Original commit message:
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Parallel IO: New collated file format
When an OpenFOAM simulation runs in parallel, the data for decomposed fields and
mesh(es) has historically been stored in multiple files within separate
directories for each processor. Processor directories are named 'processorN',
where N is the processor number.
This commit introduces an alternative "collated" file format where the data for
each decomposed field (and mesh) is collated into a single file, which is
written and read on the master processor. The files are stored in a single
directory named 'processors'.
The new format produces significantly fewer files - one per field, instead of N
per field. For large parallel cases, this avoids the restriction on the number
of open files imposed by the operating system limits.
The file writing can be threaded allowing the simulation to continue running
while the data is being written to file. NFS (Network File System) is not
needed when using the the collated format and additionally, there is an option
to run without NFS with the original uncollated approach, known as
"masterUncollated".
The controls for the file handling are in the OptimisationSwitches of
etc/controlDict:
OptimisationSwitches
{
...
//- Parallel IO file handler
// uncollated (default), collated or masterUncollated
fileHandler uncollated;
//- collated: thread buffer size for queued file writes.
// If set to 0 or not sufficient for the file size threading is not used.
// Default: 2e9
maxThreadFileBufferSize 2e9;
//- masterUncollated: non-blocking buffer size.
// If the file exceeds this buffer size scheduled transfer is used.
// Default: 2e9
maxMasterFileBufferSize 2e9;
}
When using the collated file handling, memory is allocated for the data in the
thread. maxThreadFileBufferSize sets the maximum size of memory in bytes that
is allocated. If the data exceeds this size, the write does not use threading.
When using the masterUncollated file handling, non-blocking MPI communication
requires a sufficiently large memory buffer on the master node.
maxMasterFileBufferSize sets the maximum size in bytes of the buffer. If the
data exceeds this size, the system uses scheduled communication.
The installation defaults for the fileHandler choice, maxThreadFileBufferSize
and maxMasterFileBufferSize (set in etc/controlDict) can be over-ridden within
the case controlDict file, like other parameters. Additionally the fileHandler
can be set by:
- the "-fileHandler" command line argument;
- a FOAM_FILEHANDLER environment variable.
A foamFormatConvert utility allows users to convert files between the collated
and uncollated formats, e.g.
mpirun -np 2 foamFormatConvert -parallel -fileHandler uncollated
An example case demonstrating the file handling methods is provided in:
$FOAM_TUTORIALS/IO/fileHandling
The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
- STLpoint.H
- isoAdvection.C
- checkMesh/writeFields.C
STYLE: drop construct STLpoint(Istream&), since it doesn't make much sense
- No use case for reading via an OpenFOAM stream and tokenizer.
Should always be parsing ASCII or reading binary directly.
- Constructor for bounding box of a single point.
- add(boundBox), add(point) ...
-> Extend box to enclose the second box or point(s).
Eg,
bb.add(pt);
vs.
bb.min() = Foam::min(bb.min(), pt);
bb.max() = Foam::max(bb.max(), pt);
Also works with other bounding boxes.
Eg,
bb.add(bb2);
// OR
bb += bb2;
vs.
bb.min() = Foam::min(bb.min(), bb2.min());
bb.max() = Foam::max(bb.max(), bb2.max());
'+=' operator allows the reduction to be used in parallel
gather/scatter operations.
A global '+' operator is not currently needed.
Note: may be useful in the future to have a 'clear()' method
that resets to a zero-sized (inverted) box.
STYLE: make many bounding box constructors explicit
reduce()
- parallel reduction of min/max values.
Reduces coding for the callers.
Eg,
bb.reduce();
instead of the previous method:
reduce(bb.min(), minOp<point>());
reduce(bb.max(), maxOp<point>());
STYLE:
- use initializer list for creating static content
- use point::min/point::max when defining standard boxes
- Allows passing of additional information (per-face zone ids) or possibly
other things, while reducing the number of arguments to pass.
- In sampledTriSurfaceMesh, preserve the region information that was
read in, passing it onwards via the UnsortedMeshSurface content.
The Nastran surface writer is currently the only writer making use
of this per-face zone information.
Passing it through as a PSHELL attribute, which should retain the
distinction for parts. (issue #204)
- the checking for point-connected multiple-regions now also writes the
conflicting points to a pointSet
- with the -writeSets option it now also reconstructs & writes pointSets
In parallel the sets are reconstructed. e.g.
mpirun -np 6 checkMesh -parallel -allGeometry -allTopology -writeSets vtk
will create a postProcessing/ folder with the vtk files of the
(reconstructed) faceSets and cellSets.
Also improved analysis of disconnected regions now also checks for point
connectivity with is useful for detecting if AMI regions have duplicate
points.
Patch contributed by Mattijs Janssens
- checkMesh has option to write faceSets or (outside of) cellSets as
sampledSurface format. It automatically reconstructs the set on the master
and writes it to the postProcessing folder (as any sampledSurface). E.g.
mpirun -np 6 checkMesh -allTopology -allGeometry -writeSets vtk -parallel
- fixed order writing of symmTensor in Ensight writers
