HDC - Hierarchical Dynamic Containers {#mainpage}

HDC is tiny library for exchanging hierarchical data (arrays of structures) in shared memory between multiple programming languages, currently supporting C, C++, Python, Fortran and MATLAB.

Repository

The master repository lives in IPP CAS gitlab instance.

The bitbucket repo is just a read-only mirror.

The access to the master repo can be requested via email fridrich at ipp.cas.cz

API documentation

The API documentation is available here.

Prerequisites

To build HDC, you will need:

c++14 compliant compiler (tested with intelstudio>=2018 and gcc>=5.0)
gfortran >= 4.9
Boost >= 1.48
CMake >= 3.3
Doxygen for documentation building
Cython > 0.23 (there is some parsing error in 0.23)

Optionally it can use:

Python > 3.4 (Python HDC bindings "pyHCD" and hdc-binder support)
MATLAB > 2018a (MATLAB mex interface)
Yahoo MDBM (recommended storage plugin working within shared memory)
Redis + libhiredis-dev (storage plugin working within distributed memory)
HDF5 devel libraries ((de)serialization, tested with 1.8 and 1.10)
libs3 ((de)serialization plugin)
flatbuffers ((de)serialization plugin)

Supported OS:

Currently all commits are automatically tested against:

Ubuntu 16.04 (xenial)
Ubuntu 18.04 (bionic)
Ubuntu 20.04 (focal)
Fedora 31
Centos 7

But HDC should work on any not-too-obsolette distro. If you face any problems, please, report it via email or project issue tracker.

Building HDC

Machine specific build instructions are available here.

There are several cmake options. The most important are:

-DCMAKE_INSTALL_PREFIX=/where/to/install make install destination.
-DBUILD_DOC=ON Whether to build and install documentation.
-DBUILD_EXAMPLES=ON Whether to build and install examples.
-DENABLE_HDF5=OFF Switch off HDF5 serialization.
Python, if not detected correctly:
- -DPYTHON_LIBRARY=/path/to/libpython.so
- -DPYTHON_INCLUDE_DIR=/path/to/python/include
-DDEBUG=ON Whether to print debugging messages.

Some of them can be edited using ccmake . in build directory.

The example of build follows:

clone the git repository

git clone git@bitbucket.org:compass-tokamak/hdc.git
# cd into hdc
cd hdc

build in a separate build directory

export HDC_PREFIX=$PWD/install
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$HDC_PREFIX
make -j install

Building Python bindings

Important: numpy must be installed before pyhdc.

cd  python
python setup.py build
python setup.py install
cd ..

Optionally, run Python tests:

cd python
python setup.py test
cd tests_binder
./run
cd ..

General note for some bindings (embedded vs. standalone builds)

Especially for use with multiple compiler/library versions, HDC supports two ways of of building its binding interfaces. Currently this holds for FORTRAN, MATLAB and JAVA. Unless you need the same HDC with e.g. multiple MATLAB versions, you should use embedded build, which is set by adding -DENABLE_<LANG>=TRUE to cmake arguments - e.g.:

 cmake .. -DCMAKE_INSTALL_PREFIX=$HDC_PREFIX -DENABLE_MATLAB=TRUE -DENABLE_FORTRAN=TRUE - DENABLE_JAVA=TRUE

in this way, cmake adds specific subdirectories and tries to build everything at once.

On contrary, setting -DENABLE_<LANG>=FALSE prevents <LANG> binding from being built. After you install HDC and set up PKG_CONFIG_PATH:

export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HDC_PREFIX/lib/pkgconfig

The complete how to is in the next sections.

Building FORTRAN bindings (embedded)

Just append -DENABLE_FORTRAN=TRUE to your cmake command:

 cmake .. -DCMAKE_INSTALL_PREFIX=$HDC_PREFIX -DENABLE_FORTRAN=TRUE

and you are done, make will do the rest

Building FORTRAN bindings (standalone)

Disable fortran by adding -DENABLE_FORTRAN=FALSE to your cmake - e.g.:

 cmake .. -DCMAKE_INSTALL_PREFIX=$HDC_PREFIX -DENABLE_FORTRAN=FALSE

Now you can cd into binding directory and run:

cd fortran
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$HDC_PREFIX
make -j
make install

Done. You should have it installed.

Building MATLAB bindings (embedded)

Make matlab and mex binaries findable (e.g. by modifying PATH environment variable, or by loading module), then you jus need to provide -DENABLE_MATLAB=TRUE on cmake line, i.e.:

 cmake .. -DCMAKE_INSTALL_PREFIX=$HDC_PREFIX -DENABLE_MATLAB=TRUE

Building MATLAB bindings (standalone)

export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HDC_PREFIX/lib/pkgconfig
cd matlab
mkdir build
cd build
make -j
LD_LIBRARY_PATH=../../install/lib matlab -nojvm -r "run('test_matlab')"

You should see "All tests are OK..." message - in such case, the mex interface should work fine...

Installation is up to you, e.g.:

cp *.m *.mexa64 /desired/matlab/stuff/dir

Building Java bindings (embedded)

jHDC build requires maven and openjdk-8-jdk-headless or another JDK (not tested). Please ensure you have these installed. There are several cmake options for jHDC:

-DENABLE_JAVA Enable JAVA support (OFF by default).
-DJAR_INSTALL_PREFIX Where to install resulting jar(s) (Defaults to ${CMAKE_INSTALL_PREFIX}/share/java).
-DINSTALL_JAVA_DEPENDENCIES Whether to install also dependencies (OFF by default). If enabled, all jars are put into $JAR_INSTALL_PREFIX.
-DJAR_WITH_DEPENDENCIES Build jar with all dependencies bundled inside. The result can be quite large, but no dependencies are needed. (OFF by default).
-DJAVACPP_PLATFORM Build bundled jar with only specified arch (linux-x86_64 by default). This reduces the jar size from ~460MB to ~80MB. Anybody loving huge jars can set empty string here. Detailed description here.

Clearly, not all combinations of these options make sense, but making some of them dependent does not make the sense either.

Usually you would want either:

-DENABLE_JAVA=ON -DINSTALL_JAVA_DEPENDENCIES=ON --DJAR_WITH_DEPENDENCIES=OFF

or:

-DENABLE_JAVA=ON -DJAR_WITH_DEPENDENCIES=ON -DJAVACPP_PLATFORM=linux-x86_64

depending on your preferences.

How to run jHDC example is described here.

Building Java bindings (standalone)

CMAKE options remain the same as for embedded build

cd java
mkdir build
cd build
make -j
make install

Building using IntelStudio

Instrucions are similar as above, just setup your environment and CC,CXX and FORTRAN variables:
source /sw/intel/parallel_studio_xe_2018/psxevars.sh
CC=icc FORTRAN=ifort CXX=icpc cmake .. -DCMAKE_INSTALL_PREFIX=$PWD/../install

Contributing

Everyone is welcome to contribute. Please use Git and merge resquest.

Versioning

bumpversion is used for maintaining version consistently across the repository and files.

To create a new version, use

bumpversion PART

where PART is either patch, minor or major.

Git repository needs to be synchronized afterwards:

git push
git push --tags

Basic ideas

The hierarchical structure is organized as tree.
Subtrees (Nodes) can be accessed by path similarily to file system paths like "aaa/bbb"
Each node can be one of several types:
- Empty node - this is the initial state of node. Empty node does not store any data and does not have any children. By adding subnode, slice or data it's type is automaticaly changed to another type.
- Structure/list node - the node has at least one children indexed by string path. It can only store subtrees indexed by path/integer index.
- Array node - the node has at least one children indexed by integer. It can only store subtrees indexed by integer.
- Data node - it only can be terminal node, it stores some data, currently char* buffer.

Path syntax

If working directly with HDC tree (i.e.: methods like get(), put(), set()) The path string is internally converted to

hdc_path_t = std::list<hdc_index_t>

type where

hdc_index_t = boost::variant<size_t, std::string>

type represents single level of path. Therefore every tree node can be refferenced by:

empty string representing identity, e.g.: "//" is ommited unless part of protocol specification like "json://"
key (string) referencing children of hash map/dict
index (non-negative integer) for referencing value in list/array Individual keys are separated by slash, indexes are surrounded by brakets.

For example the following string

"aaa/bbb//ccc[5]/ddd"

represents the following node within the HDC tree:

"aaa" -> "bbb" -> "ccc" -> 5 -> "ddd"

For loading from or saving to outside HDC tree (methods load() and save() ), one has to also specify protocol and file path. Is such case there are two ekvivalent options:

protocol+file path and the path within the file data are concatenated using pipe character |: HDC n = HDC::load("protocol://path/to/file|path/within/the/file")
two arguments are provided: HDC n = HDC::load("protocol://path/to/file", "path/within/the/file")

Internally the first option calls the second one, so usage of the second form spares some method calls.

The supported protocols are:

json
json_string
json_verbose
uda
uda_new
hdf5
hdc_file
hdc_string
flatbuffers
s3

Examples

The basic examples can be found in examples folder. The executables are built in CMAKE_BUILD_DIR/bin directory.

The Python examples can be run from any arbitraty folder, the only necessary thing is to set LD_LIBRARY_PATH properly:

LD_LIBRARY_PATH="../build/lib/" ipython hdc_fortran_module.py

Some benchmarks

See this file

Next steps

Read-only and/or copy-on-write potection of data.
File systems and database access (key-value, object stores) via the HDC API.
Support for metadata.
A plugin system for, e.g., data systems validation or conversion, object-oriented features (methods for particular data types), ...
Support for scientific data: dimensions, units, etc.
More features: slicing, lazy evaluation, richer API, ...

Compared to ...

HDF5

HDC holds data buffers in (shared) memory, hence passing HDC containers means
- no data copy,
- no serialization / deserialization,
- better performace.
HDC is written in C++ with bindings to Fortran, C, Python, MATLAB and other languages in mind.
HDC API can abstract out various back-end storage solutions: file systems, key-value stores, clouds, ...

Conduit

Citing Conduit: provides an intuitive model for describing hierarchical scientific data in C++, C, Fortran, and Python and is used for data coupling between packages in-core, serialization, and I/O tasks.

HDC supports (in private/shared memory) zero-copy data access.
The goals are very close to ours, the way is slightly different.

ukaea / hdc