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.
699 lines
18 KiB
C
699 lines
18 KiB
C
/*---------------------------------------------------------------------------*\
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========= |
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\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
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\\ / O peration |
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\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
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\\/ M anipulation | Copyright (C) 2016-2017 OpenCFD Ltd.
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-------------------------------------------------------------------------------
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License
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This file is part of OpenFOAM.
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OpenFOAM is free software: you can redistribute it and/or modify it
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under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
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for more details.
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You should have received a copy of the GNU General Public License
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along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
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Application
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modifyMesh
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Group
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grpMeshAdvancedUtilities
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Description
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Manipulates mesh elements.
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Actions are:
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(boundary)points:
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- move
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(boundary)edges:
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- split and move introduced point
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(boundary)faces:
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- split(triangulate) and move introduced point
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edges:
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- collapse
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cells:
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- split into polygonal base pyramids around newly introduced mid
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point
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Is a bit of a loose collection of mesh change drivers.
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\*---------------------------------------------------------------------------*/
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#include "argList.H"
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#include "Time.H"
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#include "polyMesh.H"
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#include "polyTopoChange.H"
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#include "mapPolyMesh.H"
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#include "boundaryCutter.H"
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#include "cellSplitter.H"
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#include "edgeCollapser.H"
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#include "meshTools.H"
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#include "Pair.H"
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#include "globalIndex.H"
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#include "topoSet.H"
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#include "processorMeshes.H"
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#include "IOdictionary.H"
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using namespace Foam;
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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// Locate point on patch. Returns (mesh) point label.
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label findPoint(const primitivePatch& pp, const point& nearPoint)
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{
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const pointField& points = pp.points();
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const labelList& meshPoints = pp.meshPoints();
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// Find nearest and next nearest
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scalar minDistSqr = GREAT;
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label minI = -1;
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scalar almostMinDistSqr = GREAT;
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label almostMinI = -1;
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forAll(meshPoints, i)
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{
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label pointi = meshPoints[i];
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scalar distSqr = magSqr(nearPoint - points[pointi]);
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if (distSqr < minDistSqr)
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{
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almostMinDistSqr = minDistSqr;
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almostMinI = minI;
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minDistSqr = distSqr;
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minI = pointi;
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}
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else if (distSqr < almostMinDistSqr)
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{
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almostMinDistSqr = distSqr;
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almostMinI = pointi;
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}
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}
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// Decide if nearPoint unique enough.
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Info<< "Found to point " << nearPoint << nl
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<< " nearest point : " << minI
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<< " distance " << Foam::sqrt(minDistSqr)
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<< " at " << points[minI] << nl
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<< " next nearest point : " << almostMinI
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<< " distance " << Foam::sqrt(almostMinDistSqr)
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<< " at " << points[almostMinI] << endl;
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if (almostMinDistSqr < 4*minDistSqr)
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{
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Info<< "Next nearest too close to nearest. Aborting" << endl;
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return -1;
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}
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else
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{
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return minI;
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}
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}
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// Locate edge on patch. Return mesh edge label.
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label findEdge
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(
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const primitiveMesh& mesh,
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const primitivePatch& pp,
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const point& nearPoint
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)
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{
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const pointField& localPoints = pp.localPoints();
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const pointField& points = pp.points();
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const labelList& meshPoints = pp.meshPoints();
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const edgeList& edges = pp.edges();
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// Find nearest and next nearest
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scalar minDist = GREAT;
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label minI = -1;
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scalar almostMinDist = GREAT;
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label almostMinI = -1;
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forAll(edges, edgeI)
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{
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const edge& e = edges[edgeI];
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pointHit pHit(e.line(localPoints).nearestDist(nearPoint));
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if (pHit.hit())
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{
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if (pHit.distance() < minDist)
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{
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almostMinDist = minDist;
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almostMinI = minI;
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minDist = pHit.distance();
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minI = meshTools::findEdge
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(
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mesh,
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meshPoints[e[0]],
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meshPoints[e[1]]
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);
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}
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else if (pHit.distance() < almostMinDist)
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{
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almostMinDist = pHit.distance();
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almostMinI = meshTools::findEdge
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(
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mesh,
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meshPoints[e[0]],
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meshPoints[e[1]]
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);
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}
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}
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}
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if (minI == -1)
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{
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Info<< "Did not find edge close to point " << nearPoint << endl;
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return -1;
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}
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// Decide if nearPoint unique enough.
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Info<< "Found to point " << nearPoint << nl
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<< " nearest edge : " << minI
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<< " distance " << minDist << " endpoints "
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<< mesh.edges()[minI].line(points) << nl
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<< " next nearest edge : " << almostMinI
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<< " distance " << almostMinDist << " endpoints "
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<< mesh.edges()[almostMinI].line(points) << nl
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<< endl;
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if (almostMinDist < 2*minDist)
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{
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Info<< "Next nearest too close to nearest. Aborting" << endl;
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return -1;
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}
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else
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{
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return minI;
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}
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}
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// Find face on patch. Return mesh face label.
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label findFace
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(
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const primitiveMesh& mesh,
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const primitivePatch& pp,
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const point& nearPoint
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)
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{
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const pointField& points = pp.points();
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// Find nearest and next nearest
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scalar minDist = GREAT;
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label minI = -1;
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scalar almostMinDist = GREAT;
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label almostMinI = -1;
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forAll(pp, patchFacei)
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{
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pointHit pHit(pp[patchFacei].nearestPoint(nearPoint, points));
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if (pHit.hit())
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{
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if (pHit.distance() < minDist)
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{
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almostMinDist = minDist;
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almostMinI = minI;
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minDist = pHit.distance();
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minI = patchFacei + mesh.nInternalFaces();
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}
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else if (pHit.distance() < almostMinDist)
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{
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almostMinDist = pHit.distance();
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almostMinI = patchFacei + mesh.nInternalFaces();
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}
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}
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}
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if (minI == -1)
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{
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Info<< "Did not find face close to point " << nearPoint << endl;
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return -1;
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}
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// Decide if nearPoint unique enough.
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Info<< "Found to point " << nearPoint << nl
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<< " nearest face : " << minI
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<< " distance " << minDist
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<< " to face centre " << mesh.faceCentres()[minI] << nl
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<< " next nearest face : " << almostMinI
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<< " distance " << almostMinDist
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<< " to face centre " << mesh.faceCentres()[almostMinI] << nl
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<< endl;
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if (almostMinDist < 2*minDist)
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{
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Info<< "Next nearest too close to nearest. Aborting" << endl;
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return -1;
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}
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else
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{
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return minI;
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}
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}
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// Find cell with cell centre close to given point.
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label findCell(const primitiveMesh& mesh, const point& nearPoint)
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{
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label celli = mesh.findCell(nearPoint);
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if (celli != -1)
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{
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scalar distToCcSqr = magSqr(nearPoint - mesh.cellCentres()[celli]);
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const labelList& cPoints = mesh.cellPoints()[celli];
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label minI = -1;
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scalar minDistSqr = GREAT;
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forAll(cPoints, i)
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{
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label pointi = cPoints[i];
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scalar distSqr = magSqr(nearPoint - mesh.points()[pointi]);
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if (distSqr < minDistSqr)
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{
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minDistSqr = distSqr;
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minI = pointi;
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}
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}
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// Decide if nearPoint unique enough.
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Info<< "Found to point " << nearPoint << nl
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<< " nearest cell : " << celli
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<< " distance " << Foam::sqrt(distToCcSqr)
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<< " to cell centre " << mesh.cellCentres()[celli] << nl
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<< " nearest mesh point : " << minI
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<< " distance " << Foam::sqrt(minDistSqr)
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<< " to " << mesh.points()[minI] << nl
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<< endl;
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if (minDistSqr < 4*distToCcSqr)
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{
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Info<< "Mesh point too close to nearest cell centre. Aborting"
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<< endl;
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celli = -1;
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}
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}
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return celli;
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}
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int main(int argc, char *argv[])
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{
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#include "addOverwriteOption.H"
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#include "addDictOption.H"
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#include "setRootCase.H"
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#include "createTime.H"
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runTime.functionObjects().off();
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#include "createPolyMesh.H"
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const word oldInstance = mesh.pointsInstance();
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const bool overwrite = args.optionFound("overwrite");
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Info<< "Reading modifyMeshDict\n" << endl;
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// Read meshing dictionary
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const word dictName("modifyMeshDict");
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#include "setSystemMeshDictionaryIO.H"
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const IOdictionary dict(dictIO);
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// Read all from the dictionary.
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List<Pair<point>> pointsToMove(dict.lookup("pointsToMove"));
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List<Pair<point>> edgesToSplit(dict.lookup("edgesToSplit"));
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List<Pair<point>> facesToTriangulate
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(
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dict.lookup("facesToTriangulate")
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);
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bool cutBoundary =
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(
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pointsToMove.size()
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|| edgesToSplit.size()
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|| facesToTriangulate.size()
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);
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List<Pair<point>> edgesToCollapse(dict.lookup("edgesToCollapse"));
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bool collapseEdge = edgesToCollapse.size();
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List<Pair<point>> cellsToPyramidise(dict.lookup("cellsToSplit"));
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bool cellsToSplit = cellsToPyramidise.size();
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// List<Tuple2<pointField,point>>
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// cellsToCreate(dict.lookup("cellsToCreate"));
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Info<< "Read from " << dict.name() << nl
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<< " Boundary cutting module:" << nl
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<< " points to move :" << pointsToMove.size() << nl
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<< " edges to split :" << edgesToSplit.size() << nl
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<< " faces to triangulate:" << facesToTriangulate.size() << nl
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<< " Cell splitting module:" << nl
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<< " cells to split :" << cellsToPyramidise.size() << nl
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<< " Edge collapsing module:" << nl
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<< " edges to collapse :" << edgesToCollapse.size() << nl
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//<< " cells to create :" << cellsToCreate.size() << nl
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<< endl;
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if
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(
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(cutBoundary && collapseEdge)
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|| (cutBoundary && cellsToSplit)
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|| (collapseEdge && cellsToSplit)
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)
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{
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FatalErrorInFunction
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<< "Used more than one mesh modifying module "
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<< "(boundary cutting, cell splitting, edge collapsing)" << nl
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<< "Please do them in separate passes." << exit(FatalError);
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}
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// Get calculating engine for all of outside
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const SubList<face> outsideFaces
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(
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mesh.faces(),
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mesh.nFaces() - mesh.nInternalFaces(),
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mesh.nInternalFaces()
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);
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primitivePatch allBoundary(outsideFaces, mesh.points());
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// Look up mesh labels and convert to input for boundaryCutter.
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bool validInputs = true;
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Info<< nl << "Looking up points to move ..." << nl << endl;
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Map<point> pointToPos(pointsToMove.size());
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forAll(pointsToMove, i)
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{
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const Pair<point>& pts = pointsToMove[i];
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label pointi = findPoint(allBoundary, pts.first());
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if (pointi == -1 || !pointToPos.insert(pointi, pts.second()))
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{
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Info<< "Could not insert mesh point " << pointi
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<< " for input point " << pts.first() << nl
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<< "Perhaps the point is already marked for moving?" << endl;
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validInputs = false;
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}
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}
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Info<< nl << "Looking up edges to split ..." << nl << endl;
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Map<List<point>> edgeToCuts(edgesToSplit.size());
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forAll(edgesToSplit, i)
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{
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const Pair<point>& pts = edgesToSplit[i];
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label edgeI = findEdge(mesh, allBoundary, pts.first());
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if
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(
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edgeI == -1
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|| !edgeToCuts.insert(edgeI, List<point>(1, pts.second()))
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)
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{
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Info<< "Could not insert mesh edge " << edgeI
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<< " for input point " << pts.first() << nl
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<< "Perhaps the edge is already marked for cutting?" << endl;
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validInputs = false;
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}
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}
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Info<< nl << "Looking up faces to triangulate ..." << nl << endl;
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Map<point> faceToDecompose(facesToTriangulate.size());
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forAll(facesToTriangulate, i)
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{
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const Pair<point>& pts = facesToTriangulate[i];
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label facei = findFace(mesh, allBoundary, pts.first());
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if (facei == -1 || !faceToDecompose.insert(facei, pts.second()))
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{
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Info<< "Could not insert mesh face " << facei
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<< " for input point " << pts.first() << nl
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<< "Perhaps the face is already marked for splitting?" << endl;
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validInputs = false;
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}
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}
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Info<< nl << "Looking up cells to convert to pyramids around"
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<< " cell centre ..." << nl << endl;
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Map<point> cellToPyrCentre(cellsToPyramidise.size());
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forAll(cellsToPyramidise, i)
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{
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const Pair<point>& pts = cellsToPyramidise[i];
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label celli = findCell(mesh, pts.first());
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if (celli == -1 || !cellToPyrCentre.insert(celli, pts.second()))
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{
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Info<< "Could not insert mesh cell " << celli
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<< " for input point " << pts.first() << nl
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<< "Perhaps the cell is already marked for splitting?" << endl;
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validInputs = false;
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}
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}
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Info<< nl << "Looking up edges to collapse ..." << nl << endl;
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Map<point> edgeToPos(edgesToCollapse.size());
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forAll(edgesToCollapse, i)
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{
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const Pair<point>& pts = edgesToCollapse[i];
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label edgeI = findEdge(mesh, allBoundary, pts.first());
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if (edgeI == -1 || !edgeToPos.insert(edgeI, pts.second()))
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{
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Info<< "Could not insert mesh edge " << edgeI
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<< " for input point " << pts.first() << nl
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<< "Perhaps the edge is already marked for collaping?" << endl;
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validInputs = false;
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}
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}
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if (!validInputs)
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{
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Info<< nl << "There was a problem in one of the inputs in the"
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<< " dictionary. Not modifying mesh." << endl;
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}
|
|
else if (cellToPyrCentre.size())
|
|
{
|
|
Info<< nl << "All input cells located. Modifying mesh." << endl;
|
|
|
|
// Mesh change engine
|
|
cellSplitter cutter(mesh);
|
|
|
|
// Topo change container
|
|
polyTopoChange meshMod(mesh);
|
|
|
|
// Insert commands into meshMod
|
|
cutter.setRefinement(cellToPyrCentre, meshMod);
|
|
|
|
// Do changes
|
|
autoPtr<mapPolyMesh> morphMap = meshMod.changeMesh(mesh, false);
|
|
|
|
if (morphMap().hasMotionPoints())
|
|
{
|
|
mesh.movePoints(morphMap().preMotionPoints());
|
|
}
|
|
|
|
cutter.updateMesh(morphMap());
|
|
|
|
if (!overwrite)
|
|
{
|
|
runTime++;
|
|
}
|
|
else
|
|
{
|
|
mesh.setInstance(oldInstance);
|
|
}
|
|
|
|
// Write resulting mesh
|
|
Info<< "Writing modified mesh to time " << runTime.timeName() << endl;
|
|
mesh.write();
|
|
topoSet::removeFiles(mesh);
|
|
processorMeshes::removeFiles(mesh);
|
|
}
|
|
else if (edgeToPos.size())
|
|
{
|
|
Info<< nl << "All input edges located. Modifying mesh." << endl;
|
|
|
|
// Mesh change engine
|
|
edgeCollapser cutter(mesh);
|
|
|
|
const edgeList& edges = mesh.edges();
|
|
const pointField& points = mesh.points();
|
|
|
|
pointField newPoints(points);
|
|
|
|
PackedBoolList collapseEdge(mesh.nEdges());
|
|
Map<point> collapsePointToLocation(mesh.nPoints());
|
|
|
|
// Get new positions and construct collapse network
|
|
forAllConstIter(Map<point>, edgeToPos, iter)
|
|
{
|
|
label edgeI = iter.key();
|
|
const edge& e = edges[edgeI];
|
|
|
|
collapseEdge[edgeI] = true;
|
|
collapsePointToLocation.set(e[1], points[e[0]]);
|
|
|
|
newPoints[e[0]] = iter();
|
|
}
|
|
|
|
// Move master point to destination.
|
|
mesh.movePoints(newPoints);
|
|
|
|
List<pointEdgeCollapse> allPointInfo;
|
|
const globalIndex globalPoints(mesh.nPoints());
|
|
labelList pointPriority(mesh.nPoints(), 0);
|
|
|
|
cutter.consistentCollapse
|
|
(
|
|
globalPoints,
|
|
pointPriority,
|
|
collapsePointToLocation,
|
|
collapseEdge,
|
|
allPointInfo
|
|
);
|
|
|
|
// Topo change container
|
|
polyTopoChange meshMod(mesh);
|
|
|
|
// Insert
|
|
cutter.setRefinement(allPointInfo, meshMod);
|
|
|
|
// Do changes
|
|
autoPtr<mapPolyMesh> morphMap = meshMod.changeMesh(mesh, false);
|
|
|
|
if (morphMap().hasMotionPoints())
|
|
{
|
|
mesh.movePoints(morphMap().preMotionPoints());
|
|
}
|
|
|
|
// Not implemented yet:
|
|
//cutter.updateMesh(morphMap());
|
|
|
|
|
|
if (!overwrite)
|
|
{
|
|
runTime++;
|
|
}
|
|
else
|
|
{
|
|
mesh.setInstance(oldInstance);
|
|
}
|
|
|
|
// Write resulting mesh
|
|
Info<< "Writing modified mesh to time " << runTime.timeName() << endl;
|
|
mesh.write();
|
|
topoSet::removeFiles(mesh);
|
|
processorMeshes::removeFiles(mesh);
|
|
}
|
|
else
|
|
{
|
|
Info<< nl << "All input points located. Modifying mesh." << endl;
|
|
|
|
// Mesh change engine
|
|
boundaryCutter cutter(mesh);
|
|
|
|
// Topo change container
|
|
polyTopoChange meshMod(mesh);
|
|
|
|
// Insert commands into meshMod
|
|
cutter.setRefinement
|
|
(
|
|
pointToPos,
|
|
edgeToCuts,
|
|
Map<labelPair>(0), // Faces to split diagonally
|
|
faceToDecompose, // Faces to triangulate
|
|
meshMod
|
|
);
|
|
|
|
// Do changes
|
|
autoPtr<mapPolyMesh> morphMap = meshMod.changeMesh(mesh, false);
|
|
|
|
if (morphMap().hasMotionPoints())
|
|
{
|
|
mesh.movePoints(morphMap().preMotionPoints());
|
|
}
|
|
|
|
cutter.updateMesh(morphMap());
|
|
|
|
if (!overwrite)
|
|
{
|
|
runTime++;
|
|
}
|
|
else
|
|
{
|
|
mesh.setInstance(oldInstance);
|
|
}
|
|
|
|
// Write resulting mesh
|
|
Info<< "Writing modified mesh to time " << runTime.timeName() << endl;
|
|
mesh.write();
|
|
topoSet::removeFiles(mesh);
|
|
processorMeshes::removeFiles(mesh);
|
|
}
|
|
|
|
|
|
Info<< "\nEnd\n" << endl;
|
|
return 0;
|
|
}
|
|
|
|
|
|
// ************************************************************************* //
|