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.
See tutorials/compressible/rhoPimpleFoam/RAS/squareBendLiq for exapmle
pimpleControl: Added SIMPLErho option for running in SIMPLE mode
with large time-step/Courant number and relaxation. With this option the
density is updated from thermodynamics rather than continuity after the pressure
equation which is better behaved if pressure is relaxed and/or solved to a
loose relative tolerance. The need for this option is demonstrated in the
tutorials/compressible/rhoPimpleFoam/RAS/angledDuct tutorial which is unstable
without the option.
These new names are more consistent and logical because:
primitiveField():
primitiveFieldRef():
Provides low-level access to the Field<Type> (primitive field)
without dimension or mesh-consistency checking. This should only be
used in the low-level functions where dimensional consistency is
ensured by careful programming and computational efficiency is
paramount.
internalField():
internalFieldRef():
Provides access to the DimensionedField<Type, GeoMesh> of values on
the internal mesh-type for which the GeometricField is defined and
supports dimension and checking and mesh-consistency checking.
Non-const access to the internal field now obtained from a specifically
named access function consistent with the new names for non-canst access
to the boundary field boundaryFieldRef() and dimensioned internal field
dimensionedInternalFieldRef().
See also commit a4e2afa4b3
e.g. (fvc::interpolate(HbyA) & mesh.Sf()) -> fvc::flux(HbyA)
This removes the need to create an intermediate face-vector field when
computing fluxes which is more efficient, reduces the peak storage and
improved cache coherency in addition to providing a simpler and cleaner
API.
The deprecated non-const tmp functionality is now on the compiler switch
NON_CONST_TMP which can be enabled by adding -DNON_CONST_TMP to EXE_INC
in the Make/options file. However, it is recommended to upgrade all
code to the new safer tmp by using the '.ref()' member function rather
than the non-const '()' dereference operator when non-const access to
the temporary object is required.
Please report any problems on Mantis.
Henry G. Weller
CFD Direct.
The boundary conditions of HbyA are now constrained by the new "constrainHbyA"
function which applies the velocity boundary values for patches for which the
velocity cannot be modified by assignment and pressure extrapolation is
not specified via the new
"fixedFluxExtrapolatedPressureFvPatchScalarField".
The new function "constrainPressure" sets the pressure gradient
appropriately for "fixedFluxPressureFvPatchScalarField" and
"fixedFluxExtrapolatedPressureFvPatchScalarField" boundary conditions to
ensure the evaluated flux corresponds to the known velocity values at
the boundary.
The "fixedFluxPressureFvPatchScalarField" boundary condition operates
exactly as before, ensuring the correct flux at fixed-flux boundaries by
compensating for the body forces (gravity in particular) with the
pressure gradient.
The new "fixedFluxExtrapolatedPressureFvPatchScalarField" boundary
condition may be used for cases with or without body-forces to set the
pressure gradient to compensate not only for the body-force but also the
extrapolated "HbyA" which provides a second-order boundary condition for
pressure. This is useful for a range a problems including impinging
flow, extrapolated inlet conditions with body-forces or for highly
viscous flows, pressure-induced separation etc. To test this boundary
condition at walls in the motorBike tutorial case set
lowerWall
{
type fixedFluxExtrapolatedPressure;
}
motorBikeGroup
{
type fixedFluxExtrapolatedPressure;
}
Currently the new extrapolated pressure boundary condition is supported
for all incompressible and sub-sonic compressible solvers except those
providing implicit and tensorial porosity support. The approach will be
extended to cover these solvers and options in the future.
Note: the extrapolated pressure boundary condition is experimental and
requires further testing to assess the range of applicability,
stability, accuracy etc.
Henry G. Weller
CFD Direct Ltd.
fvOptions are transferred to the database on construction using
fv::options::New which returns a reference. The same function can be
use for construction and lookup so that fvOptions are now entirely
demand-driven.
The abstract base-classes for fvOptions now reside in the finiteVolume
library simplifying compilation and linkage. The concrete
implementations of fvOptions are still in the single monolithic
fvOptions library but in the future this will be separated into smaller
libraries based on application area which may be linked at run-time in
the same manner as functionObjects.
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.
fvOptions does not have the appropriate structure to support MRF as it
is based on option selection by user-specified fields whereas MRF MUST
be applied to all velocity fields in the particular solver. A
consequence of the particular design choices in fvOptions made it
difficult to support MRF for multiphase and it is easier to support
frame-related and field related options separately.
Currently the MRF functionality provided supports only rotations but
the structure will be generalized to support other frame motions
including linear acceleration, SRF rotation and 6DoF which will be
run-time selectable.
Allows the specification of a reference height, for example the height
of the free-surface in a VoF simulation, which reduces the range of p_rgh.
hRef is a uniformDimensionedScalarField specified via the constant/hRef
file, equivalent to the way in which g is specified, so that it can be
looked-up from the database. For example see the constant/hRef file in
the DTCHull LTSInterFoam and interDyMFoam cases.
