- commit fb69a54bc3 accidentally changed the constructMap compact
order from linear ordering to local elements first order. Seems to
interact poorly with other bookkeeping so doing a partial revert,
but still replacing the old allGatherList with exchangeSizes.
Note:
the processorLOD method does actually use a constructMap with local
elements first ordering, so some inconsistency may still exist
there
Corrects turbulence viscosity field (e.g. nut) within a specified
region by applying a maximum limit, set according to a coefficient
multiplied by the laminar viscosity:
\nu_{t,max} = c \nu
Corrections applied to:
nut | Turbulence vicosity [m2/s2]
Usage
Minimal example by using \c constant/fvOptions:
\verbatim
limitTurbulenceViscosity1
{
// Mandatory entries (unmodifiable)
type limitTurbulenceViscosity;
// Optional entries (runtime modifiable)
nut nut;
c 1e5;
// Mandatory/Optional (inherited) entries
...
}
The optional areaNormalisationMode entry determines how the area normalisation
is performed. Options are:
- `project`: tri face area dotted with patch face normal; same as v2212 (default)
- `mag`: tri face area magnitude (v2206 and earlier)
Example usage:
AMI1
{
type cyclicAMI;
...
areaNormalisationMode mag;
//areaNormalisationMode project;
}
- the special MacOS dlopen handling (commit f584ec97d0)
did not fully solve the problem with SIP clearing.
Eg, sourcing the RunFunctions (for runParallel) triggers SIP and
clears DYLD_LIBRARY_PATH. With the cleared path it finds the dummy
libraries: the dummy Pstream::init() fails.
- for simulations where the yPlus is needed for other purposes or
just for obtaining information on the patches it can be useful
to disable field writing and save disk space.
The 'writeFields' flag (as per some other function objects)
has been added control writing the yPlus volume field.
If unspecified, the default value is 'true' so that the yPlus
function object continues to work as before.
However, this default may change to 'false' in the future to align
with other function objects.
ENH: wallShearStress: support disable of field writing
- similar to yPlus, the write() method combines writing information
and writing the fields. The 'writeFields' flag allows some
separation of that logic.
- replace Map with a List or DynamicList to reduce the number of
operations and allocations within the loops.
Use polyBoundaryMesh::nProcessorPatches() for initial capacity
to avoid reallocations.
- returns the number of processorPolyPatch patches (finiteVolume)
or else the number of processorFaPatch patches (finiteArea).
These can be useful when sizing lists etc.
- the changes introduced in f215ad15d1 aim to reduce unnecessary
point-to-point communication. However, if there are also
processorCyclic boundaries involved, there are multiple connections
between any two processors, so simply skipping empty sends will cause
synchronization problems.
Eg,
On the send side:
patch0to1_a is zero (doesn't send) and patch0to1_b does send
(to the same processor).
On the receive side:
patch1to0_a receives the data intended for patch1to0_b !
Remedy
======
Simply stream all of send data into PstreamBuffers
(regardless if empty or non-empty) but track the sends
as a bit operation: empty (0) or non-empty (1)
Reset the buffer slots that were only sent empty data.
This adds an additional local overhead but avoids communication
as much as possible.
- files might have been set during token reading so only on
known on master processor.
Broadcast names to all processors (even alhough they are only
checked on master) so that the watched states remain synchronised
- freeCommmunicatorComponents needs an additional bounds check.
When MPI is initialized outside of OpenFOAM, there are no
UPstream communicator equivalents
- for boundary conditions such as uniformFixed, uniformMixed etc the
optional 'value' entry (optional) is used for the initial values and
restarts. Otherwise the various Function1 or PatchFunction1 entries
are evaluated and used determine the boundary condition values.
In most cases this is OK, but in some case such coded or expression
entries with references to other fields it can be problematic since
they may reference fields (eg, phi) that have not yet been created.
For these cases the 'value' entry will be needed: documentation
updated accordingly.
STYLE: eliminate some unneeded/unused declaration headers
- provides a more succinct way of writing
{fa,fv}PatchField<Type>::patchInternalField(*this)
as well as a consistent naming that can be used for patches derived
from valuePointPatchField
ENH: readGradientEntry helper method for fixedGradient conditions
- simplifies coding and logic.
- support different read construct modes for fixedGradient
- individual processor Time databases are purely for internal logistics
and should not be introducing any new library symbols: these will
already have been loaded in the outer loop.
- MPI_THREAD_MULTIPLE is usually undesirable for performance reasons,
but in some cases may be necessary if a linked library expects it.
Provide a '-mpi-threads' option to explicitly request it.
ENH: consolidate some looping logic within argList
- can be broadly categorised as 'unthreaded'
or 'collated' (threading requirement depends on buffering)
without other opaque inheritances.
CONFIG: add hostUncollated to bash completion prompt
- The Apple SIP (System Integrity Protection) clears environment
variables, which affects the behaviour of dynamic library loading
(the DYLD_LIBRARY_PATH env variable).
OpenFOAM shadows this variable as FOAM_LD_LIBRARY_PATH, which has
been used to restore DYLD_LIBRARY_PATH (eg, in RunFunctions script).
However, this solution is not quite complete, as it
(a) requires sourcing of RunFunctions file,
(b) additional errors appear depending on a user workflow.
This changeset alleviates the problem by also iterating through
paths stored in the shadow variable when loading dynamic libraries
(if the DYLD_LIBRARY_PATH is empty).
- with C++11, static constexpr variables apparently also require
definition in a translation unit and not just as inlined quantities.
Mostly not an issue, however gcc with -O0 does not do the inlining
and thus actually requires them to be defined in a translation unit
as well.
These variables were provided for symmetry with worldComm, but only
used in low-level internal code. Changing to inlined functions
solves the linkage issue and also aligns with the commWorld()
function naming.
Mnemonics:
MPI_COMM_SELF => UPstream::commSelf()
overall MPI_COMM_WORLD => UPstream::commGlobal(), sometimes commWorld()
local COMM_WORLD => UPstream::commWorld()
- useful when speculative receives have been initiated but are no
longer required.
Combines MPI_Cancel() + MPI_Request_free() for consistent resource
management. Currently no feedback provided if the request was
satisfied by a completed send/recv or by cancellation (can be added
later if required).
- primarily relevant for finite-area meshes, in which case they can be
considered to be an additional, detailed diagnositic that is
normally not needed (clutters the file system).
Writing can be enabled with the `-write-edges` option.
- enable 'faceZones' support.
- enable 'writeFile' support to better control file output.
- rename 'PatchPostProcessing' as 'ParticlePostProcessing' for better clarity.
- fix#1808
- enable 'faceZone' support.
- introduce 'cloudFunctionObjectTools' to simplify collection of particle info
on patches or face zones.
- enable 'writeFile' support to better control file output.
- rename 'PatchParticleHistogram' as 'ParticleHistogram' for better clarity.
- extend the loadOrCreateMesh functionality to work in conjunction
with file handlers. This allows selective loading of the mesh parts
without the ugly workaround of writing zero-sized meshes to disk and
then reading them back.
Co-authored-by: Mark Olesen <>
- fatten the interface to continue allowing write control with a bool
or with a dedicated file handler. This may slim down in the future.
Co-authored-by: mattijs <mattijs>
- use local function for the decision making, whether worldComm or a
dedicated communicator is needed (and which sibling ranks are
involved)
Co-authored-by: mattijs <mattijs>
- accept plain lists (space or comma separated) as well as the
traditional OpenFOAM lists. This simplifies argument handling
with job scripts.
For example,
simpleFoam -ioRanks 0,4,8 ...
vs
simpleFoam -ioRanks '(0 4 8)' ...
It is also possible to select the IO ranks on a per-host basis:
simpleFoam -ioRanks host ...
- expose rank/subrank handling as static fileOperation methods
- previously checked on destruction, but it is robuster to check for a
locally defined communicator during construction
- add InfoProxy output for fileOperation
ENH: add fileOperation::storeComm()
- transfers management of the communicator from external to internal.
Use with caution
- for special cases it can simplify sharing of processor communication
patterns, but no visible change for most code.
- make fileHandler communicator modifiable (mutable), for special
cases. The changes from 9711b7f1b9 now make this safer to do.
Continue to support legacy global function using an autoPtr:
autoPtr<fileOperation> Foam::fileHandler(autoPtr<fileOperation>&&);
However, new code using refPtr uses the following static method since
swapping out file handlers is an infrequent operation that should
also stand out a bit more.
fileOperation::fileHandler(...);
- consolidate file synchronization checks in dynamicCode
STYLE: report missing library on master only (not every rank)
- avoid flooding the output with messages
Co-authored-by: mattijs <mattijs>
- avoid explicit isFile() check in favour of a lazy-read.
With redistributePar + fileHandler, for example, it is possible that
the master processor finds file but not the subprocs
ENH: lazy reading of tetBasePtIs
- delay reading until needed
Co-authored-by: Mark Olesen <>
- added UPstream::allGatherValues() with a direct call to MPI_Allgather.
This enables possible benefit from a variety of internal algorithms
and simplifies the caller
Old:
labelList nPerProc
(
UPstream::listGatherValues<label>(patch_.size(), myComm)
);
Pstream::broadcast(nPerProc, myComm);
New:
const labelList nPerProc
(
UPstream::allGatherValues<label>(patch_.size(), myComm)
);
- Pstream::allGatherList uses MPI_Allgather for contiguous values
instead of the hand-rolled tree walking involved with
gatherList/scatterList.
-
- simplified the calling parameters for mpiGather/mpiScatter.
Since send/recv data types are identical, the send/recv count
is also always identical. Eliminates the possibility of any
discrepancies.
Since this is a low-level call, it does not affect much code.
Currently just Foam::profilingPstream and a UPstream internal.
BUG: call to MPI_Allgather had hard-coded MPI_BYTE (not the data type)
- a latent bug since it is currently only passed char data anyhow
UPstream::allocateCommunicator
- with contiguous sub-procs. Simpler, more compact handling, ranks
are guaranteed to be monotonic
UPstream::commWorld(label)
- ignore placeholder values, prevents accidental negative values
- make communicator non-optional for UPstream::broadcast(), which
means it has three mandatory parameters and thus always fully
disambiguated from Pstream::broadcast().
ENH: relax size checking on gatherList/scatterList
- only fatal if the List size is less than nProcs.
Can silent ignore any trailing elements: they will be untouched.
- calling the mixed BC dictionary construct with NO_READ leaves the
fields properly sized, but not initialised.
ENH: add mixed BC constructor zero initialise
- sometimes the last commit is not enough information about
the tested state (especially with extensive rebasing).
Also provide the short context of some previous commits.
- this refinement of commit 81807646ca makes these methods
consistent with other objects/containers.
The 'unsigned char' access is still available via cdata()
- extend toc/sortedToc wrappers to bitSet and labelHashSet to allow
use of BitOps::toc(...) in templated code
- size_data() method to return the number of addressed integer blocks
similar to size_bytes() does, but for int instead of char.
- use typeHeaderOk<regIOobject>(false) for some generic file existence
checks. Often had something like labelIOField as a placeholder, but
that may be construed to have a particular something.
- ensures that read failures can be properly detected
COMP: include refPtr.H instead of autoPtr.H in IOobject.H
- ensures inclusion of autoPtr/refPtr/tmp/stdFoam
ENH: add IOobject::resetHeader() method
- when re-using an IOobject for repeated read operations it enforces
resetting of headerClassName, scalar/label sizes etc prior to
reading. Permits convenient resetting of the name too (optional).
Example,
IOobject rio("none", ..., IOobject::LAZY_READ);
rio.resetHeader("U")
if (returnReduceOr(rio.typeHeaderOk<volVectorField>(false)))
...
io.resetHeader("p")
if (returnReduceOr(rio.typeHeaderOk<volScalarField>(false)))
...
- coupled patches are treated distinctly and independently of
internalFacesOnly, it makes little sense to report them with a
warning about turning off boundary faces (which would not work
anyhow).
STYLE: update code style for createBaffles
- permitting a cast to a non-const pointer adds uncertainty of
ownership.
- adjust PtrDynList transfer. Remove the unused 'PtrDynList::remove()'
method, which is better handled with pop().
- initialise with Switch::INVALID and then test if good() to
trigger the initial update.
This avoids some overhead, but primarily avoids ambiguity with
implicit casting to a 'bool' that autoPtr<bool> has.
- Allows clearing or freeing pointers without touching the underlying
list size. Was previously only for PtrDynList, but now available on
UPtrList, PtrList as well.
- add transfer() method to PtrDynList to avoid potential slicing.
- provide uniformMixed conditions for finite-area and finite-volume.
These are intended to replace the exprMixed condition but allow
the full range of different PatchFunction1 and Function1 types.
- add uniformFixedGradient to finite-area for completeness.
Note:
- still some possible difficulties with the order of evaluation.
- eg, using an expression within the 'U' field that depends
of the surface 'phi' field before that is constructed.
In this case, the 'value' entry is really needed.
- multiply-connected edges can arise at the centre of a "star"
connection or because the patch faces are actually baffles.
- In the serial case these internal edges are also rather dubious in
terms of modelling. However, when they are split across multiple
processors there can only be a single processor-to-processor
connectivity.
We don't necessary have enough information to know how things should
be connected, so connect pair-wise as the first remedial solution
- Any extra dangle edges are relegated to an 'ignore' faPatch
to tag as needing different handling.
- this is a placeholder boundary BC for using with bad or illegal
edges. It is currently functionally identical to zero-gradient.
Naming and definition still subject to change.
- this complements the whichPatch(meshFacei) method [binary search]
and the list of patchID() by adding internal range checks.
eg,
Before
~~~~~~
if (facei >= mesh.nInternalFaces() && facei < mesh.nFaces())
{
patchi = pbm.patchID()[facei - mesh.nInternalFaces()];
...
}
After
~~~~~
patchi = pbm.patchID(facei);
if (patchi >= 0)
{
...
}
- functionality introduced by openfoam.org to support selective
caching of temporary fields. The purpose is two-fold: to enable
diagnostics and to allow more places to use unregistered fields by
default.
For example to cache the grad(k) field in
cacheTemporaryObjects
(
grad(k)
);
If the name of a field which in never constructed is added to the
cacheTemporaryObjects list a waning message is generated which
includes a useful list of ALL the temporary fields constructed
during the time step
Multiple regions are also supported by specifying individual region
names in a cacheTemporaryObjects dictionary.
cacheTemporaryObjects
{
porous
(
porosityBlockage:UNbr
);
}
functions
{
writePorousObjects
{
type writeObjects;
libs (utilityFunctionObjects);
region porous;
writeControl writeTime;
writeOption anyWrite;
objects (porosityBlockage:UNbr);
}
}
- for interface polling previously required that both send and recv
requests were completed before evaluating (values or matrix update).
However, only the recv needs to be complete, which helps disentangle
the inter-rank waiting.
NB: this change is possible following (1f5cf3958b) that replaced
UPstream::resetRequests() call in favour of UPstream::waitRequests()
- UPstream exit with a non-zero return code is raised by things like
exit(FatalError) which means there is no reason to believe that
any/all of the buffered sends, requests etc have completed.
Thus avoid detaching buffers, freeing communicators etc in this
situation. This makes exit(1) behave much more like abort(), but
without any stack trace. Should presumably help with avoiding
deadlocks on exit.
ENH: support transfer from a wrapped MPI request to global list
- allows coding with a list UPstream::Request and subsequently either
retain that list or transfer into the global list.
- can use traits to distinguish label vs scalar types and
setComponents to properly index into single or multi-component
types without needing template specialisations for the task.
This avoids the need for a concrete translation unit and the
reported problem of multiply-defined specialisations when the header
is included in different places.
- the default (uninitialised) value for edge connections of -1
could be confused with a tagged finiteArea patch, which used
(-patchid-1) encoding. This would lead to messages about erroneous
processor-processor addressing, but is in fact an mismatched edge
connection.
Now tag the finiteArea patch as (-patchid-2) to avoid this ambiguity
and correctly generate an "Undefined connection:" message instead.
Properly flush the VTP writers before raising a FatalError
to ensure that they are not prematurely truncated.
Open Point:
The base problem of "Undefined connection:" is largely related to
multiply-connected face edges (ie, from the underlying volume mesh).
Not easily remedied in the finiteArea generation.
TUT: basic finiteArea setup on motorBike
- have read(nullptr, count) and readRaw(nullptr, count) act like a
forward seek instead of failing.
This lets it be used to advance through a file without needing to
allocate (and discard) storage space etc.
- construct from components, or use word::null to ensure
consistent avoid naming between IOobject vs dimensioned type.
- support construct with parameter ordering as per DimensionedField
ENH: instantiate a uniformDimensionedLabelField
- eg, for registering standalone integer counters
- directory discovery originally designed for a sub-dir location
(eg, etc/openfoam) but failed if called from within the sub-dir
itself.
Now simply assume it is located in the project directory or the etc/
sub-dir, so that it can also be relocated into the project directory
in the future (pending changes to RPM and debian packaging)
- for querying all outstanding requests:
if (UPstream::finishedRequests(startRequest)) ...
if (UPstream::finishedRequests(startRequest, -1)) ...
- for querying slice of outstanding requests:
if (UPstream::finishedRequests(startRequest, 10)) ...
- simplifies communication structuring with intra-host communication.
Can be used for IO only, or for specialised communication.
Demand-driven construction. Gathers the SHA1 of host names when
determining the connectivity. Internally uses an MPI_Gather of the
digests and a MPI_Bcast of the unique host indices.
NOTE:
does not use MPI_Comm_splt or MPI_Comm_splt_type since these
return MPI_COMM_NULL on non-participating process which does not
easily fit into the OpenFOAM framework.
Additionally, if using the caching version of
UPstream::commInterHost() and UPstream::commIntraHost()
the topology is determined simultaneously
(ie, equivalent or potentially lower communication).
- make sizing of commsStruct List demand-driven as well
for more robustness, fewer unneeded allocations.
- fix potential latent bug with allBelow/allNotBelow for proc 0
(linear communication).
ENH: remove unused/unusable UPstream::communicator optional parameter
- had constructor option to avoid constructing the MPI backend,
but this is not useful and inconsistent with what the reset or
destructor expect.
STYLE: local use of UPstream::communicator
- automatically frees communicator when it leaves scope
- these are primarily when encountering sparse (eg, inter-host)
communicators. Additional UPstream convenience methods:
is_rank(comm)
=> True if process corresponds to a rank in the communicators.
Can be a master rank or a sub-rank.
is_parallel(comm)
=> True if parallel algorithm or exchange is used on the process.
same as
(parRun() && (nProcs(comm) > 1) && is_rank(comm))
- for robustness with small edges (which can occur with snappy meshes),
the Le() and magLe() are limited to SMALL (commit a0f1e98d24).
Now use factor sqrt(1/3) in the components to maintain magnitude of 1.
ENH: add fvMesh::unitSf() and faMesh::unitLe() methods
- simple wrappers around Sf()/magSf() and Le()/magLe() but with
the potential for additional/alternative corrections.
STYLE: thisDb() in faMesh code to simplify future changes in storage
ENH: do not register finite-area geometric fields
- consistent with finite-volume treatment
- replace the "one-size-fits-all" approach of tensor field inv()
with individual 'failsafe' inverts.
The inv() field function historically just checked the first entry
to detect 2D cases and adjusted/readjusted *all* tensors accordingly
(to avoid singularity tensors and/or noisy inversions).
This seems to have worked reasonably well with 3D volume meshes, but
breaks down for 2D area meshes, which can be axis-aligned
differently on different sections of the mesh.
- with (nPollProcInterfaces < 0) it does the following:
- loop, waiting for some requests to finish
- for each out-of-date interface, check if its associated
requests have now finished (ie, the ready() check).
- if ready() -> call updateInterfaceMatrix()
In contrast to (nPollProcInterfaces > 0) which loops a specified
number of times with several calls to MPI_Test each time, the
(nPollProcInterfaces < 0) variant relies on internal MPI looping
within MPI_Waitsome to progress communication.
The actual dispatch still remains non-deterministic (ie, waiting for
some requests to finish does not mean that any particular interface
is eligible for update, or in any particular order). However, using
Waitsome places the tight looping into the MPI layer, which results
in few calls and eliminates behaviour dependent on the value of
nPollProcInterfaces.
TUT: add polling to windAroundBuildings case (for testing purposes)
- fewer calls, potentially more consistent
ENH: update sendRequest state after recvRequest wait
- previously had this type of code:
// Treat send as finished when recv is done
UPstream::waitRequest(recvRequest_);
recvRequest_ = -1;
sendRequest_ = -1;
Now refined as follows:
// Require receive data. Update the send request state.
UPstream::waitRequest(recvRequest_);
recvRequest_ = -1;
if (UPstream::finishedRequest(sendRequest_)) sendRequest_ = -1;
Can potentially investigate with requiring both,
but this may be over-contrained.
Example,
// Require receive data, but also wait for sends too
UPstream::waitRequestPair(recvRequest_, sendRequest_);
- checks requests from completion, returning true when some requests
have completed and false when there are no active requests.
This allows it to be used in a polling loop to progress MPI
and then respond when as requests become satisfied.
When using as part of a dispatch loop, waitSomeRequests() is
probably more efficient than calling waitAnyRequest() and can help
avoid biasing which client requests are serviced.
Takes an optional return parameter, to retrieve the indices,
but more importantly to avoid inner-loop reallocations.
Example,
DynamicList<int> indices;
while (UPstream::waitSomeRequests(startRequest, &indices))
{
// Dispatch something ....
}
// Reset list of outstanding requests with 'Waitall' for safety
UPstream::waitRequests(startRequest);
---
If only dealing with single items and an index is required for
dispatching, it can be better to use a list of UPstream::Request
instead.
Example,
List<UPstream::Request> requests = ...;
label index = -1;
while ((index = UPstream::waitAnyRequest(requests)) >= 0)
{
// Do something at index
}
ENH: pair-wise wrappers for MPI_Test or MPI_Wait
- for send/recv pairs of requests, can bundle both together and use a
single MPI_Testsome and MPI_Waitall instead of two individual
calls.
- previously had an additional stack for freedRequests_,
which were used to 'remember' locations into the list of
outstandingRequests_ that were handled by 'waitRequest()'.
This was principally done for sanity checks on shutdown,
but we now just test for any outstanding requests that
are *not* MPI_REQUEST_NULL instead (much simpler).
The framework with freedRequests_ also had a provision to 'recycle'
them by popping from that stack, but this is rather fragile since it
would only triggered by some collectives
(MPI_Iallreduce, MPI_Ialltoall, MPI_Igather, MPI_Iscatter)
with no guarantee that these will all be properly removed again.
There was also no pruning of extraneous indices.
ENH: consolidate internal reset/push of requests
- replace duplicate code with inline functions
reset_request(), push_request()
ENH: null out trailing requests
- extra safety (paranoia) for the UPstream::Request versions
of finishedRequests(), waitAnyRequest()
CONFIG: document nPollProcInterfaces in etc/controlDict
- still experimental, but at least make the keyword known
- mechanism has been unused for at least a decade or more
(or was never used). Message tags are assigned on an ad hoc basis
locally when collision avoidance is necessary.
- not currently used, but it is possible that communicator allocation
modifies the list of sub-ranks. Ensure that the correct size is used
when (re)initialising the linear/tree structures.
STYLE: adjust MPI test applications
- remove some clutter and unneeded grouping.
Some ideas for host-only communicators
- allow reporting even when profiling is suspended
- consolidate reporting into profilingPstream itself
(avoids code scatter).
Example of possible advanced use for timing only one section of
code:
====
// Profile local operations
profilingPstream::enable();
... do something
// Don't profile elsewhere
profilingPstream::suspend();
====
- separate broadcast times from reduce/gather/scatter time
- separate wait times from all-to-all time
- support invocation counts, split off requests time/count
from others to avoid flooding the counts
- support 'detail' switch to increase the output information.
Format may change in the future
- attributes such as assignable(), coupled() etc
- common patchField types: calculatedType(), zeroGradientType() etc.
This simplifies reference to these types without actually needing a
typed patchField version.
ENH: add some basic patchField types to fieldTypes namespace
- allows more general use of the names
ENH: set extrapolated/calculated from patchInternalField directly
- avoids intermediate tmp
- with the current handling of small edges (finite-area), the LSQ
vectors can result in singular/2D tensors. However, the regular
2D handling in field inv() only detects based on the first element.
Provide a 'failsafe' inv() method for symmTensor and tensor that
follows a similar logic for avoiding zero determinates, but it is
applied on a per element basis, instead of deciding based on the
first field element.
The symmTensor::inv(bool) and tensor::inv(bool) methods have a
fairly modest additional overhead.
- unroll the field inv() function to avoid creating an intermediate
field. Reduce the number of operations when adjusting/re-adjusting
the diagonal.
- for cases where a 3D tensor is being used to represent 2D content,
the determinant is zero. Can use inv2D(excludeDirection) to compensate
and invert as if it were only 2D.
ENH: consistent definitions for magSqr of symmTensors, diagSqr() norm
COMP: return scalar not component type for magSqr
- had inconsistent definitions with SymmTensor returning the component
type and Tensor returning scalar. Only evident with complex.
- when only a partial stacktrace is desirable.
ENH: add stack trace decorators
- the 0-th frame is always printStack(), so skip that and emit
some headers/footers instead. Eg,
[stack trace]
=============
#1 Foam::SymmTensor<double> Foam::inv<double>(...)
#2 Foam::inv(Foam::UList<Foam::SymmTensor<double>> const&) ...
...
=============
- data_bytes(), size_bytes() methods to support broadcasting or
gather/scatter content. Additional construct from raw bytes
to support transmitting content.
- missed consistency in a few places.
- return nullptr (with automatic conversion to tmp) on failures
instead of tmp<....>(nullptr), for cleaner coding.
INT: add support for an 'immovable' tmp pointer
- this idea is from openfoam.org, to allow creation of a tmp that is
protected from having its memory reclaimed in field operations
ENH: tmp NewImmovable factory method, forwards as immovable/movable
- no-op implementations, but makes the call to
GeometricBoundaryField::evaluate() less dependent on PatchField type
- add updated()/manipulatedMatrix() methods to faePatchField,
fvsPatchField etc. These are mostly no-ops, but provide name
compatible with fvPatchField etc.
- similar to UPstream::parRun(), the setter returns the previous value.
The accessors are prefixed with 'comm':
Eg, commGlobal(), commWarn(), commWorld(), commSelf().
This distinguishes them from any existing variables (eg, worldComm)
and arguably more similar to MPI_COMM_WORLD etc...
If demand-driven communicators are added in the future, the function
call syntax can help encapsulate that.
Previously:
const label oldWarnComm = UPstream::warnComm;
const label oldWorldComm = UPstream::worldComm;
UPstream::warnComm = myComm;
UPstream::worldComm = myComm;
...
UPstream::warnComm = oldWarnComm;
UPstream::worldComm = oldWorldComm;
Now:
const label oldWarnComm = UPstream::commWarn(myComm);
const label oldWorldComm = UPstream::commWorld(myComm);
...
UPstream::commWarn(oldWarnComm);
UPstream::commWorld(oldWorldComm);
STYLE: check (warnComm >= 0) instead of (warnComm != -1)
- constructing with valueRequired as a bool is still supported,
but now also support more refined requirements
(eg, NO_READ, MUST_READ, LAZY_READ)
- continue with LAZY_READ for finite-area fields
- interpret as '-decomposeParDict xyz' for simpler scripting:
A empty value ("") as well as "none" or "false" values are ignored.
Eg,
unset decompDict
if some_condition; then decompDict=decomposeParDict-12; fi
runParallel -decompose-dict=$decompDict ...
ENH: more generous when scanning decomposeParDict for numberOfSubdomains
- assume file is in system/ directory if not otherwise found
- useful when regular contents are to be read via an IOobject and
returned.
Eg, dictionary propsDict(IOdictionary::readContents(dictIO));
vs. dictionary propsDict(static_cast<dictionary&&>(IOdictionary(dictIO)));
Commonly these would have simply been constructed directly as the
IO container:
eg, IOdictionary propsDict(dictIO);
However, that style may not ensure proper move semantics for return
types.
Now,
=====
labelList decomp(labelIOList::readContents(io));
... something
return decomp;
=====
Previously,
=====
labelIOList decomp(io);
// Hope for the best...
return decomp;
// Or be explicit and ensure elision occurs...
return labelList(std::move(static_cast<labelList&>(decomp)));
=====
Note:
labelList list(labelIOList(io));
looks like a good idea, but generally fails to compile
- the iterator/const_iterator now skip any nullptr entries,
which enables the following code to work even if the PtrList
contains nullptr:
for (const auto& intf : interfaces)
{
// Do something
...
}
- this is a change in behaviour compared to OpenFOAM-v2212 and earlier,
but is non-breaking:
* Lists without null entries will traverse exactly as before.
* Lists with null entries will now traverse correctly without
provoking a FatalError.
- allows unambiguous of count() for other classes.
Naming as per std::shared_ptr.
STYLE: qualify use_count() and unique() methods with the refCount base
- clearer/consistent meaning
- the null output adapter was previously used for the HashTables API
when HashSet actually stored key/value. Now that the node only
contains the key, having suppressed output is redundant, as is the
zero::null class (reduces clutter)
STYLE: replace one::minus dispatch in extendedEdgeMesh
GIT: remove Foam::nil typedef (deprecated since May-2017)
ENH: add pTraits and IO for std::int8_t
STYLE: cull some implicitly available includes
- pTraits.H is included by label/scalar etc
- zero.H is included by UList
STYLE: cull redundant forward declarations for Istream/Ostream
- in earlier versions: used 'fixed' notation
to force floating point numbers to be printed with at least
some decimal digits. However, in the meantime we are more
flexible with handling float/int input so remove this constraint.
- use ITstream::toString, which makes the string expansion of ${var}
and the expression expansion of $[var] consistent.
- other systems (eg, ARM64 linux with clang) do not have a separate
mpfr library configured so also check for mpfr (gmp is assumed to be
the same) and return corresponding cgal flavour (eg, header-no-mpfr)
Note:
in some borderline cases (eg, PDRFoam) the multiplication order
and rounding imposed by the lerp function may affect the
results slightly.
eg, (valueFraction_ * this->patch().deltaCoeffs()*refValue_)
vs. (valueFraction_ * (this->patch().deltaCoeffs()*refValue_))
- defined for lerp between two fields,
either with a constant or a field of interpolation factors.
* plain Field, DimensionedField, FieldField, GeometricFields
- using a field to lerp between two constants is not currently
supported
- clearer, more consistent parameter naming, which helps when
maintaining different field function types (eg, DimensionedFields,
GeometricFields)
- provide reuseTmpGeometricField::New taking a reference (not a tmp),
with forwarding. This helps centralise naming and acquisition etc
- split binary function macros into transform/interface
for easier support of different transform loops.
- initial field macros for looping over ternaries
- newer naming allows for less confusing code.
Eg,
max(lower) -> clamp_min(lower)
min(upper) -> clamp_max(upper)
- prefer combined method, for few operations.
Eg,
max(lower) + min(upper) -> clamp_range(lower, upper)
The updated naming also helps avoid some obvious coding errors.
Eg,
Re.min(1200.0);
Re.max(18800.0);
instead of
Re.clamp_range(1200.0, 18800.0);
- can also use implicit conversion of zero_one to MinMax<Type> for
this type of code:
lambda_.clamp_range(zero_one{});
- this is slightly longer to write (but consistent with clamp_min
etc). The main reason is that this allows easier use of the clamp()
free function.
STYLE: skip checks for bad/invalid clamping ranges
- ranges are either already validated before calling, the caller logic
has already made the branching decision.
- run-time warning about deprecated features. For example,
DeprecatedInFunction(2212)
<< "Prefer using xyz boundary condition. "
<< "This boundary condition will be removed in the future." << endl;
CONFIG: mark exprFixedValue as deprecated
- same functionality is possible with uniformFixedValue and an
expression PatchFunction1, which can also be easily changed to any
other PatchFunction1
- was using UPstream::procIDs(), which returns the sub-ranks with
respect to the parent communicator. This is normally just an
identity list (single-world) but with multi-world the indexing
is incorrect. Use UPstream::allProcs() instead.
- was only used in Pstream::combineReduce(...) with a full list,
which should have been avoided in most cases anyhow.
Much more efficient to simply gather the sizes directly
- adjust nullptr checks to discourage flip-flop when confronted with
multiple null values.
Old: (a && b) ? (*a < *b) : bool(a);
New: (a && b) ? (*a < *b) : !b;
comparing (non-null < null) and (null < non-null) behaves
identically, but comparing (null < null) now tests as true
(ie, already sorted) whereas before it would have been false
(ie, needs a swap)
- add UPtrList trimTrailingNull(), which reduces the effective
(addressable) list size to ignore any trailing null pointers, but
without reallocation. This is particularly useful when creating a
UPtrList list view. For example,
UPtrList<some_iterator> validValues(container.size());
...Loop to add valid entries, by some criteria...
// Shorten list to hide null entries
validValues.trimTrailingNull();
This list view now only needs a single allocation, whereas using
a resize (as was previously necessary) could invoke a second
allocation, as well as recopying.
- in most cases can simply construct mapDistribute with the sendMap
and have it take care of communication and addressing for the
corresponding constructMap.
This removes code duplication, which in some cases was also using
much less efficient mechanisms (eg, combineReduce on list of
lists, or an allGatherList on the send sizes etc) and also
reduces the number of places where Pstream::exchange/exchangeSizes
is being called.
ENH: reduce communication in turbulentDFSEMInlet
- was doing an allGatherList to populate a mapDistribute.
Now simply use PstreamBuffers mechanisms directly.
- dynamic sparse data exchange using Map to hold data and sizes.
Still uses the personalised exchange paradigm, but with non-blocking
consensus exchange to obtain the sizes and regular point-to-point
for the data exchange itself. This avoids an all-to-all but still
keeps the point-to-point for overlapping communication, data
chunking etc.
- to service both List and Map exchanges with limited message sizes
(termed 'data chunking' here) add a PstreamDetail for walking and
dispatching. Like other Detail components, the API is subject
to (possibly breaking) changes in the future at any time.
The regular exchangeBuf detail has this type of signature:
PstreamDetail::exchangeBuf
(
const UList<std::pair<int, stdFoam::span<const Type>>>& sends,
const UList<std::pair<int, stdFoam::span<Type>>>& recvs,
...
)
Where [rank, span] is the tuple pack.
The basic idea is to pre-process the send/receive buffers and
marshall them into a flat list of [rank, span] tuples.
The originating buffers could be any type of container (List or Map)
which is then marshalled into this given sequence that can be
processed in source-agnostic fashion.
If data chunking is required (when UPstream::maxCommsSize > 0)
it is possible to make a cheap copy of the rank/address information
and then walk different slices or views.
ENH: replace private static methods with PstreamDetail functions
- simpler to update locally.
- since List is being used to manage the storage content for
DynamicList, it needs to free old memory for zero-sized lists first.
Consider this case (slightly exaggerated):
line 0: DynamicList<label> list;
line 1: list.reserve(100000);
line 2: list.reserve(200000);
After line 0:
- list has size=0, capacity=0 and data=nullptr
After line 1:
- list has size=0, capacity=1e+5 and data != nullptr
After line 2:
- list has size=0, capacity=2e+5 and data != nullptr
---
The internal resizing associated with line 1 corresponds to what the
List resize would naturally do. Namely allocate new storage, copy/move
any overlapping elements (in this case none) before freeing the old
storage and replacing with new storage.
Applying the same resizing logic for line 2 means, however, that the
old memory (1e5) and new memory (2e5) are temporarily both
accessible - leading to an unnecessary memory peak.
Now: if there is no overlap, just remove old memory first.
- basic functionality similar to std::span (C++20).
Holds pointer and size: for lightweight handling of address ranges.
- implements cdata_bytes() and data_bytes() methods for similarity
with UList. For span, however, both container accesses are const
but the data_bytes() method is only available when the
underlying pointer is non-const.
No specializations of std::as_bytes() or std::as_writeable_bytes()
as free functions, since std::byte etc are not available anyhow.
- name and functionality similar to std::unordered_map (C++17).
Formalizes what had been previously been implemented in IOobjectList
but now manages without pointer deletion/creation.
- use persistent PstreamBuffers between iterations, restrict size
information exchange to the processor neighbours (which is what the
algorithm is handling there anyhow).
- attempted reduction in bookkeeping (commit: 068ab8ccc7) meant that
the worldComm didn't have a group from which sub-communicators could
be spun off.
- do not force reset of PstreamBuffers positions
STYLE: UPstream::globalComm instead of '0'
- functionality provided as 'found(key)' in OpenFOAM naming, since
there was no stl equivalent at the time. Now support contains(),
which is the equivalent for C++20 maps/sets.
STYLE: general contains() method for containers
STYLE: treat Enum and Switch similarly as hash-like objects
- waits for completion of any of the listed requests and returns the
corresponding index into the list.
This allows, for example, dispatching of data when the receive is
completed.
- make nProcs() independent of internal storage mechanism.
- reset receive positions with finished sends
- use size of received buffers to manage validity instead of
an separate additional gather operation.
- clearing the receive 'slots' is preferrable to clearing out the map
itself since this can potentially preserve allocated space (eg
DynamicList entries) between calls.
BUG: remove stray MPI barrier in exchange code
- permits distinction between communicators/groups that were
user-created (eg, MPI_Comm_create) versus those queried from MPI.
Previously simply relied on non-null values, but that is too fragile
ENH: support List<Request> version of UPstream::finishedRequests
- allows more independent algorithms
ENH: added UPstream::probeMessage(...). Blocking or non-blocking
- allows the possibility of using demand-driven internal buffers
and/or different storage mechanisms.
Changes:
* old: sendBuf_[proci] -> accessSendBuffer(proci)
* old: recvBuf_[proci] -> accessRecvBuffer(proci)
* old: recvBufPos_[proci] -> accessRecvPosition(proci)
only affects internals of UIPstreamBase and UOPstreamBase
BUG: reduceOr in PstreamBuffers uses world communicator
- should respect the value of the communicator defined within
PstreamBuffers
- previously built the entire adjacency table (full communication!)
but this is only strictly needed when using 'scheduled' as the
default communication mode. For blocking/nonBlocking modes this
information is not necessary at that point.
The processorTopology::New now generally creates a smaller amount of
data at startup: the processor->patch mapping and the patchSchedule.
If the default communication mode is 'scheduled', the behaviour is
almost identical to previously.
- Use Map<label> for the processor->patch mapping for a smaller memory
footprint on large (ie, sparsely connected) cases. It also
simplifies coding and allows recovery of the list of procNeighbours
on demand.
- Setup the processor initEvaluate/evaluate states with fewer loops
over the patches.
========
BREAKING: procNeighbours() method changed definition
- this was previously the entire adjacency table, but is now only the
processor-local neighbours. Now use procAdjacency() to create or
recover the entire adjacency table.
The only known use is within Cloud<ParticleType>::move and there it
was only used to obtain processor-local information.
Old:
const labelList& neighbourProcs =
mesh.globalData().topology().procNeighbours()[Pstream::myProcNo()];
New:
const labelList& neighbourProcs =
mesh.globalData().topology().procNeighbours();
// If needed, the old definition (with communication!)
const labelListList& connectivity =
mesh.globalData().topology().procAdjacency();
In the 'standard' and 'UaGradU' options for the ATC term of the adjoint
equations, there is an option to add 'aritificial dissipation', by
adding and subtracting a multiple of the adjoint convection term with
different discretizations. The implicit part was not multiplied with the
ATClimiter whereas the explicit one was, leading to mismatched
contributions in the areas affected by the ATClimiter, which could
affect the sensitivity derivatives.
- field blocking/exclusion added in commit d9ab5d54ef,
but was incorrectly doing a lookup for "blockField" for ensight
although "excludeFields" was documented (and expected).
Now corrected to use "excludeFields"
transformation support in-place modifies the data (e.g. to
add a transform). This might cause the neighbour side patch
to pick up owner side information.
- wish to deprecate and remove exprFixedValue in the future since the
same functionality is possible using patch expressions with a
uniformFixedValue condition.
- skip loading of fields with -no-internal, -no-boundary
- suppress reporting fields with -no-internal, -no-boundary
- cache loaded volume field for reuse with point interpolation.
Trade off some memory overhead against reading twice.
NOTE: this issue will not be evident with foamToEnsight since there
it only handles cell data *or* point data (not both), so a field is
only ever loaded/processed once.
- This simplifies definition of 'lazier' (READ_IF_PRESENT)
construction or assignment.
For construction:
- For MUST_READ and key not found: FatalIOError.
- For LAZY_READ and key not found: initialise field with Zero.
- For NO_READ and key not found: simply size the field.
For assignment:
- If len == 0 : a no-op and return True.
- For NO_READ : a no-op and return False.
- For MUST_READ and key not found : FatalIOError
- encompasses isReadOptional or isReadRequired check
STYLE: allow LAZY_READ as a shorter synonym for READ_IF_PRESENT
- add helper for downgrading MUST_READ... to LAZY_READ
- with geometryOrder=1, edge normal calculation is done directly from
the faces, whereas geometryOrder=2 they are calculated based on the
point normals of each end.
In both cases, the geometry calculation uses processor communication
(with corresponding waitRequests etc).
Since the final correction and the halo face normals also need
collective communication, these routines must be triggered on all
processors or they will block. Thus also include edgeAreaNormals()
triggering in addition to pointAreaNormals() triggering.
- handle lower geometryOrder values directly within edgeAreaNormals()
and reuse the results within Le().
- direct nonBlocking recv/send of edge normals instead using the
intermediate processorLduInterface buffers
- symmetrical evaluation for processor patches, eliminates
scalar/vector multiply followed by projection.
STYLE: use evaluateCoupled instead of local versions
- vector, tensor versions are defined component-wise
to avoid intermediates.
The base version uses the form "(1-t)*a + t*b" without any bounds
checking (ie, will also extrapolate).
- proper component-wise clamping for MinMax clamp().
- construct clampOp from components
- propagate clamp() method from GeometricField to FieldField and Field
- clamp_min() and clamp_max() for one-sided clamping,
as explicit alternative to min/max free functions which can
be less intuitive and often involve additional field copies.
- top-level checks to skip applying invalid min/max ranges
and bypass the internal checks of MinMax::clamp() etc.
GIT: primitives/compat with compatibility includes
GIT: primitives/traits with pTraits, contiguous, zero, one etc.
COMP: relocate base equal(a,b) definition from scalar.H -> label.H
- make more universally available
STYLE: replace occasional use of notEqual(a,b) with !equal(a,b)
- avoids implicit promotion of label to scalar for no-op,
or alternatively promotion of symmTensor to tensor for no-op
(ie, ambiguous).
- fix incorrect transform(.., symmTensor, ...) declarations.
COMP: update include for CGAL-5.5 (#2665)
old: Robust_circumcenter_filtered_traits_3
new: Robust_weighted_circumcenter_filtered_traits_3
COMP: adjust CGAL rule for OSX (#2664)
- since CGAL is now header-only, the previous OSX-specific rules have
become redundant
STYLE: rename some internal buffers with the data types
low-level : byteSendBuf_, byteRecvBuf_
field level: sendBuf_, recvBuf_
solve level: scalarSendBuf_, scalarRecvBuf_
- with alternative faceCell addressing, use the three-parameter
version only. This avoids potential future ambiguity with the
two-parameter version (eg, with a label type)
ENH: add faPatchField patchInternalField() for symmetry with fvPatchField
ENH: direct reference to mesh thisDb instead of inferring
ENH: pointMesh::boundaryMesh() method (eg, similar to fvMesh)
- UPstream::Request wrapping class provides an opaque wrapper for
vendor MPI_Request values, independent of global lists.
ENH: support for MPI barrier (blocking or non-blocking)
ENH: support for MPI sync-send variants
STYLE: deprecate waitRequests() without a position parameter
- in many cases this can indicate a problem in the program logic since
normally the startOfRequests should be tracked locally.
- reduces clutter. In some cases the Fwd typedefs were also incorrect
STYLE: combine Scalar specialisations into corresponding PatchFields.C
- reduces clutter, simplifies future adjustments
- simplifies code, consistent with other matrix transfer functions.
Use a setter method.
STYLE: AMIInterpolation::upToDate(bool) setter method
ENH: add guards to avoid float-compressed transfer of integral types
STYLE: drop unused debug member from abstract interface classes
- now simply a no-op for out-of-range values (instead of an error),
which simplifies the calling code.
Previously
==========
if (request_ >= 0 && request_ < UPstream::nRequests())
{
UPstream::waitRequest(request_);
}
Updated
=======
UPstream::waitRequest(request_);
- when 'recycling' freed request indices, ensure they are actually
within the currently addressable range
- MPI finalization now checks outstanding requests against
MPI_REQUEST_NULL to verify that they have been waited or tested on.
Previously simply checked against freed request indices
ENH: consistent initialisation of send/receive bookkeeping
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