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.
A synchronizing operation will synchronize the MPI ranks that participate in it.
For more information, please see the MPI standard documents, for example MPI-3.1 in "Section 2.4 - Semantic Terms".
| Functionality | Behavior | Synchronizing | Description |
|---|---|---|---|
Series |
collective | yes | open and close |
::flush() |
collective | yes | read and write |
::setRankTable() |
collective | no | write, performed at flush |
::rankTable() |
coll/indep. | yes/no | behavior specified by bool param |
Iteration [1] |
independent | no | declare and open |
::open() [4] |
collective | yes | explicit open |
Mesh [1] |
independent | no | declare, open, write |
ParticleSpecies [1] |
independent | no | declare, open, write |
::setAttribute [3] |
backend-specific | no | declare, write |
::getAttribute |
independent | no | open, reading |
RecordComponent [1] |
independent | no | declare, open, write |
::resetDataset [1] [2] |
backend-specific | no | declare, write |
::makeConstant [3] |
backend-specific | no | declare, write |
::storeChunk [1] |
independent | no | write |
::loadChunk |
independent | no | read |
::availableChunks [4] |
independent | no | read, immediate result |
| [1] | (1, 2, 3, 4, 5, 6) Individual backends, i.e. :ref:`parallel HDF5 <backends-hdf5>`, will only support independent operations if the default, non-collective (aka independent) behavior is kept. Otherwise these operations are collective. |
| [2] | Dataset declarations in :ref:`parallel HDF5 <backends-hdf5>` are only non-collective if :ref:`chunking <backendconfig-hdf5>` is set to none (auto by default).
Otherwise these operations are collective. |
| [3] | (1, 2) :ref:`HDF5 <backends-hdf5>` only supports collective attribute definitions/writes; :ref:`ADIOS2 <backends-adios2>` attributes can be written independently.
If you want to support all backends equally, treat as a collective operation.
Note that openPMD represents constant record components with attributes, thus inheriting this for When treating attribute definitions as collective, we advise specifying the ADIOS2 :ref:`JSON/TOML key <backendconfig>` |
| [4] | (1, 2) 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.
Alternatively, iterations might be accessed for the first time by immediate operations such as ::availableChunks(). |
Warning
The openPMD-api will by default flush only those Iterations which are dirty, i.e. have been written to.
This is somewhat unfortunate in parallel setups since only the dirty status of the current MPI rank can be considered.
As a workaround, use Attributable::seriesFlush() on an Iteration (or an object contained within an Iteration) to force flush that Iteration regardless of its dirty status.
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.
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 :ref:`implemented I/O backends <backends-overview>` for individual tuning options.