- use cellCentres() instead of volField equivalent for vtk conversion
- make looping variables more consistent
- centralize the transcription of OpenFOAM -> vtk tuples
- provide default WM_DIR if not already set, to improve robustness if a
reduced environment is used
- add etc/ to WM_PROJECT_SITE search. This makes the site directory
structure consistent with the OpenFOAM structure.
Eg,
WM_PROJECT_SITE/etc/..
WM_PROJECT_SITE/bin/..
WM_PROJECT_SITE/platforms/..
- Don't set/export WM_OSTYPE. The default is POSIX and is properly
defaulted throughout, including in CMakeLists-OpenFOAM.txt (also for
Catalyst)
- removed reliance on ParaView_INCLUDE_DIR variable for conveying the
major.minor version information when compiling. This can be somewhat
fragile and also adds variable that is an unnecessary when running
(only used when compiling).
Instead use `have_pvplugin_support` function in paraviewFunctions
wmake script to determine the maj.min from the PV_PLUGIN_PATH
since we have already defined the output path there with paraview
maj.min numbering.
Can now build with paraview from the operating system,
provided that it has develop headers available.
ParaView_VERSION=system
In the etc/config.sh/paraview setup, the maj.min is taken from
the corresponding `paraview --version` output and used when
defining the PV_PLUGIN_PATH.
During the build, the include path taken from `paraview-config`
for a system installation, from the guess installation root
of the paraview binary, or ParaView_DIR otherwise.
NB: using a system ParaView for building runTimePostProcessing is unsupported.
- these types of builds appear to have various library resolution issues
(eg, libexpat not being loaded). Additionally, the build logic does
not yet cover this type of use case.
- use std::string instead of c-string for the string constants
- centralize some definitions of resources into foamVersion.H
Now expose some of the hard-coded values used in foamEtcFiles()
so that they can be known or even overridden as required.
Relocate to src/OpenFOAM/include as a constant location.
- For compatibility, access to the old global names is provided via
macros
#define FOAMversion foamVersion::version
#define FOAMbuild foamVersion::build
#define FOAMbuildArch foamVersion::buildArch
- this isolation makes it easier to provide additional scoped methods
for dealing with version related information. Eg, printBuildInfo()
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
- simplifies usage.
Support syncPar check on names() to detect inconsistencies.
- simplify readFields, ReadFields and other routines by using these
new methods.
- what was previously termed 'setLargeCellSubset()' is now simply
'setCellSubset()' and supports memory efficient interfaces.
The new parameter ordering avoids ambiguities caused by default
parameters.
Old parameter order:
setLargeCellSubset
(
const labelList& region,
const label currentRegion,
const label patchID = -1,
const bool syncCouples = true
);
New parameter order:
setCellSubset
(
const label regioni,
const labelUList& regions,
const label patchID = -1,
const bool syncCouples = true
);
And without ambiguity:
setCellSubset
(
const labelUList& selectedCells,
const label patchID = -1,
const bool syncCouples = true
);
- support bitSet directly for specifying the selectedCells for
memory efficiency and ease of use.
- Additional constructors to perform setCellSubset() immediately,
which simplifies coding.
For example,
meshParts.set
(
zonei,
new fvMeshSubset(mesh, selectedCells)
);
Or even
return autoPtr<fvMeshSubset>::New(mesh, selectedCells);
- 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
- generalize some of the library extensions (.so vs .dylib).
Provide as wmake 'sysFunctions'
- added note about unsupported/incomplete system support
- centralize detection of ThirdParty packages into wmake/ subdirectory
by providing a series of scripts in the spirit of GNU autoconfig.
For example,
have_boost, have_readline, have_scotch, ...
Each of the `have_<package>` scripts will generally provide the
following type of functions:
have_<package> # detection
no_<package> # reset
echo_<package> # echoing
and the following type of variables:
HAVE_<package> # unset or 'true'
<package>_ARCH_PATH # root for <package>
<package>_INC_DIR # include directory for <package>
<package>_LIB_DIR # library directory for <package>
This simplifies the calling scripts:
if have_metis
then
wmake metisDecomp
fi
As well as reducing clutter in the corresponding Make/options:
EXE_INC = \
-I$(METIS_INC_DIR) \
-I../decompositionMethods/lnInclude
LIB_LIBS = \
-L$(METIS_LIB_DIR) -lmetis
Any additional modifications (platform-specific or for an external build
system) can now be made centrally.
- this provides a better typesafe means of locating predefined cell
models than relying on strings. The lookup is now ptr() or ref()
directly. The lookup functions behave like on-demand singletons when
loading "etc/cellModels".
Functionality is now located entirely in cellModel but a forwarding
version of cellModeller is provided for API (but not ABI) compatibility
with older existing user code.
STYLE: use constexpr for cellMatcher constants
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;
- previous only checked for clouds at the last instance and only
detected lagrangian fields from the first cloud.
Now check for clouds at all instances and detect all of their fields
as well.
- use allocator class to wrap the stream pointers instead of passing
them into ISstream, OSstream and using a dynamic cast to delete
then. This is especially important if we will have a bidirectional
stream (can't delete twice!).
STYLE:
- file stream constructors with std::string (C++11)
- for rewind, explicit about in|out direction. This is not currently
important, but avoids surprises with any future bidirectional access.
- combined string streams in StringStream.H header.
Similar to <sstream> include that has both input and output string
streams.
- disable automatically upgrading copyrights in files since changes to
not automatically imply a change in copyright. Eg, fixing a typo in
comments, or changing a variable from 'loopI' to 'loopi' etc.
- The reader module allows two levels of caching.
The OpenFOAM fvMesh can be cached in memory, for faster loading of
fields. Additionally, the translated VTK geometries are held in a
local cache. The cached VTK geometries should incur no additional
overhead since they use the VTK reference counting for their storage
management.
- 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.
- has the selected values directly and use these lookup names to store
directly into a hash. This replaces several parallel lists of
decomp information etc and makes it easier.
