;
result += conj(d1[q0]) * d2[q0];
result += conj(d1[q1]) * d2[q1];
}
return result;
}
};
template<typename T>
class EuclidianFourierTransform: public FourierTransform<T>
{
public:
typedef typename EuclidianFourierMapBase<T>::DimArray DimArray;
private:
typedef FFTW_Calls<T> calls;
EuclidianFourierMap<T> *realMap;
EuclidianFourierMap<std::complex<T> > *fourierMap;
EuclidianFourierMapReal<T> *realMap;
EuclidianFourierMapComplex<T> *fourierMap;
typename calls::plan_type m_analysis, m_synthesis;
double volume;
long N;
std::vector<int> m_dims;
DimArray m_dims;
std::vector<double> m_L;
public:
EuclidianFourierTransform(const std::vector<int>& dims, const std::vector<double>& L)
EuclidianFourierTransform(const DimArray& dims, const std::vector<double>& L)
{
assert(L.size() == dims.size());
std::vector<double> dk(L.size());
m_dims = dims;
m_L = L;
@ -77,16 +222,17 @@ namespace CosmoTool
{
N *= dims[i];
volume *= L[i];
dk[i] = 2*M_PI/L[i];
}
realMap = new EuclidianFourierMap<T>(
realMap = new EuclidianFourierMapReal<T>(
boost::shared_ptr<T>(calls::alloc_real(N),
std::ptr_fun(calls::free)),
dims);
fourierMap = new EuclidianFourierMap<std::complex<T> >(
fourierMap = new EuclidianFourierMapComplex<T>(
boost::shared_ptr<std::complex<T> >((std::complex<T>*)calls::alloc_complex(N),
std::ptr_fun(calls::free)),
dims);
dims, dk);
m_analysis = calls::plan_dft_r2c(dims.size(), &dims[0],
realMap->data(), (typename calls::complex_type *)fourierMap->data(),
FFTW_MEASURE);
@ -194,7 +340,64 @@ namespace CosmoTool
};
template<typename T>
typename EuclidianSpectrum_1D<T>::ptr_map
EuclidianSpectrum_1D<T>::newRandomFourier(gsl_rng *rng, const FourierMapType& like_map) const
{
typedef EuclidianFourierMapComplex<T> MapT;
typedef typename MapT::DimArray DimArray;
MapT& m_c = dynamic_cast<MapT&>(like_map);
MapT *rand_map = m_c.mimick();
std::complex<T> *d = rand_map->data();
long idx;
const DimArray& dims = rand_map->getDims();
long plane_size;
for (long p = 1; p < m_c.size(); p++)
{
double A_k = std::sqrt(0.5*f(rand_map->get_K(p)));
d[p] = std::complex<T>(gsl_ran_gaussian(rng, A_k),
gsl_ran_gaussian(rng, A_k));
}
// Generate the mean value
d[0] = std::complex<T>(std::sqrt(f(0)), 0);
// Correct the Nyquist plane
idx = dims[0]-1; // Stick to the last element of the first dimension
// 1D is special case
if (dims.size() == 1)
{
d[idx] = std::complex<T>(d[idx].real() + d[idx].imag(), 0);
return boost::shared_ptr<EuclidianSpectrum_1D<T>::FourierMapType>(rand_map);
}
plane_size = 1;
for (int q = 1; q < dims.size(); q++)
{
plane_size *= dims[q];
}
for (long p = 1; p < plane_size/2; p++)
{
long q = (p+1)*dims[0]-1;
long q2 = (plane_size-p+1)*dims[0]-1;
assert(q < plane_size*dims[0]);
assert(q2 < plane_size*dims[0]);
d[q] = conj(d[q2]);
}
long q = dims[0];
d[q] = std::complex<T>(d[q].real() + d[q].imag());
}
template<typename T>
void EuclidianSpectrum_1D<T>::mul(FourierMap<std::complex<T> >& m) const
{
EuclidianFourierMapComplex<T>& m_c = dynamic_cast<EuclidianFourierMapComplex<T>&>(m);
std::complex<T> *d = m.data();
for (long p = 0; p < m_c.size(); p++)
d[p] *= f(m.get_K(p));
}
};
#endif

View File

@ -1,24 +1,45 @@
#ifndef __COSMOTOOL_FOURIER_HEALPIX_HPP
#define __COSMOTOOL_FOURIER_HEALPIX_HPP
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include <cmath>
#include <boost/bind.hpp>
#include <boost/shared_ptr.hpp>
#include <alm.h>
#include <healpix_base.h>
#include <psht_cxx.h>
#include <exception>
#include <sharp_cxx.h>
namespace CosmoTool
{
template<typename T>
class HealpixSpectrum: public FourierSpectrum<T>
{
protected:
std::vector<T> cls;
public:
typedef typename FourierSpectrum<T>::FourierMapType FourierMapType;
HealpixSpectrum(long Lmax)
: cls(Lmax+1) {}
T *data() { return &cls[0]; }
const T *data() const { return &cls[0]; }
long size() const { return cls.size(); }
boost::shared_ptr<FourierMapType>
newRandomFourier(gsl_rng *rng, const FourierMapType& like_map) const = 0;
};
template<typename T>
class HealpixFourierMap: public FourierMap<T>, public Healpix_Base
class HealpixFourierMap: public FourierMap<T>
{
private:
T *m_data;
long Npix, Nside;
Eigen::aligned_allocator<T> alloc;
public:
HealpixFourierMap(long nSide)
: Healpix_Base(RING, nSide, SET_NSIDE)
: Npix(12*nSide*nSide), Nside(nSide)
{
m_data = alloc.allocate(Npix);
}
@ -30,27 +51,61 @@ namespace CosmoTool
virtual const T* data() const { return m_data; }
virtual T *data() { return m_data; }
virtual long size() const { return Npix(); }
virtual long size() const { return Npix; }
virtual T dot_product(const FourierMap<T>& other) const
throw(std::bad_cast)
{
const HealpixFourierMap<T>& mfm = dynamic_cast<const HealpixFourierMap<T>&>(other);
if (Npix() != mfm.Npix())
throw std::bad_cast();
MapType m1(m_data, Npix);
MapType m2(mfm.m_data, mfm.Npix);
return (m1*m2).sum();
}
virtual FourierMap<T> *mimick() const
{
return new HealpixFourierMap<T>(Nside());
return new HealpixFourierMap<T>(Nside);
}
};
template<typename T>
class HealpixFourierALM: public FourierMap<std::complex<T> >, public Alm_Base
class HealpixFourierALM: public FourierMap<std::complex<T> >
{
private:
std::complex<T> *alms;
long size;
long Lmax_, Mmax_, TVal_;
Eigen::aligned_allocator<std::complex<T> > alloc;
public:
HealpixFourierALM(long Lmax, long Mmax)
: Alm_Base(Lmax, Mmax)
typedef unsigned long LType;
LType Lmax() const { return Lmax_; }
LType Mmax() const { return Mmax_; }
LType Num_Alms() const
{
size = Num_Alms(Lmax, Mmax);
return ((Mmax_+1)*(Mmax_+2))/2 + (Mmax_+1)*(Lmax_-Mmax_);
}
LType index_l0(LType m) const
{
return ((m*(TVal_-m))/2);
}
LType index(LType l, LType m) const
{
return index_l0(m) + l;
}
HealpixFourierALM(LType lmax, LType mmax)
: Lmax_(lmax), Mmax_(mmax), TVal_(2*lmax+1)
{
size = Num_Alms();
alms = alloc.allocate(size);
}
@ -63,25 +118,41 @@ namespace CosmoTool
virtual T * data() { return alms;}
virtual long size() const { return size; }
virtual FourierMap<T> *mimick() const
virtual FourierMap<std::complex<T> > *mimick() const
{
return new HealpixFourierALM<T>(Lmax(), Mmax());
return new HealpixFourierALM<T>(Lmax_, Mmax_);
}
virtual std::complex<T> dot_product(const FourierMap<std::complex<T> >& other) const
throw(std::bad_cast)
{
const HealpixFourierALM<T>& mfm = dynamic_cast<const HealpixFourierALM<T>&>(other);
std::complex<T> S;
if (size != mfm.size)
throw std::bad_cast();
MapType m1(m_data, Npix);
MapType m2(mfm.m_data, mfm.Npix);
S = (m1.block(0,0,1,Lmax_+1).adjoint() * m2(0,0,1,Lmax_+1)).sum();
S += 2*(m1.block(0,1+Lmax_,1,size-1-Lmax_).adjoint() * m2(0,1+Lmax_,1,size-1-Lmax_)).sum();
return S;
}
};
template<typename T>
class HealpixFourierTransform: public FourierTransform<T>
class HealpixFourierTransform: public FourierTransform<T>, public sharp_base
{
private:
HealpixFourierMap<T> realMap;
HealpixFourierALM<T> fourierMap;
psht_joblist<T> jobs;
public:
HealpixFourierTransform(long nSide, long Lmax, long Mmax)
: realMap(nSide), fourierMap(Lmax, Mmax)
{
jobs.set_Healpix_geometry(nSide);
jobs.set_triangular_alm_info(Lmax, Mmax);
set_Healpix_geometry(nSide);
set_triangular_alm_info(Lmax, Mmax);
}
virtual ~HealpixFourierTransform() {}
@ -96,25 +167,23 @@ namespace CosmoTool
virtual FourierTransform<T> *mimick() const
{
return new HealpixFourierTransform<T>(realMap.Nside(), fourierMap.Lmax(), fourierMap.Mmax());
return new HealpixFourierTransform<T>(realMap.Nside, fourierMap.Lmax, fourierMap.Mmax);
}
virtual void analysis()
{
jobs.add_map2alm(realMap.data(),
reinterpret_cast<xcomplex<T> *>(fourierMap.data()),
false);
jobs.execute();
jobs.clear_jobs();
void *aptr=reinterpret_cast<void *>(fourierMap.data()), *mptr=reinterpret_cast<void *>(realMap.data());
sharp_execute (SHARP_MAP2ALM, 0, 0, &aptr, &mptr, ginfo, ainfo, 1,
cxxjobhelper__<T>::val,0,0,0);
}
virtual void synthesis()
{
jobs.add_alm2map(reinterpret_cast<xcomplex<T> *>(fourierMap.data()),
realMap.data(),
false);
jobs.execute();
jobs.clear_jobs();
void *aptr=reinterpret_cast<void *>(fourierMap.data()), *mptr=reinterpret_cast<void *>(realMap.data());
sharp_execute (SHARP_ALM2MAP, 0, 0, &aptr, &mptr, ginfo, ainfo, 1,
cxxjobhelper__<T>::val,0,0,0);
}
virtual void analysis_conjugate()
@ -130,6 +199,32 @@ namespace CosmoTool
}
};
template<typename T>
boost::shared_ptr<HealpixSpectrum<T>::FourierMapType>
HealpixSpectrum<T>::newRandomFourier(gsl_rng *rng, const FourierMapType& like_map) const
{
const HealpixFourierALM<T>& alms = dynamic_cast<const HealpixFourierALM<T>&>(like_map);
HealpixFourierALM<T> *new_alms;
boost::shared_ptr<FourierMapType> r(new_alms = new HealpixFourierALM<T>(alms.Lmax(), alms.Mmax()));
long lmaxGen = std::min(cls.size()-1, alms.Lmax());
std::complex<T> *new_data = new_alms->data();
for (long l = 0; l < lmaxGen; l++)
{
double Al = std::sqrt(cls[l]);
new_data[alms.index(l,0)] = gsl_ran_gaussian(rng, Al);
Al *= M_SQRT1_2;
for (long m = 1; m < alms.Mmax(); m++)
{
std::complex<T>& c = new_data[alms.index(l,m)];
c.real() = gsl_ran_gaussian(rng, Al);
c.imag() = gsl_ran_gaussian(rng, Al);
}
}
return r;
}
};
#endif