Conduit

repository·develop·Indexed 42 days ago

https://github.com/llnl/conduit

An open source framework from Lawrence Livermore National Laboratory designed to simplify hierarchical scientific data exchange in HPC simulations. It supports C++, C, Fortran, and Python to enable efficient data coupling, serialization, and I/O tasks.

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What's inside Conduit

  1. Overview of CivetWeb

    develop

    CivetWeb is a powerful, easy-to-use, C/C++ embeddable web server. It is designed to be used in two ways:

    1. As a library: Developers can embed it into existing applications to add HTTP/HTTPS functionality.
    2. As a stand-alone server: End users can run it as a single executable with no installation required.

    Key Features:

    • License: MIT license (permissive and commercial-friendly).
    • Platforms: Windows, Mac, Linux, UNIX, iPhone, Android, and more.
    • Capabilities: Supports CGI, HTTPS (SSL/TLS), SSI, HTTP digest (MD5) authorization, Websocket, and WEbDAV.
    • Scripting & Database: Optional support for Lua scripts, Lua Server Pages, CGI, SQLite, and Server-side JavaScript.
    • Client Functionality: Includes an HTTP client for sending arbitrary requests and a Websocket client (WS/WSS).
  2. Overview of Conduit for HPC Data Exchange

    develop

    Conduit is an open-source project designed for simplified data exchange in High-Performance Computing (HPC) simulations. It provides an intuitive model for describing hierarchical scientific data across multiple languages, including C++, C, Fortran, and Python.

    Key use cases include:

    • Data coupling between simulation packages in-core.
    • Data serialization.
    • I/O tasks.

    The core API uses a JSON-inspired data model to describe hierarchical in-core scientific data and provides a dynamic API for rapid construction and consumption of these objects. It supports both Conduit-allocated memory and externally owned memory semantics, and it does not require code generation or data repacking.

  3. Overview of Conduit for scientific data exchange

    develop

    Conduit is an open source project designed for simplified data exchange in High-Performance Computing (HPC) simulations. It provides an intuitive model for describing hierarchical scientific data across multiple languages, including C++, C, Fortran, and Python.

    Developers use Conduit for:

    • Data coupling: Facilitating exchange between different simulation packages in-core.
    • Serialization: Converting data structures into formats suitable for storage or transmission.
    • I/O tasks: Managing input and output operations for scientific datasets.
  4. Understand the Conduit source code repository layout

    develop

    The Conduit repository is organized into several key directories that separate the core libraries, testing suites, and examples:

    • src/libs/: Contains the source code for the primary libraries:
      • conduit/: The main Conduit library.
      • relay/: Relay libraries.
      • blueprint/: Blueprint library.
    • src/tests/: Contains testing suites for the libraries (conduit/, relay/, blueprint/) and third-party libraries (thirdparty/).
    • src/examples/: Provides basic examples for building and using Conduit.
    • src/docs/: Project documentation.
    • src/thirdparty_builtin/: Third-party libraries that are built and managed directly by the project.
  5. RapidJSON core features and capabilities

    develop

    RapidJSON is designed for high performance and low memory footprint. Key features include:

    • Dual API: Supports both SAX (Simple API for XML style) and DOM (Document Object Model) interfaces.
    • Performance: Highly optimized; optionally supports SSE2/SSE4.2 for hardware acceleration.
    • Memory Efficiency: Uses a fast internal allocator; JSON values are stored compactly (typically 16/20 bytes per value on 32/64-bit machines, excluding text).
    • Unicode Support: Full support for UTF-8, UTF-16, and UTF-32 (both Little and Big Endian), including validation and transcoding.
    • Compliance: Fully compliant with RFC7159 and ECMA-404 JSON standards.
  6. What is the table blueprint protocol?

    develop

    The table blueprint protocol is a convention for expressing tabular data in Conduit. It ensures that data can be easily translated to and from CSV files.

    In a table blueprint:

    • Each data entry represents a column.
    • Each column contains the same number of rows.

    To conform to the protocol, a Node must have a values child (which can be a list or an object) where:

    1. All values children are data arrays or mcarrays.
    2. All values children have the same number of elements (the number of rows).

    A Node also conforms to the protocol if it is a collection of tables (a list or object where all children are valid tables).

  7. Use the Relay I/O HDF5 Interface

    develop

    The Relay I/O HDF5 interface allows reading and writing Conduit Nodes using HDF5 handles. This interface provides fine-grained control and efficient reuse of I/O handles.

    Note: This interface is only available in C++. It serves as the underlying implementation for both the path-based and handle-based I/O interfaces for HDF5.

  8. Understand the Node concept in Conduit

    develop

    The Node class is the primary object in Conduit. It acts as a hierarchical variant object that can represent different types of data structures.

    Conduit uses a hierarchy inspired by JSON:

    • Objects: Collections of named nodes.
    • Lists: Collections of unnamed nodes.
    • Leaves: Concrete data types (e.g., numbers, arrays) that represent the end of a branch.

    You can iterate through a Node's children and fetch sub-nodes using relative paths. Note that paths are relative to the current node; leading slashes (/) or redundant slashes (///) are ignored.

    import conduit
    
    # Basic Node creation
    n = conduit.Node()
    
    # Hierarchical construction (example pattern)
    n.add_object("my_object")
    n.add_list("my_list")
  9. Accessing children in Object and List roles

    develop

    In Conduit, Node instances using the Object or List role interfaces can contain children.

    • List role: A Node holds a set of indexed children.
    • Object role: A Node holds a set of both indexed and named children.

    Children can be accessed or removed using their index. The following methods are available for both Node and Schema instances:

    • number_of_children(): Returns the count of children.
    • child(index_t): Returns a child by index.
    • child_ptr(index_t): Returns a pointer to a child by index.
    • operator=(index_t): Access/assign via index operator.
    • remove(index_t): Removes the child at the specified index.
  10. Mesh Index Protocol and Root Files

    develop

    When working with partitioned meshes, Blueprint uses a Root File to act as a hierarchical index. This allows analysis tools (like VisIt) to treat many individual Blueprint files as a single dataset.

    Root File Structure

    The root file must contain a blueprint_index node. Under each mesh node, the following sub-nodes are used to point to the actual data in individual files via path nodes:

    • coordsets: Coordinate set metadata.
    • topologies: Topology definitions.
    • fields: Field data (can include an optional display_name for visualization tools).
    • state: Mesh state metadata.

    Generating a Mesh Index

    Use conduit::blueprint::mpi::mesh::generate_index() to create the index metadata from a valid Blueprint dataset in an MPI environment.

    File Pattern Wildcards

    The file_pattern key uses C-style printf() format strings (e.g., %05d) to generate filenames. These wildcards are substituted with integers from 0 to number_of_files.

  11. Understand Material Set Layouts

    develop

    Conduit material sets (matsets) follow different layout specifications which determine how data is indexed. Understanding these is critical for efficient data access:

    • Dominance:
      • Element-dominant: The number of materials in element i is defined by sizes[i]. The offset into indices for element i is offsets[i]. Indices for volume_fractions and material_ids are found at indices[offsets[i]].
      • Material-dominant: The number of elements for material i is defined by sizes[i]. The offset into indices for material i is offsets[i]. Indices for volume_fractions and element_ids are found at indices[offsets[i]].
    • Buffering:
      • Multi-buffer: The volume_fractions child is an Object.
      • Uni-buffer: The volume_fractions child is not an Object.

    Summary Table:

    TypeIdentification
    Material-dominantHas a child called element_ids
    Element-dominantDoes not have a child called element_ids
    Multi-buffervolume_fractions is an Object
    Uni-buffervolume_fractions is not an Object