Sidre User Guide¶
The Sidre (Simulation data repository) component of Axom provides tools to centralize data management in HPC applications: data description, allocation, access, and so forth. The goal of Sidre is efficient coordination and sharing of data across physics packages in integrated applications, and between applications and tools that provide capabilities such as file I/O, in situ visualization, and analysis.
The design of Sidre is based on substantial production application experience and requirements for codes to run on advanced architectures. Such codes must carefully manage data allocation and placement to run efficiently. Sidre is intended to be used in a variety of diverse applications.
Doxygen generated API documentation can be found here: API documentation
Sidre provides simple application-level semantics to describe, allocate, deallocate, and provide access to data. Currently supported capabilities include:
Separate data description and allocation operations. This allows applications to describe their data and then decide how best to place the data in memory.
Multiple different “views” into a chunk of (shared) data. A Sidre view includes description semantics to define data type, number of elements, offset, stride, etc. Thus, a chunk of data in memory can be interpreted conceptually in different ways using different views into it.
Externally-owned “opaque” or described data. Sidre can accept a pointer to externally-allocated data and provide access to it by name. When external data is described to Sidre, it can be processed in the same ways as data that Sidre owns. When data is not described (i.e., it is “opaque”), Sidre can provide access to the data via a pointer, but the consumer of the data must know type information to do anything substantial with the data.
Support for different memory spaces and allocation schemes. Default memory space and allocation support is basic. More advanced features are available via the Umpire library when Axom is configured to be built with it.
Attributes or metadata associated with a Sidre view. This metadata is available to user code to facilitate program logic and is also used in Axom to enable selective writing of data subsets to files.
Tree-structured data hierarchies. Many mesh-based application codes organize data into hierarchies of contexts (e.g., domains, regions, blocks, mesh centerings, subsets of elements containing different materials, etc.). Sidre supports hierarchical, tree-based organizations in a simple, flexible way that aligns with the data organization in many applications.
APIs for C++, C, and Fortran along with mechanisms to ensure inter-language data consistency.
So far, Sidre development has focused on designing and building flexible and powerful concepts to build on. The Sidre API includes five main concepts:
DataStore. The main access point to data managed by Sidre; it contains a collection of Buffers, a collection of default Attributes, and a tree structure of Groups.
Buffer. Describes and holds a chunk of data in memory owned by Sidre.
Group. Defines a tree structure like a filesystem, where Groups are like folders and Views are like files.
View. Describes a conceptual layout of data in memory. Each View has a collection of its explicitly-set Attributes.
Attribute. Provides a metadata descriptor of a View.
These concepts will be described in more detail in later sections.
At this point, Sidre supports simple data types such as scalars, strings, and (multidimensional) arrays of scalars. Fundamentally, Sidre does not preclude the use of more complex data structures, but does not currently support them directly. Future Sidre development will expand core functionality to support additional features such as:
Support for more complex data types.
Complex queries and actions involving Attributes.
Support for these enhancements and others will be added based on application needs and use cases.
- An introductory example
- Core concepts
- Serial File I/O
- Parallel File I/O
- Sidre Interaction with Conduit
- Using Sidre with MFEM