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.
- The logic for switching input-mode was previously completely
encapsulated within the #inputMode directive, but without any
programming equivalent. Furthermore, the encapsulation in inputMode
made the logic less clear in other places.
Exposing the inputMode as an enum with direct access from entry
simplifies things a fair bit.
- eliminate one level of else/if nesting in entryIO.C for clearer logic
- for dictionary function entries, simply use
addNamedToMemberFunctionSelectionTable() and avoid defining a type()
as a static. For most function entries the information is only used
to get a name for the selection table lookup anyhow.
When using #include or #includeIfPresent, it is easy to generate an
empty file name. For example,
#include "~OpenFOAM/missing-path/file"
On error, findEtcFile() returns an empty fileName. This was treated as
a relative name, which meant there was an attempt to open the parent directory
as a file. The resulting error message was confusing:
--> FOAM FATAL IO ERROR:
Attempt to put back onto bad stream
file: /CASE/PATH/system at line 1.
From function void Istream::putBack(const token&)
in file db/IOstreams/IOstreams/Istream.C at line 34.
- fix by leaving empty expansions as-is
- similar to the #include directive, but does not generate an error if the
file does not exist.
Note: opted for an explicit naming #includeIfPresent rather than #cinclude
- #inputMode error
now issues a FatalError on duplicate entries
- #inputMode warn
issues a warning on duplicate entries, corresponds to the
old behaviour of 'error'
- #inputMode protect
prevents overwriting existing entries
The 'protect' mode provides a simple mechanism for supplying default values.
eg,
in file1:
#inputMode protect
intensity 0.1;
mixingLength 0.005;
#inputMode merge
inlet
{
type turbulentIntensityKineticEnergyInlet;
intensity $intensity;
}
which is included from file2:
intensity 0.05;
#include "file1"
- partial revert for commit d21869b580
* only add extra newlines for a top-level dictionary that is output as such
- make "#inputMode merge" the default instead of "#inputMode error"
* this corresponds to a very common usage case
* added '#remove' function
* changed insert() method name to more general execute()
* using #inputMode or #remove within a primitiveEntry now provokes an error
* adjusted the dictionaryTest accordingly
