d8d6030ab6
Original commit message:
------------------------
Parallel IO: New collated file format
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.
602 lines
16 KiB
C
602 lines
16 KiB
C
/*---------------------------------------------------------------------------*\
|
|
========= |
|
|
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
|
\\ / O peration |
|
|
\\ / A nd | Copyright (C) 2014-2017 OpenFOAM Foundation
|
|
\\/ M anipulation |
|
|
-------------------------------------------------------------------------------
|
|
License
|
|
This file is part of OpenFOAM.
|
|
|
|
OpenFOAM is free software: you can redistribute it and/or modify it
|
|
under the terms of the GNU General Public License as published by
|
|
the Free Software Foundation, either version 3 of the License, or
|
|
(at your option) any later version.
|
|
|
|
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
|
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
|
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
|
for more details.
|
|
|
|
You should have received a copy of the GNU General Public License
|
|
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
Application
|
|
surfaceHookUp
|
|
|
|
Group
|
|
grpSurfaceUtilities
|
|
|
|
Description
|
|
Find close open edges and stitches the surface along them
|
|
|
|
Usage
|
|
- surfaceHookUp hookDistance [OPTION]
|
|
|
|
\*---------------------------------------------------------------------------*/
|
|
|
|
#include "argList.H"
|
|
#include "Time.H"
|
|
|
|
#include "triSurfaceMesh.H"
|
|
#include "indexedOctree.H"
|
|
#include "treeBoundBox.H"
|
|
#include "PackedBoolList.H"
|
|
#include "unitConversion.H"
|
|
#include "searchableSurfaces.H"
|
|
#include "IOdictionary.H"
|
|
|
|
using namespace Foam;
|
|
|
|
// Split facei along edgeI at position newPointi
|
|
void greenRefine
|
|
(
|
|
const triSurface& surf,
|
|
const label facei,
|
|
const label edgeI,
|
|
const label newPointi,
|
|
DynamicList<labelledTri>& newFaces
|
|
)
|
|
{
|
|
const labelledTri& f = surf.localFaces()[facei];
|
|
const edge& e = surf.edges()[edgeI];
|
|
|
|
// Find index of edge in face.
|
|
|
|
label fp0 = findIndex(f, e[0]);
|
|
label fp1 = f.fcIndex(fp0);
|
|
label fp2 = f.fcIndex(fp1);
|
|
|
|
if (f[fp1] == e[1])
|
|
{
|
|
// Edge oriented like face
|
|
newFaces.append
|
|
(
|
|
labelledTri
|
|
(
|
|
f[fp0],
|
|
newPointi,
|
|
f[fp2],
|
|
f.region()
|
|
)
|
|
);
|
|
newFaces.append
|
|
(
|
|
labelledTri
|
|
(
|
|
newPointi,
|
|
f[fp1],
|
|
f[fp2],
|
|
f.region()
|
|
)
|
|
);
|
|
}
|
|
else
|
|
{
|
|
newFaces.append
|
|
(
|
|
labelledTri
|
|
(
|
|
f[fp2],
|
|
newPointi,
|
|
f[fp1],
|
|
f.region()
|
|
)
|
|
);
|
|
newFaces.append
|
|
(
|
|
labelledTri
|
|
(
|
|
newPointi,
|
|
f[fp0],
|
|
f[fp1],
|
|
f.region()
|
|
)
|
|
);
|
|
}
|
|
}
|
|
|
|
|
|
//scalar checkEdgeAngle
|
|
//(
|
|
// const triSurface& surf,
|
|
// const label edgeIndex,
|
|
// const label pointIndex,
|
|
// const scalar& angle
|
|
//)
|
|
//{
|
|
// const edge& e = surf.edges()[edgeIndex];
|
|
|
|
// vector eVec = e.vec(surf.localPoints());
|
|
// eVec /= mag(eVec) + SMALL;
|
|
|
|
// const labelList& pEdges = surf.pointEdges()[pointIndex];
|
|
//
|
|
// forAll(pEdges, eI)
|
|
// {
|
|
// const edge& nearE = surf.edges()[pEdges[eI]];
|
|
|
|
// vector nearEVec = nearE.vec(surf.localPoints());
|
|
// nearEVec /= mag(nearEVec) + SMALL;
|
|
|
|
// const scalar dot = eVec & nearEVec;
|
|
// const scalar minCos = degToRad(angle);
|
|
|
|
// if (mag(dot) > minCos)
|
|
// {
|
|
// return false;
|
|
// }
|
|
// }
|
|
|
|
// return true;
|
|
//}
|
|
|
|
|
|
void createBoundaryEdgeTrees
|
|
(
|
|
const PtrList<triSurfaceMesh>& surfs,
|
|
PtrList<indexedOctree<treeDataEdge>>& bEdgeTrees,
|
|
labelListList& treeBoundaryEdges
|
|
)
|
|
{
|
|
forAll(surfs, surfI)
|
|
{
|
|
const triSurface& surf = surfs[surfI];
|
|
|
|
// Boundary edges
|
|
treeBoundaryEdges[surfI] =
|
|
labelList
|
|
(
|
|
identity(surf.nEdges() - surf.nInternalEdges())
|
|
+ surf.nInternalEdges()
|
|
);
|
|
|
|
Random rndGen(17301893);
|
|
|
|
// Slightly extended bb. Slightly off-centred just so on symmetric
|
|
// geometry there are less face/edge aligned items.
|
|
treeBoundBox bb
|
|
(
|
|
treeBoundBox(UList<point>(surf.localPoints())).extend(rndGen, 1e-4)
|
|
);
|
|
|
|
bb.min() -= point(ROOTVSMALL, ROOTVSMALL, ROOTVSMALL);
|
|
bb.max() += point(ROOTVSMALL, ROOTVSMALL, ROOTVSMALL);
|
|
|
|
bEdgeTrees.set
|
|
(
|
|
surfI,
|
|
new indexedOctree<treeDataEdge>
|
|
(
|
|
treeDataEdge
|
|
(
|
|
false, // cachebb
|
|
surf.edges(), // edges
|
|
surf.localPoints(), // points
|
|
treeBoundaryEdges[surfI] // selected edges
|
|
),
|
|
bb, // bb
|
|
8, // maxLevel
|
|
10, // leafsize
|
|
3.0 // duplicity
|
|
)
|
|
);
|
|
}
|
|
}
|
|
|
|
|
|
class findNearestOpSubset
|
|
{
|
|
const indexedOctree<treeDataEdge>& tree_;
|
|
|
|
DynamicList<label>& shapeMask_;
|
|
|
|
public:
|
|
|
|
findNearestOpSubset
|
|
(
|
|
const indexedOctree<treeDataEdge>& tree,
|
|
DynamicList<label>& shapeMask
|
|
)
|
|
:
|
|
tree_(tree),
|
|
shapeMask_(shapeMask)
|
|
{}
|
|
|
|
void operator()
|
|
(
|
|
const labelUList& indices,
|
|
const point& sample,
|
|
|
|
scalar& nearestDistSqr,
|
|
label& minIndex,
|
|
point& nearestPoint
|
|
) const
|
|
{
|
|
const treeDataEdge& shape = tree_.shapes();
|
|
|
|
forAll(indices, i)
|
|
{
|
|
const label index = indices[i];
|
|
const label edgeIndex = shape.edgeLabels()[index];
|
|
|
|
if
|
|
(
|
|
!shapeMask_.empty()
|
|
&& findIndex(shapeMask_, edgeIndex) != -1
|
|
)
|
|
{
|
|
continue;
|
|
}
|
|
|
|
const edge& e = shape.edges()[edgeIndex];
|
|
|
|
pointHit nearHit = e.line(shape.points()).nearestDist(sample);
|
|
|
|
// Only register hit if closest point is not an edge point
|
|
if (nearHit.hit())
|
|
{
|
|
scalar distSqr = sqr(nearHit.distance());
|
|
|
|
if (distSqr < nearestDistSqr)
|
|
{
|
|
nearestDistSqr = distSqr;
|
|
minIndex = index;
|
|
nearestPoint = nearHit.rawPoint();
|
|
}
|
|
}
|
|
}
|
|
}
|
|
};
|
|
|
|
|
|
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
|
|
|
int main(int argc, char *argv[])
|
|
{
|
|
argList::addNote
|
|
(
|
|
"hook surfaces to other surfaces by moving and retriangulating their"
|
|
"boundary edges to match other surface boundary edges"
|
|
);
|
|
argList::noParallel();
|
|
argList::validArgs.append("hookTolerance");
|
|
|
|
#include "addDictOption.H"
|
|
|
|
#include "setRootCase.H"
|
|
#include "createTime.H"
|
|
|
|
const word dictName("surfaceHookUpDict");
|
|
#include "setSystemRunTimeDictionaryIO.H"
|
|
|
|
Info<< "Reading " << dictName << nl << endl;
|
|
|
|
const IOdictionary dict(dictIO);
|
|
|
|
const scalar dist(args.argRead<scalar>(1));
|
|
const scalar matchTolerance(max(1e-6*dist, SMALL));
|
|
const label maxIters = 100;
|
|
|
|
Info<< "Hooking distance = " << dist << endl;
|
|
|
|
searchableSurfaces surfs
|
|
(
|
|
IOobject
|
|
(
|
|
"surfacesToHook",
|
|
runTime.constant(),
|
|
"triSurface",
|
|
runTime
|
|
),
|
|
dict,
|
|
true // assume single-region names get surface name
|
|
);
|
|
|
|
Info<< nl << "Reading surfaces: " << endl;
|
|
forAll(surfs, surfI)
|
|
{
|
|
Info<< incrIndent;
|
|
Info<< nl << indent << "Surface = " << surfs.names()[surfI] << endl;
|
|
|
|
const wordList& regions = surfs[surfI].regions();
|
|
forAll(regions, surfRegionI)
|
|
{
|
|
Info<< incrIndent;
|
|
Info<< indent << "Regions = " << regions[surfRegionI] << endl;
|
|
Info<< decrIndent;
|
|
}
|
|
Info<< decrIndent;
|
|
}
|
|
|
|
PtrList<indexedOctree<treeDataEdge>> bEdgeTrees(surfs.size());
|
|
labelListList treeBoundaryEdges(surfs.size());
|
|
|
|
List<DynamicList<labelledTri>> newFaces(surfs.size());
|
|
List<DynamicList<point>> newPoints(surfs.size());
|
|
List<PackedBoolList> visitedFace(surfs.size());
|
|
|
|
PtrList<triSurfaceMesh> newSurfaces(surfs.size());
|
|
forAll(surfs, surfI)
|
|
{
|
|
const triSurfaceMesh& surf =
|
|
refCast<const triSurfaceMesh>(surfs[surfI]);
|
|
|
|
newSurfaces.set
|
|
(
|
|
surfI,
|
|
new triSurfaceMesh
|
|
(
|
|
IOobject
|
|
(
|
|
"hookedSurface_" + surfs.names()[surfI],
|
|
runTime.constant(),
|
|
"triSurface",
|
|
runTime
|
|
),
|
|
surf
|
|
)
|
|
);
|
|
}
|
|
|
|
label nChanged = 0;
|
|
label nIters = 1;
|
|
|
|
do
|
|
{
|
|
Info<< nl << "Iteration = " << nIters++ << endl;
|
|
nChanged = 0;
|
|
|
|
createBoundaryEdgeTrees(newSurfaces, bEdgeTrees, treeBoundaryEdges);
|
|
|
|
forAll(newSurfaces, surfI)
|
|
{
|
|
const triSurface& newSurf = newSurfaces[surfI];
|
|
|
|
newFaces[surfI] = newSurf.localFaces();
|
|
newPoints[surfI] = newSurf.localPoints();
|
|
visitedFace[surfI] = PackedBoolList(newSurf.size(), false);
|
|
}
|
|
|
|
forAll(newSurfaces, surfI)
|
|
{
|
|
const triSurface& surf = newSurfaces[surfI];
|
|
|
|
List<pointIndexHit> bPointsTobEdges(surf.boundaryPoints().size());
|
|
labelList bPointsHitTree(surf.boundaryPoints().size(), -1);
|
|
|
|
const labelListList& pointEdges = surf.pointEdges();
|
|
|
|
forAll(bPointsTobEdges, bPointi)
|
|
{
|
|
pointIndexHit& nearestHit = bPointsTobEdges[bPointi];
|
|
|
|
const label pointi = surf.boundaryPoints()[bPointi];
|
|
const point& samplePt = surf.localPoints()[pointi];
|
|
|
|
const labelList& pEdges = pointEdges[pointi];
|
|
|
|
// Add edges connected to the edge to the shapeMask
|
|
DynamicList<label> shapeMask;
|
|
shapeMask.append(pEdges);
|
|
|
|
forAll(bEdgeTrees, treeI)
|
|
{
|
|
const indexedOctree<treeDataEdge>& bEdgeTree =
|
|
bEdgeTrees[treeI];
|
|
|
|
pointIndexHit currentHit =
|
|
bEdgeTree.findNearest
|
|
(
|
|
samplePt,
|
|
sqr(dist),
|
|
findNearestOpSubset
|
|
(
|
|
bEdgeTree,
|
|
shapeMask
|
|
)
|
|
);
|
|
|
|
if
|
|
(
|
|
currentHit.hit()
|
|
&&
|
|
(
|
|
!nearestHit.hit()
|
|
||
|
|
(
|
|
magSqr(currentHit.hitPoint() - samplePt)
|
|
< magSqr(nearestHit.hitPoint() - samplePt)
|
|
)
|
|
)
|
|
)
|
|
{
|
|
nearestHit = currentHit;
|
|
bPointsHitTree[bPointi] = treeI;
|
|
}
|
|
}
|
|
|
|
scalar dist2 = magSqr(nearestHit.rawPoint() - samplePt);
|
|
|
|
if (nearestHit.hit())
|
|
{
|
|
// bool rejectEdge =
|
|
// checkEdgeAngle
|
|
// (
|
|
// surf,
|
|
// nearestHit.index(),
|
|
// pointi,
|
|
// 30
|
|
// );
|
|
|
|
if (dist2 > Foam::sqr(dist))
|
|
{
|
|
nearestHit.setMiss();
|
|
}
|
|
}
|
|
}
|
|
|
|
forAll(bPointsTobEdges, bPointi)
|
|
{
|
|
const pointIndexHit& eHit = bPointsTobEdges[bPointi];
|
|
|
|
if (eHit.hit())
|
|
{
|
|
const label hitSurfI = bPointsHitTree[bPointi];
|
|
const triSurface& hitSurf = newSurfaces[hitSurfI];
|
|
|
|
const label eIndex =
|
|
treeBoundaryEdges[hitSurfI][eHit.index()];
|
|
const edge& e = hitSurf.edges()[eIndex];
|
|
|
|
const label pointi = surf.boundaryPoints()[bPointi];
|
|
|
|
const labelList& eFaces = hitSurf.edgeFaces()[eIndex];
|
|
|
|
if (eFaces.size() != 1)
|
|
{
|
|
WarningInFunction
|
|
<< "Edge is attached to " << eFaces.size()
|
|
<< " faces." << endl;
|
|
|
|
continue;
|
|
}
|
|
|
|
const label facei = eFaces[0];
|
|
|
|
if (visitedFace[hitSurfI][facei])
|
|
{
|
|
continue;
|
|
}
|
|
|
|
DynamicList<labelledTri> newFacesFromSplit(2);
|
|
|
|
const point& pt = surf.localPoints()[pointi];
|
|
|
|
if
|
|
(
|
|
(
|
|
magSqr(pt - hitSurf.localPoints()[e.start()])
|
|
< matchTolerance
|
|
)
|
|
|| (
|
|
magSqr(pt - hitSurf.localPoints()[e.end()])
|
|
< matchTolerance
|
|
)
|
|
)
|
|
{
|
|
continue;
|
|
}
|
|
|
|
nChanged++;
|
|
|
|
label newPointi = -1;
|
|
|
|
// Keep the points in the same place and move the edge
|
|
if (hitSurfI == surfI)
|
|
{
|
|
newPointi = pointi;
|
|
}
|
|
else
|
|
{
|
|
newPoints[hitSurfI].append(newPoints[surfI][pointi]);
|
|
newPointi = newPoints[hitSurfI].size() - 1;
|
|
}
|
|
|
|
// Split the other face.
|
|
greenRefine
|
|
(
|
|
hitSurf,
|
|
facei,
|
|
eIndex,
|
|
newPointi,
|
|
newFacesFromSplit
|
|
);
|
|
|
|
visitedFace[hitSurfI][facei] = true;
|
|
|
|
forAll(newFacesFromSplit, newFacei)
|
|
{
|
|
const labelledTri& fN = newFacesFromSplit[newFacei];
|
|
|
|
if (newFacei == 0)
|
|
{
|
|
newFaces[hitSurfI][facei] = fN;
|
|
}
|
|
else
|
|
{
|
|
newFaces[hitSurfI].append(fN);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
Info<< " Number of edges split = " << nChanged << endl;
|
|
|
|
forAll(newSurfaces, surfI)
|
|
{
|
|
newSurfaces.set
|
|
(
|
|
surfI,
|
|
new triSurfaceMesh
|
|
(
|
|
IOobject
|
|
(
|
|
"hookedSurface_" + surfs.names()[surfI],
|
|
runTime.constant(),
|
|
"triSurface",
|
|
runTime
|
|
),
|
|
triSurface
|
|
(
|
|
newFaces[surfI],
|
|
newSurfaces[surfI].patches(),
|
|
pointField(newPoints[surfI])
|
|
)
|
|
)
|
|
);
|
|
}
|
|
|
|
} while (nChanged > 0 && nIters <= maxIters);
|
|
|
|
Info<< endl;
|
|
|
|
forAll(newSurfaces, surfI)
|
|
{
|
|
const triSurfaceMesh& newSurf = newSurfaces[surfI];
|
|
|
|
Info<< "Writing hooked surface " << newSurf.searchableSurface::name()
|
|
<< endl;
|
|
|
|
newSurf.searchableSurface::write();
|
|
}
|
|
|
|
Info<< "\nEnd\n" << endl;
|
|
|
|
return 0;
|
|
}
|
|
|
|
|
|
// ************************************************************************* //
|