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Merge remote-tracking branch 'origin/master' into natalia/qlpt_feature

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This commit is contained in:
Guilhem Lavaux 2020-10-22 09:27:58 +02:00
commit 1cf9966e1f
16 changed files with 369 additions and 20 deletions
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2
CMakeLists.txt
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@ -54,7 +54,7 @@ IF(YORICK_SUPPORT)
ENDIF((EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") OR (INTERNAL_NETCDF))
ENDIF(YORICK_SUPPORT)
find_program(CYTHON cython3 cython)
find_program(CYTHON NAMES cython3 cython)
find_library(ZLIB_LIBRARY z)
find_library(DL_LIBRARY dl)
find_library(MATH_LIBRARY m)

7
builder/build-wheels.sh
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@ -1,6 +1,11 @@
#!/bin/bash
set -e -x
CC=cc
CXX=c++
export CC CXX
# Install a system package required by our library
#yum install -y atlas-devel
yum install -y cmake3 gsl-devel zlib-devel
@ -8,7 +13,7 @@ yum install -y cmake3 gsl-devel zlib-devel
ln -fs /usr/bin/cmake3 /usr/bin/cmake
ALL_PYTHON="cp37-cp37m cp38-cp38"
ALL_PYTHON="cp36-cp36m cp37-cp37m cp38-cp38"
# Compile wheels
for pkg in $ALL_PYTHON; do

2
builder/start.sh
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@ -9,4 +9,4 @@ if ! [ -e ${d}/setup.py ] ; then
exit 1
fi
podman run -ti --rm -e PLAT=manylinux2014_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2014_x86_64 /io/builder/build-wheels.sh
podman run -ti --rm -e PLAT=manylinux2010_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2010_x86_64 /io/builder/build-wheels.sh

1
conda/build.sh Normal file
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@ -0,0 +1 @@
$PYTHON setup.py install

7
conda/conda_build_config.yaml Normal file
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@ -0,0 +1,7 @@
python:
- 3.7
- 3.8
numpy:
- 1.11
- 1.19

38
conda/meta.yaml Normal file
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@ -0,0 +1,38 @@
package:
name: cosmotool
version: "1.0.0a7"
source:
git_rev: 7fce73e
git_url: https://bitbucket.org/glavaux/cosmotool
requirements:
build:
- numpy >=1.11
- gcc_linux-64
- gxx_linux-64
- python
- setuptools
- cython
- healpy
- numexpr
- cffi
- pyfftw
- gsl
- h5py
run:
- numpy
- python
- healpy
- numexpr
- cffi
- pyfftw
- h5py
test:
imports:
- cosmotool
about:
home: https://bitbucket.org/glavaux/cosmotool

18
external/external_build.cmake vendored
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@ -3,7 +3,7 @@ include(FindOpenMP)
OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE STRING "URL to download FFTW from")
SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE STRING "URL to download Eigen from")
SET(EIGEN_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" CACHE STRING "URL to download Eigen from")
SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from")
SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz" CACHE STRING "URL to download NetCDF from")
@ -255,8 +255,8 @@ ELSE (INTERNAL_BOOST)
set(Boost_VERSION ${TMP_MAJOR}.${TMP_MINOR}.${TMP_PATCHLEVEL})
ENDIF()
if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0)
set(Boost_DEP Boost::headers)
set(Boost_TARGET Boost::headers)
set(Boost_DEP Boost::boost)
set(Boost_TARGET Boost::boost)
endif()
endif()
if (NOT Boost_FOUND)
@ -291,13 +291,19 @@ IF(INTERNAL_GSL)
set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
SET(cosmotool_DEPS ${cosmotool_DEPS} gsl)
ELSE(INTERNAL_GSL)
find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
IF (NOT DEFINED GSL_LIBRARY OR NOT GSL_LIBRARY)
find_library(GSL_LIBRARY gsl)
ENDIF()
IF (NOT DEFINED GSL_INCLUDE_PATH OR NOT GSL_INCLUDE_PATH)
find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
ENDIF()
IF (NOT DEFINED GSL_CBLAS_LIBRARY OR NOT GSL_CBLAS_LIBRARY)
find_library(GSLCBLAS_LIBRARY gslcblas)
ENDIF()
set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
ENDIF(INTERNAL_GSL)
mark_as_advanced(GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
@ -350,7 +356,7 @@ ENDIF(INTERNAL_FFTW)
IF (INTERNAL_EIGEN)
ExternalProject_Add(eigen
URL ${EIGEN_URL}
URL_HASH SHA256=04f8a4fa4afedaae721c1a1c756afeea20d3cdef0ce3293982cf1c518f178502
URL_HASH MD5=b9e98a200d2455f06db9c661c5610496
PREFIX ${BUILD_PREFIX}/eigen-prefix
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

10
python/CMakeLists.txt
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@ -30,6 +30,10 @@ IF(CYTHON)
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx ${CMAKE_CURRENT_SOURCE_DIR}/project_tool.hpp )
add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmomath.pyx
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmomath.pyx )
ENDIF(CYTHON)
@ -38,12 +42,13 @@ add_library(_cosmo_power MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp)
add_library(_cosmo_cic MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp)
add_library(_fast_interp MODULE ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp)
add_library(_project MODULE ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp)
add_library(_cosmomath MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp)
target_include_directories(_cosmotool PRIVATE ${PYTHON_INCLUDES})
target_include_directories(_cosmo_power PRIVATE ${PYTHON_INCLUDES})
target_include_directories(_cosmo_cic PRIVATE ${PYTHON_INCLUDES})
target_include_directories(_fast_interp PRIVATE ${PYTHON_INCLUDES})
target_include_directories(_project PRIVATE ${PYTHON_INCLUDES})
target_include_directories(_cosmomath PRIVATE ${PYTHON_INCLUDES})
SET(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -Bsymbolic-functions")
if(APPLE)
@ -53,10 +58,11 @@ endif()
target_link_libraries(_cosmotool PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
target_link_libraries(_cosmo_power PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
target_link_libraries(_cosmo_cic PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
target_link_libraries(_cosmomath PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
target_link_libraries(_project )
target_link_libraries(_fast_interp PRIVATE ${CosmoTool_local} )
SET(ct_TARGETS _cosmotool _project _cosmo_power _cosmo_cic _fast_interp )
SET(ct_TARGETS _cosmotool _project _cosmo_power _cosmo_cic _fast_interp _cosmomath)
if (Boost_FOUND)
message(STATUS "Building bispectrum support (path = ${Boost_INCLUDE_DIRS})")

38
python/_cosmomath.pyx Normal file
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@ -0,0 +1,38 @@
import numpy as np
cimport numpy as np
np.import_array()
np.import_ufunc()
cdef extern from "sys/types.h":
ctypedef np.int64_t int64_t
cdef extern from "special_math.hpp" namespace "CosmoTool":
T log_modified_bessel_first_kind[T](T v, T z) nogil except +
cdef np.PyUFuncGenericFunction loop_func[1]
cdef char input_output_types[3]
cdef void *elementwise_funcs[1]
loop_func[0] = np.PyUFunc_dd_d
input_output_types[0] = np.NPY_DOUBLE
input_output_types[1] = np.NPY_DOUBLE
input_output_types[2] = np.NPY_DOUBLE
elementwise_funcs[0] = <void*>log_modified_bessel_first_kind[double]
log_modified_I = np.PyUFunc_FromFuncAndData(
loop_func,
elementwise_funcs,
input_output_types,
1, # number of supported input types
2, # number of input args
1, # number of output args
0, # `identity` element, never mind this
"log_modified_bessel_first_kind", # function name
"log_modified_bessel_first_kind(v: Float, z: Float) -> Float", # docstring
0 # unused
)

3
python/_cosmotool.pyx
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@ -513,7 +513,8 @@ def writeGadget(str filename, object simulation):
simdata.TotalNumPart = NumPart
simdata.NumPart = NumPart
cxx_writeGadget(filename, &simdata)
filename_b = bytes(filename, 'utf-8')
cxx_writeGadget(filename_b, &simdata)
def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = False, bool loadPosition = True, bool loadVelocity = False, bool loadId = False, bool loadMass = False):
""" loadRamses(basepath, snapshot_id, cpu_id, doublePrecision = False, loadPosition = True, loadVelocity = False)

1
python/cosmotool/__init__.py
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@ -3,6 +3,7 @@ from ._project import *
from ._cosmo_power import *
from ._cosmo_cic import *
from ._fast_interp import *
from ._cosmomath import *
from .grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
from .borg import read_borg_vol
from .cic import cicParticles

4
python/cosmotool/simu.py
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@ -98,12 +98,12 @@ def simpleWriteGadget(filename, positions, boxsize=1.0, Hubble=100, Omega_M=0.30
s.positions = positions
if velocities:
if velocities is not None:
s.velocities = velocities
else:
s.velocities = [np.zeros(positions[0].size,dtype=np.float32)]*3
if identifiers:
if identifiers is not None:
s.identifiers = identifiers
else:
s.identifiers = np.arange(positions[0].size, dtype=np.int64)

3
sample/CMakeLists.txt
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@ -114,6 +114,9 @@ if (Boost_FOUND)
add_dependencies(graficToDensity ${all_deps})
endif()
endif()
add_executable(test_special test_special.cpp)
target_link_libraries(test_special ${tolink})
endif (Boost_FOUND)
IF (ENABLE_OPENMP AND YORICK_SUPPORT)

12
sample/test_special.cpp Normal file
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@ -0,0 +1,12 @@
#include <iostream>
#include "special_math.hpp"
int main()
{
std::cout << CosmoTool::log1p_exp(2.0) << std::endl;
std::cout << CosmoTool::log_modified_bessel_first_kind(100.0, 0.1) << std::endl;
return 0;
}

8
setup.py
View File

@ -156,9 +156,8 @@ class BuildCMakeExt(build_ext):
cython_code = os.path.join(str(build_dir.absolute()),'mycython')
with open(cython_code, mode="wt") as ff:
ff.write(f"#!{sys.executable}\n"
"from Cython.Compiler.Main import setuptools_main\n"
"setuptools_main()")
ff.write("#!/bin/sh\n"
f"{sys.executable} -c 'from Cython.Compiler.Main import setuptools_main; setuptools_main()' $@")
os.chmod(cython_code, stat.S_IXUSR|stat.S_IWUSR|stat.S_IRUSR|stat.S_IRGRP)
# Now that the necessary directories are created, build
@ -169,6 +168,7 @@ class BuildCMakeExt(build_ext):
# Below is just an example set of arguments for building Blender as a Python module
self.spawn(['cmake', '-H'+SOURCE_DIR, '-B'+self.build_temp,
'-DCMAKE_C_COMPILER=' + os.environ["CC"], "-DCMAKE_CXX_COMPILER=" + os.environ["CXX"],
'-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON',
'-DINTERNAL_HDF5=ON','-DINTERNAL_NETCDF=ON',
'-DBUILD_PYTHON=ON', '-DINSTALL_PYTHON_LOCAL=OFF',
@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext):
CosmoTool_extension = CMakeExtension(name="cosmotool")
setup(name='cosmotool',
version='1.0.0a5',
version='1.1.0',
packages=["cosmotool"],
package_dir={'cosmotool': 'python/cosmotool'},
install_requires=['numpy','cffi','numexpr','pyfftw','h5py'],

231
src/special_math.hpp Normal file
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@ -0,0 +1,231 @@
// Original code derived from Boost and is distributed here
// under the Boost license (licenses/boost-license.txt)
// Copyright (c) 2006 Xiaogang Zhang
// Copyright (c) 2007, 2017 John Maddock
// Secondary code copyright by its author and is distributed here
// under the BSD-3 license (LICENSE.md). Derived from
// stan/math/prim/fun/log_modified_bessel_first_kind.hpp
#ifndef __COSMOTOOL_SPECIAL_MATH_HPP
#define __COSMOTOOL_SPECIAL_MATH_HPP
#include "algo.hpp"
#include <boost/math/constants/constants.hpp>
#include <boost/math/tools/rational.hpp>
#include <cmath>
#include <limits>
// Taken and adapted from
// https://github.com/stan-dev/math/blob/develop/stan/math/prim/fun/log_modified_bessel_first_kind.hpp
namespace CosmoTool {
template <typename T> T log1p_exp(T x) {
if (x > T(0)) {
return x + std::log1p(std::exp(-x));
}
return std::log1p(std::exp(x));
}
template <typename T> T multiply_log(T a, T b) {
if (a == 0 && b == 0)
return 0;
return a * std::log(b);
}
template <typename T> T inf() { return std::numeric_limits<T>::infinity(); }
template <typename T> T log_sum_exp(T const a, T const b) {
if (a == -inf<T>()) {
return b;
}
if (a == inf<T>() && b == inf<T>()) {
return inf<T>();
}
if (a > b) {
return a + log1p_exp(b - a);
}
return b + log1p_exp(a - b);
}
/* Log of the modified Bessel function of the first kind,
* which is better known as the Bessel I function. See
* modified_bessel_first_kind.hpp for the function definition.
* The derivatives are known to be incorrect for v = 0 because a
* simple constant 0 is returned.
*
* @tparam T common type for calculation
* @param v Order, can be a non-integer but must be at least -1
* @param z Real non-negative number
* @throws std::domain_error if either v or z is NaN, z is
* negative, or v is less than -1
* @return log of Bessel I function
*/
template <typename T> T log_modified_bessel_first_kind(T const v, T const z) {
using boost::math::tools::evaluate_polynomial;
using std::log;
using std::pow;
using std::sqrt;
static const double LOG_TWO = std::log(2.0);
static const double EPSILON = std::numeric_limits<double>::epsilon();
static const double TWO_PI = 2.0 * boost::math::constants::pi<double>();
if (z == 0) {
if (v == 0) {
return 0.0;
}
if (v > 0) {
return -std::numeric_limits<T>::infinity();
}
return std::numeric_limits<T>::infinity();
}
if (std::isinf(z)) {
return z;
}
if (v == 0) {
// Modified Bessel function of the first kind of order zero
// we use the approximating forms derived in:
// "Rational Approximations for the Modified Bessel Function of the
// First Kind -- I0(x) for Computations with Double Precision"
// by Pavel Holoborodko, see
// http://www.advanpix.com/2015/11/11/rational-approximations-for-the-modified-bessel-function-of-the-first-kind-i0-computations-double-precision
// The actual coefficients used are [Boost's] own, and extend
// Pavel's work to precisions other than double.
if (z < 7.75) {
// Bessel I0 over[10 ^ -16, 7.75]
// Max error in interpolated form : 3.042e-18
// Max Error found at double precision = Poly : 5.106609e-16
// Cheb : 5.239199e-16
static const double P[] = {
1.00000000000000000e+00, 2.49999999999999909e-01,
2.77777777777782257e-02, 1.73611111111023792e-03,
6.94444444453352521e-05, 1.92901234513219920e-06,
3.93675991102510739e-08, 6.15118672704439289e-10,
7.59407002058973446e-12, 7.59389793369836367e-14,
6.27767773636292611e-16, 4.34709704153272287e-18,
2.63417742690109154e-20, 1.13943037744822825e-22,
9.07926920085624812e-25};
return log1p_exp(multiply_log(2.0, z) - log(4.0) +
log(evaluate_polynomial(P, 0.25 * square(z))));
}
if (z < 500) {
// Max error in interpolated form : 1.685e-16
// Max Error found at double precision = Poly : 2.575063e-16
// Cheb : 2.247615e+00
static const double P[] = {
3.98942280401425088e-01, 4.98677850604961985e-02,
2.80506233928312623e-02, 2.92211225166047873e-02,
4.44207299493659561e-02, 1.30970574605856719e-01,
-3.35052280231727022e+00, 2.33025711583514727e+02,
-1.13366350697172355e+04, 4.24057674317867331e+05,
-1.23157028595698731e+07, 2.80231938155267516e+08,
-5.01883999713777929e+09, 7.08029243015109113e+10,
-7.84261082124811106e+11, 6.76825737854096565e+12,
-4.49034849696138065e+13, 2.24155239966958995e+14,
-8.13426467865659318e+14, 2.02391097391687777e+15,
-3.08675715295370878e+15, 2.17587543863819074e+15};
return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
}
// Max error in interpolated form : 2.437e-18
// Max Error found at double precision = Poly : 1.216719e-16
static const double P[] = {3.98942280401432905e-01, 4.98677850491434560e-02,
2.80506308916506102e-02, 2.92179096853915176e-02,
4.53371208762579442e-02};
return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
}
if (v == 1) { // WARNING: will not autodiff for v = 1 correctly
// modified from Boost's bessel_i1_imp in the double precision case
// see credits above in the v == 0 case
if (z < 7.75) {
// Bessel I0 over[10 ^ -16, 7.75]
// Max error in interpolated form: 5.639e-17
// Max Error found at double precision = Poly: 1.795559e-16
static const double P[] = {
8.333333333333333803e-02, 6.944444444444341983e-03,
3.472222222225921045e-04, 1.157407407354987232e-05,
2.755731926254790268e-07, 4.920949692800671435e-09,
6.834657311305621830e-11, 7.593969849687574339e-13,
6.904822652741917551e-15, 5.220157095351373194e-17,
3.410720494727771276e-19, 1.625212890947171108e-21,
1.332898928162290861e-23};
T a = square(z) * 0.25;
T Q[3] = {1, 0.5, evaluate_polynomial(P, a)};
return log(z) + log(evaluate_polynomial(Q, a)) - LOG_TWO;
}
if (z < 500) {
// Max error in interpolated form: 1.796e-16
// Max Error found at double precision = Poly: 2.898731e-16
static const double P[] = {
3.989422804014406054e-01, -1.496033551613111533e-01,
-4.675104253598537322e-02, -4.090895951581637791e-02,
-5.719036414430205390e-02, -1.528189554374492735e-01,
3.458284470977172076e+00, -2.426181371595021021e+02,
1.178785865993440669e+04, -4.404655582443487334e+05,
1.277677779341446497e+07, -2.903390398236656519e+08,
5.192386898222206474e+09, -7.313784438967834057e+10,
8.087824484994859552e+11, -6.967602516005787001e+12,
4.614040809616582764e+13, -2.298849639457172489e+14,
8.325554073334618015e+14, -2.067285045778906105e+15,
3.146401654361325073e+15, -2.213318202179221945e+15};
return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
}
// Max error in interpolated form: 1.320e-19
// Max Error found at double precision = Poly: 7.065357e-17
static const double P[] = {
3.989422804014314820e-01, -1.496033551467584157e-01,
-4.675105322571775911e-02, -4.090421597376992892e-02,
-5.843630344778927582e-02};
return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
}
if (z > 100) {
// Boost does something like this in asymptotic_bessel_i_large_x
T lim = pow((square(v) + 2.5) / (2 * z), 3) / 24;
if (lim < (EPSILON * 10)) {
T s = 1;
T mu = 4 * square(v);
T ex = 8 * z;
T num = mu - 1;
T denom = ex;
s -= num / denom;
num *= mu - 9;
denom *= ex * 2;
s += num / denom;
num *= mu - 25;
denom *= ex * 3;
s -= num / denom;
s = z - log(sqrt(z * TWO_PI)) + log(s);
return s;
}
}
T log_half_z = log(0.5 * z);
T lgam = (v > -1) ? lgamma(v + 1.0) : 0;
T lcons = (2.0 + v) * log_half_z;
T out;
if (v > -1) {
out = log_sum_exp(v * log_half_z - lgam, lcons - lgamma(v + 2));
lgam += log1p(v);
} else {
out = lcons;
}
double m = 2;
double lfac = 0;
T old_out;
do {
lfac += log(m);
lgam += log(v + m);
lcons += 2 * log_half_z;
old_out = out;
out = log_sum_exp(out, lcons - lfac - lgam); // underflows eventually
m++;
} while (out > old_out || out < old_out);
return out;
}
} // namespace CosmoTool
#endif