steven-varga/h5cpp

C++17 templates between [stl::vector | armadillo | eigen3 | ublas | blitz++] and HDF5 datasets

Easy to use HDF5 C++ templates for Serial and Paralell HDF5

News: optional custom dataype is added to h5::create to allow custom dataypes passed along the other arguments.

hsize_t dataset_size = 1'000'000;

using custom_t = char[42];
h5::dt_t<custom_t> hdf5_data_type{H5Tcreate(H5T_STRING, sizeof(custom_t))};
H5Tset_cset(hdf5_data_type, H5T_CSET_UTF8); // you can always call HDF5 CAPI functions on any H5CPP resource 

// `custom_t` is passed as template parameter, 
h5::ds_t ds = h5::create<custom_t>(fd, "my/dataset", h5::chunk{4096}, h5::current_dims{dataset_size},
    hdf5_data_type)); // <- h5::dt_t<custom_t> argument is passed along 

//example interop with HDF5 CAPI, where you need to pass `dt_t<custom_t>` type descriptor
h5::sp_t mem_space{H5Screate_simple(1, &dataset_size, nullptr )};
H5Sselect_all(mem_space);
// file space
h5::sp_t file_space{H5Dget_space(ds)};
H5Sselect_all(file_space);

H5Dwrite( ds[idx], hdf5_data_type, mem_space, file_space, H5P_DEFAULT, data.data());

h5cpp compiler can easily be compiled with stock LLVM6.0 and clang6.0 binary release h5cpp-dev_1.10.4-5.xxx contains bug fixes, and half float support, deb,rpm,tarball

Hierarchical Data Format prevalent in high performance scientific computing, sits directly on top of sequential or parallel file systems, providing block and stream operations on standardized or custom binary/text objects. Scientific computing platforms such as Python, R, Matlab, Fortran, Julia [and many more...] come with the necessary libraries to read write HDF5 dataset. This edition simplifies interactions with popular linear algebra libraries, provides compiler assisted seamless object persistence, Standard Template Library support and equipped with novel error handling architecture.

H5CPP is a novel approach to persistence in the field of machine learning, it provides high performance sequential and block access to HDF5 containers through modern C++ Download packages from here. If you are interested in h5cpp LLVM/clang based source code transformation tool you find it in this separate project.

You can read this blog post published on HDFGroup Blog site to find out where the project is originated. Click here Doxygen based Documentation pages. Browse highlighted examples, follow this link to our spring presentation or take a peek at the upcoming ISC'19 BOF, where I am presenting H5CPP.

H5CPP for MPI

Proud to announce to the HPC community that H5CPP is now MPI capable. The prerequisites are: c++17 capable MPI compiler, and linking against the Parallel HDF5 library. The template system provides the same easy to use functionality as in the serial version, and may be enabled by including parallel hdf5.h then passing h5::mpiio({mpi_com, mpi_info}) to h5::create | h5::open | h5::write | h5::read , as well as h5::independent and h5::collective data transfer properties. There are examples for independent, collective IO, as well as a short program to demonstrate throughput. The MPI extension supports all parallel HDF5 features, while the documentation is in progress please look at the tail end of H5Pall.hpp for details.

Note: h5::append operator and attributes are not yet tested, and probably are non-functional.

Tested against:

• gcc 7.4.0, gcc 8.3.0, gcc 9.0.1
• clang 6.0

Note: the preferred compiler is gcc, however there is work put in to broaden the support for major modern C++ compilers. Please contact me if there is any shortcomings.

Templates:

create dataset within an opened hdf5 file

file ::= const h5::fd_t& fd | const std::string& file_path;
dataspace ::= const h5::sp_t& dataspace | const h5::current_dims& current_dim [, const h5::max_dims& max_dims ] |  
    [,const h5::current_dims& current_dim] , const h5::max_dims& max_dims;

template <typename T> h5::ds_t create( file, const std::string& dataset_path, dataspace, 
    [, const h5::lcpl_t& lcpl] [, const h5::dcpl_t& dcpl] [, const h5::dapl_t& dapl] [const h5::dt_t<T>]);

read a dataset and return a reference of the created object

dataset ::= (const h5::fd_t& fd | const std::string& file_path, const std::string& dataset_path ) | const h5::ds_t& ds;

template <typename T> T read( dataset
    [, const h5::offset_t& offset]  [, const h5::stride_t& stride] [, const h5::count_t& count]
    [, const h5::dxpl_t& dxpl ] ) const;
template <typename T> h5::err_t read( dataset, T& ref 
    [, const h5::offset_t& offset]  [, const h5::stride_t& stride] [, const h5::count_t& count]
    [, const h5::dxpl_t& dxpl ] ) [noexcept] const;						 

write dataset into a specified location

dataset ::= (const h5::fd_t& fd | const std::string& file_path, const std::string& dataset_path ) | const h5::ds_t& ds;

template <typename T> h5::err_t write( dataset, const T* ptr
    [,const hsize_t* offset] [,const hsize_t* stride] ,const hsize_t* count [, const h5::dxpl_t dxpl ]  ) noexcept;
template <typename T> h5::err_t write( dataset,  const T& ref
    [,const h5::offset_t& offset] [,const h5::stride_t& stride]  [,const& h5::dxcpl_t& dxpl] ) [noexept];

append to extendable C++/C struct dataset

#include <h5cpp/core>
	#include "your_data_definition.h"
#include <h5cpp/io>
template <typename T> void h5::append(h5::pt_t& ds, const T& ref) [noexcept];

All file and dataset io descriptors implement raii idiom and close underlying resource when going out of scope, and may be seamlessly passed to HDF5 CAPI calls when implicit conversion enabled. Similarly templates can take CAPI hid_t identifiers as arguments where applicable provided conversion policy allows. See conversion policy for details.

install:

On the projects download page you find debian, rpm and general tar.gz packages with detailed instructions. Or get the download link to the header only h5cpp-dev_1.10.4.deb and the binary compiler h5cpp_1.10.4.deb directly from this page.

supported classes:

T := ([unsigned] ( int8_t | int16_t | int32_t | int64_t )) | ( float | double  )
S := T | c/c++ struct | std::string
ref := std::vector<S> 
	| arma::Row<T> | arma::Col<T> | arma::Mat<T> | arma::Cube<T> 
	| Eigen::Matrix<T,Dynamic,Dynamic> | Eigen::Matrix<T,Dynamic,1> | Eigen::Matrix<T,1,Dynamic>
	| Eigen::Array<T,Dynamic,Dynamic>  | Eigen::Array<T,Dynamic,1>  | Eigen::Array<T,1,Dynamic>
	| blaze::DynamicVector<T,rowVector> |  blaze::DynamicVector<T,colVector>
	| blaze::DynamicVector<T,blaze::rowVector> |  blaze::DynamicVector<T,blaze::colVector>
	| blaze::DynamicMatrix<T,blaze::rowMajor>  |  blaze::DynamicMatrix<T,blaze::colMajor>
	| itpp::Mat<T> | itpp::Vec<T>
	| blitz::Array<T,1> | blitz::Array<T,2> | blitz::Array<T,3>
	| dlib::Matrix<T>   | dlib::Vector<T,1> 
	| ublas::matrix<T>  | ublas::vector<T>
ptr 	:= T* 
accept 	:= ref | ptr 

In addition to the standard data types offered by BLAS/LAPACK systems and POD struct -s, std::vector also supports std::string data-types mapping N dimensional variable-length C like string HDF5 data-sets to std::vector<std::string> objects.

short examples:

to read/map a 10x5 matrix from a 3D array from location {3,4,1}

#include <armadillo>
#include <h5cpp/all>
...
auto fd = h5::open("some_file.h5", H5F_ACC_RDWR);
/* the RVO arma::Mat<double> object will have the size 10x5 filled*/
try {
	/* will drop extents of unit dimension returns a 2D object */
	auto M = h5::read<arma::mat>(fd,"path/to/object", 
        h5::offset{3,4,1}, h5::count{10,1,5}, h5::stride{3,1,1} ,h5::block{2,1,1} );
} catch (const std::runtime_error& ex ){
	...
}
// fd closes underlying resource (raii idiom)

to write the entire matrix back to a different file

#include <Eigen/Dense>
#include <h5cpp/all>

h5::fd_t fd = h5::create("some_file.h5",H5F_ACC_TRUNC);
h5::write(fd,"/result",M);

to create an dataset recording a stream of struct into an extendable chunked dataset with GZIP level 9 compression:

#include <h5cpp/core>
	#include "your_data_definition.h"
#include <h5cpp/io>
...
auto ds = h5::create<some_type>(fd,"bids", h5::max_dims{H5S_UNLIMITED}, h5::chunk{1000} | h5::gzip{9});

to append records to an HDF5 datastream

#include <h5cpp/core>
	#include "your_data_definition.h"
#include <h5cpp/io>
auto fd = h5::create("NYSE high freq dataset.h5");
h5::pt_t pt = h5::create<ns::nyse_stock_quote>( fd, 
		"price_quotes/2018-01-05.qte",h5::max_dims{H5S_UNLIMITED}, h5::chunk{1024} | h5::gzip{9} );
quote_update_t qu;

bool having_a_good_day{true};
while( having_a_good_day ){
	try{
		recieve_data_from_udp_stream( qu )
		h5::append(pt, qu);
	} catch ( ... ){
        if( cant_fix_connection() )
	  		having_a_good_day = false; 
	}
}

h5cpp's Issues

Not installing correctly on Mint 19

I tried following both the automatic instructions using conan and cmake, but neither one is installing correctly. Conan seems to work, but then when I try to import h5cpp.h in my code I get the error:

CMake Error at CMakeLists.txt:34 (find_package):
  By not providing "Findh5cpp.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "h5cpp", but
  CMake did not find one.

  Could not find a package configuration file provided by "h5cpp" with any of
  the following names:

    h5cppConfig.cmake
    h5cpp-config.cmake

  Add the installation prefix of "h5cpp" to CMAKE_PREFIX_PATH or set
  "h5cpp_DIR" to a directory containing one of the above files.  If "h5cpp"
  provides a separate development package or SDK, be sure it has been
  installed.


-- Configuring incomplete, errors occurred!
See also "/home/glicka/GEANT/B4a/build/CMakeFiles/CMakeOutput.log".

And when I try to install h5cpp using cmake I get the error:

ERROR: boost_filesystem/1.65.1@bincrafters/stable: 'settings.compiler' value not defined
CMake Error at cmake/conan.cmake:322 (message):
  Conan install failed='1'
Call Stack (most recent call first):
  cmake/conan.cmake:399 (conan_cmake_install)
  CMakeLists.txt:21 (conan_cmake_run)


-- Configuring incomplete, errors occurred!
See also "/home/glicka/h5cpp-0.1.0/build/CMakeFiles/CMakeOutput.log".

What do I need to do to get this to work?

Example Provided - Packet Table and Dataset Attributes

Below is an example of how one can add attributes to a pack table-generated dataset. This tripped me up for a bit, so an example may be useful to others.

Please adapt as you see fit to work with packet-table example.

I didn't add to the packet-table example myself because it needs to be tested in Linux which I can't currently do.

The important points are creating ds_t, adding attributes to it, then casting to pt_t for data appending.

#include <h5cpp/all>
#include <cstddef>
#include <vector>

int main(){

	const size_t count = 2048;
	const std::size_t chunk_size = 1024;

	try
	{
		h5::fd_t fd = h5::create("example.h5", H5F_ACC_TRUNC);
		
		// Create a dataset.
		h5::ds_t ds = h5::create<double>(fd, "some_path", h5::max_dims{ H5S_UNLIMITED },
			h5::chunk{ chunk_size } | h5::gzip{ 6 } | h5::fill_value<double>(0));

		// Add attributes to dataset.
		ds["attr1"] = 1.23;
		ds["attr2"] = "string";

		// Cast dataset to packet table.
		h5::pt_t pt = static_cast<h5::pt_t>(ds);

		// Append data to packet table.
		for (std::size_t i = 0; i < count; ++i)
			h5::append(pt, i * 0.999);

	}
	catch (const std::exception& e)
	{
		std::cout << e.what() << std::endl;
	}
}

h5::pt_t move assignment behaves oddly.

Hi,
I got one more issue, it's small for any pull request, so decided to describe it here and you will decide how to fix or maybe I'm just using it not correctly...

Ok,
the h5::dt_t has a move assignment operator

h5cpp/h5cpp/H5Dappend.hpp

Line 25 in 9b9b90c

pt_t& operator=( h5::pt_t&& pt ){

that not correctly working in the next situation

struct logger {
   logger() {
     fd = h5::create(...);
     pt = h5::create( fd, "first_dataset", ...);
   }
   void createNextTable() {
      pt = h5::create( fd, "name_of_next_dataset", ...);
   }
   private:
   h5::pt_t pt{};
   h5::fd_t fd{};
};

so, the line pt = h5::create( fd, "name_of_next_dataset", ...); will call conversion constructor

h5cpp/h5cpp/H5Dappend.hpp

Line 21 in 9b9b90c

pt_t( const h5::pt_t& pt ) : h5::pt_t(pt.ds) {

and after that move assignment. For some reason the result is that pt.n stores number of samples in cache of previous first_dataset.

the next code

h5::pt_t pt = h5::create( fd, "first_dataset", ...);
std::cout << pt;
h5::append(pt, some_data );
h5::append(pt, some_data );
h5::append(pt, some_data );
pt.flush();
std::cout << pt;

pt = h5::create( fd, "next_dataset", ...);
std::cout << pt;

will generate the next output

packet table:
------------------------------------------
rank: 1 N:1000 n:0
element size: 24 block size: 24000
current dims: [0]
chunk dims: [0]
offset : [0] count : [1]
ds: 360287970189639680 dxpl: 720575940379279425
fill value: 0x55c6dfecc2a0 buffer: 0x55c6dfedff00
packet table:
------------------------------------------
rank: 1 N:3e8 n:3
element size: 18 block size: 5dc0
current dims: [3]
chunk dims: [3]
offset : [0] count : [1]
ds: 500000000000000 dxpl: a00000000000041
fill value: 0x55c6dfecc2a0 buffer: 0x55c6dfedff00
packet table:
------------------------------------------
rank: 1 N:3e8 n:3
element size: 18 block size: 5dc0
current dims: [0]
chunk dims: [0]
offset : [0] count : [1]
ds: 500000000000001 dxpl: a00000000000041
fill value: 0x55c6dfec3980 buffer: 0x55c6dfef7800

FIX

I did fixed it in a next way, however not sure that it's correct way...

		pt_t& operator=( h5::pt_t&& pt ){
			this->n = pt.n;
			init(pt.ds);
			return pt;
		}

Is it correct to reuse h5::pt_t object as I did? Is dataset closed properly when I reuse it?

And one more question, is it really required to call init(pt.ds) in move assignment, seems like it's done twice...

Regards, Max 73!

Possible Compilation or Run Time Issues with String-Based Attributes

Hi,

I am finding compilation or run time issues when attempting to use std::string and std::vector<std::string> to read dataset attributes.

Can you confirm that you see these issues too?

Perhaps I am missing something in my code

#include <iostream>
#include <string>
#include <vector>
#include "h5cpp/all"

int main()
{
	// Create a file.
	h5::fd_t fd = h5::create("a.h5", H5F_ACC_TRUNC, h5::default_fcpl, h5::libver_bounds({ H5F_LIBVER_LATEST, H5F_LIBVER_LATEST }));

	// Add a simple dataset.
	std::vector<int> data = { 1,2,3,4,5 };
	h5::ds_t ds = h5::write(fd, "/test/path", data, h5::create_path | h5::utf8);

	// Employ the two methods for adding attributes to dataset to add std::string's.
	std::string str1 = "std::string #1";
	ds["attr1"] = str1;
	std::string str2 = "std::string #2";
	h5::awrite(ds, "attr2", str2);

	// Employ the two methods for added attributes to dataset to add std::vector<std::string>'s.
	std::vector<std::string> vs1 = { "Millicent", "Judith", "Jennifer" };
	ds["attr3"] = vs1;
	std::vector<std::string> vs2 = { "Duke", "Melvin", "Claude" };
	h5::awrite(ds, "attr4", vs2);

	// Read and dump the two std::string attributes.
	auto attr_1 = h5::aread<std::string>(ds, "attr1");
	std::cout << "attr1 : " << attr_1 << std::endl;

	auto attr_2 = h5::aread<std::string>(ds, "attr2");
	std::cout << "attr2 : " << attr_2 << std::endl;

	// Read and dump the two std::vector<std::string> attributes.
	auto attr_3 = h5::aread<std::vector<std::string>>(ds, "attr3");
	std::cout << "attr3 : ";
	for (auto v : attr_3)
		std::cout << v << ", ";
	std::cout << std::endl;

	auto attr_4 = h5::aread<std::vector<std::string>>(ds, "attr4");
	std::cout << "attr4 : ";
	for (auto v : attr_4)
		std::cout << v << ", ";
	std::cout << std::endl;
}

extend supported stl types for std::array

I think I see 2 spaces where std::array should be incorporated

The first is in simply writing or reading std::array<T, N> to a dataset/attribute.

The second is writing a collection of std::array<T, N>, like std::vector<std::array<T, N>>

H5CPP doesn't differentiate between HDF5 CAPI versions

using stock ubuntu 18.04LTS with minimal dependencies there are compile time errors triggered by the following HDF5 CAPI properties:
H5Pset_file_space_page_size, H5Pset_page_buffer_size, H5Pset_evict_on_close, H5Pset_mdc_image_config

how to reproduce error:

sudo apt-get install -y build-essential libhdf5-serial-dev
wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key|sudo apt-key add -
sudo sh -c 'echo "deb http://apt.llvm.org/bionic/ llvm-toolchain-bionic-7 main" >> /etc/apt/sources.list'
sudo sh -c 'echo "deb-src http://apt.llvm.org/bionic/ llvm-toolchain-bionic-7 main" >> /etc/apt/sources.list'
sudo apt-get update
sudo apt-get -y install clang-tools-7 llvm-7-tools libclang-7-dev
git clone https://github.com/steven-varga/h5cpp.git
git checkout ubuntu-18.04LTS
cd h5cpp && make install

note:

on dev suite: [email protected] the the offending lines are commented out

Update Links to New Repo for Windows Port of H5CPP

Hi,

I created a new repo for the Windows port of H5CPP. It is here:
https://github.com/ChrisDrozdowski/h5cpp-windows

Please modify links to the old repos on this to reflect the new repo.

My rationale is that it puts the h5cpp source and examples in one unified repo. I also included the source for Armadillo and Eigen so that the examples can be compiled out of box with minimal work.

I will be maintaining this repo as the Windows port from now on.

h5cpp compiler doesn't work with attributes

Attribute operations are not yet handled with h5cpp compiler, because of the difference in templating mechanism.
Expect fix in early November.

VC++ Complains About strdup Function

Compiling with VC++ in Visual Studio 2017, the compiler complains about strdup usage:

Error C4996 'strdup': The POSIX name for this item is deprecated. Instead, use the ISO C and C++ conformant name: _strdup.

It is referring to line 88 in H5Dwrite.hpp:

try {
	for( const auto& reference:ref)
		ptr.push_back( strdup( reference.data()) );
} catch( ... ){
	throw h5::error::io::dataset::write( h5::error::msg::mem_alloc );
}

'after' example returns an error

./before
reading back data previously written:
        1 0.5 0.333333 0.25 0.2 0.166667 0.142857 0.125 0.111111 0.1
./after
terminate called after throwing an instance of 'h5::error::io::dataset::create'
  what():  /usr/local/include/h5cpp/H5capi.hpp line#  186 : couldn't create dataset...

Issue reading dataset into std::vector<std::string> when testing "string" example

Steven, please confirm whether or not you see this issue when compiling/running "string" example in Linux. Is this a general issue or only in VC++ that I should look into fixing for VC++.

Issue: H5CPP cannot read a string dataset into std::vector<std::string>.
Dev Environment: Visual Studio 2017 (141) compiling as x64 with Win 8.1 64-bit.

Issue was discovered and is reproducible while testing the "string" example project.

Details:
Writing std::vector<std::string> to a dataset works properly.

But reading the same dataset back into a std::vector<std::string> triggers a std::bad_alloc exception when iterating the returned vector.

If you read the dataset into a std::vector<const char*>, the dataset is read properly and iterates without exception.

However, using std::vector<const char*> won't compile because it can't get by:
static_assert( utils::is_supported<T>, "error: " H5CPP_supported_elementary_types );
in H5Dread.hpp, line 36.

Commenting out that line allows for compilation and successful execution.

The code below (essentially from string.cpp) is a working example.

// CHD !!! This is important for Windows!
#define H5_BUILT_AS_DYNAMIC_LIB

/* Copyright (c) 2018 vargaconsulting, Toronto,ON Canada
 * Author: Varga, Steven <[email protected]>
 */
#include <vector>
#include <string>

#include <h5cpp/all>

int main(){
	//RAII will close resource, noo need H5Fclose( any_longer ); 
	h5::fd_t fd = h5::create("example.h5",H5F_ACC_TRUNC);
	{
		// CHD: This works correctly.
		std::vector<std::string> vec = h5::utils::get_test_data<std::string>(20);
		h5::write(fd, "/strings.txt", vec);
	}
	{
		// CHD: This will result in a std::bad_alloc exception when the returned
		// std::vector<std::string> is iterated.
		//auto vec = h5::read<std::vector<std::string>>(fd, "strings.txt");
		//for( auto i : vec )
			//std::cout << i <<"\n";

		// CHD: This will return vector properly and will iterate properly.
		// But only if the utils::is_supported assert in H5Dread.hpp, line
		// 36 is commented out.
		auto vec = h5::read<std::vector<const char*>>(fd, "strings.txt");
		for( auto i : vec )
			std::cout << i <<"\n";
	}
}

What is the status of and where is this project heading

This seems like a really great tool and would like to be a user, however I am wondering what the future of this project will be in terms of vision and timing. It sounds like maybe this is on the development back burner due to other exigencies or funding. If there is a better forum for this I am happy to move this somewhere else. I am mostly curious where it's going or could go.

guidance for OpenCV cv::Mat support

Hi, I would like to add support for OpenCV matrices (cv::Mat). All supported matrix classes in H5M* are templated based on scalar type (plus other things); cv::Mat, on the other hand, stores its datatype internally. I usually use a simple switch/case function to map OpenCV type constants to HDF5 constants and vice verse.

Could I get some guidance how to hook that into h5cpp? I appreciate very much compactness of the code, esthetically and as programmer, but need a bit of help at first :)

H5CPP doesn't comply with C++11

error:
There are if constrexpr ( condition) { } in code base that prevent the code to parse as c++11

workaround: --std=c++17 until conditionally removing the offending constructs

attributes handle only limited object types

Due to template system rework the newly added attributes can only handle armadillo objects in addition to scalars, strings and arrays.

missing include guards from h5cpp commpiler generated files

error:
redefinition of H5CPP_REGISTER_STRUCT( ... )
At most only one unique symbol may be present in TU translation unit. Include guards are a good method to prevent errors in the linking phase.

workaround: be certain the generated header file is included only once.

Eigen simplification (almost-patch)

I simplified most of the code in H5Meigen.hpp by using Eigen base types.

There are 4 parts: size, data, get and decay.

For size, data, it is straightforward to write the function like this (handles all of Matrix and Array, bot row-major and column-major):

template<class T>
typename T::Scalar* data(const ::Eigen::PlainObjectBase<T>& ref ){
		return const_cast<typename T::Scalar*>( ref.data() );
}
template<class T>
inline std::array<size_t,2> size( const ::Eigen::PlainObjectBase<T>& ref){
	if constexpr(T::IsRowMajor) return {(hsize_t)ref.rows(),(hsize_t)ref.cols()};
	return {(hsize_t)ref.cols(),(hsize_t)ref.rows()};
}

The others are not as straightforward, as they are class templates (which are matched differently than function templates, like data and size — those use overload resolution).

For get, I had to change the base template in H5Mstl.hpp, adding typename = void:

template <class T, typename = void> struct get {
   	static inline T ctor( std::array<size_t,impl::rank<T>::value> dims ){
		return T(); }};

so that the Eigen template is then more specialized:

template<class T>
struct get<T,std::enable_if_t<std::is_base_of_v<Eigen::PlainObjectBase<T>,T>>>{
	static inline T ctor( std::array<size_t,2> dims ){
		if constexpr(T::IsRowMajor) return T( dims[0], dims[1] );
		return T( dims[1], dims[0] );
}};

Finally, for decay, I could not use the extra parameter trick as decay is declared with ellipsis template <T, ...>, so no solution for that one so far.

What do you think? Would this be worth putting as a pull request?

---

Incidentally, I was checking out HighFive recently (they use too much whitespace in the code for my taste, though ;) ) and was helping there with a similar issue. The most elegant solution seemed to be to put all such common functions into a class template, one for each supported array types (one has to write the type-matching code only once, for the whole class).

An example is here: https://gist.github.com/eudoxos/43f11cfb04d33b4f3e5cf309ad628365 : io_impl is specialized for each supported array type, containing all the functions. For h5cpp, those 4 would be obviously decay, data, size and ctor and they would be called as (e.g.) h5::impl::support<T>::decay rather than h5::impl::decay<T> and so on.

h5::append not working as intended

TL;DR

• It seems h5::fill_value does not work as intended.
• There should be some diagnostic in case h5::gzip is used and one chunk is t0o small.

Long version:

I am trying to append data and it did not work.

Since i was not sure whether I am doing something wrong, I decided to check the current master for examples and tests.

There i found this problem:

$ ./tests/test-packettable
$ h5dump -d "/stream of struct" test.h5
HDF5 "test.h5" {
DATASET "/stream of struct" {
   DATATYPE  H5T_COMPOUND {
      H5T_STD_U16LE "field1";
      H5T_IEEE_F64LE "field2";
      H5T_IEEE_F32LE "field3";
      H5T_STD_I8LE "field4";
      H5T_IEEE_F64LE "field5";
      H5T_IEEE_F64LE "field6";
      H5T_IEEE_F64LE "field7";
      H5T_IEEE_F64LE "field8";
      H5T_IEEE_F64LE "field9";
   }
   DATASPACE  SIMPLE { ( 0 ) / ( H5S_UNLIMITED ) }
   DATA {
   }
}
}

The test test-packettable creates an empty dataset /stream of struct even though it writes 200 elements.

I looked at the example examples-packettable, since it also uses append.
In this example I looked at the dataset /stream of integral which is created with:

h5::pt_t pt = h5::create<int>(fd, "stream of integral",
    h5::max_dims{H5S_UNLIMITED,3,5}, h5::chunk{2,3,5} | h5::gzip{9} | h5::fill_value<int>(3) );

If I dump it, I get this:

$ ./examples/examples-packettable
$ h5dump -d "/stream of integral" example.h5 
HDF5 "example.h5" {
DATASET "/stream of integral" {
   DATATYPE  H5T_STD_I32LE
   DATASPACE  SIMPLE { ( 6, 3, 5 ) / ( H5S_UNLIMITED, 3, 5 ) }
   DATA {
   (0,0,0): 1, 2, 3, 4, 5,
   (0,1,0): 6, 7, 8, 9, 10,
   (0,2,0): 11, 12, 13, 14, 15,
   (1,0,0): 16, 17, 18, 19, 20,
   (1,1,0): 21, 22, 23, 24, 25,
   (1,2,0): 26, 27, 28, 29, 30,
   (2,0,0): 31, 32, 33, 34, 35,
   (2,1,0): 36, 37, 38, 39, 40,
   (2,2,0): 41, 42, 43, 44, 45,
   (3,0,0): 46, 47, 48, 49, 50,
   (3,1,0): 51, 52, 53, 54, 55,
   (3,2,0): 56, 57, 58, 59, 60,
   (4,0,0): 61, 62, 63, 64, 65,
   (4,1,0): 66, 67, 68, 69, 70,
   (4,2,0): 71, 72, 73, 74, 75,
   (5,0,0): 76, 77, 78, 79, 80,
   (5,1,0): 81, 82, 83, 0, 0,
   (5,2,0): 0, 0, 0, 0, 0
   }
}
}

Here the values are written, but the fill value is 0 instead of 3,

Since my data is one dimensional, I added this code to the example:

try { // centrally used error handling
    std::vector<int> stream(83);
    std::iota(std::begin(stream), std::end(stream), 1);
    // the leading dimension is extended once chunk is full, chunk is filled in row major order
    // zero copy writes directly to chunk buffer then pushed through filter chain if specified
    // works up to H5CPP_MAX_RANK default to 7
    // last chunk if partial filled with h5::fill_value<T>( some_value )  
	h5::pt_t pt = h5::create<int>(fd, "stream of integral2",
                                  h5::max_dims{H5S_UNLIMITED}, h5::chunk{2} | h5::gzip{9} | h5::fill_value<int>(3) );
    for( auto record : stream )
        h5::append(pt, record);
} catch ( const h5::error::any& e ){
    std::cerr << "ERROR:" << e.what();
}

It is a copy of /stream of integral, but I changed the dimensions and chunk size (and name).

$ ./examples/examples-packettable
$ h5dump -d "/stream of integral2" example.h5 
HDF5 "example.h5" {
DATASET "/stream of integral2" {
   DATATYPE  H5T_STD_I32LE
   DATASPACE  SIMPLE { ( 83 ) / ( H5S_UNLIMITED ) }
   DATA {h5dump error: unable to print data

   }
}
}

Dumping it, I get corrupted data (but the dimensions are correct).

I got the same results with:

• h5::max_dims{H5S_UNLIMITED }, h5::chunk{1 }
• h5::max_dims{H5S_UNLIMITED,1 }, h5::chunk{2,1 }
• h5::max_dims{H5S_UNLIMITED,2 }, h5::chunk{2,2 }
• h5::max_dims{H5S_UNLIMITED,1,1}, h5::chunk{2,1,1}
• h5::max_dims{H5S_UNLIMITED,2,1}, h5::chunk{2,1,1}
• h5::max_dims{H5S_UNLIMITED,2,1}, h5::chunk{2,2,1}
• h5::max_dims{H5S_UNLIMITED,2,2}, h5::chunk{2,2,1}
• h5::max_dims{H5S_UNLIMITED,1,2}, h5::chunk{2,1,2}
• h5::max_dims{H5S_UNLIMITED }, h5::chunk{5 }

It worked with (correct values, but wrong fill value):

• h5::max_dims{H5S_UNLIMITED,2,2 }, h5::chunk{2,2,2 }
• h5::max_dims{H5S_UNLIMITED,2,2,2}, h5::chunk{2,2,2,2}
• h5::max_dims{H5S_UNLIMITED,2,2,1}, h5::chunk{2,2,2,1}
• h5::max_dims{H5S_UNLIMITED,8 }, h5::chunk{2,8 }
• h5::max_dims{H5S_UNLIMITED }, h5::chunk{16 }
• h5::max_dims{H5S_UNLIMITED }, h5::chunk{ 8 }
• h5::max_dims{H5S_UNLIMITED }, h5::chunk{ 6 }

If I remove h5::gzip{9}, i can use h5::max_dims{H5S_UNLIMITED}, h5::chunk{2}.
Hence my guess is: This problem is caused by the minimum gzip block size (or at least the minimum size in the implementation used by hdf5).

I think some diagnostic would be good, since this error is not easy to track down.

Packet Table Behavior When Appending Vector

I want to confirm whether this is expected behavior or not for packet table functionality.

When appending a vector to h5:pt_t and size of vector != chunk size, an exception is thrown.

(This occurs with my MSVC code- does it happen with Linux???)

Example code:

#include <h5cpp/all>
#include <cstddef>
#include <vector>

int main(){

	const size_t count = 2048; // Some arbitrary length not known at compile time.

	std::vector<double> data(count);
	for (std::size_t i = 0; i < count; ++i) { data[i] = i * 0.123; }

	const std::size_t chunk_size = 1024;

	try
	{
		h5::fd_t fd = h5::create("pt1.h5", H5F_ACC_TRUNC);
		h5::pt_t pt = h5::create<double>(fd, "some_path", h5::max_dims{ H5S_UNLIMITED },
			h5::create_path | h5::utf8, h5::chunk{ chunk_size } | h5::fill_value<double>(0));

		h5::append(pt, data); // Exception is thrown in this call.
	}
	catch (const std::exception& e)
	{
		std::cout << e.what() << std::endl;
	}
}

Coding conventions

Since i am currently extending h5cpp in my fork and plan to make a pull request at some point, it would be useful to know the coding conventions for this project.

The best option would be to use a tool for reformatting (astyle, clang-tidy etc.).
This would make it much easier to collaborate and keep the same style throughout the project (this would improve readability and thus maintainability) since collaborators could configure their editor to apply the file.

Request for .clangformat

Hello,

I have a couple of pull requests I'd like to submit, one of which enables Eigen::Tensor objects. Before I do so is it possible for you to add a .clangformat file, so I can ensure I stick with your chosen style?

Read single std::string attribute?

Hello,

Looking at https://github.com/steven-varga/h5cpp/blob/master/examples/attributes/attributes.cpp it appears that string array attributes (std::aread<std::vector<std::string>>) is supported. However, I can't find an example for only a single string, i.e. std::aread<std::string>, and indeed, this fails to compile. Is this not supported? Is there a way to read a single string/char* attribute into a std::string?

Thanks in advance!

Missing LDFLAGS from h5cpp recipe

The recipe for the h5cpp target in compiler/Makefile should read

h5cpp: h5cpp.o
        $(CXX)  $^  $(LDFLAGS) $(LIBS)  -o $@

Otherwise we get a linker error because the Clang libs aren't found.

'compound' example returns an error

h5cpp  struct.cpp -- -std=c++11  -I/usr/local/include -I/usr/local/h5cpp-llvm  -Dgenerated.h
H5CPP: Copyright (c) 2018     , VargaConsulting, Toronto,ON Canada
LLVM : Copyright (c) 2003-2010, University of Illinois at Urbana-Champaign.
g++ -o struct.o  -std=c++11  -I/usr/local/include -I/usr/local/h5cpp-llvm -c struct.cpp
g++ struct.o -lhdf5  -lz -ldl -lm -o struct
./struct
HDF5-DIAG: Error detected in HDF5 (1.11.4) thread 0:
  #000: H5D.c line 164 in H5Dcreate2(): unable to create dataset
    major: Dataset
    minor: Unable to initialize object
  #001: H5VLcallback.c line 1787 in H5VL_dataset_create(): dataset create failed
    major: Virtual Object Layer
    minor: Unable to create file
  #002: H5VLcallback.c line 1754 in H5VL__dataset_create(): dataset create failed
    major: Virtual Object Layer
    minor: Unable to create file
  #003: H5VLnative_dataset.c line 76 in H5VL__native_dataset_create(): not a datatype ID
    major: Invalid arguments to routine
    minor: Inappropriate type
terminate called after throwing an instance of 'h5::error::io::dataset::create'
  what():  /usr/local/include/h5cpp/H5capi.hpp line#  186 : couldn't create dataset...

std::complex support

Complex numbers are prevalent in signal processing and more generally scientific computing. BLAS | LAPACK supports complex numbers therefore it is reasonable to have the ability to store the content of objects with complex datatypes in a straightforward way. While the HDF5 CAPI doesn't provide predefined complex datatypes ie: H5T_IEEE_C32LE is not present, the library allows creating a custom representation of such types.
Since the in memory layout of std::complex is guaranteed to be contiguous by the c++11 standard section §26.4 see this stack overflow notes the implementation is indeed straightforward and will follow pattern with the newly added half float dataypes

This section is opened to leave comments/observations for the upcoming std::complex support.

Windows Support?

Is there a Windows support?
Can I use this library in the Windows 10 x64 environment?

Error: HDF5 library configure

Following the H5Cpp INSTALL file documentation, I'm trying to configure and install the HDF5 library in my Ubuntu machine.

I downloaded the lasted HDF5 source code from here: official website
Here is my output:

vm@vm:~/Desktop/hdf5-1.10.6$ sudo ./configure --prefix=/usr/local --enable-build-mode=production --enable-shared --enable-static --enable-optimization=high --with-default-api-version=v110

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/home/vm/Desktop/hdf5-1.10.6/bin/missing: line 3: $'\r': command not found
/home/vm/Desktop/hdf5-1.10.6/bin/missing: line 5: $'\r': command not found
/home/vm/Desktop/hdf5-1.10.6/bin/missing: line 8: $'\r': command not found
/home/vm/Desktop/hdf5-1.10.6/bin/missing: line 13: $'\r': command not found
/home/vm/Desktop/hdf5-1.10.6/bin/missing: line 18: $'\r': command not found
/home/vm/Desktop/hdf5-1.10.6/bin/missing: line 21: $'\r': command not found
/home/vm/Desktop/hdf5-1.10.6/bin/missing: line 26: $'\r': command not found
/home/vm/Desktop/hdf5-1.10.6/bin/missing: line 32: syntax error near unexpected token `$'in\r''
'home/vm/Desktop/hdf5-1.10.6/bin/missing: line 32: `case $1 in
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
configure: error: cannot run /bin/bash bin/config.sub

How can I fix it?

My setup is:
OS: Ubuntu 18 x64
HDF5 Library: 1.10.6
gcc version: 7.4.0
CMake version: 3.10.2

Amend README.md for vs2017-windows branch

When porting h5cpp to Visual C++ in the vs2017-windows branch, I am only adapting file source code files in the h5cpp directory. I am not adapting any other files from the master repo.

Perhaps a note to this effect should be added to the main README.md for the vs2017-windows branch.

Also, even though I have included MPI and Kita based h5cpp code in the vs2017-windows branch, perhaps we should note that those feature areas will not work in a Windows environment.

If it is agreed upon, I'll be happy to provide a PR.

h5cpp dumps core w/ before-after, compound, and packet-table

Check this out.

LLVM 7.0.0 and up is crashing

A recent error report by @mrj10 motivated to check compiler compatibility, and as it turns out the LLVM based Clang toolchain is crashing while parsing the C++ templates.
The workaround is to use gcc 7.4.0, gcc 8.3.0, gcc 9.0.1 or clang 6.0.0 until the problem is located and fixed.

Error report: clang_9.0.1-error.tar.gz

Examination of Compiler Compatibility

H5CPP increasing popularity justifies the survey of compiler/OS compatibility starting with Linux, expanding to other mainstream Unix Like OS-s and Windows OS. This thread is to report and accumulate user experiences then take action on acute cases; as well as to aim for thorough treatment across major platform and compilers providing much similar experience as of the HDF5 CAPI.

To facilitate this process feel free to report success or failure on this thread filling in the blanks:
OS: Linux (distro name) | Apple (MAC | IOS | ...) | Windows (version) | ...
C++ Compiler: clang | gcc | ... version
STL: if different from default
HDF5 CAPI: version serial | parallel | VOL
File System: local | pvfs | lustre | Kita S3 | ...
Result: success | failure

Current C++17 compilers are not quite accommodating when reporting template (meta) programming errors, to limit the verbose output please do: make my_target |& head -n20.

= operator overload in H5Dappend.hpp missing return statement

Return statement missing from = operator overload in H5Dappend.hpp (lines 26-28):

pt_t& operator=( h5::pt_t&& pt ){
    init(pt.ds);
}

Request for Example of Creating Group

Can an example be provided for creating a group, assigning attributes to that group, and assigning one or more datasets to the group?

Perhaps I am missing something.

Help on serializing Eigen::Array< double, Eigen::Dynamic, 3, Eigen::RowMajor >

Hello @steven-varga ,

I would like to serialize the following Eigen array, with specific number of columns and memory layout. From a quick read of documentation, I thought the following would work. But compilation log is full of errors. After a careful reading, I see that this king of array is not directly supported. Do I have to go to raw data pointer to serialize my array?

typedef Eigen::Array< double, Eigen::Dynamic, 3, Eigen::RowMajor > ArrayX3D;
ArrayX3D res2 = ArrayX3D::Zero(10, 3);
h5::write(fd, "/res",  res2);

Below is my test program

#include <Eigen/Dense>
typedef Eigen::Array< double, Eigen::Dynamic, 1 > ArrayXD;
typedef Eigen::Array< double, Eigen::Dynamic, 3, Eigen::RowMajor > ArrayX3D;
#include <h5cpp/all>

int main()
{
    ArrayXD res = ArrayXD::Zero(10);
    h5::fd_t fd = h5::create("eigen.h5",H5F_ACC_TRUNC);
    h5::write(fd, "/res",  res);
    ArrayX3D res2 = ArrayX3D::Zero(10, 3);
    h5::write(fd, "/res2",  res2);
    // auto ds_3 = h5::create<double>(fd,"/type/short max_dims", h5::max_dims{res2.rows(),3});
    // h5::write(fd, "/res2",  res2,h5::current_dims{res2.rows(),3});
}

Can't compile 'packet-table' example

I have Eigen installed in /usr/local/include/eigen3 but still get this error:

h5cpp  packettable.cpp -- -std=c++11  -I/usr/local/include -I/usr/local/h5cpp-llvm  -Dgenerated.h
H5CPP: Copyright (c) 2018     , VargaConsulting, Toronto,ON Canada
LLVM : Copyright (c) 2003-2010, University of Illinois at Urbana-Champaign.
g++ -o packettable.o  -std=c++11  -I/usr/local/include -I/usr/local/h5cpp-llvm -c packettable.cpp
packettable.cpp:7:10: fatal error: Eigen/Dense: No such file or directory
 #include <Eigen/Dense> // must include Eigen before <h5cpp/core>
          ^~~~~~~~~~~~~
compilation terminated.

Not sure what's amiss.

Simple example error

Hi, I copy and paste this short example source-code in a new Qt C++ console project (using C++17)

Code example link: http://h5cpp.org/eigen3_8cpp-example.html

And I got these compile time errors:

So I tryed another simple Eigen example:

#include <QCoreApplication>
#include <iostream>
#include <Eigen/Dense> // must include Eigen before <h5cpp/core>
#include <h5cpp/all>

using Eigen::MatrixXd;

int main(int argc, char *argv[])
{
    QCoreApplication a(argc, argv);

    MatrixXd m(2,2);
    m(0,0) = 3;
    m(1,0) = 2.5;
    m(0,1) = -1;
    m(1,1) = m(1,0) + m(0,1);

    h5::fd_t fd = h5::create("some_file.h5", H5F_ACC_TRUNC);
    h5::write(fd,"/result", m);

    return a.exec();
}

And I got a lot of compilation errors again:

What I have to do?

VS 2017 Compiler Errors When h5cpp/all is Included After windows.h

Visual Studio 2017 (v141)
Windows SDK Version: 10.0.17763.0
C++ Language Standard: ISO C++ Latest Draft Standard (/std:c++latest)

These issues is not caused by improvements provided by Commit: 8061fbd or this Pull Request: #20

Compiler reports the following errors when h5cpp/all is included after windows.h. If h5cpp/all is included before windows.h, these errors are not reported.

In: h5zpipeline.hpp

Error	C2589	'(': illegal token on right side of '::'	h5cpptest	c:\users\c drozdowski\source\repos\h5cpptest\h5cpptest\h5cpp\h5zpipeline.hpp	184	
Error	C2589	'(': illegal token on right side of '::'	h5cpptest	c:\users\c drozdowski\source\repos\h5cpptest\h5cpptest\h5cpp\h5zpipeline.hpp	221	

In: h5capi.hpp

Error	C2589	'(': illegal token on right side of '::'	h5cpptest	c:\users\c drozdowski\source\repos\h5cpptest\h5cpptest\h5cpp\h5capi.hpp	217	

I will attempt to find out why the errors are happening and will report if I can find out the answers.

Explanation of Half Float Support Code in H5Tall.hpp

Steve,

Can you provide a brief explanation of the half float support code in H5Tall.hpp ? I don't quite see how the data type is registered, etc. Perhaps big naivety on my part though.

Packet table flush fails with one element in cache.

Hi Steven, good piece of obstruction; I really like this wrapper for hdf5.

The next code

h5::pt_t pt = h5::create<mc:sometype_t>(fd, getDataSetName(),
	h5::max_dims{ H5S_UNLIMITED }, h5::chunk{ 1000 } | h5::gzip{9} );
std::cout << pt;
h5::append( pt, sample );
pt.flush();
std::cout << pt;

will generate output

packet table:
------------------------------------------
rank: 1 N:1000 n:0
element size: 24 block size: 24000
current dims: [0]
chunk dims: [0]
offset : [0] count : [1]
ds: 360287970189639680 dxpl: 720575940379279425
fill value: 0x562efb0632a0 buffer: 0x562efb076f00

HDF5-DIAG: Error detected in HDF5 (1.10.6) thread 0:
  #000: H5Dio.c line 400 in H5Dwrite_chunk(): failure to copy offset array
    major: Dataset
    minor: Can't allocate space
  #001: H5Dio.c line 120 in H5D__get_offset_copy(): offset doesn't fall on chunks's boundary
    major: Dataspace
    minor: Inappropriate type

packet table:
------------------------------------------
rank: 1 N:3e8 n:1
element size: 18 block size: 5dc0
current dims: [1]
chunk dims: [1]
offset : [0] count : [1]
ds: 500000000000000 dxpl: a00000000000041
fill value: 0x562efb0632a0 buffer: 0x562efb076f00

I almost didn't work with hdf5 before, is it some kind of limitation of packet tables or a bug.
I can spend some time to fix it if you give me some clues.

This is not common case to flush chunk with only one element, but I have a system where I don't have constant sample rate and flushing and moving to other table on a timeframe base, so quite possible.

Regards,
Max 73!

Exception Thrown when Using HDF5 1.10.6

Steve,

I compiled h5cpp using HDF5 1.10.6. When I run the compound example, I'm getting an exception in H5Pall.hpp on line 260:

const static h5::elink_acc_flags acc_rdwr{H5F_ACC_RDWR};

No problems with 1.10.5.

If you don't see the same issue with your Linux environment, let me know and I'll provide much more detail.

property lists template parser requires multiple arguments embedded in double braces

error:
auto some_fapl_prop = h5::libver_bounds(H5F_LIBVER_LATEST, H5F_LIBVER_LATEST); or h5::libver_bounds{H5F_LIBVER_LATEST, H5F_LIBVER_LATEST}; fails to parse properly @gheber

workaround is to embed arguments in an extra pair of braces, to force the template parser to recognize std::tuple. This suggested workaround will work even after a fix is provided.

correct syntax until fix:

h5::libver_bounds( { H5F_LIBVER_LATEST, H5F_LIBVER_LATEST } );
or the less visually appealing but functional:
h5::libver_bounds {{ H5F_LIBVER_LATEST, H5F_LIBVER_LATEST }};

explanation:
the arguments require std::tuple<args type> and the correct way to denote this is {arg0, arg1, ..., argn} which is turned into:
std::tuple<type0,type1,...,typen>( arg0, arg1, ..., argn );

this is a compile time operation, doesn't affect performance

c++14 support

I can definitely understand the usage of C++17, but it's still a bit too new for my usages.

I'm not sure how many c++17 features h5cpp uses but one I am seeing is if-constexpr variations.

I see some attempt at constexpr version handling with h5cpp__constexpr, but it seems there's several instances of the if constexprs. I wonder if this is all that stands in the way?

Repo for H5CPP MSVC Specific Examples

Steven,

I created a separate repo for the MSVC specific H5CPP examples I've adapted:
https://github.com/ChrisDrozdowski/h5cpp-msvc-examples

I created it because it is essentially different than the structure of the H5CPP repo and I don't want to mix in Visual studio-specific files such a solution or project files.

Please let me know if you have any issues with this.

hid_t-related compilation errors on recent clang++

I tried to compile ToT of the master branch on macOS, using the default Xcode clang++-based toolchain, and ran into the errors below.

It could be that the first error is the cause of all the rest, I'm not sure.

A using directive with the same name as the enclosing class does seem like a legitimate complaint, but I'm not enough of a template guru to figure out how to fix it :)

In file included from /Users/mrj10/h5cpp/examples/basics/basics.cpp:1:
In file included from /Users/mrj10/h5cpp/h5cpp/all:8:
In file included from /Users/mrj10/h5cpp/h5cpp/core:50:
/Users/mrj10/h5cpp/h5cpp/H5Tall.hpp:24:17: error: member 'hid_t' has the same name as its class
                using parent::hid_t; // is a must because of ds_t{hid_t} ctor 
                              ^
error: no member named '' in 'h5::impl::detail::hid_t<h5::impl::fapl_t, &H5Pclose, true, true, 0>'
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:15:28: note: in instantiation of template class 'h5::impl::detail::hid_t<h5::impl::fapl_t, &H5Pclose, true, true, 1>' requested here
                using hidtype = typename phid_t::parent::hidtype;
                                         ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:69:18: note: in instantiation of template class 'h5::impl::prop_base<h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::fapl_t,
      &H5Pclose, true, true, 1>, &h5::impl::default_fapl, h5::impl::capi_t<long long, H5F_libver_t, H5F_libver_t>, &H5Pset_libver_bounds>,
      h5::impl::detail::hid_t<h5::impl::fapl_t, &H5Pclose, true, true, 1> >' requested here
        struct prop_t : prop_base<prop_t<phid_t,init,capi,capi_call>,phid_t> {
                        ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:215:32: note: in instantiation of template class 'h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::fapl_t, &H5Pclose, true, true,
      1>, &h5::impl::default_fapl, h5::impl::capi_t<long long, H5F_libver_t, H5F_libver_t>, &H5Pset_libver_bounds>' requested here
const static h5::libver_bounds latest_version({H5F_LIBVER_LATEST, H5F_LIBVER_LATEST});
                               ^
error: no member named '' in 'h5::impl::detail::hid_t<h5::impl::lcpl_t, &H5Pclose, true, true, 0>'
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:15:28: note: in instantiation of template class 'h5::impl::detail::hid_t<h5::impl::lcpl_t, &H5Pclose, true, true, 1>' requested here
                using hidtype = typename phid_t::parent::hidtype;
                                         ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:69:18: note: in instantiation of template class 'h5::impl::prop_base<h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::lcpl_t,
      &H5Pclose, true, true, 1>, &h5::impl::default_lcpl, h5::impl::capi_t<long long, H5T_cset_t>, &H5Pset_char_encoding>, h5::impl::detail::hid_t<h5::impl::lcpl_t,
      &H5Pclose, true, true, 1> >' requested here
        struct prop_t : prop_base<prop_t<phid_t,init,capi,capi_call>,phid_t> {
                        ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:242:32: note: in instantiation of template class 'h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::lcpl_t, &H5Pclose, true, true,
      1>, &h5::impl::default_lcpl, h5::impl::capi_t<long long, H5T_cset_t>, &H5Pset_char_encoding>' requested here
const static h5::char_encoding ascii{H5T_CSET_ASCII};
                               ^
error: no member named '' in 'h5::impl::detail::hid_t<h5::impl::lapl_t, &H5Pclose, true, true, 0>'
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:15:28: note: in instantiation of template class 'h5::impl::detail::hid_t<h5::impl::lapl_t, &H5Pclose, true, true, 1>' requested here
                using hidtype = typename phid_t::parent::hidtype;
                                         ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:69:18: note: in instantiation of template class 'h5::impl::prop_base<h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::lapl_t,
      &H5Pclose, true, true, 1>, &h5::impl::default_lapl, h5::impl::capi_t<long long, unsigned int>, &H5Pset_elink_acc_flags>, h5::impl::detail::hid_t<h5::impl::lapl_t,
      &H5Pclose, true, true, 1> >' requested here
        struct prop_t : prop_base<prop_t<phid_t,init,capi,capi_call>,phid_t> {
                        ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:254:34: note: in instantiation of template class 'h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::lapl_t, &H5Pclose, true, true,
      1>, &h5::impl::default_lapl, h5::impl::capi_t<long long, unsigned int>, &H5Pset_elink_acc_flags>' requested here
const static h5::elink_acc_flags acc_rdwr{H5F_ACC_RDWR};
                                 ^
error: no member named '' in 'h5::impl::detail::hid_t<h5::impl::dcpl_t, &H5Pclose, true, true, 0>'
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:15:28: note: in instantiation of template class 'h5::impl::detail::hid_t<h5::impl::dcpl_t, &H5Pclose, true, true, 1>' requested here
                using hidtype = typename phid_t::parent::hidtype;
                                         ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:69:18: note: in instantiation of template class 'h5::impl::prop_base<h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::dcpl_t,
      &H5Pclose, true, true, 1>, &h5::impl::default_dcpl, h5::impl::capi_t<long long>, &H5Pset_fletcher32>, h5::impl::detail::hid_t<h5::impl::dcpl_t, &H5Pclose, true,
      true, 1> >' requested here
        struct prop_t : prop_base<prop_t<phid_t,init,capi,capi_call>,phid_t> {
                        ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:279:31: note: in instantiation of template class 'h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::dcpl_t, &H5Pclose, true, true,
      1>, &h5::impl::default_dcpl, h5::impl::capi_t<long long>, &H5Pset_fletcher32>' requested here
const static flag::fletcher32 fletcher32;
                              ^
error: no member named '' in 'h5::impl::detail::hid_t<h5::impl::ocrl_t, &H5Pclose, true, true, 0>'
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:15:28: note: in instantiation of template class 'h5::impl::detail::hid_t<h5::impl::ocrl_t, &H5Pclose, true, true, 1>' requested here
                using hidtype = typename phid_t::parent::hidtype;
                                         ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:69:18: note: in instantiation of template class 'h5::impl::prop_base<h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::ocrl_t,
      &H5Pclose, true, true, 1>, &h5::impl::default_ocrl, h5::impl::capi_t<long long, unsigned int>, &H5Pset_attr_creation_order>,
      h5::impl::detail::hid_t<h5::impl::ocrl_t, &H5Pclose, true, true, 1> >' requested here
        struct prop_t : prop_base<prop_t<phid_t,init,capi,capi_call>,phid_t> {
                        ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:316:38: note: in instantiation of template class 'h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::ocrl_t, &H5Pclose, true, true,
      1>, &h5::impl::default_ocrl, h5::impl::capi_t<long long, unsigned int>, &H5Pset_attr_creation_order>' requested here
const static h5::attr_creation_order crt_order_tracked{H5P_CRT_ORDER_TRACKED};
                                     ^
error: no member named '' in 'h5::impl::detail::hid_t<h5::impl::ocpl_t, &H5Pclose, true, true, 0>'
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:15:28: note: in instantiation of template class 'h5::impl::detail::hid_t<h5::impl::ocpl_t, &H5Pclose, true, true, 1>' requested here
                using hidtype = typename phid_t::parent::hidtype;
                                         ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:69:18: note: in instantiation of template class 'h5::impl::prop_base<h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::ocpl_t,
      &H5Pclose, true, true, 1>, &h5::impl::default_ocpl, h5::impl::capi_t<long long, unsigned int>, &H5Pset_copy_object>, h5::impl::detail::hid_t<h5::impl::ocpl_t,
      &H5Pclose, true, true, 1> >' requested here
        struct prop_t : prop_base<prop_t<phid_t,init,capi,capi_call>,phid_t> {
                        ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:323:30: note: in instantiation of template class 'h5::impl::prop_t<h5::impl::detail::hid_t<h5::impl::ocpl_t, &H5Pclose, true, true,
      1>, &h5::impl::default_ocpl, h5::impl::capi_t<long long, unsigned int>, &H5Pset_copy_object>' requested here
const static h5::copy_object shallow_hierarchy{H5O_COPY_SHALLOW_HIERARCHY_FLAG};
                             ^
error: no member named '' in 'h5::impl::detail::hid_t<h5::impl::acpl_t, &H5Pclose, true, true, 0>'
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:382:33: note: in instantiation of template class 'h5::impl::detail::hid_t<h5::impl::acpl_t, &H5Pclose, true, true, 1>' requested here
        const static h5::acpl_t acpl = static_cast<h5::acpl_t>( H5P_DEFAULT );
                                       ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:383:33: error: no matching conversion for static_cast from 'hid_t' (aka 'long long') to 'h5::dcpl_t' (aka 'hid_t<h5::impl::dcpl_t,
      &H5Pclose, true, true, detail::hdf5::property>')
        const static h5::dcpl_t dcpl = static_cast<h5::dcpl_t>( H5P_DEFAULT);
                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit copy constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'const h5::impl::detail::hid_t<h5::impl::dcpl_t, &H5Pclose, true, true, 1>' for 1st argument
        struct hid_t final {
               ^
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit move constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'h5::impl::detail::hid_t<h5::impl::dcpl_t, &H5Pclose, true, true, 1>' for 1st argument
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:112:9: note: candidate constructor (the implicit default constructor) not viable: requires 0 arguments, but 1 was provided
        struct hid_t<T,capi_close, true,true,hdf5::property> : public hid_t<T,capi_close,true,true,hdf5::any> {
               ^
error: no member named '' in 'h5::impl::detail::hid_t<h5::impl::dxpl_t, &H5Pclose, true, true, 0>'
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:384:33: note: in instantiation of template class 'h5::impl::detail::hid_t<h5::impl::dxpl_t, &H5Pclose, true, true, 1>' requested here
        const static h5::dxpl_t dxpl = static_cast<h5::dxpl_t>( H5P_DEFAULT );
                                       ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:385:66: error: invalid operands to binary expression ('h5::char_encoding' (aka 'prop_t<hid_t<h5::impl::lcpl_t, &H5Pclose, true, true,
      detail::hdf5::property>, default_lcpl, h5::impl::capi_t<long long, H5T_cset_t>, &H5Pset_char_encoding>') and 'h5::create_intermediate_group' (aka
      'prop_t<hid_t<h5::impl::lcpl_t, &H5Pclose, true, true, detail::hdf5::property>, default_lcpl, h5::impl::capi_t<long long, unsigned int>,
      &H5Pset_create_intermediate_group>'))
        const static h5::lcpl_t lcpl = h5::char_encoding{H5T_CSET_UTF8} | h5::create_intermediate_group{1};
                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:386:33: error: no matching conversion for static_cast from 'hid_t' (aka 'long long') to 'h5::fapl_t' (aka 'hid_t<h5::impl::fapl_t,
      &H5Pclose, true, true, detail::hdf5::property>')
        const static h5::fapl_t fapl = static_cast<h5::fapl_t>( H5P_DEFAULT );
                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit copy constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'const h5::impl::detail::hid_t<h5::impl::fapl_t, &H5Pclose, true, true, 1>' for 1st argument
        struct hid_t final {
               ^
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit move constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'h5::impl::detail::hid_t<h5::impl::fapl_t, &H5Pclose, true, true, 1>' for 1st argument
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:112:9: note: candidate constructor (the implicit default constructor) not viable: requires 0 arguments, but 1 was provided
        struct hid_t<T,capi_close, true,true,hdf5::property> : public hid_t<T,capi_close,true,true,hdf5::any> {
               ^
error: no member named '' in 'h5::impl::detail::hid_t<h5::impl::fcpl_t, &H5Pclose, true, true, 0>'
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:387:33: note: in instantiation of template class 'h5::impl::detail::hid_t<h5::impl::fcpl_t, &H5Pclose, true, true, 1>' requested here
        const static h5::fcpl_t fcpl = static_cast<h5::fcpl_t>( H5P_DEFAULT );
                                       ^
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:389:41: error: no matching conversion for static_cast from 'hid_t' (aka 'long long') to 'h5::acpl_t' (aka 'hid_t<h5::impl::acpl_t,
      &H5Pclose, true, true, detail::hdf5::property>')
        const static h5::acpl_t default_acpl = static_cast<h5::acpl_t>( H5P_DEFAULT );
                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit copy constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'const h5::impl::detail::hid_t<h5::impl::acpl_t, &H5Pclose, true, true, 1>' for 1st argument
        struct hid_t final {
               ^
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit move constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'h5::impl::detail::hid_t<h5::impl::acpl_t, &H5Pclose, true, true, 1>' for 1st argument
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:112:9: note: candidate constructor (the implicit default constructor) not viable: requires 0 arguments, but 1 was provided
        struct hid_t<T,capi_close, true,true,hdf5::property> : public hid_t<T,capi_close,true,true,hdf5::any> {
               ^
In file included from /Users/mrj10/h5cpp/examples/basics/basics.cpp:1:
In file included from /Users/mrj10/h5cpp/h5cpp/all:8:
In file included from /Users/mrj10/h5cpp/h5cpp/core:52:
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:390:41: error: no matching conversion for static_cast from 'hid_t' (aka 'long long') to 'h5::dcpl_t' (aka 'hid_t<h5::impl::dcpl_t,
      &H5Pclose, true, true, detail::hdf5::property>')
        const static h5::dcpl_t default_dcpl = static_cast<h5::dcpl_t>( H5P_DEFAULT );
                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit copy constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'const h5::impl::detail::hid_t<h5::impl::dcpl_t, &H5Pclose, true, true, 1>' for 1st argument
        struct hid_t final {
               ^
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit move constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'h5::impl::detail::hid_t<h5::impl::dcpl_t, &H5Pclose, true, true, 1>' for 1st argument
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:112:9: note: candidate constructor (the implicit default constructor) not viable: requires 0 arguments, but 1 was provided
        struct hid_t<T,capi_close, true,true,hdf5::property> : public hid_t<T,capi_close,true,true,hdf5::any> {
               ^
In file included from /Users/mrj10/h5cpp/examples/basics/basics.cpp:1:
In file included from /Users/mrj10/h5cpp/h5cpp/all:8:
In file included from /Users/mrj10/h5cpp/h5cpp/core:52:
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:391:41: error: no matching conversion for static_cast from 'hid_t' (aka 'long long') to 'h5::dxpl_t' (aka 'hid_t<h5::impl::dxpl_t,
      &H5Pclose, true, true, detail::hdf5::property>')
        const static h5::dxpl_t default_dxpl = static_cast<h5::dxpl_t>( H5P_DEFAULT );
                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit copy constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'const h5::impl::detail::hid_t<h5::impl::dxpl_t, &H5Pclose, true, true, 1>' for 1st argument
        struct hid_t final {
               ^
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit move constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'h5::impl::detail::hid_t<h5::impl::dxpl_t, &H5Pclose, true, true, 1>' for 1st argument
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:112:9: note: candidate constructor (the implicit default constructor) not viable: requires 0 arguments, but 1 was provided
        struct hid_t<T,capi_close, true,true,hdf5::property> : public hid_t<T,capi_close,true,true,hdf5::any> {
               ^
In file included from /Users/mrj10/h5cpp/examples/basics/basics.cpp:1:
In file included from /Users/mrj10/h5cpp/h5cpp/all:8:
In file included from /Users/mrj10/h5cpp/h5cpp/core:52:
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:392:74: error: invalid operands to binary expression ('h5::char_encoding' (aka 'prop_t<hid_t<h5::impl::lcpl_t, &H5Pclose, true, true,
      detail::hdf5::property>, default_lcpl, h5::impl::capi_t<long long, H5T_cset_t>, &H5Pset_char_encoding>') and 'h5::create_intermediate_group' (aka
      'prop_t<hid_t<h5::impl::lcpl_t, &H5Pclose, true, true, detail::hdf5::property>, default_lcpl, h5::impl::capi_t<long long, unsigned int>,
      &H5Pset_create_intermediate_group>'))
        const static h5::lcpl_t default_lcpl = h5::char_encoding{H5T_CSET_UTF8} | h5::create_intermediate_group{1};
                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:393:41: error: no matching conversion for static_cast from 'hid_t' (aka 'long long') to 'h5::fapl_t' (aka 'hid_t<h5::impl::fapl_t,
      &H5Pclose, true, true, detail::hdf5::property>')
        const static h5::fapl_t default_fapl = static_cast<h5::fapl_t>( H5P_DEFAULT );
                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit copy constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'const h5::impl::detail::hid_t<h5::impl::fapl_t, &H5Pclose, true, true, 1>' for 1st argument
        struct hid_t final {
               ^
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit move constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'h5::impl::detail::hid_t<h5::impl::fapl_t, &H5Pclose, true, true, 1>' for 1st argument
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:112:9: note: candidate constructor (the implicit default constructor) not viable: requires 0 arguments, but 1 was provided
        struct hid_t<T,capi_close, true,true,hdf5::property> : public hid_t<T,capi_close,true,true,hdf5::any> {
               ^
In file included from /Users/mrj10/h5cpp/examples/basics/basics.cpp:1:
In file included from /Users/mrj10/h5cpp/h5cpp/all:8:
In file included from /Users/mrj10/h5cpp/h5cpp/core:52:
/Users/mrj10/h5cpp/h5cpp/H5Pall.hpp:394:41: error: no matching conversion for static_cast from 'hid_t' (aka 'long long') to 'h5::fcpl_t' (aka 'hid_t<h5::impl::fcpl_t,
      &H5Pclose, true, true, detail::hdf5::property>')
        const static h5::fcpl_t default_fcpl = static_cast<h5::fcpl_t>( H5P_DEFAULT );
                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit copy constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'const h5::impl::detail::hid_t<h5::impl::fcpl_t, &H5Pclose, true, true, 1>' for 1st argument
        struct hid_t final {
               ^
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:53:9: note: candidate constructor (the implicit move constructor) not viable: no known conversion from 'hid_t' (aka 'long long') to
      'h5::impl::detail::hid_t<h5::impl::fcpl_t, &H5Pclose, true, true, 1>' for 1st argument
/Users/mrj10/h5cpp/h5cpp/H5Iall.hpp:112:9: note: candidate constructor (the implicit default constructor) not viable: requires 0 arguments, but 1 was provided
        struct hid_t<T,capi_close, true,true,hdf5::property> : public hid_t<T,capi_close,true,true,hdf5::any> {
               ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.

Tensor support

Where the Matrix is just not enough, there exists Tensor.

This page is to report request or possible mishaps while I am adding tensor support to H5CPP. The list here lifted from StackOverflow

• ftensor
• eigen tensor
• taco
• xtensor
• dealii
• boost tensor extension
• tensor by Juan José García Ripoll
• DyND
• ltensor
• itensor
• acrotensor
• tensors nongnu

Clang (LLVM) Windows Issue

Clang 9.0.0 (LLVM) Visual Studio 2019 as IDE.

Using my h5cpp-windows version of h5cpp, some examples compile fine, some fail (e.g. stl) with this error:

h5cpp/H5Dwrite.hpp(60): error : call to 'write' is ambiguous

Do you have a suggestion on which direction to go to address this issue? Is it not seen on different platforms?

Half-precision float support?

Hi! I want to know, is there any methods for me to use fp16 in hdf5-C++?

I intend to use the Half precision floating-point format for storing data that do not need as much precision in order to save space. So does this code support half-precision float storage?

I know that h5py provides an option to store data as fp16, like this:

file.create_dataset(key, data=data,  dtype = np.float16)

But no predefined type provided for fp16 storage on the official documentation of hdf5 for C++ , linking here https://support.hdfgroup.org/HDF5/doc1.8/RM/PredefDTypes.html. And I found hdf5 has an C interface named H5Tset_precision, so does this interface have a corresponding implementation in h5cpp?

memset requires cstring include

Please include <cstring> in h5cpp/core.

Error in ublas example

g++ ublas.cpp -lhdf5 -lz -ldl -lm  -o ublas
HDF5-DIAG: Error detected in HDF5 (1.11.3) thread 0:
  #000: H5Dio.c line 322 in H5Dwrite(): could not get a validated dataspace from file_space_id
    major: Invalid arguments to routine
    minor: Bad value
  #001: H5S.c line 254 in H5S_get_validated_dataspace(): selection + offset not within extent
    major: Dataspace
    minor: Out of range
   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
   3.0000   3.0000   3.0000   3.0000   1.0000   3.0000   1.0000   3.0000   1.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
   3.0000   3.0000   3.0000   3.0000   1.0000   3.0000   1.0000   3.0000   1.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000   3.0000
HDF5-DIAG: Error detected in HDF5 (1.11.3) thread 0:
  #000: H5Dio.c line 322 in H5Dwrite(): could not get a validated dataspace from file_space_id
    major: Invalid arguments to routine
    minor: Bad value
  #001: H5S.c line 254 in H5S_get_validated_dataspace(): selection + offset not within extent
    major: Dataspace
    minor: Out of range
HDF5-DIAG: Error detected in HDF5 (1.11.3) thread 0:
  #000: H5Dio.c line 322 in H5Dwrite(): could not get a validated dataspace from file_space_id
    major: Invalid arguments to routine
    minor: Bad value
  #001: H5S.c line 254 in H5S_get_validated_dataspace(): selection + offset not within extent
    major: Dataspace
    minor: Out of range
HDF5-DIAG: Error detected in HDF5 (1.11.3) thread 0:
  #000: H5Dio.c line 322 in H5Dwrite(): could not get a validated dataspace from file_space_id
    major: Invalid arguments to routine
    minor: Bad value
  #001: H5S.c line 254 in H5S_get_validated_dataspace(): selection + offset not within extent
    major: Dataspace
    minor: Out of range
HDF5-DIAG: Error detected in HDF5 (1.11.3) thread 0:
  #000: H5Dio.c line 322 in H5Dwrite(): could not get a validated dataspace from file_space_id
    major: Invalid arguments to routine
    minor: Bad value
  #001: H5S.c line 254 in H5S_get_validated_dataspace(): selection + offset not within extent
    major: Dataspace
    minor: Out of range
make[1]: Leaving directory '/home/ubuntu/h5cpp/examples/linalg'
make -C raw_memory
make[1]: Entering directory '/home/ubuntu/h5cpp/examples/raw_memory'
g++ -std=c++11 -Wno-deprecated   -c -o raw.o raw.cpp
g++ raw.o -lhdf5  -lz -ldl -lm -o raw
valued read: 2 3 4 5 6 7 8 9 0 0 
h5dump -d dataset raw.h5
HDF5 "raw.h5" {
DATASET "dataset" {
   DATATYPE  H5T_IEEE_F64LE
   DATASPACE  SIMPLE { ( 1, 10 ) / ( 1, 10 ) }
   DATA {
   (0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9
   }
}
}

H5CPP on android armv7f

Currently the HDF5 library is hard to cross compile because of some internals, to ease on the process here are the binaries: hdf5-1.10.6-arm7f.tar.gz

The H5CPP library is currently broken for android armv7f platform due to the size differences between some integral types, however only minor adjustment is needed to make this port happen. Will keep this errata up until the fix is provided.