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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

Added

General

  • Added conduit_json_external protocol. Creates a json schema representation of a node that includes all addresses that the node is pointing to. Parsing this schema will create a node equivalent to set_external().
  • Added a conduit_generate_data executable that can generate datasets using the tiled() and braid() functions and save the datasets to files.

Relay

  • Added ability to read N-dimensional hyperslabs from HDF5 leaf arrays into linear memory arrays.

Blueprint

  • Added a conduit::blueprint::mesh::examples::tiled() function that can generate meshes by repeating a tiled pattern.
  • Added a conduit::blueprint::mpi::mesh::utils::adjset::compare_pointwise() function that can compare adjsets for multi-domain meshes in parallel. The function is used to diagnose adjsets with points that are out of order on either side of the boundary. The comparison is done point by point within each group and it checks to ensure that the points reference the same spatial location.
  • Added a conduit::blueprint::mesh::utils::reorder() function that can accept a vector of element ids and create a reordered topology. The points and coordinates are re-ordered according to their first use in the new element ordering.
  • Added a conduit::blueprint::mesh::utils::topology::spatial_ordering() function that takes a topology and computes centroids for each element, passes them through a kdtree, and returns the new element ordering. The new ordering can be used with the reorder() function.
  • Added a conduit::blueprint::mesh::utils::slice_array() function that can slice Conduit nodes that contain arrays. A new node with the same type is created but it contains only the selected indices.
  • Added a conduit::blueprint::mesh::utils::slice_field() function. It is like slice_array() but it can handle the mcarray protocol. This functionality was generalized from the partitioner.
  • Added blueprint.mesh.examples.strided_structured to the blueprint python module.

Changed

General

  • Improved the efficiency of json parsing logic.
  • The conduit_relay_io_convert program was enhanced so it can read/write Blueprint root files by passing "blueprint" for the read or write protocols.

Blueprint

  • The conduit::blueprint::mpi::mesh::partition_map_back() function was enhanced so it accepts a "field_prefix" value in its options. The prefix is used when looking for the global_vertex_ids field, which could have been created with a prefix by the same option in the conduit::blueprint::mpi::mesh::generate_partition_field() function.

Fixed

Blueprint

  • The conduit::blueprint::mesh::partition() function no longer issues an error when it receives a "maxshare" adjset.
  • The partitioner is better about outputting a "material_map" node for matsets. The "material_map" node is optional for some varieties of matset but they can also help the conduit::blueprint::mesh::matset::to_silo() function generate the right material numbers when a domain does not contain all materials.
  • The conduit::Node::swap() and conduit::Node::move() functions no longer cause node names to disappear.

0.8.8 - Released 2023-05-18

Added

General

  • Added Python 3 Stable ABI compatibility (Py_LIMITED_API) build support. Enabled by default when building against Python 3.11 or newer.
  • Added conduit_adjset_validate tool which can read root files for a multiple domain dataset and check whether the adjsets (vertex or element associations) in it are correct. Any errors are printed to the console.

Blueprint

  • Added PointQuery class that can query points in a topology and return whether the query points hit a point in that topology's coordset. There are serial and parallel versions of this class. In parallel, the query domain may exist on a different MPI rank and the result will be communicated to the calling rank.
  • Added MatchQuery class that can be used to ask remote domains whether they contain an entity given using a set of point ids in the current rank's topology. The query builds up a query topology that it sends to the neighboring rank (if the query domain is not owned by the current MPI rank) and the topology is matched against the remote topology by matching points in the remote coordset. The results are returned to the calling MPI rank and can be retrieved using the query.
  • Added TopologyBuilder class that can be used to build up a new topology subset from a source topology. The new topology shape does not have to match the original topology shape. A new coordset is created based on the points that are referenced from the original topology.
  • Added topology::search function that allows one topology to be searched for in another topology. The topologies must have the same shape type and their respective coordsets can have points in different orders. The shapes are matched using coordinate matching.
  • Added adjset::validate function which tests adjacency sets for correctness and flags any errors in a Conduit node. There are serial and parallel versions of the function. The functions apply PointQuery for vertex association adjsets and MatchQuery for element association adjsets. Each domain's adjset will make queries to its neighboring domains as to whether the vertex or element of interest exists in the neighbor's topology.
  • Added utils::kdtree class that can be used to accelerate point lookups for coordsets.
  • Field selections for the conduit::blueprint::mesh::partition() function support a new destination_ranks property that contains a list of integers that map domain numbers to MPI ranks. This property tells the partitioner the ranks where it should place each domain. If the property is not supplied, the partitioner is free to place domains as before.

Fixed

General

  • Added explicit control for OpenMP Features with CMake ENABLE_OPENMP option (default = OFF). Adds CONDUIT_USE_OPENMP define to conduit_config.h. Guards all use of OpenMP with CONDUIT_USE_OPENMP. Prior to these guards, downstream users could enable OpenMP and macros could evaluate inconsistently with how Conduit was built causing OpenMP related linking errors.

Blueprint

  • Functions such as generate_corners or generate_faces that accept adjsets now include a filtering stage to improve adjset quality. This filtering stage uses PointQuery and MatchQuery to ensure that entities referenced in a remote domain actually exist in the neighboring domain.

0.8.7 - Released 2023-03-23

Added

General

  • Added public default and copy constructor to DataAccessor. Enables more flexibility with initializing DataAccessors from Nodes.
  • Added Node.name(), Node.path(), Schema.name(), and Schema.path() to Python API.
  • Added Node.as_index_t_ptr()
  • Added conduit::execution namespace, which contains for_all() and sort() functions.
  • Added DataType support to the Fortran API

Blueprint

  • Added conduit::blueprint::mpi::mesh::distribute, which enables sending mesh domains to arbitrary MPI ranks (suppo
  • Added conduit::blueprint::mesh::utils::NDIndex class. Instantiate with shape, offset, and stride in array or conduit::Node. Get flatindex for N-D coordinates.
  • Added conduit::blueprint::o2mrelation::O2MIndex class. Instantiate with O2M relation Node; get flatindex for a given one_index and many_index. Alternative to Java-style iterator.
  • Added conduit::blueprint::examples::mesh::rz_cylinder function that generates example 2D cylindrical (RZ) meshes.

Relay

  • Added verbose mode option for Relay I/O HDF5 diagnostic messages. See src/tests/relay/t_relay_io_hdf5_diag_verbose.cpp for an example of how to enable verbose output.

Fixed

General

  • Fixed a logic issue undermining C++ type mapping when using CMake 3.26.

Blueprint

  • Performance improvements to Mesh Blueprint topology metadata, used by generate_points, generate_sides, etc. The class was rewritten and the old one was moved to conduit::blueprint::mesh::utils::reference::TopologyMetadata. The new implementation is faster, often about 6-20x depending on options.
  • Performance improvements to O2M Iterators.
  • Performance improvements to functions that underpin centroid generation.

Relay

  • Fixed MPI baton logic error in conduit::relay::io::blueprint::save_mesh() that caused MPI tasks to serialize writes to files in the N domains to M files case. Fix restores parallel write performance. This bug did not impact cases where where N domains were written to N files (N to N) or N domains were written to a single file (N to 1).

Changed

General

  • Changed diff of string types to respect null terminated strings instead of described length
  • Improved diff_compatible of string types to look for substring match, to implement expected compatible semantics.

Blueprint

  • Changed the recommended axis order for 2D cylindrical meshes to be Z as the first axis, and R as the second. This choice aligns with expected visualization cases where Z varies with the horizontal axis and R varies with the vertical axis.

0.8.6 - Released 2023-01-11

Added

General

  • Added C++ int DataType::sizeof_index_t() and C int conduit_datatype_sizeof_index_t() methods to provide a stable ABI to determine configured size (number of bytes) of Conduit's index_t type.

Fixed

General

  • Build fixes for Conda Forge (mpi -fallow-argument-mismatch clang protection)

Relay

  • Fixed a directory creation bug in relay::io::blueprint::{save_mesh|write_mesh} that occurred with sparse topologies with no domains on rank 0.
  • Fixed a bug in relay::io::blueprint::{save_mesh|write_mesh} with the suffix=cycle option that could cause int max to erroneously be used as the cycle number in the output directory.

0.8.5 - Released 2022-12-22

Added

General

  • Added Node::move and Node::swap methods, which provide efficient ways to help build Node trees by consuming other Nodes.
  • Added Node::reset methods to C and Fortran interfaces.
  • Added initial optional support for Caliper performance annotations.
  • Added Python support for Node.set and Node.set_external with a schema and external buffer.

Blueprint

  • Added support for Wedges and Pyramids.
  • Added helper function blueprint::mesh::generate_strip to generate a 2D "strip mesh" topology, and dependent other Blueprint mesh parts, from a 1D mesh.

Changed

General

  • Changed Schema::has_path() (and transitively Node::has_path() ) to ignore leading / s.
  • Updated to BLT v0.5.2

Relay

  • When using HDF5 1.10 or newer, default to use libver 1.8 when creating HDF5 files for wider read compatibly. This setting can be controlled via the hdf5 relay option libver, accepted values: default, none, latest, v108, and v110.

Relay

  • Updated C++ and Python tutorial docs for Compatible Schemas with a new example to outline the most common use case.

Fixed

Blueprint

  • Fixed bug with blueprint::mesh::examples::strided_structured so it correctly generates a coordset with padding
  • Fixes (correctness and performance) to topology::unstructured::generate_offsets
  • Updated conduit.relay.io.blueprint.{load_mesh|read_mesh} to use improved logic to auto detect the format (hdf5 ,yaml, or json) of mesh blueprint root files.
  • Leading / s in mesh tree paths no longer undermine conduit.relay.io.blueprint.{load_mesh|read_mesh} reading json and yaml flavored files.
  • Fixed indexing and offsets in blueprint mixed element topology examples.

Relay

  • Leading / s in tree paths no longer undermine io::IOHandle reads for conduit_bin, json, conduit_json, conduit_base64_json, and yaml flavored files.
  • Updated conduit.relay.io.blueprint.{load_mesh|read_mesh} to only the read the necessary subset of root file entries. Updated MPI version to only read root file entries on rank 0 and broadcast them to other ranks.
  • Fixed write compatibly check in relay::mpi::gather, relay::mpi::all_gather, and relay::mpi::broadcast_using_schema. Node compatible check is not commutative and checks in leaf zero-copy logic were reversed.

0.8.4 - Released 2022-08-22

Added

General

  • Added variants of Node::to_json, Node::to_yaml, and Node::to_string that take formatting options via a Conduit Node.
  • Added C API methods conduit_node_to_json, conduit_node_to_yaml, conduit_node_to_string, and conduit_node_to_summary_string.
  • Added DataArray::count method.
  • Added DataAccessor::{min,max,sum,mean,count} methods.
  • Added Schema and Python Buffer variants to Python Node.set() and Node.set_external().

Blueprint

  • Added blueprint::mesh::paint_adjset, which paints fields that encode adjacency set counts and ordering details.
  • Added blueprint::mesh::examples::strided_structured which creates a structured mesh with arbitrarily strided vertex and element fields.
  • Added support for mixed element topologies to the mesh blueprint.
  • Added blueprint::mesh::examples::braid examples with mixed element topologies (mesh_type={"mixed", "mixed_2d"})
  • Added 1D mesh example support to blueprint::mesh::examples::basic().
  • Added adjacency set aware generate functions (genearte_points(), etc) to the non-mpi blueprint library.
  • Added generate_offsets_inline(Node &) for cases where we want topology offsets created in an existing tree.
  • Added support to write and read per-mesh blueprint index entires with partition_pattern and partition_map.

Relay

  • Added any source, any tag variants of mpi receive functions: recv, recv_using_schema, and irecv.
  • Added subpath support for relay::io::{save,load,save_merged,load_merged} for basic protocols (json, yaml, etc).

Changed

Blueprint

  • Removed field type entries from braid examples, since that info is not required by the Mesh Blueprint.
  • Fixed a const-ignoring crime related to polyhedral element and subelement offset generation.
  • Refactored unstructured case in blueprint::mesh::topology::logical_dims calculation to directly calculate number of elements instead of generating offsets.

Relay

  • Changed HDF5 CMake sanity checks to issue WARNING instead of FATAL_ERROR, since Cray system HDF5 installs do not always present the info we use for sanity checks.
  • Changed HDF5 version guards to also check requested HDF5 API.

Fixed

General

  • Fixed bug with to_json() where leaf arrays of size 0 lead to malformed json.
  • Fixed parsing issue with conduit_json protocol for leaf arrays of size 0.
  • Fixed roundtrip parsing of numeric arrays with nan, infs, etc for JSON cases (Node::to_json() followed by Node::parse(...,"json")).

Blueprint

  • Fixed a bug with blueprint::mesh::index::generate, where a uniform grid with no origin would lead to invalid coordinate system name logical in the resulting index. This case now defaults to cartesian.
  • Improved relay::io::blueprint::{save_mesh|write_mesh} blueprint index generation for cases where fields do not exist on all domains.
  • Fixed a bug that labeled internal faces as shared in generated adjsets.

Relay

  • Fixed a bug with blueprint root file creation, where the file_pattern was not relative to the root file location
  • Fixed missing header include for relay io csv support.
  • Fixed a bug with relay mpi all reduce.

0.8.3 - Released 2022-04-14

Added

General

  • Added C/C++ version macros CONDUIT_VERSION_MAJOR, CONDUIT_VERSION_MINOR, CONDUIT_VERSION_PATCH and these values as separate entries in conduit::about() to provide more support for compile time and runtime conduit version detection.

Blueprint

  • Added blueprint::mesh::examples::polystar, which creates a mesh with a polyhedral star pattern that demonstrates hanging vertices in a topology, along with its representations from generate_sides and generate_corners.
  • Added blueprint::mesh::examples::related_boundary, which creates a multi-domain mesh with a related boundary topology and several fileds that encode relationships between the main topology and the boundary.
  • Expanded blueprint::mpi::mesh::generate_partition_field to support all topology types.

Fixed

Blueprint

  • Fixed a bug with conduit::blueprint::mesh::examples::braid, where 2D cases for points and structured examples would create coordsets with all entries being zero.

Changed

General

  • Improved pip install logic

Relay

  • Added szip and zlib linking fix for older version of HDF5 (1.8.14)
  • Fixed a bug with relay::io::blueprint::write_mesh and relay::io::blueprint::save_mesh for the multi domain case, removing unintended :mesh file name suffix for json and yaml domain files.

0.8.2 - Released 2022-02-01

Fixed

Blueprint

  • Fixed missing C++ include used by Blueprint Parmetis support.

0.8.1 - Released 2022-01-25

Added

General

  • Added CONDUIT_DLL_DIR env var support on windows, for cases where Conduit DLLs are not installed directly inside the Python Module.

Blueprint

  • Allow adjsets to be used in blueprint::mesh::partition to determine global vertex ids.
  • Added partial matset support to blueprint::mesh::partition and blueprint::mesh::combine.

Fixed

General

  • Fixed CMake bug with ENABLE_RELAY_WEBSERVER option.
  • Fixed build and test issues with Python >= 3.8 on Windows.

Blueprint

  • Fixed a bug in blueprint::mesh::partition where adjsets could be missing in new domains.
  • Fixed a bug with blueprint::mesh::matset::to_silo and uni-buffer matsets.

0.8.0 - Released 2021-12-20

Added

General

  • Added setup.py for building and installing Conduit and its Python module via pip
  • Added DataAccessor class that helps write generic algorithms that consume data arrays using expected types.
  • Added support to register custom memory allocators and a custom data movement handler. This allows conduit to move trees of data between heterogenous memory spaces (e.g. CPU and GPU memory). See conduit_utils.hpp for API details.

Blueprint

  • Added conduit::blueprint::{mpi}::partition function that provides a general N-to-M partition capability for Blueprint Meshes. This helps with load balancing and other use cases, including fusing multi-domain data to simplifying post processing. This capability supports several options, see (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh_partition.html) for more details.
  • Added a Table blueprint used to represent tables of numeric data. See (https://llnl-conduit.readthedocs.io/en/latest/blueprint_table.html) more details.
  • Added conduit::blueprint::{mpi}::flatten which transforms Blueprint Meshes into Blueprint Tables. This transforms Mesh Blueprint data into a form that is more easily digestible in machine learning applications.
  • Added conduit::blueprint::mpi::generate_partition_field, which uses Parmetis to create a field that identifies how to load balance an input mesh elements. This field can be used as a Field selection input to conduit::blueprint::mpi::partition function.
  • Added theblueprint::mesh::examples::polychain example. It is an example of a polyhedral mesh. See Mesh Blueprint Examples docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#polychain) for more details.
  • Added a new function signature for blueprint::mesh::topology::unstructured::generate_sides, which performs the same task as the original and also takes fields from the original topology and maps them onto the new topology.
  • Added blueprint::mpi::mesh::to_polygonal, which provides a MPI aware conversion Blueprint Structured AMR meshes to a Blueprint Polyhedral meshes.
  • Added a host of conduit::blueprint::mpi::mesh::generate_* methods, which are the MPI parallel equivalents of the conduit::blueprint::mesh::topology::unstructured::generate_* functions.
  • Added the conduit::blueprint::mpi::mesh::find_delegate_domain function, which returns a single delegate domain for the given mesh across MPI ranks (useful when all ranks need mesh information and some ranks can have empty meshes).
  • Added check and transform functions for the newly-designated pairwise and maxshare variants of adjsets. For more information, see the conduit::blueprint::mesh::adjset namespace.
  • Added mesh::topology::unstructured::to_polytopal as an alias to mesh::topology::unstructured::to_polygonal, to reflect that both polygonal and polyhedral are supported.
  • Added conduit::blueprint::mpi::mesh::to_polytopal as an alias to conduit::blueprint::mpi::mesh::to_polygonal and conduit::blueprint::mpi::mesh::to_polyhedral.

Relay

  • Added conduit::relay::io::hdf5_identifier_report methods, which create conduit nodes that describes active hdf5 resource handles.

Changed

General

  • Updated CMake logic to provide more robust Python detection and better support for HDF5 installs that were built with CMake.
  • Improved Node::diff and Node::diff_compatible to show string values when strings differ.
  • conduit::Node::print() and in Python Node repr and str now use to_summary_string(). This reduces the output for large Nodes. Full output is still supported via to_string(), to_yaml(), etc methods.

Blueprint

  • The blueprint::mesh::examples::polytess function now takes a new argument, called nz, which allows it to be extended into 3 dimensions. See Mesh Blueprint Examples docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#polytess) for more details.
  • Added support for both const and non-const inputs to the conduit::blueprint::mesh::domains function.
  • Improved mesh blueprint index generation logic (local and MPI) to support domains with different topos, fields, etc.
  • Deprecated accepting npts_z !=0 for 2D shape types in conduit::blueprint::mesh::examples::{braid,basic,grid}. They issue a CONDUIT_INFO message when this detected and future versions will issue a CONDUIT_ERROR.
  • An empty Conduit Node is now considered a valid multi-domain mesh. This change was made to make serial uses cases better match sparse MPI multi-domain use cases. Existing code that relied mesh::verify to exclude empty Nodes will now need an extra check to see if an input mesh has data.
  • Added MPI communicator argument to conduit::blueprint::mpi::mesh::to_polygonal and conduit::blueprint::mpi::mesh::to_polyhedral.

Relay

  • Added CMake option (ENABLE_RELAY_WEBSERVER, default = ON) to control if Conduit's Relay Web Server support is built. Down stream codes can check for support via header ifdef CONDUIT_RELAY_WEBSERVER_ENABLED or at runtime in conduit::relay::about.
  • Added support to compile against HDF5 1.12.

Fixed

General

  • Avoid compile issue with using _Pragma() with Python 3.8 on Windows
  • conduit_node and conduit_datatype in the C API are no longer aliases to void so that callers cannot pass just any pointer to the APIs.
  • Fixed memory over read issue with Fortran API due to int vs bool binding error. Fortran API still provides logical returns for methods like conduit_node_has_path() however the binding implementation now properly translates C_INT return codes into logical values.
  • Fixed a subtle bug with Node fetch and Object role initialization.

Blueprint

  • Fixed a bug that was causing the conduit::blueprint::mesh::topology::unstructured::generate_* functions to produce bad results for polyhedral input topologies with heterogeneous elements (e.g. tets and hexs).
  • Fixed a bug with conduit::relay::io::blueprint::write_mesh that undermined truncate=true option for root-only style output.
  • Fixed options parsing bugs and improved error messages for the conduit_blueprint_verify exe.

Relay

  • Changed HDF5 offset support to use 64-bit unsigned integers for offsets, strides, and sizes.
  • Fixed a bug with conduit::relay::mpi::io::blueprint::save_mesh where file_style=root_only could crash or truncate output files.
  • Fixed a bug with inconsistent HDF5 handles being used in some cases when converting existing HDF5 Datasets from fixed to extendable.

0.7.2 - Released 2021-05-19

Added

General

  • Added the cpp_fort_and_py standalone example. It demos passing Conduit Nodes between C++, Fortran, and Python. See the related tutorial docs (https://llnl-conduit.readthedocs.io/en/latest/tutorial_cpp_fort_and_py.html) for more details.
  • Added conduit::utils::info_handler(), conduit::utils::warning_handler(), and conduit::utils::error_handler() methods, which provide access to the currently registered info, warning, and error handlers.
  • Added DataType::index_t method. Creates a DataType instance that describes an index_t, which is an alias to either int32, or int 64 controlled by the CONDUIT_INDEX_32 compile time option.
  • Added several more methods to Python DataType interface
  • Removed duplicate install of CMake exported target files that served as a bridge for clients using old style paths.

Changed

General

  • Updated to newer version of uberenv and changed to track spack fork https://github.com/alpine-dav/spack (branch: conduit/develop).
  • Updated to newer version of BLT to leverage CMake's FindMPI defined targets when using CMake 3.15 or newer.
  • Changed rapidjson namespace to conduit_rapidjson to avoid symbol collisions with other libraries using RapidJSON.

Blueprint

  • The semantics of conduit::blueprint::mesh::verify changed. An empty conduit Node is now considered a valid multi-domain mesh with zero domains. If you always expect mesh data, you can add an additional check for empty to craft code that works for both the old and new verify semantics.

Relay

  • Added Relay HDF5 support for reading and writing to an HDF5 dataset with offset.
  • Added conduit::relay::io::hdf5::read_info which allows you to obtain metadata from an HDF5 file.
  • Added configure error when conduit lacks MPI support and HDF5 has MPI support

Fixed

General

  • Fixed missing implementation of DataType::is_index_t
  • Fixed issue with compiling t_h5z_zfp_smoke.cpp against an MPI-enabled HDF5.

Blueprint

  • Fixed a bug that caused HDF5 reference paths to appear twice in Relay HDF5 Error messages.

Blueprint

  • conduit::relay::io::blueprint.read_mesh now uses read only I/O handles.

0.7.1 - Released 2021-02-11

Fixed

General

  • Fixed a bug with Conduit's C interface including C++ headers.

Blueprint

  • Fixed a bug with blueprint::mesh::matset::to_silo and blueprint::mesh::field::to_silo that could modify input values.

0.7.0 - Released 2021-02-08

Changed

General

  • Conduit now requires C++11 support.
  • Python Node repr string construction now uses Node.to_summary_string()

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.
  • Added conduit::utils::format methods. These methods use fmt to format strings that include fmt style patterns. The formatting arguments are passed as a conduit::Node tree. The args case allows named arguments (args passed as object) or ordered args (args passed as list). The maps case also supports named or ordered args and works in conjunction with a map_index. The map_index is used to fetch a value from an array, or list of strings, which is then passed to fmt. The maps style of indexed indirection supports generating path strings for non-trivial domain partition mappings in Blueprint. This functionality is also available in Python, via the conduit.utils.format method.
  • Added DataArray::fill method, which set all elements of a DataArray to a given value.
  • Added Node::to_summary_string methods, which allow you to create truncated strings that describe a node tree, control the max number of children and max number of elements shown.
  • Added python support for Node.to_summary_string

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.
  • Added yaml detection support to conduit::relay::io:identify_file_type.

Blueprint

  • Added conduit::blueprint::mesh::matset::to_silo() which converts a valid blueprint matset to a node that contains arrays that follow Silo's sparse mix slot volume fraction representation.
  • Added conduit::blueprint::mesh::field::to_silo() which converts a valid blueprint field and matset to a node that contains arrays that follow Silo's sparse mix slot volume fraction representation.
  • Added material_map to conduit::blueprint::mesh:matset::index, to provide an explicit material name to id mapping.
  • Added mat_check field to blueprint::mesh::examples::venn. This field encodes the material info in a scalar field and in the matset_values in a way that can be used to easily compare and verify proper construction in other tools.

Fixed

Relay

  • Fixed bug in the Relay IOHandle Basic that would create unnecessary "_json" schema files to be written to disk upon open().

Removed

General

  • Removed Node::fetch_child and Schema::fetch_child methods for v0.7.0. (Deprecated in v0.6.0 -- prefer fetch_existing)
  • Removed Schema::to_json method variants with detailed for v0.7.0. (Deprecated in v0.6.0 -- prefer standard to_json)
  • Removed Schema::save method variant with detailed for v0.7.0. (Deprecated in v0.6.0 -- prefer standard save)
  • The master branch was removed from GitHub (Deprecated in v0.6.0 -- replaced by the develop branch)

Relay

  • Removed conduit::relay::io_blueprint::save methods for v0.7.0. (Deprecated in v0.6.0 -- prefer conduit::relay::io::blueprint::save_mesh)

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: LLNL#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