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.
Fixed reaction source terms in the energy and species fraction equations
by multiplying by the phase fraction.
Resolves bug report https://bugs.openfoam.org/view.php?id=2591
Added a grow time and better allocate the CPU time to either add or grow. This
gives much more information to the user and helps changing the settings
accordingly.
Patch contributed by Francesco Contino
vectorField or vector2DField from scalarField components. To do this
properly and have it work for field-type combinations would require some
new field function macros.
Initially the listSwitches functions depended directly on argList functionality
but this has now been factored out so that the listSwitches functions are more
general and require only debug functionality.
Provides better context for the available boundary conditions, fvOptions,
functionObjects etc. and thus returns only those available to and compatible
with the particular application.
e.g.
pimpleFoam -help
Usage: pimpleFoam [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-listFunctionObjects
List functionObjects
-listFvOptions List fvOptions
-listRegisteredSwitches
List switches registered for run-time modification
-listScalarBCs List scalar field boundary conditions (fvPatchField<scalar>)
-listSwitches List switches declared in libraries but not set in
etc/controlDict
-listTurbulenceModels
List turbulenceModels
-listUnsetSwitches
List switches declared in libraries but not set in
etc/controlDict
-listVectorBCs List vector field boundary conditions (fvPatchField<vector>)
-noFunctionObjects
do not execute functionObjects
-parallel run in parallel
-postProcess Execute functionObjects only
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage
pimpleFoam listTurbulenceModels
pimpleFoam -listTurbulenceModels
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: dev |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : dev-39c46019e44f
Exec : pimpleFoam -listTurbulenceModels
Date : Jun 10 2017
Time : 21:37:49
Host : "dm"
PID : 675
Case : /home/dm2/henry/OpenFOAM/OpenFOAM-dev
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
SetNaN : Initialising allocated memory to NaN (FOAM_SETNAN).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Turbulence models
3
(
LES
RAS
laminar
)
RAS models
18
(
LRR
LamBremhorstKE
LaunderSharmaKE
LienCubicKE
LienLeschziner
RNGkEpsilon
SSG
ShihQuadraticKE
SpalartAllmaras
kEpsilon
kOmega
kOmegaSST
kOmegaSSTLM
kOmegaSSTSAS
kkLOmega
qZeta
realizableKE
v2f
)
LES models
10
(
DeardorffDiffStress
Smagorinsky
SpalartAllmarasDDES
SpalartAllmarasDES
SpalartAllmarasIDDES
WALE
dynamicKEqn
dynamicLagrangian
kEqn
kOmegaSSTDES
)
Further work will be needed to support the -listTurbulenceModels option in
multiphase solvers.
discontinuous fields, with the discontinuity defined by a level set. The
functions do a proper integration of the discontinuous fields by tet-
and tri-cutting along the plane of the level set.
- provides a summary hash of classes used and their associated object names.
The HashTable representation allows us to leverage various HashTable
methods. This hashed summary view can be useful when querying
particular aspects, but is most useful when reducing the objects in
consideration to a particular subset. For example,
const wordHashSet interestingTypes
{
volScalarField::typeName,
volVectorField::typeName
};
IOobjectList objects(runTime, runTime.timeName());
HashTable<wordHashSet> classes = objects.classes();
classes.retain(interestingTypes);
// Or do just the opposite:
classes.erase(unsupportedTypes);
Can also use the underlying HashTable filter methods
STYLE: use templated internals to avoid findString() when matching subsets
- Generalized means over filtering table entries based on their keys,
values, or both. Either filter (retain), or optionally prune elements
that satisfy the specified predicate.
filterKeys and filterValues:
- Take a unary predicate with the signature
bool operator()(const Key& k);
- filterEntries:
Takes a binary predicate with the signature
bool operator()(const Key& k, const T& v);
==
The predicates can be normal class methods, or provide on-the-fly
using a C++ lambda. For example,
wordRes goodFields = ...;
allFieldNames.filterKeys
(
[&goodFields](const word& k){ return goodFields.match(k); }
);
Note that all classes that can match a string (eg, regExp, keyType,
wordRe, wordRes) or that are derived from a Foam::string (eg, fileName,
word) are provided with a corresponding
bool operator()(const std::string&)
that either performs a regular expression or a literal match.
This allows such objects to be used directly as a unary predicate
when filtering any string hash keys.
Note that HashSet and hashedWordList both have the proper
operator() methods that also allow them to be used as a unary
predicate.
- Similar predicate selection with the following:
* tocKeys, tocValues, tocEntries
* countKeys, countValues, countEntries
except that instead of pruning, there is a simple logic inversion.
- predicates::always and predicates::never returning true and false,
respectively. These simple classes make it easier when writing
templated code.
As well as unary and binary predicate forms, they also contain a
match(std::string) method for compatibility with regex-based classes.
STYLE: write bool and direction as primitive 'int' not as 'label'.
- ensure that the string-related classes have consistently similar
matching methods. Use operator()(const std::string) as an entry
point for the match() method, which makes it easier to use for
filters and predicates. In some cases this will also permit using
a HashSet as a match predicate.
regExp
====
- the set method now returns a bool to signal that the requested
pattern was compiled.
wordRe
====
- have separate constructors with the compilation option (was previously
a default parameter). This leaves the single parameter constructor
explicit, but the two parameter version is now non-explicit, which
makes it easier to use when building lists.
- renamed compile-option from REGEX (to REGEXP) for consistency with
with the <regex.h>, <regex> header names etc.
wordRes
====
- renamed from wordReListMatcher -> wordRes. For reduced typing and
since it behaves as an entity only slightly related to its underlying
list nature.
- Provide old name as typedef and include for code transition.
- pass through some list methods into wordRes
hashedWordList
====
- hashedWordList[const word& name] now returns a -1 if the name is is
not found in the list of indices. That has been a pending change
ever since hashedWordList was generalized out of speciesTable
(Oct-2010).
- add operator()(const word& name) for easy use as a predicate
STYLE: adjust parameter names in stringListOps
- reflect if the parameter is being used as a primary matcher, or the
matcher will be derived from the parameter.
For example,
(const char* re), which first creates a regExp
versus (const regExp& matcher) which is used directly.
- can run doxygen with an alternative Doxyfile, which is useful
when verifying generated content for particular classes.
Eg,
PATH/doc/Allwmake -dir $PWD
- this allows filling in the VTK structures without intermediate data
and without sequencial insertion. Should be faster and smaller
than the previous cell-wise insertion methods.
Most importantly, it improves code reuse.
- Previously matched name against the object->name() method
but saved with iter.key(). Now use iter.key() more consistently.
STYLE: consistent parameter names (doxygen)
