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.
- OSspecific: chmod() -> chMod(), even although it's not used anywhere
- ListOps get subset() and inplaceSubset() templated on BoolListType
- added UList<bool>::operator[](..) const specialization.
Returns false (actually pTraits<bool>::zero) for out-of-range elements.
This lets us use List<bool> with lazy evaluation and no noticeable
change in performance.
- use rcIndex() and fcIndex() wherever possible.
Could check if branching or modulus is faster for fcIndex().
- UList and FixedList get 'const T* cdata() const' and 'T* data()' members.
Similar to the STL front() and std::string::data() methods, they return a
pointer to the first element without needing to write '&myList[0]', recast
begin() or violate const-ness.
- can use 'XX.empty()' instead of 'XX.size() == 0', 'XX.size() < 1' or
'XX.size() <= 0' or for simpler coding.
It also has the same number of characters as '!XX.size()' and /might/ be
more readable
- many size checking had 'XX.size() > 0', 'XX.size() != 0', or 'XX.size() >= 1'
when a simple 'XX.size()' suffices
