From cf90393c36172c6690d424d239972c36408df6bd Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Mon, 10 Feb 2020 08:40:17 +0100 Subject: [PATCH 01/38] Portability fixes --- CMakeLists.txt | 2 +- src/CMakeLists.txt | 2 +- src/loadRamses.cpp | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 0e21c7d..2690baf 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -55,7 +55,7 @@ IF(YORICK_SUPPORT) ENDIF(YORICK_SUPPORT) find_program(CYTHON cython3 cython) -find_library(ZLIB z) +find_library(ZLIB_LIBRARY z) find_library(DL_LIBRARY dl) find_library(MATH_LIBRARY m) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 196ed36..a4c81e8 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -79,7 +79,7 @@ if(YORICK_SUPPORT) endif(YORICK_SUPPORT) if (HDF5_FOUND) - set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${ZLIB}) + set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${ZLIB_LIBRARY}) message(STATUS "CosmoTool_LIBS: ${CosmoTool_LIBS}") endif (HDF5_FOUND) diff --git a/src/loadRamses.cpp b/src/loadRamses.cpp index 0c628f8..3e841d5 100644 --- a/src/loadRamses.cpp +++ b/src/loadRamses.cpp @@ -34,7 +34,7 @@ knowledge of the CeCILL license and that you accept its terms. +*/ #include -#include "/usr/include/regex.h" +#include #include #include #include From bc2e126075a295d1dc9f5881b92ee731b7fd25c2 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Fri, 6 Mar 2020 08:23:55 +0100 Subject: [PATCH 02/38] Add support for multiple attributes in CTPV --- python/cosmotool/ctpv.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/python/cosmotool/ctpv.py b/python/cosmotool/ctpv.py index 22a9d22..4d90f1a 100644 --- a/python/cosmotool/ctpv.py +++ b/python/cosmotool/ctpv.py @@ -87,7 +87,7 @@ class ProgrammableParticleHistoryLoad(object): class ProgrammableDensityLoad(object): @staticmethod - def main_script(source, density, extents=None, aname="default"): + def main_script(source, density, extents=None, aname="default", extra_arrays={}): import vtk from vtk.util import numpy_support @@ -116,6 +116,11 @@ class ProgrammableDensityLoad(object): arr = numpy_support.numpy_to_vtk(density.transpose().astype(np.float64).ravel(), deep=1) arr.SetName(aname) ido.GetPointData().AddArray(arr) + + for k in extra_arrays.keys(): + arr = numpy_support.numpy_to_vtk(extra_arrays[k].transpose().astype(np.float64).ravel(), deep=1) + arr.SetName(k) + ido.GetPointData().AddArray(arr) @staticmethod def request_information(source, density=None, dims=None): From a3f30b5d8fb8a596feb5f295d88a0915b9d27c37 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Fri, 3 Apr 2020 19:17:27 +0200 Subject: [PATCH 03/38] Fixes to support ninja --- external/external_build.cmake | 17 +++++++++-------- src/CMakeLists.txt | 2 ++ 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index c8fedcf..53037ed 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -56,19 +56,19 @@ if (ENABLE_SHARP) IF(NOT ENABLE_OPENMP) SET(SHARP_OPENMP --disable-openmp) ENDIF() - ExternalProject_Add(sharp - URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz - PREFIX ${BUILD_PREFIX}/sharp-prefix - BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP} - BUILD_COMMAND ${CMAKE_MAKE_PROGRAM} - INSTALL_COMMAND echo "No install" - ) SET(CUTILS_LIBRARY ${DEP_BUILD}/lib/libc_utils.a) SET(FFTPACK_LIBRARY ${DEP_BUILD}/lib/libfftpack.a) SET(SHARP_LIBRARY ${DEP_BUILD}/lib/libsharp.a) SET(SHARP_LIBRARIES ${SHARP_LIBRARY} ${FFTPACK_LIBRARY} ${CUTILS_LIBRARY}) SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include) + ExternalProject_Add(sharp + URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz + PREFIX ${BUILD_PREFIX}/sharp-prefix + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP} + INSTALL_COMMAND echo "No install" + BUILD_BYPRODUCTS ${SHARP_LIBRARIES} + ) endif (ENABLE_SHARP) @@ -375,6 +375,7 @@ ExternalProject_Add(omptl BUILD_COMMAND echo "No build" PATCH_COMMAND patch -p1 -t -N < ${CMAKE_SOURCE_DIR}/external/patch-omptl INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${OMPTL_BUILD_DIR} ${EXT_INSTALL}/include/omptl + BUILD_BYPRODUCTS ${EXT_INSTALL}/include/omptl ) include_directories(${EXT_INSTALL}/include) ##include_directories(${OMPTL_BUILD_DIR}/src/) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index a4c81e8..2cc4b29 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -92,11 +92,13 @@ if (BUILD_SHARED_LIBS) add_library(CosmoTool_static STATIC ${CosmoTool_SRCS} $) target_link_libraries(CosmoTool_static) set_property(TARGET CosmoTool_static PROPERTY POSITION_INDEPENDENT_CODE ON) + add_dependencies(CosmoTool_static ${cosmotool_DEPS}) endif(BUILD_STATIC_LIBS) else (BUILD_SHARED_LIBS) add_library(CosmoTool STATIC ${CosmoTool_SRCS} $) target_link_libraries(CosmoTool) set_property(TARGET CosmoTool PROPERTY POSITION_INDEPENDENT_CODE ON) + add_dependencies(CosmoTool ${cosmotool_DEPS}) endif (BUILD_SHARED_LIBS) IF(NOT COSMOTOOL_PYTHON_PACKAGING) From e4924917b9ddc145f802a19c714df35e9fe96021 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Fri, 10 Apr 2020 18:02:18 +0200 Subject: [PATCH 04/38] Add some support for boost >= 1.70 --- external/external_build.cmake | 13 ++++++++----- src/CMakeLists.txt | 2 +- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index 53037ed..458b803 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -2,8 +2,8 @@ include(FindOpenMP) OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF) -SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE URL "URL to download FFTW from") -SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE URL "URL to download Eigen from") +SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE STRING "URL to download FFTW from") +SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE STRING "URL to download Eigen from") SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from") SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from") SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz" CACHE STRING "URL to download NetCDF from") @@ -246,10 +246,13 @@ if (INTERNAL_BOOST) set(Boost_DEP boost) ELSE (INTERNAL_BOOST) - find_package(Boost 1.53 QUIET) - set(Boost_DEP) + find_package(Boost 1.69 QUIET) if (NOT Boost_FOUND) - cmessage(CWARNING "Boost >= 1.53 was not found") + cmessage(CWARNING "Boost >= 1.69 was not found") + endif() + if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0) + set(Boost_DEP Boost::headers) + set(Boost_TARGET Boost::headers PARENT_SCOPE) endif() endif (INTERNAL_BOOST) mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 2cc4b29..3d6b1ff 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -72,7 +72,7 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS} include_directories(${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src) -set(CosmoTool_LIBS ${GSL_LIBRARIES}) +set(CosmoTool_LIBS ${GSL_LIBRARIES} ${Boost_TARGET}) if(YORICK_SUPPORT) set(CosmoTool_LIBS ${CosmoTool_LIBS} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES}) include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH}) From 3773c1ab43af2b3b0f871436cdf84fa8568a0952 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 14 Apr 2020 17:46:14 +0200 Subject: [PATCH 05/38] Add support for newer boost --- external/external_build.cmake | 2 +- src/CMakeLists.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index 458b803..780dff6 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -252,7 +252,7 @@ ELSE (INTERNAL_BOOST) endif() if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0) set(Boost_DEP Boost::headers) - set(Boost_TARGET Boost::headers PARENT_SCOPE) + set(Boost_TARGET Boost::headers) endif() endif (INTERNAL_BOOST) mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 3d6b1ff..4f39695 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -96,7 +96,7 @@ if (BUILD_SHARED_LIBS) endif(BUILD_STATIC_LIBS) else (BUILD_SHARED_LIBS) add_library(CosmoTool STATIC ${CosmoTool_SRCS} $) - target_link_libraries(CosmoTool) + target_link_libraries(CosmoTool ${CosmoTool_LIBS}) set_property(TARGET CosmoTool PROPERTY POSITION_INDEPENDENT_CODE ON) add_dependencies(CosmoTool ${cosmotool_DEPS}) endif (BUILD_SHARED_LIBS) From 8d91ec20fabef7c0c18366340a31af8076f149ad Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 26 Apr 2020 09:36:40 +0200 Subject: [PATCH 06/38] Better test of boost --- external/external_build.cmake | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index 780dff6..43e0021 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -249,10 +249,14 @@ ELSE (INTERNAL_BOOST) find_package(Boost 1.69 QUIET) if (NOT Boost_FOUND) cmessage(CWARNING "Boost >= 1.69 was not found") + else() + cmessage(STATUS "Boost has been found (version=${Boost_VERSION})") endif() - if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0) - set(Boost_DEP Boost::headers) - set(Boost_TARGET Boost::headers) + if (Boost_VERSION) + if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0) + set(Boost_DEP Boost::headers) + set(Boost_TARGET Boost::headers) + endif() endif() endif (INTERNAL_BOOST) mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES) From 74a59cb21b4e7e4a5bdfa4f708db93d213f4bf96 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 14:12:36 +0200 Subject: [PATCH 07/38] Adjust linkage --- python/CMakeLists.txt | 8 ++++---- python/_cosmo_power.pyx | 2 +- setup.py | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt index 6045aca..90d3e6e 100644 --- a/python/CMakeLists.txt +++ b/python/CMakeLists.txt @@ -50,11 +50,11 @@ if(APPLE) set(CMAKE_MODULE_LINKER_FLAGS "-undefined dynamic_lookup") endif() -target_link_libraries(_cosmotool ${CosmoTool_local} ${GSL_LIBRARIES}) -target_link_libraries(_cosmo_power ${CosmoTool_local} ${GSL_LIBRARIES}) -target_link_libraries(_cosmo_cic ${CosmoTool_local} ${GSL_LIBRARIES}) +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(_project ) -target_link_libraries(_fast_interp ${CosmoTool_local} ) +target_link_libraries(_fast_interp PRIVATE ${CosmoTool_local} ) SET(ct_TARGETS _cosmotool _project _cosmo_power _cosmo_cic _fast_interp ) diff --git a/python/_cosmo_power.pyx b/python/_cosmo_power.pyx index 2d01e72..bf4bd4b 100644 --- a/python/_cosmo_power.pyx +++ b/python/_cosmo_power.pyx @@ -81,7 +81,7 @@ cdef class CosmologyPower: if 'ns' in cosmo: self.power.n = cosmo['ns'] if 'T27' in cosmo: - self.power.THETA_27 = cosmo['T27'] + self.power.Theta_27 = cosmo['T27'] assert self.power.OMEGA_C > 0 diff --git a/setup.py b/setup.py index a3d1a58..74d4925 100644 --- a/setup.py +++ b/setup.py @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a2', + version='1.0.0a3', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, setup_requires=['cython','cffi','numexpr'], From f35d0cc6944370175169456cb6ca81c77f9165c1 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 14:52:59 +0200 Subject: [PATCH 08/38] Add dummy source code --- python/dummy.c | 1 + setup.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) create mode 100644 python/dummy.c diff --git a/python/dummy.c b/python/dummy.c new file mode 100644 index 0000000..ad8787c --- /dev/null +++ b/python/dummy.c @@ -0,0 +1 @@ +static void dummyFunc() {} diff --git a/setup.py b/setup.py index 74d4925..f1cf6d6 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ class CMakeExtension(Extension): doesn't try to build your sources for you """ - def __init__(self, name, sources=[]): + def __init__(self, name, sources=["python/dummy.c"]): super().__init__(name = name, sources = sources) @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a3', + version='1.0.0a4', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, setup_requires=['cython','cffi','numexpr'], From 6bc0b80e3986deb2b7f4fabd78181b2a30f9e545 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 18:23:44 +0200 Subject: [PATCH 09/38] Add script and metadata to build binary packages. --- LICENCE.txt | 508 ++++++++++++++++++++++++++++++++++++++++ MANIFEST.in | 169 +++++++++++++ builder/build-wheels.sh | 27 +++ builder/start.sh | 12 + setup.py | 3 +- 5 files changed, 718 insertions(+), 1 deletion(-) create mode 100644 LICENCE.txt create mode 100644 MANIFEST.in create mode 100755 builder/build-wheels.sh create mode 100755 builder/start.sh diff --git a/LICENCE.txt b/LICENCE.txt new file mode 100644 index 0000000..acde39e --- /dev/null +++ b/LICENCE.txt @@ -0,0 +1,508 @@ +Copyright (C) 2009-2020 Guilhem Lavaux + + +CeCILL FREE SOFTWARE LICENSE AGREEMENT + + + Notice + +This Agreement is a Free Software license agreement that is the result +of discussions between its authors in order to ensure compliance with +the two main principles guiding its drafting: + + * firstly, compliance with the principles governing the distribution + of Free Software: access to source code, broad rights granted to + users, + * secondly, the election of a governing law, French law, with which + it is conformant, both as regards the law of torts and + intellectual property law, and the protection that it offers to + both authors and holders of the economic rights over software. + +The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) +license are: + +Commissariat à l'Energie Atomique - CEA, a public scientific, technical +and industrial research establishment, having its principal place of +business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France. + +Centre National de la Recherche Scientifique - CNRS, a public scientific +and technological establishment, having its principal place of business +at 3 rue Michel-Ange, 75794 Paris cedex 16, France. + +Institut National de Recherche en Informatique et en Automatique - +INRIA, a public scientific and technological establishment, having its +principal place of business at Domaine de Voluceau, Rocquencourt, BP +105, 78153 Le Chesnay cedex, France. + + + Preamble + +The purpose of this Free Software license agreement is to grant users +the right to modify and redistribute the software governed by this +license within the framework of an open source distribution model. + +The exercising of these rights is conditional upon certain obligations +for users so as to preserve this status for all subsequent redistributions. + +In consideration of access to the source code and the rights to copy, +modify and redistribute granted by the license, users are provided only +with a limited warranty and the software's author, the holder of the +economic rights, and the successive licensors only have limited liability. + +In this respect, the risks associated with loading, using, modifying +and/or developing or reproducing the software by the user are brought to +the user's attention, given its Free Software status, which may make it +complicated to use, with the result that its use is reserved for +developers and experienced professionals having in-depth computer +knowledge. 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Therefore, +the Licensor disclaims any and all liability towards the Licensee +arising out of any or all proceedings for infringement that may be +instituted in respect of the use, modification and redistribution of the +Software. Nevertheless, should such proceedings be instituted against +the Licensee, the Licensor shall provide it with technical and legal +assistance for its defense. Such technical and legal assistance shall be +decided on a case-by-case basis between the relevant Licensor and the +Licensee pursuant to a memorandum of understanding. The Licensor +disclaims any and all liability as regards the Licensee's use of the +name of the Software. No warranty is given as regards the existence of +prior rights over the name of the Software or as regards the existence +of a trademark. + + + Article 10 - TERMINATION + +10.1 In the event of a breach by the Licensee of its obligations +hereunder, the Licensor may automatically terminate this Agreement +thirty (30) days after notice has been sent to the Licensee and has +remained ineffective. + +10.2 A Licensee whose Agreement is terminated shall no longer be +authorized to use, modify or distribute the Software. However, any +licenses that it may have granted prior to termination of the Agreement +shall remain valid subject to their having been granted in compliance +with the terms and conditions hereof. + + + Article 11 - MISCELLANEOUS + + + 11.1 EXCUSABLE EVENTS + +Neither Party shall be liable for any or all delay, or failure to +perform the Agreement, that may be attributable to an event of force +majeure, an act of God or an outside cause, such as defective +functioning or interruptions of the electricity or telecommunications +networks, network paralysis following a virus attack, intervention by +government authorities, natural disasters, water damage, earthquakes, +fire, explosions, strikes and labor unrest, war, etc. + +11.2 Any failure by either Party, on one or more occasions, to invoke +one or more of the provisions hereof, shall under no circumstances be +interpreted as being a waiver by the interested Party of its right to +invoke said provision(s) subsequently. + +11.3 The Agreement cancels and replaces any or all previous agreements, +whether written or oral, between the Parties and having the same +purpose, and constitutes the entirety of the agreement between said +Parties concerning said purpose. No supplement or modification to the +terms and conditions hereof shall be effective as between the Parties +unless it is made in writing and signed by their duly authorized +representatives. + +11.4 In the event that one or more of the provisions hereof were to +conflict with a current or future applicable act or legislative text, +said act or legislative text shall prevail, and the Parties shall make +the necessary amendments so as to comply with said act or legislative +text. All other provisions shall remain effective. Similarly, invalidity +of a provision of the Agreement, for any reason whatsoever, shall not +cause the Agreement as a whole to be invalid. + + + 11.5 LANGUAGE + +The Agreement is drafted in both French and English and both versions +are deemed authentic. + + + Article 12 - NEW VERSIONS OF THE AGREEMENT + +12.1 Any person is authorized to duplicate and distribute copies of this +Agreement. + +12.2 So as to ensure coherence, the wording of this Agreement is +protected and may only be modified by the authors of the License, who +reserve the right to periodically publish updates or new versions of the +Agreement, each with a separate number. These subsequent versions may +address new issues encountered by Free Software. + +12.3 Any Software distributed under a given version of the Agreement may +only be subsequently distributed under the same version of the Agreement +or a subsequent version, subject to the provisions of Article 5.3.4. + + + Article 13 - GOVERNING LAW AND JURISDICTION + +13.1 The Agreement is governed by French law. The Parties agree to +endeavor to seek an amicable solution to any disagreements or disputes +that may arise during the performance of the Agreement. + +13.2 Failing an amicable solution within two (2) months as from their +occurrence, and unless emergency proceedings are necessary, the +disagreements or disputes shall be referred to the Paris Courts having +jurisdiction, by the more diligent Party. + + +Version 2.0 dated 2006-09-05. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..8d92fca --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,169 @@ +include .gitignore +include CMakeLists.txt +include FindNumPy.cmake +include FindPyLibs.cmake +include GetGitRevisionDescription.cmake +include GetGitRevisionDescription.cmake.in +include LICENCE.txt +include LICENCE_CeCILL_V2 +include README.md +include build_tools/gather_sources.py +include color_msg.cmake +include doc/Makefile +include doc/make.bat +include doc/source/conf.py +include doc/source/cpplibrary.rst +include doc/source/index.rst +include doc/source/intro.rst +include doc/source/pythonmodule.rst +include external/external_build.cmake +include external/libsharp-6077806.tar.gz +include external/omptl-20120422.tar.bz2 +include external/patch-omptl +include python/CMakeLists.txt +include python/_cosmo_bispectrum.cpp +include python/_cosmo_cic.pyx +include python/_cosmo_power.pyx +include python/_cosmotool.pyx +include python/_fast_interp.pyx +include python/_project.pyx +include python/copy.pxd +include python/cosmotool/__init__.py +include python/cosmotool/bispectrum.py +include python/cosmotool/borg.py +include python/cosmotool/cic.py +include python/cosmotool/cl_cic.py +include python/cosmotool/config.py.in +include python/cosmotool/ctpv.py +include python/cosmotool/fftw.py +include python/cosmotool/grafic.py +include python/cosmotool/simu.py +include python/cosmotool/smooth.py +include python/cosmotool/timing.py +include python/cppHelper.hpp +include python/dummy.c +include python/project_tool.hpp +include python/safe_gadget.hpp +include python_sample/build_2lpt_ksz.py +include python_sample/build_2lpt_skymap.py +include python_sample/build_dipole_ksz_from_galaxies.py +include python_sample/build_nbody_ksz.py +include python_sample/build_nbody_ksz_from_galaxies.py +include python_sample/build_nbody_skymap.py +include python_sample/gen_2lpt_asmooth.py +include python_sample/gen_2lpt_density.py +include python_sample/icgen/__init__.py +include python_sample/icgen/borgadaptor.py +include python_sample/icgen/borgicgen.py +include python_sample/icgen/cosmogrowth.py +include python_sample/icgen/gen_ic_from_borg.py +include python_sample/icgen/test_ic_from_borg.py +include python_sample/icgen/test_whitify.py +include python_sample/ksz/__init__.py +include python_sample/ksz/constants.py +include python_sample/ksz/gal_prof.py +include python_sample/ramsesToArray.py +include python_sample/test_bispectrum.py +include python_sample/test_spheric_proj.py +include sample/CMakeLists.txt +include sample/Hartmann_Matrix.txt +include sample/gadgetToArray.cpp +include sample/gadgetToDensity.cpp +include sample/graficToDensity.cpp +include sample/simple3DFilter.cpp +include sample/simpleDistanceFilter.cpp +include sample/testAlgo.cpp +include sample/testBQueue.cpp +include sample/testBSP.cpp +include sample/testDelaunay.cpp +include sample/testEskow.cpp +include sample/testHDF5.cpp +include sample/testInterpolate.cpp +include sample/testNewton.cpp +include sample/testPool.cpp +include sample/testReadFlash.cpp +include sample/testSmooth.cpp +include sample/test_cosmopower.cpp +include sample/test_fft_calls.cpp +include sample/test_healpix_calls.cpp +include sample/testkd.cpp +include sample/testkd2.cpp +include sample/testkd3.cpp +include setup.py +include src/CMakeLists.txt +include src/algo.hpp +include src/bqueue.hpp +include src/bqueue.tcc +include src/bsp_simple.hpp +include src/bsp_simple.tcc +include src/cic.cpp +include src/cic.hpp +include src/config.hpp +include src/cosmopower.cpp +include src/cosmopower.hpp +include src/dinterpolate.hpp +include src/dinterpolate.tcc +include src/eskow.hpp +include src/field.hpp +include src/fixArray.hpp +include src/fortran.cpp +include src/fortran.hpp +include src/fourier/base_types.hpp +include src/fourier/details/euclidian_maps.hpp +include src/fourier/details/euclidian_spectrum_1d.hpp +include src/fourier/details/euclidian_spectrum_1d_bin.hpp +include src/fourier/details/euclidian_transform.hpp +include src/fourier/details/healpix_alms.hpp +include src/fourier/details/healpix_map.hpp +include src/fourier/details/healpix_spectrum.hpp +include src/fourier/details/healpix_transform.hpp +include src/fourier/details/healpix_utility.hpp +include src/fourier/euclidian.hpp +include src/fourier/fft/fftw_calls.hpp +include src/fourier/fft/fftw_calls_mpi.hpp +include src/fourier/fft/fftw_complex.hpp +include src/fourier/healpix.hpp +include src/growthFactor.cpp +include src/growthFactor.hpp +include src/h5_readFlash.cpp +include src/h5_readFlash.hpp +include src/hdf5_array.hpp +include src/hdf5_flash.h +include src/interpolate.cpp +include src/interpolate.hpp +include src/interpolate3d.hpp +include src/kdtree_leaf.hpp +include src/kdtree_leaf.tcc +include src/kdtree_splitters.hpp +include src/loadFlash.cpp +include src/loadFlash.hpp +include src/loadFlash_dummy.cpp +include src/loadGadget.cpp +include src/loadGadget.hpp +include src/loadRamses.cpp +include src/loadRamses.hpp +include src/loadSimu.hpp +include src/load_data.cpp +include src/load_data.hpp +include src/mach.hpp +include src/miniargs.cpp +include src/miniargs.hpp +include src/mykdtree.hpp +include src/mykdtree.tcc +include src/newton.hpp +include src/octTree.hpp +include src/octTree.tcc +include src/openmp.hpp +include src/pool.hpp +include src/powerSpectrum.cpp +include src/powerSpectrum.hpp +include src/replicateGenerator.hpp +include src/sparseGrid.hpp +include src/sparseGrid.tcc +include src/sphSmooth.hpp +include src/sphSmooth.tcc +include src/symbol_visible.hpp +include src/tf_fit.hpp +include src/yorick.hpp +include src/yorick_nc3.cpp +include src/yorick_nc4.cpp diff --git a/builder/build-wheels.sh b/builder/build-wheels.sh new file mode 100755 index 0000000..32ecd8b --- /dev/null +++ b/builder/build-wheels.sh @@ -0,0 +1,27 @@ +#!/bin/bash +set -e -x + +# Install a system package required by our library +#yum install -y atlas-devel +yum install -y cmake3 + + +ALL_PYTHON=cp38-cp38 + +# Compile wheels +for pkg in $ALL_PYTHON; do + PYBIN=/opt/python/${pkg}/bin +# "${PYBIN}/pip" install -r /io/dev-requirements.txt + "${PYBIN}/pip" wheel -v /io/ -w wheelhouse/ +done + +# Bundle external shared libraries into the wheels +for whl in wheelhouse/*.whl; do + auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/ +done + +# Install packages and test +for pkg in $ALL_PYTHON; do + PYBIN=/opt/python/${pkg}/bin + "${PYBIN}/pip" install cosmotool --no-index -f /io/wheelhouse +done diff --git a/builder/start.sh b/builder/start.sh new file mode 100755 index 0000000..31f95f0 --- /dev/null +++ b/builder/start.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +d=$(pwd) +if test x"$(basename $d)" = xbuilder; then + d=${d}/../ +fi +if ! [ -e ${d}/setup.py ] ; then + echo "Unknown directory. Please move to the root of cosmotool source tree." + exit 1 +fi + +podman run -ti --rm -e PLAT=manylinux2014_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2014_x86_64 /io/builder/build-wheels.sh diff --git a/setup.py b/setup.py index f1cf6d6..226be38 100644 --- a/setup.py +++ b/setup.py @@ -241,5 +241,6 @@ setup(name='cosmotool', 'build_ext': BuildCMakeExt, 'install_data': InstallCMakeLibsData, 'install_lib': InstallCMakeLibs, - } + }, + python_requires='>=3.6' ) From 9703cbfd70af34ab19dc908ed458976a39b25e2b Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 21:08:27 +0200 Subject: [PATCH 10/38] Improvement for Boost detection --- external/external_build.cmake | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index 43e0021..6f00ec6 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -247,17 +247,23 @@ if (INTERNAL_BOOST) ELSE (INTERNAL_BOOST) find_package(Boost 1.69 QUIET) - if (NOT Boost_FOUND) - cmessage(CWARNING "Boost >= 1.69 was not found") - else() - cmessage(STATUS "Boost has been found (version=${Boost_VERSION})") - endif() if (Boost_VERSION) + if (${Boost_VERSION} VERSION_GREATER 1000) + math(EXPR TMP_MAJOR "${Boost_VERSION} / 100000") + math(EXPR TMP_MINOR "(${Boost_VERSION} - ${TMP_MAJOR} * 100000) / 100") + math(EXPR TMP_PATCHLEVEL "${Boost_VERSION} - ${TMP_MAJOR} * 100000 - ${TMP_MINOR} * 100") + 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) endif() endif() + if (NOT Boost_FOUND) + cmessage(CWARNING "Boost >= 1.69 was not found") + else() + cmessage(STATUS "Boost has been found (version=${Boost_VERSION}), Boost_TARGET=${Boost_Target}") + endif() endif (INTERNAL_BOOST) mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES) From 772677590c83d40cc83886d33ba29c1d367aad8f Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 22:34:49 +0200 Subject: [PATCH 11/38] Automate building --- builder/build-wheels.sh | 9 ++++++--- setup.py | 5 +++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/builder/build-wheels.sh b/builder/build-wheels.sh index 32ecd8b..ffef437 100755 --- a/builder/build-wheels.sh +++ b/builder/build-wheels.sh @@ -3,16 +3,19 @@ set -e -x # Install a system package required by our library #yum install -y atlas-devel -yum install -y cmake3 +yum install -y cmake3 gsl-devel zlib-devel + +ln -fs /usr/bin/cmake3 /usr/bin/cmake -ALL_PYTHON=cp38-cp38 +ALL_PYTHON="cp37-cp37m cp38-cp38" # Compile wheels for pkg in $ALL_PYTHON; do PYBIN=/opt/python/${pkg}/bin # "${PYBIN}/pip" install -r /io/dev-requirements.txt - "${PYBIN}/pip" wheel -v /io/ -w wheelhouse/ + "${PYBIN}/pip" install -r /io/requirements.txt + "${PYBIN}/pip" wheel -vvv /io/ -w wheelhouse/ done # Bundle external shared libraries into the wheels diff --git a/setup.py b/setup.py index 226be38..90aa9d6 100644 --- a/setup.py +++ b/setup.py @@ -218,10 +218,11 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a4', + version='1.0.0a5', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, - setup_requires=['cython','cffi','numexpr'], + install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], + setup_requires=['cython','cffi','numpy','numexpr'], ext_modules=[CosmoTool_extension], description='A small cosmotool box of useful functions', long_description=open("./README.md", 'r').read(), From f6b99a084e5338174c3c9aa63bb10eeaaf633485 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 22:35:26 +0200 Subject: [PATCH 12/38] Add python requirements --- requirements.txt | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..ef3f5d4 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,5 @@ +numpy +cffi +numexpr +pyfftw +cython From 689cc70daa8006f4e4eeeda29d7bc460f37bf5a7 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Wed, 29 Apr 2020 14:36:41 +0200 Subject: [PATCH 13/38] Fix some warnings --- src/algo.hpp | 2 +- src/config.hpp | 2 +- src/hdf5_array.hpp | 6 ++---- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/src/algo.hpp b/src/algo.hpp index 5f896ef..9dcf1bc 100644 --- a/src/algo.hpp +++ b/src/algo.hpp @@ -93,6 +93,6 @@ namespace CosmoTool -}; +} #endif diff --git a/src/config.hpp b/src/config.hpp index 6fa7b63..940919b 100644 --- a/src/config.hpp +++ b/src/config.hpp @@ -165,6 +165,6 @@ namespace CosmoTool FilesystemFullException() : Exception() {} }; -}; +} #endif diff --git a/src/hdf5_array.hpp b/src/hdf5_array.hpp index 11762bb..4cab937 100644 --- a/src/hdf5_array.hpp +++ b/src/hdf5_array.hpp @@ -78,8 +78,6 @@ namespace CosmoTool { } }; - //, typename boost::enable_if >::type> \ - // #define HDF5_TYPE(tl, thdf5) \ template struct get_hdf5_data_type >::type > \ { static H5::DataType type() { return H5::PredType::thdf5; }; } @@ -122,7 +120,7 @@ namespace CosmoTool { template<> struct hdf5_extent_gen<0> { - static inline boost::multi_array_types::extent_gen build(hsize_t *d) + static inline boost::multi_array_types::extent_gen build(hsize_t *) { return boost::extents; } @@ -513,7 +511,7 @@ namespace CosmoTool { \ }; \ }; -}; +} #endif From 46831ba9abc1eb41d48732632c91daf54cdf4e5d Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Tue, 4 Aug 2020 10:43:45 +0200 Subject: [PATCH 14/38] Fixes for gadget IO --- builder/build-wheels.sh | 2 +- builder/start.sh | 2 +- python/_cosmotool.pyx | 3 ++- python/cosmotool/simu.py | 4 ++-- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/builder/build-wheels.sh b/builder/build-wheels.sh index ffef437..e5c1b6f 100755 --- a/builder/build-wheels.sh +++ b/builder/build-wheels.sh @@ -8,7 +8,7 @@ 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 diff --git a/builder/start.sh b/builder/start.sh index 31f95f0..9fbc185 100755 --- a/builder/start.sh +++ b/builder/start.sh @@ -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 diff --git a/python/_cosmotool.pyx b/python/_cosmotool.pyx index 61ba1a0..ed9195e 100644 --- a/python/_cosmotool.pyx +++ b/python/_cosmotool.pyx @@ -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) diff --git a/python/cosmotool/simu.py b/python/cosmotool/simu.py index 2389926..157e107 100644 --- a/python/cosmotool/simu.py +++ b/python/cosmotool/simu.py @@ -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) From 11f732bd16fbd8565fa6426c69ec4c86f5c7c25a Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Tue, 4 Aug 2020 11:51:05 +0200 Subject: [PATCH 15/38] Bump version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 90aa9d6..9bdbd96 100644 --- a/setup.py +++ b/setup.py @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a5', + version='1.0.0a6', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], From 55f4dde852d2325c67acf49c1133723c8d0f47e0 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Fri, 18 Sep 2020 11:06:16 +0300 Subject: [PATCH 16/38] Update eigen --- external/external_build.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index c8fedcf..070686c 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -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 URL "URL to download FFTW from") -SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE URL "URL to download Eigen from") +SET(EIGEN_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" CACHE URL "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") @@ -337,7 +337,7 @@ 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} From 8f14192dab4a3977c05a942758a6e8b89ecd94a8 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Fri, 18 Sep 2020 11:07:30 +0300 Subject: [PATCH 17/38] Bump version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9bdbd96..5e89069 100644 --- a/setup.py +++ b/setup.py @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a6', + version='1.0.0a7', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], From fe5da8198212b711687c9b52d07bee73fcd8bbad Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 20 Sep 2020 12:08:18 +0300 Subject: [PATCH 18/38] Add compiler spec --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index 5e89069..dca81c0 100644 --- a/setup.py +++ b/setup.py @@ -169,6 +169,7 @@ 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.env["CC"], "-DCMAKE_CXX_COMPILER=" + os.env["CXX"], '-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON', '-DINTERNAL_HDF5=ON','-DINTERNAL_NETCDF=ON', '-DBUILD_PYTHON=ON', '-DINSTALL_PYTHON_LOCAL=OFF', From ec308c1759b7de9c84d555bbac424a91ad1d5928 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 20 Sep 2020 12:08:42 +0300 Subject: [PATCH 19/38] Fix dict access --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index dca81c0..6086a36 100644 --- a/setup.py +++ b/setup.py @@ -169,7 +169,7 @@ 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.env["CC"], "-DCMAKE_CXX_COMPILER=" + os.env["CXX"], + '-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', From b509f7146477f0538b8967ecf4dd02aa49bfca87 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 20 Sep 2020 13:42:05 +0300 Subject: [PATCH 20/38] Use another script command --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 6086a36..2e8081e 100644 --- a/setup.py +++ b/setup.py @@ -156,7 +156,7 @@ 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" + ff.write(f"#!/usr/bin/env sh -c '${PYTHON}'\n" "from Cython.Compiler.Main import setuptools_main\n" "setuptools_main()") os.chmod(cython_code, stat.S_IXUSR|stat.S_IWUSR|stat.S_IRUSR|stat.S_IRGRP) From f09b35c4905c67a54493486dc950e80496d95002 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 20 Sep 2020 15:11:05 +0300 Subject: [PATCH 21/38] Remove inline formatting --- setup.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index 2e8081e..ab343ad 100644 --- a/setup.py +++ b/setup.py @@ -156,9 +156,9 @@ 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"#!/usr/bin/env sh -c '${PYTHON}'\n" - "from Cython.Compiler.Main import setuptools_main\n" - "setuptools_main()") + ff.write("#!/usr/bin/env sh -c '${PYTHON}'\n" + "from Cython.Compiler.Main import setuptools_main\n" + "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 From 83778c3b1f88a66f389e5165f15147483e688c91 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 20 Sep 2020 15:32:53 +0300 Subject: [PATCH 22/38] Fix shebang --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index ab343ad..1123641 100644 --- a/setup.py +++ b/setup.py @@ -156,7 +156,7 @@ class BuildCMakeExt(build_ext): cython_code = os.path.join(str(build_dir.absolute()),'mycython') with open(cython_code, mode="wt") as ff: - ff.write("#!/usr/bin/env sh -c '${PYTHON}'\n" + ff.write("#!/usr/bin/env -S sh -c '${PYTHON}'\n" "from Cython.Compiler.Main import setuptools_main\n" "setuptools_main()") os.chmod(cython_code, stat.S_IXUSR|stat.S_IWUSR|stat.S_IRUSR|stat.S_IRGRP) From 3920970326315638ef1fedcf4398f1f3658076d5 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 20 Sep 2020 16:38:18 +0300 Subject: [PATCH 23/38] Use shell script instead --- setup.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index 1123641..7c04629 100644 --- a/setup.py +++ b/setup.py @@ -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("#!/usr/bin/env -S sh -c '${PYTHON}'\n" - "from Cython.Compiler.Main import setuptools_main\n" - "setuptools_main()") + ff.write("#!/bin/sh\n" + "${PYTHON} -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 From 7fce73ef6c366420edc378d1896389e669c2eadf Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 20 Sep 2020 16:56:25 +0300 Subject: [PATCH 24/38] Fix typo --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 7c04629..6c83310 100644 --- a/setup.py +++ b/setup.py @@ -157,7 +157,7 @@ class BuildCMakeExt(build_ext): cython_code = os.path.join(str(build_dir.absolute()),'mycython') with open(cython_code, mode="wt") as ff: ff.write("#!/bin/sh\n" - "${PYTHON} -c 'from Cython.Compiler.Main import setuptools_main; setuptools_main()' #@") + "${PYTHON} -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 From 8658acfde6064c5d27b6e6850ec801f1c7fe1dca Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Tue, 22 Sep 2020 15:27:12 +0300 Subject: [PATCH 25/38] Use Boost::boost which has better cmake compatiblity --- external/external_build.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index ebb122f..bd4b18b 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -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) From 441691c0d84fa1d6ff21a95a13e69d8b824ea82c Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Wed, 23 Sep 2020 11:26:48 +0300 Subject: [PATCH 26/38] Bump version in setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 6c83310..6ed753e 100644 --- a/setup.py +++ b/setup.py @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a7', + version='1.0.0a8', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], From 06b9b2291e2c200c9767306aed13c2b51cd0f4f5 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Mon, 28 Sep 2020 13:30:48 +0200 Subject: [PATCH 27/38] Add first conda packaging instructions --- conda/build.sh | 1 + conda/conda_build_config.yaml | 7 +++++++ conda/meta.yaml | 38 +++++++++++++++++++++++++++++++++++ 3 files changed, 46 insertions(+) create mode 100644 conda/build.sh create mode 100644 conda/conda_build_config.yaml create mode 100644 conda/meta.yaml diff --git a/conda/build.sh b/conda/build.sh new file mode 100644 index 0000000..5a5aeeb --- /dev/null +++ b/conda/build.sh @@ -0,0 +1 @@ +$PYTHON setup.py install diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml new file mode 100644 index 0000000..b120466 --- /dev/null +++ b/conda/conda_build_config.yaml @@ -0,0 +1,7 @@ +python: + - 3.7 + - 3.8 + +numpy: + - 1.11 + - 1.19 diff --git a/conda/meta.yaml b/conda/meta.yaml new file mode 100644 index 0000000..8cc271b --- /dev/null +++ b/conda/meta.yaml @@ -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 From 47f2e247e9c158be66e4791306ab4d9373fc1173 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Tue, 29 Sep 2020 15:56:52 +0200 Subject: [PATCH 28/38] Harden build procedure --- CMakeLists.txt | 2 +- external/external_build.cmake | 18 ++++++++++++------ 2 files changed, 13 insertions(+), 7 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 2690baf..565a80e 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -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) diff --git a/external/external_build.cmake b/external/external_build.cmake index bd4b18b..5459427 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -2,8 +2,8 @@ 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 URL "URL to download FFTW from") -SET(EIGEN_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" CACHE URL "URL to download Eigen from") +SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE STRING "URL to download FFTW 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") @@ -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) - find_library(GSL_LIBRARY gsl) - find_library(GSLCBLAS_LIBRARY gslcblas) + 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) From 0ff1b04b3d8c3f9912e9c03c2ea99eaf97885cef Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 3 Oct 2020 20:17:07 +0200 Subject: [PATCH 29/38] Add some special math function --- sample/CMakeLists.txt | 3 + sample/test_special.cpp | 12 +++ src/special_math.hpp | 231 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 246 insertions(+) create mode 100644 sample/test_special.cpp create mode 100644 src/special_math.hpp diff --git a/sample/CMakeLists.txt b/sample/CMakeLists.txt index 561751c..03709a7 100644 --- a/sample/CMakeLists.txt +++ b/sample/CMakeLists.txt @@ -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) diff --git a/sample/test_special.cpp b/sample/test_special.cpp new file mode 100644 index 0000000..ae463d6 --- /dev/null +++ b/sample/test_special.cpp @@ -0,0 +1,12 @@ +#include +#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; +} + diff --git a/src/special_math.hpp b/src/special_math.hpp new file mode 100644 index 0000000..ccff170 --- /dev/null +++ b/src/special_math.hpp @@ -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 +#include +#include +#include +#include + +// 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 T log1p_exp(T x) { + if (x > T(0)) { + return x + std::log1p(std::exp(-x)); + } + return std::log1p(std::exp(x)); +} + +template T multiply_log(T a, T b) { + if (a == 0 && b == 0) + return 0; + return a * std::log(b); +} + +template T inf() { return std::numeric_limits::infinity(); } + +template T log_sum_exp(T const a, T const b) { + if (a == -inf()) { + return b; + } + if (a == inf() && b == inf()) { + return inf(); + } + 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 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::epsilon(); + static const double TWO_PI = 2.0 * boost::math::constants::pi(); + + if (z == 0) { + if (v == 0) { + return 0.0; + } + if (v > 0) { + return -std::numeric_limits::infinity(); + } + return std::numeric_limits::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 \ No newline at end of file From e179544422a8f8adf52248c1a357621dffd32ad8 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 3 Oct 2020 20:51:39 +0200 Subject: [PATCH 30/38] Import cosmomath in __init__ --- python/CMakeLists.txt | 10 ++++++++-- python/cosmotool/__init__.py | 1 + 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt index 90d3e6e..e2ea884 100644 --- a/python/CMakeLists.txt +++ b/python/CMakeLists.txt @@ -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})") diff --git a/python/cosmotool/__init__.py b/python/cosmotool/__init__.py index c5b1c79..fd1eb0e 100644 --- a/python/cosmotool/__init__.py +++ b/python/cosmotool/__init__.py @@ -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 From 1ea268f654b999aa5c12d2c148df0847ac1fb22a Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sat, 3 Oct 2020 20:52:43 +0200 Subject: [PATCH 31/38] Bump version and add missing file --- python/_cosmomath.pyx | 38 ++++++++++++++++++++++++++++++++++++++ setup.py | 2 +- 2 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 python/_cosmomath.pyx diff --git a/python/_cosmomath.pyx b/python/_cosmomath.pyx new file mode 100644 index 0000000..4b2b21f --- /dev/null +++ b/python/_cosmomath.pyx @@ -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] = 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 + ) + diff --git a/setup.py b/setup.py index 6ed753e..6437ecf 100644 --- a/setup.py +++ b/setup.py @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a8', + version='1.1.0', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], From 7f5c04be930827c86f8ad4468070412905b5a69b Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 4 Oct 2020 08:29:48 +0200 Subject: [PATCH 32/38] Fixup for building --- src/special_math.hpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/special_math.hpp b/src/special_math.hpp index ccff170..19e1414 100644 --- a/src/special_math.hpp +++ b/src/special_math.hpp @@ -9,7 +9,7 @@ #ifndef __COSMOTOOL_SPECIAL_MATH_HPP #define __COSMOTOOL_SPECIAL_MATH_HPP -#include +#include "algo.hpp" #include #include #include @@ -228,4 +228,4 @@ template T log_modified_bessel_first_kind(T const v, T const z) { } // namespace CosmoTool -#endif \ No newline at end of file +#endif From 179c905c36a38127bcf9391d94a09a8ad31d5db1 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 4 Oct 2020 09:46:38 +0200 Subject: [PATCH 33/38] Fix wheel building --- builder/build-wheels.sh | 5 +++++ setup.py | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/builder/build-wheels.sh b/builder/build-wheels.sh index e5c1b6f..1e310aa 100755 --- a/builder/build-wheels.sh +++ b/builder/build-wheels.sh @@ -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 diff --git a/setup.py b/setup.py index 6437ecf..08d94d9 100644 --- a/setup.py +++ b/setup.py @@ -157,7 +157,7 @@ class BuildCMakeExt(build_ext): cython_code = os.path.join(str(build_dir.absolute()),'mycython') with open(cython_code, mode="wt") as ff: ff.write("#!/bin/sh\n" - "${PYTHON} -c 'from Cython.Compiler.Main import setuptools_main; setuptools_main()' $@") + 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 From 9f7fc424ec3915708cfc85ecc249a7779242ba71 Mon Sep 17 00:00:00 2001 From: nataliaporqueres Date: Wed, 21 Oct 2020 16:40:11 +0100 Subject: [PATCH 34/38] Add plan for c2c 2d transform --- src/fourier/fft/fftw_calls.hpp | 3 +++ src/fourier/fft/fftw_calls_mpi.hpp | 3 +++ 2 files changed, 6 insertions(+) diff --git a/src/fourier/fft/fftw_calls.hpp b/src/fourier/fft/fftw_calls.hpp index 16426cf..a5ef225 100644 --- a/src/fourier/fft/fftw_calls.hpp +++ b/src/fourier/fft/fftw_calls.hpp @@ -114,6 +114,9 @@ public: \ static plan_type plan_dft_3d(int Nx, int Ny, int Nz, complex_type *in, complex_type *out, int sign, unsigned flags) { \ return prefix ## _plan_dft_3d(Nx, Ny, Nz, in, out, sign, flags); \ } \ + static plan_type plan_dft_2d(int Nx, int Ny, complex_type *in, complex_type *out, int sign, unsigned flags) { \ + return prefix ## _plan_dft_2d(Nx, Ny, in, out, sign, flags); \ + } \ static void destroy_plan(plan_type plan) { prefix ## _destroy_plan(plan); } \ } diff --git a/src/fourier/fft/fftw_calls_mpi.hpp b/src/fourier/fft/fftw_calls_mpi.hpp index 0a7a508..b592220 100644 --- a/src/fourier/fft/fftw_calls_mpi.hpp +++ b/src/fourier/fft/fftw_calls_mpi.hpp @@ -97,6 +97,9 @@ public: \ static plan_type plan_dft_3d(int Nx, int Ny, int Nz, complex_type *in, complex_type *out, MPI_Comm comm, int sign, unsigned flags) { \ return prefix ## _mpi_plan_dft_3d(Nx, Ny, Nz, in, out, comm, sign, flags); \ } \ + static plan_type plan_dft_2d(int Nx, int Ny, complex_type *in, complex_type *out, MPI_Comm comm, int sign, unsigned flags) { \ + return prefix ## _mpi_plan_dft_2d(Nx, Ny, in, out, comm, sign, flags); \ + } \ static void destroy_plan(plan_type plan) { prefix ## _destroy_plan(plan); } \ } From 84a1d3bf4792717ed985c2290c7a9e37e8b860a4 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Mon, 26 Oct 2020 08:49:12 +0100 Subject: [PATCH 35/38] Add omp parallelization for bessel function --- .gitignore | 5 +++++ CMakeLists.txt | 4 ++-- python/_cosmomath.pyx | 9 ++++++++- setup.py | 2 +- 4 files changed, 16 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index 9e4c862..a33a7a3 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,9 @@ *~ +.eggs/ +dist/ +wheelhouse/ +cosmotool.egg-info/ +build/ *.o *.prog *.pyc diff --git a/CMakeLists.txt b/CMakeLists.txt index 565a80e..ca6f9ca 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -70,8 +70,8 @@ SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A toolbox for impatient cosmologists") SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux") SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2") SET(CPACK_PACKAGE_VERSION_MAJOR "1") -SET(CPACK_PACKAGE_VERSION_MINOR "0") -SET(CPACK_PACKAGE_VERSION_PATCH "0${EXTRA_VERSION}") +SET(CPACK_PACKAGE_VERSION_MINOR "1") +SET(CPACK_PACKAGE_VERSION_PATCH "1${EXTRA_VERSION}") SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}") SET(CPACK_STRIP_FILES "lib/libCosmoTool.so") SET(CPACK_SOURCE_IGNORE_FILES diff --git a/python/_cosmomath.pyx b/python/_cosmomath.pyx index 4b2b21f..0aa5fd4 100644 --- a/python/_cosmomath.pyx +++ b/python/_cosmomath.pyx @@ -1,3 +1,4 @@ +#cython: language_level=3 import numpy as np cimport numpy as np @@ -7,15 +8,21 @@ np.import_ufunc() cdef extern from "sys/types.h": ctypedef np.int64_t int64_t +cdef extern from "numpy/npy_common.h": + ctypedef npy_intp + cdef extern from "special_math.hpp" namespace "CosmoTool": T log_modified_bessel_first_kind[T](T v, T z) nogil except + +cdef extern from "numpy_adaptor.hpp" namespace "CosmoTool": + void parallel_ufunc_dd_d[T,IT](char **args, IT* dimensions, IT* steps, void *func) + cdef np.PyUFuncGenericFunction loop_func[1] cdef char input_output_types[3] cdef void *elementwise_funcs[1] -loop_func[0] = np.PyUFunc_dd_d +loop_func[0] = parallel_ufunc_dd_d[double,npy_intp] input_output_types[0] = np.NPY_DOUBLE input_output_types[1] = np.NPY_DOUBLE diff --git a/setup.py b/setup.py index 08d94d9..04e9df0 100644 --- a/setup.py +++ b/setup.py @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.1.0', + version='1.1.1', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], From 3f7da964ee025f6c4838d190997442cf30a1a797 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Mon, 26 Oct 2020 11:40:44 +0100 Subject: [PATCH 36/38] Add adaptor --- src/numpy_adaptors.hpp | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 src/numpy_adaptors.hpp diff --git a/src/numpy_adaptors.hpp b/src/numpy_adaptors.hpp new file mode 100644 index 0000000..fe3962c --- /dev/null +++ b/src/numpy_adaptors.hpp @@ -0,0 +1,30 @@ +#ifndef __COSMOTOOL_NUMPY_ADAPTOR_HPP +#define __COSMOTOOL_NUMPY_ADAPTOR_HPP + +namespace CosmoTool { + + template + void parallel_ufunc_dd_d(char **args, IT* dimensions, IT* steps, void *func) { + IT i; + IT n = dimensions[0]; + char *in = args[0], *in2 = args[1], *out = args[2]; + IT in_step = steps[0], in2_step = args[1], out_step = steps[2]; + + double tmp; + typedef double (*F_t)(double,double); + + F_t f = (F_t)func; + +#pragma omp parallel for schedule(static) + for (i = 0; i < n; i++) { + T *out_t = (T *)(out + i * out_step); + T *in_t = (T *)(in + i * in_step); + T *in2_t = (T *)(in2 + i * in2_step); + *out_t = f(*in_t, *in2_t); + } + } + + +} + +#endif From 5e6d69f017c331a0982df2de2448e3babebad201 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Mon, 26 Oct 2020 12:00:50 +0100 Subject: [PATCH 37/38] Fixed missing files --- python/_cosmomath.pyx | 2 +- src/numpy_adaptors.hpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/python/_cosmomath.pyx b/python/_cosmomath.pyx index 0aa5fd4..e5ab880 100644 --- a/python/_cosmomath.pyx +++ b/python/_cosmomath.pyx @@ -14,7 +14,7 @@ cdef extern from "numpy/npy_common.h": cdef extern from "special_math.hpp" namespace "CosmoTool": T log_modified_bessel_first_kind[T](T v, T z) nogil except + -cdef extern from "numpy_adaptor.hpp" namespace "CosmoTool": +cdef extern from "numpy_adaptors.hpp" namespace "CosmoTool": void parallel_ufunc_dd_d[T,IT](char **args, IT* dimensions, IT* steps, void *func) diff --git a/src/numpy_adaptors.hpp b/src/numpy_adaptors.hpp index fe3962c..196206b 100644 --- a/src/numpy_adaptors.hpp +++ b/src/numpy_adaptors.hpp @@ -8,7 +8,7 @@ namespace CosmoTool { IT i; IT n = dimensions[0]; char *in = args[0], *in2 = args[1], *out = args[2]; - IT in_step = steps[0], in2_step = args[1], out_step = steps[2]; + IT in_step = steps[0], in2_step = steps[1], out_step = steps[2]; double tmp; typedef double (*F_t)(double,double); From 75de5fb4d90826fe4b6b739366791f6e88b74b2f Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Mon, 26 Oct 2020 13:58:07 +0100 Subject: [PATCH 38/38] Add Py3.9 --- builder/build-wheels.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/builder/build-wheels.sh b/builder/build-wheels.sh index 1e310aa..90f87a9 100755 --- a/builder/build-wheels.sh +++ b/builder/build-wheels.sh @@ -13,7 +13,7 @@ yum install -y cmake3 gsl-devel zlib-devel ln -fs /usr/bin/cmake3 /usr/bin/cmake -ALL_PYTHON="cp36-cp36m cp37-cp37m cp38-cp38" +ALL_PYTHON="cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39" # Compile wheels for pkg in $ALL_PYTHON; do