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.
using a run-time selectable preconditioner
References:
Van der Vorst, H. A. (1992).
Bi-CGSTAB: A fast and smoothly converging variant of Bi-CG
for the solution of nonsymmetric linear systems.
SIAM Journal on scientific and Statistical Computing, 13(2), 631-644.
Barrett, R., Berry, M. W., Chan, T. F., Demmel, J., Donato, J.,
Dongarra, J., Eijkhout, V., Pozo, R., Romine, C. & Van der Vorst, H.
(1994).
Templates for the solution of linear systems:
building blocks for iterative methods
(Vol. 43). Siam.
See also: https://en.wikipedia.org/wiki/Biconjugate_gradient_stabilized_method
Tests have shown that PBiCGStab with the DILU preconditioner is more
robust, reliable and shows faster convergence (~2x) than PBiCG with
DILU, in particular in parallel where PBiCG occasionally diverges.
This remarkable improvement over PBiCG prompted the update of all
tutorial cases currently using PBiCG to use PBiCGStab instead. If any
issues arise with this update please report on Mantis: http://bugs.openfoam.org
See http://www.openfoam.org/mantisbt/view.php?id=2076
- .org is the file extension for emacs org-mode as well
- .orig is more to the point (.org isn't always recognized as "original")
- .original is too long, although more consistent with the convention
of source code file naming
Update script contributed by Bruno Santos
so that the specification of the name and dimensions are optional in property dictionaries.
Update tutorials so that the name of the dimensionedScalar property is
no longer duplicated but optional dimensions are still provided and are
checked on read.
Description
Specify an etc file to include when reading dictionaries, expects a
single string to follow.
Searches for files from user/group/shipped directories.
The search scheme allows for version-specific and
version-independent files using the following hierarchy:
- \b user settings:
- ~/.OpenFOAM/\<VERSION\>
- ~/.OpenFOAM/
- \b group (site) settings (when $WM_PROJECT_SITE is set):
- $WM_PROJECT_SITE/\<VERSION\>
- $WM_PROJECT_SITE
- \b group (site) settings (when $WM_PROJECT_SITE is not set):
- $WM_PROJECT_INST_DIR/site/\<VERSION\>
- $WM_PROJECT_INST_DIR/site/
- \b other (shipped) settings:
- $WM_PROJECT_DIR/etc/
An example of the \c \#includeEtc directive:
\verbatim
#includeEtc "etcFile"
\endverbatim
The usual expansion of environment variables and other constructs is
retained.
For multi-region cases the default location of blockMeshDict is now system/<region name>
If the blockMeshDict is not found in system then the constant directory
is also checked providing backward-compatibility
The old separate incompressible and compressible libraries have been removed.
Most of the commonly used RANS and LES models have been upgraded to the
new framework but there are a few missing which will be added over the
next few days, in particular the realizable k-epsilon model. Some of
the less common incompressible RANS models have been introduced into the
new library instantiated for incompressible flow only. If they prove to
be generally useful they can be templated for compressible and
multiphase application.
The Spalart-Allmaras DDES and IDDES models have been thoroughly
debugged, removing serious errors concerning the use of S rather than
Omega.
The compressible instances of the models have been augmented by a simple
backward-compatible eddyDiffusivity model for thermal transport based on
alphat and alphaEff. This will be replaced with a separate run-time
selectable thermal transport model framework in a few weeks.
For simplicity and ease of maintenance and further development the
turbulent transport and wall modeling is based on nut/nuEff rather than
mut/muEff for compressible models so that all forms of turbulence models
can use the same wall-functions and other BCs.
All turbulence model selection made in the constant/turbulenceProperties
dictionary with RAS and LES as sub-dictionaries rather than in separate
files which added huge complexity for multiphase.
All tutorials have been updated so study the changes and update your own
cases by comparison with similar cases provided.
Sorry for the inconvenience in the break in backward-compatibility but
this update to the turbulence modeling is an essential step in the
future of OpenFOAM to allow more models to be added and maintained for a
wider range of cases and physics. Over the next weeks and months more
turbulence models will be added of single and multiphase flow, more
additional sub-models and further development and testing of existing
models. I hope this brings benefits to all OpenFOAM users.
Henry G. Weller
