Original commit message:
------------------------
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.
- this shifts responsibility away from caller to the individual writers
for knowing which file formats are supported and which file ending is
appropriate. When the writer receives the output format request,
it can elect to downgrade or otherwise adjust it to what it can
actually manage (eg, legacy vs xml vs xml-append).
But currently still just with legacy format backends.
- Place common code under OSspecific.
By including "endian.H", either one of WM_BIG_ENDIAN or WM_LITTLE_ENDIAN
will be defined.
Provides inline 32-bit and 64-bit byte swap routines that can be
used/re-used elsewhere.
The inplace memory swaps currently used by the VTK output are left for
the moment pending further cleanup of that code.
To compile with 64bit labels set
WM_LABEL_SIZE=64
in ~/OpenFOAM/dev/prefs.sh
source ~/.bashrc
then Allwmake in OpenFOAM-dev.
This will build into for example OpenFOAM-dev/platforms/linux64ClangDPInt64Opt
If WM_LABEL_SIZE is unset or set to 32:
WM_LABEL_SIZE=32
the build would be placed into OpenFOAM-dev/platforms/linux64ClangDPInt32Opt
Thus both 32bit and 64bit label builds can coexist without problem.
Some tools now output sets at the pointsInstance (if relating to geometry),
some at the facesInstance (if relating to topology).
So when loading them we now search for them from current time down
to facesInstance. They cannot be beyond facesInstance.
Adapted Time::findInstance to take optional limiting instance. Adapted
topoSet to use this. Adapted all uses of IOobjectList on sets to do the
same.
