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

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This commit is contained in:
Guilhem Lavaux 2018-01-23 10:13:09 +01:00
commit 4f250969ac
12 changed files with 205 additions and 42 deletions
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34
external/external_build.cmake vendored
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@ -5,8 +5,8 @@ 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(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.gz" CACHE STRING "URL to download HDF5 from")
SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.4.1.1.tar.gz" CACHE STRING "URL to download NetCDF 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")
SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.0.tar.gz" CACHE STRING "URL to download NetCDF-C++ from")
SET(BOOST_URL "http://sourceforge.net/projects/boost/files/boost/1.61.0/boost_1_61_0.tar.gz/download" CACHE STRING "URL to download Boost from")
SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ")
@ -52,11 +52,14 @@ SET(CONFIGURE_LDFLAGS "")
if (ENABLE_SHARP)
SET(DEP_BUILD ${BUILD_PREFIX}/sharp-prefix/src/sharp/auto)
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}
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"
)
@ -78,6 +81,7 @@ if (INTERNAL_HDF5)
ExternalProject_Add(hdf5
PREFIX ${BUILD_PREFIX}/hdf5-prefix
URL ${HDF5_URL}
URL_HASH MD5=29117bf488887f89888f9304c8ebea0b
CMAKE_ARGS
-DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
@ -93,9 +97,11 @@ if (INTERNAL_HDF5)
SET(HDF5_ROOTDIR ${HDF5_BIN_DIR})
SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib")
SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl")
set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE)
set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl.a CACHE STRING "HDF5 HL lib" FORCE)
set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp.a CACHE STRING "HDF5 C++ lib" FORCE)
set(HDF5_C_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5-static.a)
set(HDF5_HL_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl-static.a)
set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5-static.a CACHE STRING "HDF5 lib" FORCE)
set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl-static.a CACHE STRING "HDF5 HL lib" FORCE)
set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp-static.a CACHE STRING "HDF5 C++ lib" FORCE)
SET(HDF5_INCLUDE_DIRS ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE)
mark_as_advanced(HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIRS)
@ -114,6 +120,7 @@ else (INTERNAL_HDF5)
cmessage(STATUS "HDF5 lib: ${HDF5_LIBRARIES}")
cmessage(STATUS "HDF5 includes: ${HDF5_INCLUDE_DIRS}")
cmessage(STATUS "HDF5 C lib: ${HDF5_C_LIBRARY}")
cmessage(STATUS "HDF5 HL lib: ${HDF5_HL_LIBRARY}")
cmessage(STATUS "HDF5 BIN: ${HDF5_BIN_DIR}")
foreach(hdf5lib IN LISTS HDF5_LIBRARIES)
if (${hdf5lib} MATCHES "(hdf5)|(HDF5)")
@ -165,8 +172,13 @@ if (INTERNAL_NETCDF)
-DBUILD_TESTING=OFF
-DCMAKE_BUILD_TYPE=Release
-DENABLE_NETCDF4=ON
-DENABLE_DAP=OFF
-DCMAKE_POSITION_INDEPENDENT_CODE=ON
-DENABLE_DAP=OFF
-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
-DHDF5_C_LIBRARY=${HDF5_C_STATIC_LIBRARY}
-DHDF5_HL_LIBRARY=${HDF5_HL_STATIC_LIBRARY}
-DHDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIRS}
-DCMAKE_INSTALL_LIBDIR=lib
)
SET(NETCDFCXX_SOURCE_DIR ${BUILD_PREFIX}/netcdf-c++-prefix/src/netcdf-c++)
@ -178,13 +190,17 @@ if (INTERNAL_NETCDF)
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DBUILD_SHARED_LIBS=OFF
-DCMAKE_POSITION_INDEPENDENT_CODE=ON
-DBUILD_TESTING=OFF
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
-DCMAKE_INSTALL_LIBDIR=lib
)
# SET(CONFIGURE_CPP_LDFLAGS "${CONFIGURE_LDFLAGS}")
# SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_CPP_LDFLAGS})
SET(cosmotool_DEPS ${cosmotool_DEPS} netcdf netcdf-c++)
# find_library(NETCDF_LIBRARY netcdf NO_DEFAULT_PATH HINTS ${NETCDF_BIN_DIR}/lib ${NETCDF_BIN_DIR}/lib32 ${NETCDF_BIN_DIR}/lib64)
# find_library(NETCDFCPP_LIBRARY netcdf-cxx4 NO_DEFAULT_PATH HINTS ${NETCDF_BIN_DIR}/lib ${NETCDF_BIN_DIR}/lib32 ${NETCDF_BIN_DIR}/lib64)
SET(NETCDF_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf.a CACHE STRING "NetCDF lib" FORCE)
SET(NETCDFCPP_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf-cxx4.a CACHE STRING "NetCDF-C++ lib" FORCE)
SET(NETCDF_INCLUDE_PATH ${NETCDF_BIN_DIR}/include CACHE STRING "NetCDF include" FORCE)
@ -321,9 +337,11 @@ IF (INTERNAL_EIGEN)
SET(EIGEN3_INCLUDE_DIRS ${EXT_INSTALL}/include/eigen3)
ELSE (INTERNAL_EIGEN)
pkg_check_modules(EIGEN3 QUIET eigen3 )
pkg_check_modules(EIGEN3 eigen3 )
if (NOT EIGEN3_FOUND)
cmessage(CWARNING "Eigen library not found")
else()
cmessage(STATUS "Found EIGEN3 in ${EIGEN3_INCLUDE_DIRS}")
endif()
ENDIF(INTERNAL_EIGEN)

13
python/CMakeLists.txt
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@ -1,7 +1,8 @@
set(CMAKE_SHARED_MODULE_PREFIX)
include_directories(${NUMPY_INCLUDE_DIRS} ${PYTHON_INCLUDE_PATH} ${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src ${CMAKE_SOURCE_DIR}/python)
set(PYTHON_INCLUDES ${NUMPY_INCLUDE_DIRS} ${PYTHON_INCLUDE_PATH} ${CMAKE_SOURCE_DIR}/python)
include_directories(${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src)
IF(CYTHON)
add_custom_command(
@ -37,7 +38,11 @@ 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)
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 ${PYTHON_INCLUDES})
SET(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -Bsymbolic-functions")
@ -95,10 +100,12 @@ if (WIN32 AND NOT CYGWIN)
SET_TARGET_PROPERTIES(_cosmotool PROPERTIES SUFFIX ".pyd")
endif (WIN32 AND NOT CYGWIN)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cosmotool/config.py.in ${CMAKE_CURRENT_BINARY_DIR}/cosmotool/config.py @ONLY)
INSTALL(TARGETS
${ct_TARGETS}
LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool
)
INSTALL(DIRECTORY cosmotool DESTINATION ${PYTHON_SITE_PACKAGES}
INSTALL(DIRECTORY cosmotool ${CMAKE_CURRENT_BINARY_DIR}/cosmotool DESTINATION ${PYTHON_SITE_PACKAGES}
FILES_MATCHING PATTERN "*.py")

14
python/_cosmotool.pyx
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@ -452,7 +452,7 @@ def loadParallelGadget(object filename_list, int gadgetFormat = 1, bool loadPosi
filenames.resize(num_files)
data = alloc_simudata(num_files)
for i,l in enumerate(filename_list):
filenames[i] = l
filenames[i] = l.encode('utf-8')
with nogil:
for i in prange(num_files):
@ -515,7 +515,7 @@ def writeGadget(str filename, object simulation):
cxx_writeGadget(filename, &simdata)
def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = False, bool loadPosition = True, bool loadVelocity = False, bool loadId = False):
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)
Loads the indicated snapshot based on the cpu id, snapshot id and basepath. It is important to specify the correct precision in doublePrecision otherwise the loading will fail. There is no way of auto-detecting properly the precision of the snapshot file.
@ -528,7 +528,8 @@ def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision =
doublePrecision (bool): By default it is False, thus singlePrecision
loadPosition (bool): Whether to load positions
loadVelocity (bool): Whether to load velocities
loadId (bol): Whether to load identifiers
loadId (bool): Whether to load identifiers
loadMass (bool): Whether to load mass value
Returns:
An object derived from PySimulationBase_.
@ -544,13 +545,16 @@ def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision =
flags |= NEED_VELOCITY
if loadId:
flags |= NEED_GADGET_ID
if loadMass:
flags |= NEED_MASS
encpath = basepath.encode('utf-8')
try:
data = loadRamsesSimu(basepath, snapshot_id, cpu_id, doublePrecision, flags)
data = loadRamsesSimu(encpath, snapshot_id, cpu_id, doublePrecision, flags)
if data == <SimuData*>0:
return None
except RuntimeError as e:
raise RuntimeError(e.message + ' (check the float precision in snapshot)')
raise RuntimeError(str(e) + ' (check the float precision in snapshot)')
return PySimulationAdaptor(wrap_simudata(data, flags))

1
python/cosmotool/__init__.py
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@ -15,6 +15,7 @@ except:
from .simu import loadRamsesAll, simpleWriteGadget, SimulationBare
from .timing import time_block, timeit, timeit_quiet
from .bispectrum import bispectrum, powerspectrum
from .smooth import smooth_particle_density
try:
from .fftw import CubeFT

1
python/cosmotool/config.py.in Normal file
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@ -0,0 +1 @@
install_prefix="@CMAKE_INSTALL_PREFIX@"

18
python/cosmotool/grafic.py
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@ -15,16 +15,22 @@ def readGrafic(filename):
* the mean matter density :math:`\Omega_\mathrm{m}`
* the dark energy density :math:`\Omega_\Lambda`
* the hubble constant, relative to 100 km/s/Mpc
* xoffset
* yoffset
* zoffset
"""
with file(filename, mode="rb") as f:
with open(filename, mode="rb") as f:
p = struct.unpack("IIIIffffffffI", f.read(4*11 + 2*4))
checkPoint0, Nx, Ny, Nz, delta, _, _, _, scalefac, omega0, omegalambda0, h, checkPoint1 = p
checkPoint0, Nx, Ny, Nz, delta, xoff, yoff, zoff, scalefac, omega0, omegalambda0, h, checkPoint1 = p
if checkPoint0 != checkPoint1 or checkPoint0 != 4*11:
raise ValueError("Invalid unformatted access")
a = np.empty((Nx,Ny,Nz), dtype=np.float32)
BoxSize = delta * Nx * h
xoff *= h
yoff *= h
zoff *= h
checkPoint = 4*Ny*Nz
for i in range(Nx):
@ -38,11 +44,11 @@ def readGrafic(filename):
if checkPoint != 4*Ny*Nz:
raise ValueError("Invalid unformatted access")
return a, BoxSize, scalefac, omega0, omegalambda0, h
return a, BoxSize, scalefac, omega0, omegalambda0, h, xoff, yoff,zoff
def writeGrafic(filename, field, BoxSize, scalefac, **cosmo):
with file(filename, mode="wb") as f:
with open(filename, mode="wb") as f:
checkPoint = 4*11
Nx,Ny,Nz = field.shape
@ -65,7 +71,7 @@ def writeGrafic(filename, field, BoxSize, scalefac, **cosmo):
def writeWhitePhase(filename, field):
with file(filename, mode="wb") as f:
with open(filename, mode="wb") as f:
Nx,Ny,Nz = field.shape
checkPoint = 4*4
@ -80,7 +86,7 @@ def writeWhitePhase(filename, field):
def readWhitePhase(filename):
with file(filename, mode="rb") as f:
with open(filename, mode="rb") as f:
_, Nx, Ny, Nz, _, _ = struct.unpack("IIIIII", f.read(4*4+2*4))
a = np.empty((Nx,Ny,Nz), dtype=np.float32)

105
python/cosmotool/smooth.py Normal file
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@ -0,0 +1,105 @@
from .config import install_prefix
import subprocess
import os
from tempfile import TemporaryDirectory
import h5py as h5
import numpy as np
import weakref
def smooth_particle_density(
position,
velocities=None,
radius=1e6,
boxsize=None,
resolution=128,
center=None, tmpprefix=None ):
"""Use adaptive smoothing to produce density and momentum fields.
The algorithm is originally described in [1].
Parameters:
position : numpy array NxQ
the particle positions
if Q==3, only positions. Q==6 means full space phase
velocities : Optional numpy array Nx3.
It is only optional if the above Q is 6.
radius : float
Maximum radius to which we need to compute fields
boxsize : float
Size of the box for the generated fields
resolution : int
Resolution of the output boxes
center : list of 3 floats
Center of the new box. It depends on the convention
for particles. If those are between [0, L], then [0,0,0]
is correct. If those are [-L/2,L/2] then you should set
[L/2,L/2,L/2].
tmpprefix : string
prefix of the temporary directory that will be used.
It needs to have a lot of space available. By default
'/tmp/ will be typically used.
Returns
-------
dictionnary
The dict has two entries: 'rho' for the density, and 'p' for the momenta.
Once the dictionary is garbage collected all temporary files and directories
will be cleared automatically.
Raises
------
ValueError
if arguments are invalid
.. [1] S. Colombi, M. Chodorowski,
"Cosmic velocity-gravity in redshift space", MNRAS, 2007, 375, 1
"""
if len(position.shape) != 2:
raise ValueError("Invalid position array shape")
if velocities is None:
if position.shape[1] != 6:
raise ValueError("Position must be phase space if no velocities are given")
if boxsize is None:
raise ValueError("Need a boxsize")
cx,cy,cz=center
tmpdir = TemporaryDirectory(prefix=tmpprefix)
h5_file = os.path.join(tmpdir.name, 'particles.h5')
with h5.File(h5_file, mode="w") as f:
data = f.create_dataset('particles', shape=(position.shape[0],7), dtype=np.float32)
data[:,:3] = position[:,:3]
if velocities is not None:
data[:,3:6] = velocities[:,:3]
else:
data[:,3:6] = position[:,3:]
data[:,6] = 1
ret = \
subprocess.run([
os.path.join(install_prefix,'bin','simple3DFilter'),
h5_file,
str(radius),
str(boxsize),
str(resolution),
str(cx), str(cy), str(cz)
], cwd=tmpdir.name)
f0 = h5.File(os.path.join(tmpdir.name,'fields.h5'), mode="r")
def cleanup_f0():
f0.close()
tmpdir.cleanup()
class Dict(dict):
pass
t = Dict(rho=f0['density'], p=[f0['p0'], f0['p1'], f0['p2']])
t._tmpdir_=tmpdir
weakref.finalize(t, cleanup_f0)
return t

14
sample/CMakeLists.txt
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@ -68,7 +68,9 @@ if (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
include_directories(${SHARP_INCLUDE_PATH})
add_executable(test_healpix_calls test_healpix_calls.cpp)
target_link_libraries(test_healpix_calls ${tolink} ${SHARP_LIBRARIES})
set_target_properties(test_healpix_calls PROPERTIES COMPILE_FLAGS "${OpenMP_CXX_FLAGS}" LINK_FLAGS "${OpenMP_CXX_FLAGS}")
if (ENABLE_OPENMP)
set_target_properties(test_healpix_calls PROPERTIES COMPILE_FLAGS "${OpenMP_CXX_FLAGS}" LINK_FLAGS "${OpenMP_CXX_FLAGS}")
endif()
add_dependencies(test_healpix_calls sharp)
endif (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
@ -82,10 +84,16 @@ if (Boost_FOUND)
add_executable(testSmooth testSmooth.cpp)
target_link_libraries(testSmooth ${tolink})
add_executable(simple3DFilter simple3DFilter.cpp)
target_link_libraries(simple3DFilter ${tolink})
ENDIF (YORICK_SUPPORT)
if (HDF5_FOUND)
add_executable(simple3DFilter simple3DFilter.cpp)
target_link_libraries(simple3DFilter ${tolink})
install(TARGETS simple3DFilter
RUNTIME DESTINATION bin
LIBRARY DESTINATION lib
ARCHIVE DESTINATION lib)
add_executable(gadgetToArray gadgetToArray.cpp)
target_link_libraries(gadgetToArray ${tolink})

18
src/CMakeLists.txt
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@ -34,12 +34,13 @@ ENDIF(YORICK_SUPPORT)
if (HDF5_FOUND)
set(CosmoTool_SRCS ${CosmoTool_SRCS}
add_library(CosmoHDF5 OBJECT
h5_readFlash.cpp
loadFlash.cpp
)
target_include_directories(CosmoHDF5 BEFORE PRIVATE ${HDF5_INCLUDE_DIR})
else(HDF5_FOUND)
set(CosmoTool_SRCS ${CosmoTool_SRCS}
add_library(CosmoHdf5 OBJECT
loadFlash_dummy.cpp
)
endif (HDF5_FOUND)
@ -78,22 +79,23 @@ endif(YORICK_SUPPORT)
if (HDF5_FOUND)
set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES} ${ZLIB})
include_directories(${HDF5_INCLUDE_DIR})
message(STATUS "CosmoTool_LIBS: ${CosmoTool_LIBS}")
endif (HDF5_FOUND)
set(CosmoTool_LIBS ${CosmoTool_LIBS} PARENT_SCOPE)
if (BUILD_SHARED_LIBS)
add_library(CosmoTool SHARED ${CosmoTool_SRCS})
add_library(CosmoTool SHARED ${CosmoTool_SRCS} $<TARGET_OBJECTS:CosmoHDF5>)
target_link_libraries(CosmoTool ${CosmoTool_LIBS})
if (BUILD_STATIC_LIBS)
add_library(CosmoTool_static STATIC ${CosmoTool_SRCS})
set_target_properties(CosmoTool_static PROPERTIES COMPILE_FLAGS "${CMAKE_C_COMPILE_OPTIONS_PIC}")
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)
endif(BUILD_STATIC_LIBS)
else (BUILD_SHARED_LIBS)
add_library(CosmoTool STATIC ${CosmoTool_SRCS})
set_target_properties(CosmoTool PROPERTIES COMPILE_FLAGS "${CMAKE_C_COMPILE_OPTIONS_PIC}")
add_library(CosmoTool STATIC ${CosmoTool_SRCS} $<TARGET_OBJECTS:CosmoHDF5>)
target_link_libraries(CosmoTool)
set_property(TARGET CosmoTool PROPERTY POSITION_INDEPENDENT_CODE ON)
endif (BUILD_SHARED_LIBS)
install(TARGETS CosmoTool

2
src/fortran.cpp
View File

@ -51,6 +51,7 @@ UnformattedRead::UnformattedRead(const string& fname)
swapOrdering = false;
cSize = Check_32bits;
checkPointRef = checkPointAccum = 0;
recordBuffer = 0;
}
UnformattedRead::UnformattedRead(const char *fname)
@ -130,6 +131,7 @@ void UnformattedRead::beginCheckpoint(bool bufferRecord)
throw EndOfFileException();
if (bufferRecord) {
std::cout << "Use fast I/O mode" << std::endl;
recordBuffer = new uint8_t[checkPointRef];
f->read(reinterpret_cast<char *>(recordBuffer), checkPointRef);
}

19
src/hdf5_array.hpp
View File

@ -51,6 +51,11 @@ knowledge of the CeCILL license and that you accept its terms.
#include <H5Cpp.h>
namespace CosmoTool {
#if (H5_VERS_MAJOR == 1) && (H5_VERS_MINOR <= 8)
typedef H5::CommonFG H5_CommonFileGroup;
#else
typedef H5::Group H5_CommonFileGroup;
#endif
//!_______________________________________________________________________________________
//!
@ -129,7 +134,7 @@ namespace CosmoTool {
//!
//!_______________________________________________________________________________________
template<typename ArrayType, typename hdf5_data_type>
void hdf5_write_array(H5::CommonFG& fg, const std::string& data_set_name,
void hdf5_write_array(H5_CommonFileGroup& fg, const std::string& data_set_name,
const ArrayType& data,
const hdf5_data_type& datatype,
const std::vector<hsize_t>& dimensions,
@ -156,7 +161,7 @@ namespace CosmoTool {
template<typename ArrayType, typename hdf5_data_type>
void hdf5_write_array(H5::CommonFG& fg, const std::string& data_set_name,
void hdf5_write_array(H5_CommonFileGroup& fg, const std::string& data_set_name,
const ArrayType& data,
const hdf5_data_type& datatype,
bool doCreate = true,
@ -165,7 +170,7 @@ namespace CosmoTool {
std::vector<hsize_t> dimensions(data.shape(), data.shape() + data.num_dimensions());
hdf5_write_array(fg, data_set_name, data, datatype, dimensions, doCreate, useBases);
}
/* HDF5 complex type */
template<typename T>
class hdf5_ComplexType
@ -255,14 +260,14 @@ namespace CosmoTool {
};
template<typename ArrayType>
void hdf5_write_array(H5::CommonFG& fg, const std::string& data_set_name, const ArrayType& data )
void hdf5_write_array(H5_CommonFileGroup& fg, const std::string& data_set_name, const ArrayType& data )
{
typedef typename ArrayType::element T;
get_hdf5_data_type<T> hdf_data_type;
hdf5_write_array(fg, data_set_name, data, hdf_data_type.type());
}
// HDF5 array reader
//
// Author Guilhem Lavaux (May 2014)
@ -341,7 +346,7 @@ namespace CosmoTool {
// ----------------------------------------------------------------------
template<typename ArrayType, typename hdf5_data_type>
void hdf5_read_array_typed(H5::CommonFG& fg, const std::string& data_set_name,
void hdf5_read_array_typed(H5_CommonFileGroup& fg, const std::string& data_set_name,
ArrayType& data,
const hdf5_data_type& datatype, bool auto_resize = true, bool useBases = false)
{
@ -377,7 +382,7 @@ namespace CosmoTool {
}
template<typename ArrayType>
void hdf5_read_array(H5::CommonFG& fg, const std::string& data_set_name, ArrayType& data, bool auto_resize = true,
void hdf5_read_array(H5_CommonFileGroup& fg, const std::string& data_set_name, ArrayType& data, bool auto_resize = true,
bool useBases = false )
{
typedef typename ArrayType::element T;

8
src/loadRamses.cpp
View File

@ -417,6 +417,9 @@ CosmoTool::SimuData *CosmoTool::loadRamsesSimu(const char *basename, int outputI
data->Vel[1] = new float[nPar];
data->Vel[2] = new float[nPar];
}
if (flags & NEED_MASS) {
data->Mass = new float[nPar];
}
if (flags & NEED_GADGET_ID)
{
data->Id = new int64_t[nPar];
@ -455,9 +458,10 @@ CosmoTool::SimuData *CosmoTool::loadRamsesSimu(const char *basename, int outputI
float minMass = INFINITY;
infile.beginCheckpoint();
for (uint32_t i = nPar; i > 0; i--)
{
for (uint32_t i = 0; i < nPar; i++) {
float dummyF = dp ? infile.readReal64() : infile.readReal32();
if (flags & NEED_MASS)
data->Mass[i] = dummyF;
if (dummyF < minMass) minMass = dummyF;
}
infile.endCheckpoint();