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.
This change changes the point-tetIndices-face interpolation function
method to take barycentric-tetIndices-face arguments instead. This
function is, at present, only used for interpolating Eulerian data to
Lagrangian particles.
This change prevents an inefficiency in cellPointInterpolation whereby
the position of the particle is calculated from it's barycentric
coordinates, before immediately being converted back to barycentric
coordinates to perform the interpolation.
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.
The averaging methods now take the particle barycentric coordinates as
inputs rather than global positions. This change significantly optimises
Dual averaging, which is the most commonly used method. The run time of
the lagrangian/MPPICFoam/Goldschmidt tutorial has been reduced by a
factor of about two.
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
for consistency with reactingTwoPhaseEulerFoam and to ensure correct operation
of models requiring formal boundedness of phase-fractions.
Resolves bug-report https://bugs.openfoam.org/view.php?id=2589
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
"pos" now returns 1 if the argument is greater than 0, otherwise it returns 0.
This is consistent with the common mathematical definition of the "pos" function:
https://en.wikipedia.org/wiki/Sign_(mathematics)
However the previous implementation in which 1 was also returned for a 0
argument is useful in many situations so the "pos0" has been added which returns
1 if the argument is greater or equal to 0. Additionally the "neg0" has been
added which returns 1 if if the argument is less than or equal to 0.
Temporal variation of Ta is generally more useful than spatial variation but
a run-time switch between the two modes of operation could be implemented in
needed.
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.
