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Merge branch 'master' of https://bitbucket.org/glavaux/cosmotool

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Guilhem Lavaux 2020-09-18 11:06:54 +03:00
commit 00a9a2ab64
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2
CMakeLists.txt
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@ -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)

508
LICENCE.txt Normal file
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@ -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
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In consideration of access to the source code and the rights to copy,
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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. Users are therefore encouraged to load and test the
suitability of the software as regards their requirements in conditions
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This Agreement may apply to any or all software for which the holder of
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Article 1 - DEFINITIONS
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intellectual property rights over this Contribution as defined by
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govern its distribution.
6.4 JOINT PROVISIONS
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notices attached to the Software;
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of the Software modified or not.
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measures required to ensure respect of said intellectual property rights
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Article 7 - RELATED SERVICES
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provide technical assistance or maintenance services for the Software.
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terms and conditions of such technical assistance, and/or such
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shall incur liability therefor.
7.2 Similarly, any Licensor is entitled to offer to its licensees, under
its sole responsibility, a warranty, that shall only be binding upon
itself, for the redistribution of the Software and/or the Modified
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warranty, and the financial terms and conditions of its application,
shall be subject of a separate instrument executed between the Licensor
and the Licensee.
Article 8 - LIABILITY
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entitled to claim compensation for any direct loss it may have suffered
from the Software as a result of a fault on the part of the relevant
Licensor, subject to providing evidence thereof.
8.2 The Licensor's liability is limited to the commitments made under
this Agreement and shall not be incurred as a result of in particular:
(i) loss due the Licensee's total or partial failure to fulfill its
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agree that any or all pecuniary or business loss (i.e. loss of data,
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opportunity cost, any disturbance to business activities) or any or all
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any or all compensation from the Licensor.
Article 9 - WARRANTY
9.1 The Licensee acknowledges that the scientific and technical
state-of-the-art when the Software was distributed did not enable all
possible uses to be tested and verified, nor for the presence of
possible defects to be detected. In this respect, the Licensee's
attention has been drawn to the risks associated with loading, using,
modifying and/or developing and reproducing the Software which are
reserved for experienced users.
The Licensee shall be responsible for verifying, by any or all means,
the suitability of the product for its requirements, its good working
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or properties.
9.2 The Licensor hereby represents, in good faith, that it is entitled
to grant all the rights over the Software (including in particular the
rights set forth in Article 5).
9.3 The Licensee acknowledges that the Software is supplied "as is" by
the Licensor without any other express or tacit warranty, other than
that provided for in Article 9.2 and, in particular, without any warranty
as to its commercial value, its secured, safe, innovative or relevant
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Specifically, the Licensor does not warrant that the Software is free
from any error, that it will operate without interruption, that it will
be compatible with the Licensee's own equipment and software
configuration, nor that it will meet the Licensee's requirements.
9.4 The Licensor does not either expressly or tacitly warrant that the
Software does not infringe any third party intellectual property right
relating to a patent, software or any other property right. 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
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decided on a case-by-case basis between the relevant Licensor and the
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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
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hereunder, the Licensor may automatically terminate this Agreement
thirty (30) days after notice has been sent to the Licensee and has
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10.2 A Licensee whose Agreement is terminated shall no longer be
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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
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fire, explosions, strikes and labor unrest, war, etc.
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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.

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MANIFEST.in Normal file
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@ -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

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builder/build-wheels.sh Executable file
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#!/bin/bash
set -e -x
# Install a system package required by our library
#yum install -y atlas-devel
yum install -y cmake3 gsl-devel zlib-devel
ln -fs /usr/bin/cmake3 /usr/bin/cmake
ALL_PYTHON="cp36-cp36m 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" install -r /io/requirements.txt
"${PYBIN}/pip" wheel -vvv /io/ -w wheelhouse/
done
# Bundle external shared libraries into the wheels
for whl in wheelhouse/*.whl; do
auditwheel repair "$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

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builder/start.sh Executable file
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#!/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=manylinux2010_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2010_x86_64 /io/builder/build-wheels.sh

36
external/external_build.cmake vendored
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@ -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 ${SHARP_LIBRARIES}
)
endif (ENABLE_SHARP)
@ -246,10 +246,23 @@ if (INTERNAL_BOOST)
set(Boost_DEP boost)
ELSE (INTERNAL_BOOST)
find_package(Boost 1.53 QUIET)
set(Boost_DEP)
find_package(Boost 1.69 QUIET)
if (Boost_VERSION)
if (${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 >= 1.53 was not 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)
@ -375,6 +388,7 @@ 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/)

8
python/CMakeLists.txt
View File

@ -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 )

4
python/_cosmo_bispectrum.cpp
View File

@ -171,6 +171,7 @@ void CosmoTool_compute_bispectrum(
size_t *Ntriangles,
double* B, double delta_k, size_t Nk )
{
#if 0
// First remap to multi_array for easy access
size_t kNz = Nz/2+1;
#ifdef _OPENMP
@ -246,6 +247,7 @@ void CosmoTool_compute_bispectrum(
#else
#warning Serial version not implemented
#endif
#endif
}
@ -255,6 +257,7 @@ void CosmoTool_compute_powerspectrum(
size_t *Ncounts,
double* P, double delta_k, size_t Nk )
{
#if 0
// First remap to multi_array for easy access
size_t kNz = Nz/2+1;
boost::multi_array_ref<std::complex<double>, 3> a_delta(reinterpret_cast<std::complex<double>*>(delta_hat), boost::extents[Nx][Ny][kNz]);
@ -275,4 +278,5 @@ void CosmoTool_compute_powerspectrum(
a_Nc[q1] ++;
a_P[q1] += std::norm(v1);
}
#endif
}

12
python/_cosmo_power.pyx
View File

@ -65,18 +65,30 @@ cdef class CosmologyPower:
cdef CosmoPower power
def __init__(self,**cosmo):
"""Constructor
Keyword arguments:
* omega_B_0
* omega_M_0
* h
* ns
* T27
"""
self.power = CosmoPower()
self.power.OMEGA_B = cosmo['omega_B_0']
self.power.OMEGA_C = cosmo['omega_M_0']-cosmo['omega_B_0']
self.power.h = cosmo['h']
if 'ns' in cosmo:
self.power.n = cosmo['ns']
if 'T27' in cosmo:
self.power.Theta_27 = cosmo['T27']
assert self.power.OMEGA_C > 0
self.power.updateCosmology()
def setNormalization(self,A):
"""Set manual normalization for A_S"""
self.power.setNormalization(A)
def normalize(self,s8,k_min=-1,k_max=-1):

3
python/_cosmotool.pyx
View File

@ -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)

10
python/_project.pyx
View File

@ -509,19 +509,17 @@ cdef void INTERNAL_project_cic_with_mass_periodic(DTYPE_t[:,:,:] g,
cdef int b1[3]
for i in range(x.shape[0]):
for j in range(3):
a[j] = (x[i,j]+shifter)*delta_Box
b[j] = int(floor(a[j]))
b1[j] = b[j]+1
while b1[j] < 0:
b1[j] += Ngrid
while b1[j] >= Ngrid:
b1[j] -= Ngrid
b1[j] = (b[j]+1) % Ngrid
a[j] -= b[j]
c[j] = 1-a[j]
b[j] %= Ngrid
m0 = mass[i]
g[b[0],b[1],b[2]] += c[0]*c[1]*c[2]*m0
g[b1[0],b[1],b[2]] += a[0]*c[1]*c[2]*m0

7
python/cosmotool/ctpv.py
View File

@ -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
@ -117,6 +117,11 @@ class ProgrammableDensityLoad(object):
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):
import vtk

4
python/cosmotool/simu.py
View File

@ -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)

1
python/dummy.c Normal file
View File

@ -0,0 +1 @@
static void dummyFunc() {}

5
requirements.txt Normal file
View File

@ -0,0 +1,5 @@
numpy
cffi
numexpr
pyfftw
cython

2
sample/simple3DFilter.cpp
View File

@ -146,7 +146,7 @@ int main(int argc, char **argv)
if (rx < 0 || rx >= Nres || ry < 0 || ry >= Nres || rz < 0 || rz >= Nres)
continue;
#pragma omp atomic update
//#pragma omp atomic update
bins[rx][ry][rz]++;
}
v1_data.resize(boost::extents[1][1]);

10
setup.py
View File

@ -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)
@ -218,10 +218,11 @@ class BuildCMakeExt(build_ext):
CosmoTool_extension = CMakeExtension(name="cosmotool")
setup(name='cosmotool',
version='1.0.0a0',
version='1.0.0a6',
packages=["cosmotool"],
package_dir={'cosmotool': 'python/cosmotool'},
setup_requires=['cython'],
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(),
@ -241,5 +242,6 @@ setup(name='cosmotool',
'build_ext': BuildCMakeExt,
'install_data': InstallCMakeLibsData,
'install_lib': InstallCMakeLibs,
}
},
python_requires='>=3.6'
)

8
src/CMakeLists.txt
View File

@ -72,14 +72,14 @@ 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})
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)
@ -92,11 +92,13 @@ if (BUILD_SHARED_LIBS)
add_library(CosmoTool_static STATIC ${CosmoTool_SRCS} $<TARGET_OBJECTS:CosmoHDF5>)
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_OBJECTS:CosmoHDF5>)
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)
IF(NOT COSMOTOOL_PYTHON_PACKAGING)

2
src/algo.hpp
View File

@ -93,6 +93,6 @@ namespace CosmoTool
};
}
#endif

2
src/config.hpp
View File

@ -165,6 +165,6 @@ namespace CosmoTool
FilesystemFullException()
: Exception() {}
};
};
}
#endif

35
src/hdf5_array.hpp
View File

@ -78,8 +78,6 @@ namespace CosmoTool {
}
};
//, typename boost::enable_if<boost::is_same<T, tl> >::type> \
//
#define HDF5_TYPE(tl, thdf5) \
template<typename T> struct get_hdf5_data_type<T, typename boost::enable_if<boost::is_same<T,tl> >::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;
}
@ -263,6 +261,35 @@ namespace CosmoTool {
}
};
struct CosmoString {
char const * s;
operator char const *() { return s; }
char const *operator=(char const *s0) {
s = s0;
return s0;
}
};
class hdf5_CosmoStringType {
public:
H5::StrType type;
hdf5_CosmoStringType() : type(H5::PredType::C_S1, H5T_VARIABLE) {
}
static const hdf5_CosmoStringType *ctype()
{
static hdf5_CosmoStringType singleton;
return &singleton;
}
};
template<> struct get_hdf5_data_type<CosmoString> {
static H5::DataType type() {
return hdf5_CosmoStringType::ctype()->type;
}
};
template<typename ArrayType>
void hdf5_write_array(H5_CommonFileGroup& fg, const std::string& data_set_name, const ArrayType& data )
{
@ -484,7 +511,7 @@ namespace CosmoTool { \
}; \
};
};
}
#endif

2
src/loadRamses.cpp
View File

@ -34,7 +34,7 @@ knowledge of the CeCILL license and that you accept its terms.
+*/
#include <sys/types.h>
#include "/usr/include/regex.h"
#include <regex.h>
#include <cmath>
#include <cstring>
#include <cstdlib>

4
src/mykdtree.tcc
View File

@ -277,7 +277,7 @@ namespace CosmoTool {
coords tmpBound;
NodeIntType nodeId;
#pragma omp atomic capture
//#pragma omp atomic capture
nodeId = (this->lastNode)++;
node = &nodes[nodeId];
@ -293,7 +293,7 @@ namespace CosmoTool {
tmpBound[axis] = node->value->coord[axis];
depth++;
#pragma omp task private(tmpBound)
//#pragma omp task private(tmpBound)
{
node->children[0] = buildTree(cell0, mid, depth, minBound, tmpBound);
}