- accept IOobjectOption::registerOption with (MUST_READ, NO_WRITE)
being implicit. Direct handling of IOobjectOption itself, for
consistency with IOobject.
The disabling of object registration is currently the only case
where IOobjectList doesn't use default construction parameters,
but it was previously a bit awkward to specify.
- include -no-libs option by default, similar to '-lib',
which makes it available to all solvers/utilities.
Add argList allowLibs() method to query it.
- relocate with/no functionObjects logic from Time to argList
itself as argList allowFunctionObjects()
- add libs/functionObjects override handling to decomposePar etc
ENH: report the stream relativeName for IOerrors (see c9333a5ac8)
- in various situations with mesh regions it is also useful to
filter out or remove the defaultRegion name (ie, "region0").
Can now do that conveniently from the polyMesh itself or as a static
function. Simply use this
const word& regionDir = polyMesh::regionName(regionName);
OR mesh.regionName()
instead of
const word& regionDir =
(
regionName != polyMesh::defaultRegion
? regionName
: word::null
);
Additionally, since the string '/' join operator filters out empty
strings, the following will work correctly:
(polyMesh::regionName(regionName)/polyMesh::meshSubDir)
(mesh.regionName()/polyMesh::meshSubDir)
- simplify procAddressing read/write
- avoid accessing points in faMeshReconstructor.
Can rely on the patch meshPoints (labelList), which does not need
access to a pointField
- report number of points on decomposed mesh.
Can be useful additional information.
Additional statistics for finite area decomposition
- provide bundled reconstructAllFields for various reconstructors
- remove reconstructPar checks for very old face addressing
(from foam2.0 - ie, older than OpenFOAM itself)
- bundle all reading into fieldsDistributor tools,
where it can be reused by various utilities as required.
- combine decomposition fields as respective fieldsCache
which eliminates most of the clutter from decomposePar
and similfies reuse in the future.
STYLE: remove old wordHashSet selection (deprecated in 2018)
BUG: incorrect face flip handling for faMeshReconstructor
- a latent bug which is not yet triggered since the faMesh faces are
currently only definable on boundary faces (which never flip)
- previously filtered on the existence of area fields, but with
faMesh::TryNew this is not required anymore.
STYLE: enable -verbose for various parallel utilities (consistency)
- decomposePar: -no-fields to suppress decomposition of fields
- makeFaMesh: -no-decompose to suppress creation of *ProcAddressing
and fields, -no-fields to suppress decomposition of fields only
- similar to -dry-run handling, can be interrogated from argList,
which makes it simpler to add into utilities.
- support multiple uses of -dry-run and -verbose to increase the
level. For example, could have
someApplication -verbose -verbose
and inside of the application:
if (args.verbose() > 2) ...
BUG: error with empty distributed roots specification (fixes#2196)
- previously used the size of distributed roots to transmit if the
case was running in distributed mode, but this behaves rather poorly
with bad input. Specifically, the following questionable setup:
distributed true;
roots ( /*none*/ );
Now transmit the ParRunControl distributed() value instead,
and also emit a gentle warning for the user:
WARNING: running distributed but did not specify roots!
- argList::envExecutable() static method.
This is identical to getEnv("FOAM_EXECUTABLE"), where the name of
the executable has typically been set from the argList construction.
Provides a singleton access to this value from locations that
do not have knowledge of the originating command args (argList).
This is a similar rationale as for the argList::envGlobalPath() static.
- additional argList::envRelativePath() static method.
- make -dry-run handling more central and easier to use by adding into
argList itself.
STYLE: drop handling of -srcDoc (v1706 option)
- replaced with -doc-source for 1712 and never used much anyhow
- noticed by Robin Knowles with `decomposePar -fields -copyZero`
The internals for the Foam:cp method combine the behaviour of
a regular `cp` and `cp -R` combined.
When source and target are both directories, the old implementation
created a subdirectory for the contents.
This normally fine,
ok: cp "path1/0/" to "path2/1" -> "path2/1/2"
BUT: cp "path1/0/" to "path2/0" -> "path2/0/0" !!
Now add check for the basenames first.
If they are identical, we probably meant to copy directory contents
only, without the additional subdir layer.
BUG: decomposePar -fields -copyZero copies the wrong directory
- was using the current time name (usually latest) instead of copying
the 0 directory
ENH: accept 0.orig directories as a fallback to copy if the 0 directory
is missing
- can now drop older Test-decomposePar for exploration purposes
and simply use -dry-run with the -domains and -method options.
- write VTK file instead of volScalarField in combination
with -dry-run and -cellDist.
Avoids adding any OpenFOAM fields and is usually faster to load.
Also easier to rename than a volScalarField would be when exploring
multiple decompositions.
Step 1.
include "addAllRegionOptions.H"
Adds the -allRegions, -regions and -region options to argList.
Step 2.
include "getAllRegionOptions.H"
Processes the options with -allRegions selecting everything
from the regionProperties.
OR use -regions to specify multiple regions (from
regionProperties), and can also contain regular expressions
OR use the -region option
Specifying a single -regions NAME (not a regular expresssion)
is the same as -region NAME and doesn't use regionProperties
Creates a `wordList regionNames`
Step 3.
Do something with the region names.
Either directly, or quite commonly with the following
include "createNamedMeshes.H"
Creates a `PtrList<fvMesh> meshes`
STYLE: add description to some central include files
- make regionName an optional constructor parameter, which eliminates
a separate set of constructors and construction tables. Adjust
internals to treat a missing/empty regionName as a no-op.
- pass in fallback dictionary content via new IOdictionary constructor
with a pointer
ENH: further relax check for matching number of processor dirs
- if the "numberOfSubdomains" entry is missing (or even zero)
ignore checks of processor dirs as meaningless.
- robuster matching behaviour when encountering paths that themselves
contain the word "processor" in them. For example,
"/path/processor0generation2/case1/processor10/system"
will now correctly match on processor10 instead of failing.
- use procRangeType for encapsulating the processor ranges
- provision for information of distributed vs non-distributed roots.
The information is currently available from the initial setup, but
can useful to access directly within fileOperation.
STYLE: modernize list iteration
- Favour use of argList methods that are more similar to dictionary
method names with the aim of reducing the cognitive load.
* Silently deprecate two-parameter get() method in favour of the
more familiar getOrDefault.
* Silently deprecate opt() method in favour of get()
These may be verbosely deprecated in future versions.
This method waits until all the threads have completed IO operations and
then clears any cached information about the files on disk. This
replaces the deactivation of threading by means of zeroing the buffer
size when writing and reading of a file happen in sequence. It also
allows paraFoam to update the list of available times.
Patch contributed by Mattijs Janssens
Resolves bug report https://bugs.openfoam.org/view.php?id=2962
- centralizes IOobject handling and treatment of alternative locations.
If an alternative file location is specified, it will be used instead.
- provide decompositionMethod::canonicalName instead of using
"decomposeParDict" in various places.
General:
* -roots, -hostRoots, -fileHandler
Specific:
* -to <coordinateSystem> -from <coordinateSystem>
- Display -help-compat when compatibility or ignored options are available
STYLE: capitalization of options text
- can be used to test the behaviour of the decomposion and its
characteristics without writing any decomposition to disk.
Combine with -cellDist to visualize the expected decomposition
result.
- improves backward compatibility and more naming consistency.
Retain setMany(iter1, iter2) to avoid ambiguity with the
PackedList::set(index, value) method.
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
- use succincter method names that more closely resemble dictionary
and HashTable method names. This improves method name consistency
between classes and also requires less typing effort:
args.found(optName) vs. args.optionFound(optName)
args.readIfPresent(..) vs. args.optionReadIfPresent(..)
...
args.opt<scalar>(optName) vs. args.optionRead<scalar>(optName)
args.read<scalar>(index) vs. args.argRead<scalar>(index)
- the older method names forms have been retained for code compatibility,
but are now deprecated
Within decomposeParDict, it is now possible to specify a different
decomposition method, methods coefficients or number of subdomains
for each region individually.
The top-level numberOfSubdomains remains mandatory, since this
specifies the number of domains for the entire simulation.
The individual regions may use the same number or fewer domains.
Any optional method coefficients can be specified in a general
"coeffs" entry or a method-specific one, eg "metisCoeffs".
For multiLevel, only the method-specific "multiLevelCoeffs" dictionary
is used, and is also mandatory.
----
ENH: shortcut specification for multiLevel.
In addition to the longer dictionary form, it is also possible to
use a shorter notation for multiLevel decomposition when the same
decomposition method applies to each level.
old "positions" file form
The change to barycentric-based tracking changed the contents of the
cloud "positions" file to a new format comprising the barycentric
co-ordinates and other cell position-based info. This broke
backwards compatibility, providing no option to restart old cases
(v1706 and earlier), and caused difficulties for dependent code, e.g.
for post-processing utilities that could only infer the contents only
after reading.
The barycentric position info is now written to a file called
"coordinates" with provision to restart old cases for which only the
"positions" file is available. Related utilities, e.g. for parallel
running and data conversion have been updated to be able to support both
file types.
To write the "positions" file by default, use set the following option
in the InfoSwitches section of the controlDict:
writeLagrangianPositions 1;
