Improvements to existing functionality
--------------------------------------
- MPI is initialised without thread support if it is not needed e.g. uncollated
- Use native c++11 threading; avoids problem with static destruction order.
- etc/cellModels now only read if needed.
- etc/controlDict can now be read from the environment variable FOAM_CONTROLDICT
- Uniform files (e.g. '0/uniform/time') are now read only once on the master only
(with the masterUncollated or collated file handlers)
- collated format writes to 'processorsNNN' instead of 'processors'. The file
format is unchanged.
- Thread buffer and file buffer size are no longer limited to 2Gb.
The global controlDict file contains parameters for file handling. Under some
circumstances, e.g. running in parallel on a system without NFS, the user may
need to set some parameters, e.g. fileHandler, before the global controlDict
file is read from file. To support this, OpenFOAM now allows the global
controlDict to be read as a string set to the FOAM_CONTROLDICT environment
variable.
The FOAM_CONTROLDICT environment variable can be set to the content the global
controlDict file, e.g. from a sh/bash shell:
export FOAM_CONTROLDICT=$(foamDictionary $FOAM_ETC/controlDict)
FOAM_CONTROLDICT can then be passed to mpirun using the -x option, e.g.:
mpirun -np 2 -x FOAM_CONTROLDICT simpleFoam -parallel
Note that while this avoids the need for NFS to read the OpenFOAM configuration
the executable still needs to load shared libraries which must either be copied
locally or available via NFS or equivalent.
New: Multiple IO ranks
----------------------
The masterUncollated and collated fileHandlers can now use multiple ranks for
writing e.g.:
mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)'
In this example ranks 0 ('processor0') and 3 ('processor3') now handle all the
I/O. Rank 0 handles 0,1,2 and rank 3 handles 3,4,5. The set of IO ranks should always
include 0 as first element and be sorted in increasing order.
The collated fileHandler uses the directory naming processorsNNN_XXX-YYY where
NNN is the total number of processors and XXX and YYY are first and last
processor in the rank, e.g. in above example the directories would be
processors6_0-2
processors6_3-5
and each of the collated files in these contains data of the local ranks
only. The same naming also applies when e.g. running decomposePar:
decomposePar -fileHandler collated -ioRanks '(0 3)'
New: Distributed data
---------------------
The individual root directories can be placed on different hosts with different
paths if necessary. In the current framework it is necessary to specify the
root per slave process but this has been simplified with the option of specifying
the root per host with the -hostRoots command line option:
mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)' \
-hostRoots '("machineA" "/tmp/" "machineB" "/tmp")'
The hostRoots option is followed by a list of machine name + root directory, the
machine name can contain regular expressions.
New: hostCollated
-----------------
The new hostCollated fileHandler automatically sets the 'ioRanks' according to
the host name with the lowest rank e.g. to run simpleFoam on 6 processors with
ranks 0-2 on machineA and ranks 3-5 on machineB with the machines specified in
the hostfile:
mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler hostCollated
This is equivalent to
mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler collated -ioRanks '(0 3)'
This example will write directories:
processors6_0-2/
processors6_3-5/
A typical example would use distributed data e.g. no two nodes, machineA and
machineB, each with three processes:
decomposePar -fileHandler collated -case cavity
# Copy case (constant/*, system/*, processors6/) to master:
rsync -a cavity machineA:/tmp/
# Create root on slave:
ssh machineB mkdir -p /tmp/cavity
# Run
mpirun --hostfile hostfile icoFoam \
-case /tmp/cavity -parallel -fileHandler hostCollated \
-hostRoots '("machineA" "/tmp" "machineB" "/tmp")'
Contributed by Mattijs Janssens
In early versions of OpenFOAM the scalar limits were simple macro replacements and the
names were capitalized to indicate this. The scalar limits are now static
constants which is a huge improvement on the use of macros and for consistency
the names have been changed to camel-case to indicate this and improve
readability of the code:
GREAT -> great
ROOTGREAT -> rootGreat
VGREAT -> vGreat
ROOTVGREAT -> rootVGreat
SMALL -> small
ROOTSMALL -> rootSmall
VSMALL -> vSmall
ROOTVSMALL -> rootVSmall
The original capitalized are still currently supported but their use is
deprecated.
Specifying default fields for complex and multi-phase cases is simplified and
generalized by using wildcards to select sets of related field names, e.g.
defaultFields (p p_rgh U "U\..*" T "T\..*" "alpha\..*");
selects the velocity, temperature and phase-fraction fields of all phases in
addition to the pressure fields.
The default patch types specified in the new defaultPatchTypes entry of the
etc paraFoam configuration dictionaries:
defaultPatchTypes (patch wall);
Wildcards are supported, for example to specify that all patches loaded simply set
defaultPatchTypes to
defaultPatchTypes (".*");
The new default paraFoam configuration is in the files OpenFOAM-dev/etc/paraFoam
containing the entry
defaultFields (U p p_rgh T alpha.water alpha.air);
specifying the set of fields which are loaded by default if available. This
setting maybe overridden by providing additional paraFoam configuration files in
any of the OpenFOAM etc directories searched, listed using
foamEtcFile -list
e.g.
~/.OpenFOAM/dev
~/.OpenFOAM
~/OpenFOAM/site/dev
~/OpenFOAM/site
~/OpenFOAM/OpenFOAM-dev/etc
The new configurable set of default fields loaded replaces the original hard-coded default of
"p" and "U" and is much more convenient for current OpenFOAM usage.
The "Refresh Times" button now triggers a re-render of the visualisation
as well as scanning for new times and fields. This prevents old
overwritten data from remaining on screen despite everything else having
been updated.
ParaView has been updated to version 5.4.0. The C++ panel has been
deleted and replaced with a panel based on the new(er) XML API. This
reader works for ParaView-4.0.1 and newer. The ParaView 3 reader remains
unchanged.
Update issues have also been fixed. All the time directories are now
scanned for fields and clouds when filling the selection lists. This
stops fields from disappearing when the time is changed. The scan is
only done on startup and when the refresh button is pressed.
The list of available Lagrangian fields also now shows a combined set of
all the clouds. Previously, only fields from the first cloud were shown.
If a field does not apply to all the clouds, ParaView will display it's
name in the dropdown menu with a "(partial)" qualifier.
Some undocumented and incomplete bits of code, which were not being
compiled, have been removed.
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:
$FOAM_TUTORIALS/IO/fileHandling
The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
For example, to mesh a sphere with a single block the geometry is defined in the
blockMeshDict as a searchableSurface:
geometry
{
sphere
{
type searchableSphere;
centre (0 0 0);
radius 1;
}
}
The vertices, block topology and curved edges are defined in the usual
way, for example
v 0.5773502;
mv -0.5773502;
a 0.7071067;
ma -0.7071067;
vertices
(
($mv $mv $mv)
( $v $mv $mv)
( $v $v $mv)
($mv $v $mv)
($mv $mv $v)
( $v $mv $v)
( $v $v $v)
($mv $v $v)
);
blocks
(
hex (0 1 2 3 4 5 6 7) (10 10 10) simpleGrading (1 1 1)
);
edges
(
arc 0 1 (0 $ma $ma)
arc 2 3 (0 $a $ma)
arc 6 7 (0 $a $a)
arc 4 5 (0 $ma $a)
arc 0 3 ($ma 0 $ma)
arc 1 2 ($a 0 $ma)
arc 5 6 ($a 0 $a)
arc 4 7 ($ma 0 $a)
arc 0 4 ($ma $ma 0)
arc 1 5 ($a $ma 0)
arc 2 6 ($a $a 0)
arc 3 7 ($ma $a 0)
);
which will produce a mesh in which the block edges conform to the sphere
but the faces of the block lie somewhere between the original cube and
the spherical surface which is a consequence of the edge-based
transfinite interpolation.
Now the projection of the block faces to the geometry specified above
can also be specified:
faces
(
project (0 4 7 3) sphere
project (2 6 5 1) sphere
project (1 5 4 0) sphere
project (3 7 6 2) sphere
project (0 3 2 1) sphere
project (4 5 6 7) sphere
);
which produces a mesh that actually conforms to the sphere.
See OpenFOAM-dev/tutorials/mesh/blockMesh/sphere
This functionality is experimental and will undergo further development
and generalization in the future to support more complex surfaces,
feature edge specification and extraction etc. Please get involved if
you would like to see blockMesh become a more flexible block-structured
mesher.
Henry G. Weller, CFD Direct.
- There will be triangles rendered inside the mesh (when
surface-rendering), because one of the cell's triangles is defined
as a quadrangle in VTK_WEDGE.
- Therefore, this VTK_WEDGE representation is only used when
decomposing the mesh, otherwise the correct representation is done
by VTK_POLYHEDRON.
- Furthermore, using VTK_PYRAMID gave worse result, because it renders
2 triangles inside the mesh for the collapsed quadrangle, likely due
to mismatch with the adjacent cell's face.
- Using VTK_HEXAHEDRON was not tested in this iteration, given that it
should give even worse results, when compared to using VTK_PYRAMID.
Patch contributed by Bruno Santos
Resolves bug-report http://bugs.openfoam.org/view.php?id=2099
splitMeshRegions: handle flipping of faces for surface fields
subsetMesh: subset dimensionedFields
decomposePar: use run-time selection of decomposition constraints. Used to
keep cells on particular processors. See the decomposeParDict in
$FOAM_UTILITIES/parallel/decomposePar:
- preserveBaffles: keep baffle faces on same processor
- preserveFaceZones: keep faceZones owner and neighbour on same processor
- preservePatches: keep owner and neighbour on same processor. Note: not
suitable for cyclicAMI since these are not coupled on the patch level
- singleProcessorFaceSets: keep complete faceSet on a single processor
- refinementHistory: keep cells originating from a single cell on the
same processor.
decomposePar: clean up decomposition of refinement data from snappyHexMesh
reconstructPar: reconstruct refinement data (refineHexMesh, snappyHexMesh)
reconstructParMesh: reconstruct refinement data (refineHexMesh, snappyHexMesh)
redistributePar:
- corrected mapping surfaceFields
- adding processor patches in order consistent with decomposePar
argList: check that slaves are running same version as master
fvMeshSubset: move to dynamicMesh library
fvMeshDistribute:
- support for mapping dimensionedFields
- corrected mapping of surfaceFields
parallel routines: allow parallel running on single processor
Field: support for
- distributed mapping
- mapping with flipping
mapDistribute: support for flipping
AMIInterpolation: avoid constructing localPoints
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.
