CHANGELOG.md

Conduit Changelog

Notable changes to Conduit are documented in this file.

The format is based on Keep a Changelog, and this project aspires to adhere to Semantic Versioning.

Unreleased

Changed

General

• Conduit now requires C++11 support.

Added

• CMake: Added extra check for include dir vs fully resolved hdf5 path.

General

• Added a builtin sandboxed header-only version of fmt. The namespace and directory paths were changed to conduit_fmt to avoid potential symbol collisions with other codes using fmt. Downstream software can use by including conduit_fmt/conduit_fmt.h.
• Added support for using C++11 initializer lists to set Node and DataArray values from numeric arrays. See C++ tutorial docs (https://llnl-conduit.readthedocs.io/en/latest/tutorial_cpp_numeric.html#c-11-initializer-lists) for more details.
• Added a Node::describe() method. This method creates a new node that mirrors the current Node, however each leaf is replaced by summary stats and a truncated display of the values. For use cases with large leaves, printing the describe() output Node is much more helpful for debugging and understanding vs wall of text from other to_string() methods.

Relay

• Added Relay IO Handle mode support for a (append) and t (truncate). Truncate allows you to overwrite files when the handle is opened. The default is append, which preserves prior IO Handle behavior.
• Added conduit::relay::io::blueprint::save_mesh variants, these overwrite existing files (providing relay save semantics) instead of adding mesh data to existing files. We recommend using save_mesh for most uses cases, b/c in many cases write_mesh to an existing HDF5 file set can fail due to conflicts with the current HDF5 tree.
• Added conduit::relay::io::blueprint::load_mesh variants, these reset the passed node before reading mesh data (providing relay load semantics). We recommend using load_mesh for most uses cases.
• Added truncate option to conduit::relay::io::blueprint::write_mesh, this is used by save_mesh.
• Improve capture and reporting of I/O errors in conduit::relay::[mpi::]io::blueprint::{save_mesh|write_mesh}. Now in the MPI case, If any rank fails to open or write to a file all ranks will throw an exception.

[0.6.0] - Released 2020-11-02

Added

General

• Added support for children with names that include /. Since slashes are part of Conduit's hierarchical path mechanism, you must use explicit methods (add_child(), child(), etc) to create and access children with these types of names. These names are also supported in all basic i/o cases (JSON, YAML, Conduit Binary).
• Added Node::child and Schema::child methods, which provide access to existing children by name.
• Added Node::fetch_existing and Schema::fetch_existing methods, which provide access to existing paths or error when given a bad path.
• Added Node::add_child() and Node::remove_child() to support direct operations and cases where names have / s.
• Added a set of conduit::utils::log::remove_* filtering functions, which process conduit log/info nodes and strip out the requested information (useful for focusing the often verbose output in log/info nodes).
• Added to_string() and to_string_default() methods to Node, Schema, DataType, and DataArray. These methods alias either to_yaml() or to_json(). Long term yaml will be preferred over json.
• Added helper script (scripts/regen_docs_outputs.py) that regenerates all example outputs used Conduit's Sphinx docs.
• Added to_yaml() and to_yaml_stream methods() to Schema, DataType, and DataArray.
• Added support for C++-style iterators on node children. You can now do for (Node &node : node.children()) {}. You can also do node.children.begin() and node.children.end() to work with the iterators directly.

Relay

• Added an open mode option to Relay IOHandle. See Relay IOHandle docs (https://llnl-conduit.readthedocs.io/en/latest/relay_io.html#relay-i-o-handle-interface) for more details.
• Added the conduit.relay.mpi Python module to support Relay MPI in Python.
• Added support to write and read Conduit lists to HDF5 files. Since HDF5 Groups do not support unnamed indexed children, each list child is written using a string name that represents its index and a special attribute is written to the HDF5 group to mark the list case. On read, the special attribute is used to detect and read this style of group back into a Conduit list.
• Added preliminary support to read Sidre Datastore-style HDF5 using Relay IOHandle, those grouped with a root file.
• Added conduit::relay::io::blueprint::read_mesh functions, were pulled in from Ascent's Blueprint import logic.
• Added conduit::relay::mpi::wait and conduit::relay::mpi::wait_all functions. These functions consolidate the logic supporting both isend and irecv requests. wait_all supports cases where both sends and receives were posted, which is a common for non-trivial point-to-point communication use cases.

Blueprint

• Added support for sparse one-to-many relationships with the new blueprint::o2mrelation protocol. See the blueprint::o2mrelation::examples::uniform example for details.
• Added sparse one-to-many, uni-buffer, and material-dominant specification support to Material sets. See the Material sets documentation (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#material-sets) for more details.
• Added support for Adjacency sets for Structured Mesh Topologies. See the blueprint::mesh::examples::adjset_uniform example.
• Added blueprint::mesh::examples::julia_nestsets_simple and blueprint::mesh::examples::julia_nestsets_complex examples represent Julia set fractals using patch-based AMR meshes and the Mesh Blueprint Nesting Set protocol. See the Julia AMR Blueprint docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#julia-amr-examples) for more details.
• Added blueprint::mesh::examples::venn example that demonstrates different ways to encode volume fraction based multi-material fields. See the Venn Blueprint docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#venn) for more details.
• Added blueprint::mesh::number_of_domains property method for trees that conform to the mesh blueprint.
• Added MPI mesh blueprint methods, blueprint::mpi::mesh::verify and blueprint::mpi::mesh::number_of_domains (available in the conduit_blueprint_mpi library)
• Added blueprint::mpi::mesh::examples::braid_uniform_multi_domain and blueprint::mpi::mesh::examples::spiral_round_robin distributed-memory mesh examples to the conduit_blueprint_mpi library.
• Added state/path to the Mesh Blueprint index, needed for consumers to know the proper path to read extended state info (such as domain_id)

Fixed

General

• Updated to newer BLT to resolve BLT/FindMPI issues with rpath linking commands when using OpenMPI.
• Fixed internal object name string for the Python Iterator object. It used to report Schema, which triggered both puzzling and concerned emotions.
• Fixed a bug with Node.set in the Python API that undermined setting NumPy arrays with sliced views and complex striding. General slices should now work with set. No changes to the set_external case, which requires 1-D effective striding and throws an exception when more complex strides are presented.
• Fixed a bug with auto detect of protocol for Node.load
• Fixed bugs with auto detect of protocol for Node.load and Node.save in the Python interface

Relay

• Use H5F_ACC_RDONLY in relay::io::is_hdf5_file to avoid errors when checking files that already have open HDF5 handles.
• Fixed compatibility check for empty Nodes against HDF5 files with existing paths

Changed

General

• Conduit's main git branch was renamed from master to develop. To allow time for folks to migrate, the master branch is active but frozen and will be removed during the 0.7.0 release.
• We recommend a C++11 (or newer) compiler, support for older C++ standards is deprecated and will be removed in a future release.
• Node::fetch_child and Schema::fetch_child are deprecated in favor of the more clearly named Node::fetch_existing and Schema::fetch_existing. fetch_child variants still exist, but will be removed in a future release.
• Python str() methods for Node, Schema, and DataType now use their new to_string() methods.
• DataArray::to_json(std::ostring &) is deprecated in favor DataArray::to_json_stream. to_json(std::ostring &) will be removed in a future release.
• Schema::to_json and Schema::save variants with detailed (bool) arg are deprecated. The detailed arg was never used. These methods will be removed in a future release.
• Node::print() now prints yaml instead of json.
• The string return variants of about methods now return yaml strings instead of json strings.
• Sphinx Docs code examples and outputs are now included using start-after and end-before style includes.
• Schema to_json() and to_json_stream() methods were expanded to support indent, depth, pad and end-of-element args.
• In Python, conduit.Node() repr now returns the YAML string representation of the Node. Perviously verbose conduit_json was used, which was overwhelming.
• conduit.about() now reports the git tag if found, and version was changed to add git sha and status (dirty) info to avoid confusion between release and development installs.

Relay

• Provide more context when a Conduit Node cannot be written to a HDF5 file because it is incompatible with the existing HDF5 tree. Error messages now provide the full path and details about the incompatibility.
• conduit::relay::io_blueprint::save functions are deprecated in favor of conduit::relay::io::blueprint::write_mesh
• conduit::relay::io::blueprint::write_mesh functions were pulled in from Ascent's Blueprint export logic.
• conduit_relay_io_mpi lib now depends on conduit_relay_io. Due to this change, a single build supports either ADIOS serial (no-mpi) or ADIOS with MPI support, but not both. If conduit is configured with MPI support, ADIOS MPI is used.
• The functions conduit::relay::mpi::wait_send and conduit::relay::mpi::wait_recv now use conduit::relay::mpi::wait. The functions wait_send and wait_recv exist to preserve the old API, there is no benefit to use them over wait.
• The functions conduit::relay::mpi::wait_all_send and conduit::relay::mpi::wait_all_recv now use conduit::relay::mpi::wait_all. The functions wait_all_send and wait_all_recv exist to preserve the old API, there is no benefit to use them over wait_all.

Blueprint

• Refactored the Polygonal and Polyhedral mesh blueprint specification to leverage one-to-many concepts and to allow more zero-copy use cases.
• The conduit_blueprint_mpi library now depends on conduit_relay_mpi.
• The optional Mesh Blueprint structured topology logical element origin is now specified using {i,j,k} instead of {i0,j0,k0}.

0.5.1 - Released 2020-01-18

Added

General

• Added Node::parse() method, (C++, Python and Fortran) which supports common json and yaml parsing use cases without creating a generator instance.
• Use FOLDER target property to group targets for Visual Studio
• Added Node load(), and save() support to the C and Fortran APIs

Changed

General

• Node::load() and Node::save() now auto detect which protocol to use when protocol argument is an empty string
• Changed Node::load() and Node::save() default protocol value to empty (default now is to auto detect)
• Changed Python linking strategy to defer linking for our compiler modules
• Conduit Error Exception message strings now print cleaner (avoiding nesting doll string escaping headaches)
• Build system improvements to support conda-forge builds for Linux, macOS, and Windows

Fixed

General

• Fixed install paths for CMake exported target files to follow standard CMake find_package() search conventions. Also perserved duplicate files to support old import path structure for this release.
• python: Fixed Node.set_external() to accept conduit nodes as well as numpy arrays
• Fixed dll install locations for Windows

0.5.0 - Released 2019-10-25

Added

General

• Added support to parse YAML into Conduit Nodes and to create YAML from Conduit Nodes. Support closely follows the "json" protocol, making similar choices related to promoting YAML string leaves to concrete data types.
• Added several more Conduit Node methods to the C and Fortran APIs. Additions are enumerated here: #426
• Added Node set support for Python Tuples and Lists with numeric and string entires
• Added Node set support for Numpy String Arrays. String Arrays become Conduit lists with child char8_str arrays

Blueprint

• Added support for a "zfparray" blueprint that holds ZFP compressed array data.
• Added the the "specsets" top-level section to the Blueprint schema, which can be used to represent multi-dimensional per-material quantities (most commonly per-material atomic composition fractions).
• Added explicit topological data generation functions for points, lines, and faces
• Added derived topology generation functions for element centroids, sides, and corners
• Added the basic example function to the conduit.mesh.blueprint.examples module

Relay

• Added optional ZFP support to relay, that enables wrapping and unwraping zfp arrays into conduit Nodes.
• Extended relay HDF5 I/O support to read a wider range of HDF5 string representations including H5T_VARIABLE strings.

Changed

General

• Conduit's automatic build process (uberenv + spack) now defaults to using Python 3
• Improved CMake export logic to make it easier to find and use Conduit install in a CMake-based build system. (See using-with-cmake example for new recipe)

Relay

• Added is_open() method to IOHandle in the C++ and Python interfaces
• Added file name information to Relay HDF5 error messages

Fixed

General

• Fixed bug that caused memory access after free during Node destruction

Relay

• Fixed crash with mpi broadcast_using_schema() when receiving tasks pass a non empty Node.
• Fixed a few Windows API export issues for relay io

0.4.0 - Released 2019-03-01

Added

General

• Added Generic IO Handle class (relay::io::IOHandle) with C++ and Python APIs, tests, and docs.
• Added rename_child method to Schema and Node
• Added generation and install of conduit_config.mk for using-with-make example
• Added datatype helpers for long long and long double
• Added error for empty path fetch
• Added C functions for setting error, warning, info handlers.
• Added limited set of C bindings for DataType
• Added C bindings for relay IO
• Added several more functions to conduit node python interfaces

Blueprint

• Added implicit point topology docs and example
• Added julia and spiral mesh bp examples
• Added mesh topology transformations to blueprint
• Added polygonal mesh support to mesh blueprint
• Added verify method for mesh blueprint nestset

Relay

• Added ADIOS Support, enabling ADIOS read and write of Node objects.
• Added a relay::mpi::io library that mirrors the API of relay::io, except that all functions take an MPI communicator. The functions are implemented in parallel for the ADIOS protocol. For other protocols, they will behave the same as the serial functions in relay::io. For the ADIOS protocol, the save() and save_merged() functions operate collectively within a communicator to enable multiple MPI ranks to save data to a single file as separate "domains".
• Added an add_time_step() function to that lets the caller append data collectively to an existing ADIOS file
• Added a function to query the number of time steps and the number of domains in a ADIOS file.
• Added versions of save and save_merged that take an options node.
• Added C API for new save, save_merged functions.
• Added method to list an HDF5 group's child names
• Added save and append methods to the HDF5 I/O interface
• Added docs and examples for relay io

Changed

General

• Changed mapping of c types to bit-width style to be compatible with C++11 std bit-width types when C++11 is enabled
• Several improvements to uberenv, our automated build process, and building directions
• Upgraded the type system with more explicit signed support

Relay

• Improvements to the Silo mesh writer
• Refactor to support both relay::io and relay::mpi::io namespaces.
• Refactor to add support for steps and domains to I/O interfaces
• Changed to only use libver latest setting for for hdf5 1.8 to minimize compatibility issues

Fixed

General

• Fixed bugs with std::vector gap methods
• Fixed A few C function names in conduit_node.h
• Fixed bug in python that was requesting unsigned array for signed cases
• Fixed issue with Node::diff failing for string data with offsets
• Fixes for building on BlueOS with the xl compiler

Blueprint

• Fixed validity status for blueprint functions
• Fixed improper error reporting for Blueprint references

Relay

• Relay I/O exceptions are now forwarded to python
• Fixed MPI send_with_schema bug when data was compact but not contiguous
• Switched to use MPI bit-width style data type enums in relay::mpi

0.3.1 - Released 2018-02-26

Added

General

• Added new Node::diff and Node::diff_compatible methods
• Expanded the Node Python Capsule API
• Added Python version of basic tutorial

Blueprint

• Added Multi-level Array Protocol (conduit::blueprint::mlarray)

Changed

General

• Updated uberenv to use a newer spack and removed several custom packages
• C++ Node::set methods now take const pointers for data

Fixed

General

• Various Python API bug fixes
• Fixed API exports for static libs on Windows

Relay

• Bug fixes for HDF5 support on Windows

Removed

Blueprint

• Removed unnecessary state member in the braid example

0.3.0 - Released 2017-08-21

Added

General

• Exposed more of the Conduit API in Python

Blueprint

• Added support for multi-material fields via matsets (volume fractions and per-material values)
• Added initial support for domain boundary info via adjsets for distributed-memory unstructured meshes

Relay

• Added support for MPI reductions and broadcast
• Added support zero-copy pass to MPI for a wide set of calls
• Hardened notion of known schema vs generic MPI support
• Add heuristics with knobs for controlling use of HDF5 compact datasets and compression support

Changed

General

• Moved to use BLT (https://github.com/llnl/blt) as our core CMake-based build system
• Use ints instead of bools in the Conduit C-APIs for wider compiler compatibility

Relay

• Improved error checking and error messages for HDF5 I/O support

Fixed

General

• Fixed memory leaks in conduit
• Bug fixes to support building on Visual Studio 2013
• Bug fixes for conduit::Nodes in the List Role

Relay

• Fixed memory leaks in conduit_relay

0.2.1 - Released 2017-01-06

Added

Blueprint

• Added support to the blueprint python module for the mesh and mcarray protocol methods
• Added stand alone blueprint verify executable

Changed

General

• Eliminated separate fortran libs by moving fortran symbols into their associated main libs
• Change Node set_external to support const Node ref
• Refactor path and file systems utils functions for clarity

Fixed

General

• Added fixes to support static builds on BGQ using xlc and gcc
• Fixed missing install of fortran module files

Blueprint

• Fixed bug with verify of mesh/coords for rectilinear case

Relay

• Updated the version of civetweb used to avoid dlopen issues with SSL for static builds

0.2.0 - Released 2016-11-03

Added

General

• Added const access to conduit::Node's children and a new NodeConstIterator
• Added support for building on Windows
• Added more Python, C, and Fortran API support

Blueprint

• Added verify support for the mcarray and mesh protocols
• Added functions that create examples instances of mcarrays and meshes
• Added memory layout transform helpers for mcarrays
• Added a helper that creates a mesh blueprint index from a valid mesh

Relay

• Added entangle, a python script ssh tunneling solution
• Added extensive HDF5 I/O support for reading and writing between HDF5 files and conduit Node trees

Changed

General

• Changes to clarify concepts in the conduit::Node API
• Improved unit test coverage
• Renamed source and header files for clarity and to avoid potential conflicts with other projects

Relay

• Changed I/O protocol string names for clarity
• Refactored the relay::WebServer and the Conduit Node Viewer application

Fixed

General

• Resolved several bugs across libraries
• Resolved compiler warnings and memory leaks

0.1.0 - Released 2016-03-30

Added

• Initial Open Source Release on GitHub