- avoid meshModifier contents from being read immediately upon
construction, since this recreates an existing modifier instead of
allowing us to specify our own.
- improve functional compatibility with DynList (remove methods)
* eg, remove an element from any position in a DynamicList
* reduce the number of template parameters
* remove/subset regions of DynamicList
- propagate Swap template specializations for lists, hashtables
- move construct/assignment to various containers.
- add find/found methods for FixedList and UList for a more succinct
(and clearer?) usage than the equivalent global findIndex() function.
- simplify List_FOR_ALL loops
Previously:
- bad command-line input such as -label 1234xyz would parse as a
label (with value 1234) and the trailing junk would be silently
ignored. This may or may not be appropriate. If the trailing junk
looked like this '100E' or '1000E-' (ie, forgot to type the
exponent), the incorrectly parsed values can be quite bad:
label = 32684
scalar = 6.93556e-310
Now:
- use the updated readLabel/readScalar routines that trigger a
FatalIOError on bad input:
--> FOAM FATAL IO ERROR:
Trailing content found parsing '1234xyz'
--> FOAM FATAL IO ERROR:
Trailing content found parsing '100E'
This traps erroneous command-line input immediately.
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.
Updated the tetrahedron and triangle classes to use the barycentric
primitives. Removed duplicate code for generating random positions in
tets and tris, and fixed bug in tri random position.
now possible with level-sets as well as planes. Removed tetPoints class
as this wasn't really used anywhere except for the old tet-cutting
routines. Restored tetPointRef.H to be consistent with other primitive
shapes. Re-wrote tet-overlap mapping in terms of the new cutting.
- consolidate word::validated() into word::validate() and also allow
as short form for string::validate<word>(). Also less confusing than
having similarly named methods that essentially do the same thing.
- more consistent const access when iterating over strings
- add valid(char) for keyType and wordRe
- 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.
- 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.
- disable automatically upgrading copyrights in files since changes to
not automatically imply a change in copyright. Eg, fixing a typo in
comments, or changing a variable from 'loopI' to 'loopi' etc.
