Documentation: https://bluebrain.github.io/HighFive/
HighFive is a modern header-only C++11 friendly interface for libhdf5.
HighFive supports STL vector/string, Boost::UBLAS, Boost::Multi-array and Xtensor. It handles C++ from/to HDF5 with automatic type mapping. HighFive does not require additional libraries (see dependencies).
It integrates nicely with other CMake projects by defining (and exporting) a HighFive target.
- Simple C++-ish minimalist interface
- No other dependency than libhdf5
- Zero overhead
- Support C++11
- create/read/write files, datasets, attributes, groups, dataspaces.
- automatic memory management / ref counting
- automatic conversion of
std::vector
and nestedstd::vector
from/to any dataset with basic types - automatic conversion of
std::string
to/from variable length string dataset - selection() / slice support
- parallel Read/Write operations from several nodes with Parallel HDF5
- Advanced types: Compound, Enum, Arrays of Fixed-length strings, References
- half-precision (16-bit) floating-point datasets
std::byte
in C++17 mode (with-DCMAKE_CXX_STANDARD=17
or higher)- etc... (see ChangeLog)
- hdf5 (dev)
- hdf5-mpi (optional, opt-in with -DHIGHFIVE_PARALLEL_HDF5=ON)
- boost >= 1.41 (recommended, opt-out with -DHIGHFIVE_USE_BOOST=OFF)
- eigen3 (optional, opt-in with -DHIGHFIVE_USE_EIGEN=ON)
- xtensor (optional, opt-in with -DHIGHFIVE_USE_XTENSOR=ON)
- half (optional, opt-in with -DHIGHFIVE_USE_HALF_FLOAT=ON)
- HighFive is not thread-safe. At best it has the same limitations as the HDF5 library. However, HighFive objects modify their members without protecting these writes. Users have reported that HighFive is not thread-safe even when using the threadsafe HDF5 library, e.g., BlueBrain#675.
- Eigen support in core HighFive is broken. See BlueBrain#532. H5Easy is not affected.
- The support of fixed length strings isn't ideal.
#include <highfive/highfive.hpp>
using namespace HighFive;
std::string filename = "/tmp/new_file.h5";
{
// We create an empty HDF55 file, by truncating an existing
// file if required:
File file(filename, File::Truncate);
std::vector<int> data(50, 1);
file.createDataSet("grp/data", data);
}
{
// We open the file as read-only:
File file(filename, File::ReadOnly);
auto dataset = file.getDataSet("grp/data");
// Read back, with allocating:
auto data = dataset.read<std::vector<int>>();
// Because `data` has the correct size, this will
// not cause `data` to be reallocated:
dataset.read(data);
}
Note: H5File.hpp
is the top-level header of HighFive core which should be always included.
Note: For advanced usecases the dataset can be created without immediately writing to it. This is common in MPI-IO related patterns, or when growing a dataset over the course of a simulation.
See select_partial_dataset_cpp11.cpp
See create_attribute_string_integer.cpp
See src/examples/ subdirectory for more info.
For several 'standard' use cases the highfive/H5Easy.hpp interface is available. It allows:
-
Reading/writing in a single line of:
- scalars (to/from an extendible DataSet),
- strings,
- vectors (of standard types),
- Eigen::Matrix (optional, enable CMake option
HIGHFIVE_USE_EIGEN
), - xt::xarray and xt::xtensor
(optional, enable CMake option
HIGHFIVE_USE_XTENSOR
). - cv::Mat_
(optional, enable CMake option
HIGHFIVE_USE_OPENCV
).
-
Getting in a single line:
- the size of a DataSet,
- the shape of a DataSet.
#include <highfive/H5Easy.hpp>
int main() {
H5Easy::File file("example.h5", H5Easy::File::Overwrite);
int A = ...;
H5Easy::dump(file, "/path/to/A", A);
A = H5Easy::load<int>(file, "/path/to/A");
}
whereby the int
type of this example can be replaced by any of the above types. See easy_load_dump.cpp for more details.
Note: Classes such as H5Easy::File
are just short for the regular HighFive
classes (in this case HighFive::File
). They can thus be used interchangeably.
There's two common paths of integrating HighFive into a CMake based project. The first is to "vendor" HighFive, the second is to install HighFive as a normal C++ library. Due to how HighFive CMake code works, sometimes following the third Bailout Approach is needed.
In this approach the HighFive sources are included in a subdirectory of the
project (typically as a git submodule), for example in third_party/HighFive
.
The projects CMakeLists.txt
add the following lines
add_executable(foo foo.cpp)
# You might want to turn off Boost support:
if(NOT DEFINED HIGHFIVE_USE_BOOST)
set(HIGHFIVE_USE_BOOST Off)
endif()
# Include the subdirectory and use the target HighFive.
add_subdirectory(third_party/HighFive)
target_link_libraries(foo HighFive)
Note: add_subdirectory(third_party/HighFive)
will search and "link" HDF5
and optional dependencies such as Boost.
Alternatively you can install HighFive once and use it in several projects via
find_package()
. First one should clone the sources:
git clone --recursive https://github.com/BlueBrain/HighFive.git HighFive-src
By default CMake will install systemwide, which is likely not appropriate. The
instruction below allow users to select a custom path where HighFive will be
installed, e.g. HIGHFIVE_INSTALL_PREFIX=${HOME}/third_party/HighFive
or some
other location. The CMake invocations would be
cmake -DHIGHFIVE_EXAMPLES=Off \
-DHIGHFIVE_USE_BOOST=Off \
-DHIGHFIVE_UNIT_TESTS=Off \
-DCMAKE_INSTALL_PREFIX=${HIGHFIVE_INSTALL_PREFIX} \
-B HighFive-src/build \
HighFive-src
cmake --build HighFive-src/build
cmake --install HighFive-src/build
This will install (i.e. copy) the headers to
${HIGHFIVE_INSTALL_PREFIX}/include
and some CMake files into an appropriate
subfolder of ${HIGHFIVE_INSTALL_PREFIX}
.
The projects CMakeLists.txt
should add the following:
# ...
add_executable(foo foo.cpp)
find_package(HighFive REQUIRED)
target_link_libraries(foo HighFive)
Note: If HighFive hasn't been installed in a default location, CMake needs
to be told where to find it which can be done by adding
-DCMAKE_PREFIX_PATH=${HIGHFIVE_INSTALL_PREFIX}
to the CMake command for
building the project using HighFive. The variable CMAKE_PREFIX_PATH
is a
semi-colon ;
separated list of directories.
Note: find_package(HighFive)
will search and "link" HDF5 and optional
dependencies such as Boost.
Since both add_subdirectory
and find_package
will trigger finding HDF5 and
other optional dependencies of HighFive as well as the target_link_libraries
code for "linking" with the dependencies, things can go wrong.
Fortunately, HighFive is a header only library and all that's needed is the
headers. Preferably, the version obtained by installing HighFive, since those
include H5Version.hpp
. Let's assume they've been copied to
third_party/HighFive
. Then one could create a target:
add_library(HighFive INTERFACE)
target_include_directory(HighFive INTERFACE ${CMAKE_CURRENT_SOURCE_DIR}/third_party/HighFive/include)
add_executable(foo foo.cpp)
target_link_libraries(foo HighFive)
One known case where this is required is when vendoring the optional dependencies of HighFive.
Do you have questions on how to use HighFive? Would you like to share an interesting example or discuss HighFive features? Head over to the Discussions forum and join the community.
For bugs and issues please use Issues.
The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.
Copyright © 2015-2022 Blue Brain Project/EPFL
Boost Software License 1.0