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.
- use allocator class to wrap the stream pointers instead of passing
them into ISstream, OSstream and using a dynamic cast to delete
then. This is especially important if we will have a bidirectional
stream (can't delete twice!).
STYLE:
- file stream constructors with std::string (C++11)
- for rewind, explicit about in|out direction. This is not currently
important, but avoids surprises with any future bidirectional access.
- combined string streams in StringStream.H header.
Similar to <sstream> include that has both input and output string
streams.
- the heuristic for matching unresolved intersections is a relatively
simple matching scheme that seems to be more robust than attempting to walk
the geometry or the cuts.
- avoid false positives for self intersection
- adjust for updates in 'develop'
- change surfaceIntersection constructor to take a dictionary of
options.
tolerance | Edge-length tolerance | scalar | 1e-3
allowEdgeHits | Edge-end cuts another edge | bool | true
avoidDuplicates | Reduce the number of duplicate points | bool | true
warnDegenerate | Number of warnings about degenerate edges | label | 0
- If the dictionary is named 'surfaces', a 'surfaces' entry is mandatory.
This is a list of wordRe, which is used to load multiple surfaces from
constant/triSurface directory.
- Other dictionaries may contain a 'surfaces' entry.
In which case the behaviour is as above (loading multiple surfaces).
The dictionary name will *NOT* be taken as a surface name itself.
- Regardless of how the surfaces are loaded or features extracted,
an additional selfIntersection test may be used.
Eg,
surfaces
{
extractionMethod extractFromSurface;
surfaces (surface1.stl surface2.nas);
// Generate features from self-intersect
selfIntersection true;
// Base output name (optiona)
output surfaces;
// Tolerance for self-intersect
planarTolerance 1e-3;
extractFromSurfaceCoeffs
{
includedAngle 120;
// Do not mark region edges
geometricTestOnly yes;
}
}
- use InfoSwitch to disable, or via static method.
- respect the state of the argList banner when deciding to emit
initialization information. Can otherwise end up with unwanted
output rubbish on things like foamDictionary and foamListTimes.
- the purpose is more explicit, without needing to check documentation
about what the bool parameter means.
STYLE: improve formatting of fileName documentation
- identical code was present in surfaceCheck (original source),
and isoSurface, isoSurfaceCell (copies).
- add in a MeshedSurface<face> variant as well, since this will likely
be needed in the near future
- these directories are sometimes used for a central, non-thirdparty, non-system
installation
- leave gmp and mpfr as is, since it is not clear how these would interact with system
versions
- only occurs in combination with distributedTriSurfaceMesh in snappy.
- workaround similar to that previously used for surfaceRedistributePar
(issue #60).
Minor adjustment of incompressible motorBike tutorial to detect use of
distributedTriSurfaceMesh.
- there was a slight mix of MUST_READ and MUST_READ_IF_MODIFIED
but with no obvious code to handle runtime modified values
of the decomposition, or how this works with alternative
dictionaries.
- A special purpose MeshedSurface that exposes the stored values
for direct modification.
- Its usage should be restricted to special cases where the surface
needs modifications as an atomic operation.
- Cleanup/centralize handling of -decomposeParDict by relocating
common code into argList. Ensures that all processes receive
identical information about the -decomposeParDict opton.
- Only use alternative decomposeParDict for simpleFoam/motorBike
tutorial so that this will be included in the test loop for snappy.
- Added Mattijs' fix for surfaceRedistributePar.
