MPI

Collective Behavior

openPMD-api is designed to support both serial as well as parallel I/O. The latter is implemented through the Message Passing Interface (MPI).

A collective operation needs to be executed by all MPI ranks of the MPI communicator that was passed to openPMD::Series. Contrarily, independent operations can also be called by a subset of these MPI ranks. For more information, please see the MPI standard documents, for example MPI-3.1 in “Section 2.4 - Semantic Terms”.

Functionality	Behavior	Description
Series	collective	open and close
::flush()	collective	read and write
Iteration 1	independent	declare and open
::open() 3	collective	explicit open
Mesh 1	independent	declare, open, write
ParticleSpecies 1	independent	declare, open, write
::setAttribute 2	backend-specific	declare, write
::getAttribute	independent	open, reading
::storeChunk 1	independent	write
::loadChunk	independent	read

1(1,2,3,4)

Individual backends, e.g. HDF5, will only support independent operations if the default, non-collective behavior is kept. (Otherwise these operations are collective.)

2

HDF5 only supports collective attribute definitions/writes; ADIOS1 and ADIOS2 attributes can be written independently. If you want to support all backends equally, treat as a collective operation.

3

We usually open iterations delayed on first access. This first access is usually the flush() call after a storeChunk/loadChunk operation. If the first access is non-collective, an explicit, collective Iteration::open() can be used to have the files already open.

Tip

Just because an operation is independent does not mean it is allowed to be inconsistent. For example, undefined behavior will occur if ranks pass differing values to ::setAttribute or try to use differing names to describe the same mesh.

Efficient Parallel I/O Patterns

Note

This section is a stub. We will improve it in future versions.

Write as large data set chunks as possible in ::storeChunk operations.

Read in large, non-overlapping subsets of the stored data (::loadChunk). Ideally, read the same chunk extents as were written, e.g. through ParticlePatches (example to-do).

See the implemented I/O backends for individual tuning options.