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Fixed HDF5 hyperslab

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This commit is contained in:
Guilhem Lavaux 2015-04-08 21:01:27 +02:00
parent bf0be4fb61
commit 9b47369d0e
3 changed files with 12 additions and 10 deletions
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2
CMakeLists.txt
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@ -45,7 +45,7 @@ find_program(CYTHON cython)
if(HDF5_ROOTDIR) if(HDF5_ROOTDIR)
SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR}) SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})
endif(HDF5_ROOTDIR) endif(HDF5_ROOTDIR)
find_package(HDF5 COMPONENTS HL CXX) find_package(HDF5 COMPONENTS CXX HL)
set(NETCDF_FIND_REQUIRED TRUE) set(NETCDF_FIND_REQUIRED TRUE)

10
external/external_build.cmake vendored
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@ -66,8 +66,8 @@ if (INTERNAL_HDF5)
SET(hdf5_built hdf5) SET(hdf5_built hdf5)
set(HDF5_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE) set(HDF5_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE)
set(HDF5_CPP_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_cpp.a CACHE STRING "HDF5 C++ lib" FORCE) set(HDF5_CPP_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_cpp.a CACHE STRING "HDF5 C++ lib" FORCE)
set(HDF5HL_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl.a CACHE STRING "HDF5-HL lib" FORCE) set(HDF5_HL_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl.a CACHE STRING "HDF5-HL lib" FORCE)
set(HDF5HL_CPP_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl_cpp.a CACHE STRING "HDF5-HL C++ lib" FORCE) set(HDF5_HL_CPP_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl_cpp.a CACHE STRING "HDF5-HL C++ lib" FORCE)
SET(HDF5_INCLUDE_PATH ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE) SET(HDF5_INCLUDE_PATH ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE)
SET(ENV{HDF5_ROOT} ${HDF5_BIN_DIR}) SET(ENV{HDF5_ROOT} ${HDF5_BIN_DIR})
SET(HDF5_ROOTDIR ${HDF5_BIN_DIR}) SET(HDF5_ROOTDIR ${HDF5_BIN_DIR})
@ -76,11 +76,11 @@ else(INTERNAL_HDF5)
find_path(HDF5_INCLUDE_PATH hdf5.h) find_path(HDF5_INCLUDE_PATH hdf5.h)
find_library(HDF5_LIBRARY hdf5) find_library(HDF5_LIBRARY hdf5)
find_library(HDF5_CPP_LIBRARY hdf5_cpp) find_library(HDF5_CPP_LIBRARY hdf5_cpp)
find_library(HDF5HL_CPP_LIBRARY hdf5_hl_cpp) find_library(HDF5_HL_CPP_LIBRARY hdf5_hl_cpp)
find_library(HDF5HL_LIBRARY hdf5_hl) find_library(HDF5_HL_LIBRARY hdf5_hl)
endif (INTERNAL_HDF5) endif (INTERNAL_HDF5)
SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${HDF5_INCLUDE_PATH}") SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${HDF5_INCLUDE_PATH}")
mark_as_advanced(HDF5_INCLUDE_PATH HDF5_LIBRARY HDF5_CPP_LIBRARY HDF5HL_LIBRARY HDF5HL_CPP_LIBRARY) mark_as_advanced(HDF5_INCLUDE_PATH HDF5_LIBRARY HDF5_CPP_LIBRARY HDF5_HL_LIBRARY HDF5_HL_CPP_LIBRARY)
############### ###############
# Build NetCDF # Build NetCDF

10
src/hdf5_array.hpp
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@ -105,11 +105,13 @@ namespace CosmoTool {
bool doCreate = true, bool doCreate = true,
bool useBases = false) bool useBases = false)
{ {
H5::DataSpace dataspace(data.num_dimensions(), dimensions.data()); std::vector<hsize_t> memdims(data.shape(), data.shape() + data.num_dimensions());
H5::DataSpace dataspace(dimensions.size(), dimensions.data());
H5::DataSpace memspace(memdims.size(), memdims.data());
if (useBases) { if (useBases) {
std::vector<hssize_t> offsets(data.index_bases(), data.index_bases() + data.num_dimensions()); std::vector<hsize_t> offsets(data.index_bases(), data.index_bases() + data.num_dimensions());
dataspace.offsetSimple(offsets.data()); dataspace.selectHyperslab(H5S_SELECT_SET, memdims.data(), offsets.data());
} }
H5::DataSet dataset; H5::DataSet dataset;
@ -118,7 +120,7 @@ namespace CosmoTool {
else else
dataset = fg.openDataSet(data_set_name); dataset = fg.openDataSet(data_set_name);
dataset.write(data.data(), datatype); dataset.write(data.data(), datatype, memspace, dataspace);
} }