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INT: Integration of Mattijs' collocated parallel IO additions

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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.
This commit is contained in:
Andrew Heather
2017-07-07 11:39:56 +01:00
parent 03c114010f
commit d8d6030ab6
221 changed files with 11118 additions and 1946 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
applications/utilities/mesh/advanced/modifyMesh/modifyMesh.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2016-2017 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
@ -64,6 +64,7 @@ Description
#include "globalIndex.H"
#include "topoSet.H"
#include "processorMeshes.H"
#include "IOdictionary.H"
using namespace Foam;

15
applications/utilities/mesh/advanced/selectCells/edgeStats.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2014 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -28,6 +28,7 @@ License
#include "polyMesh.H"
#include "Ostream.H"
#include "twoDPointCorrector.H"
#include "IOdictionary.H"
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
@ -143,10 +144,8 @@ Foam::scalar Foam::edgeStats::minLen(Ostream& os) const
const edgeList& edges = mesh_.edges();
forAll(edges, edgeI)
forAll(const edge& e : edges)
{
const edge& e = edges[edgeI];
vector eVec(e.vec(mesh_.points()));
scalar eMag = mag(eVec);
@ -209,13 +208,5 @@ Foam::scalar Foam::edgeStats::minLen(Ostream& os) const
}
// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * Friend Functions * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
// ************************************************************************* //

4
applications/utilities/mesh/conversion/foamToStarMesh/foamToStarMesh.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2016 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
@ -57,6 +57,7 @@ See also
#include "Time.H"
#include "polyMesh.H"
#include "STARCDMeshWriter.H"
#include "IOdictionary.H"
using namespace Foam;
@ -134,4 +135,5 @@ int main(int argc, char *argv[])
return 0;
}
// ************************************************************************* //

2
applications/utilities/mesh/conversion/foamToSurface/foamToSurface.C
View File

@ -47,7 +47,7 @@ Usage
#include "timeSelector.H"
#include "Time.H"
#include "polyMesh.H"
#include "IOdictionary.H"
#include "MeshedSurfaces.H"
using namespace Foam;

6
applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/DelaunayMesh/DelaunayMeshIO.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2012-2016 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2012-2017 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -387,7 +387,7 @@ Foam::DelaunayMesh<Triangulation>::createMesh
IOobject::NO_READ,
IOobject::AUTO_WRITE
),
Triangulation::number_of_vertices()
label(Triangulation::number_of_vertices())
);
labelIOField processorIndices
@ -401,7 +401,7 @@ Foam::DelaunayMesh<Triangulation>::createMesh
IOobject::NO_READ,
IOobject::AUTO_WRITE
),
Triangulation::number_of_vertices()
label(Triangulation::number_of_vertices())
);
for

1
applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C
View File

@ -531,6 +531,7 @@ void extractSurface
? runTime.path()/".."/outFileName
: runTime.path()/outFileName
);
globalCasePath.clean();
Info<< "Writing merged surface to " << globalCasePath << endl;

3
applications/utilities/mesh/manipulation/checkMesh/checkMesh.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2015-2017 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
@ -67,6 +67,7 @@ Usage
#include "globalMeshData.H"
#include "surfaceWriter.H"
#include "vtkSetWriter.H"
#include "IOdictionary.H"
#include "checkTools.H"
#include "checkTopology.H"

9
applications/utilities/mesh/manipulation/checkMesh/checkTools.C
View File

@ -281,7 +281,7 @@ void Foam::mergeAndWrite
mesh.points()
);
const fileName outputDir
fileName outputDir
(
set.time().path()
/ (Pstream::parRun() ? ".." : "")
@ -289,6 +289,7 @@ void Foam::mergeAndWrite
/ mesh.pointsInstance()
/ set.name()
);
outputDir.clean();
mergeAndWrite(mesh, writer, set.name(), setPatch, outputDir);
}
@ -374,7 +375,7 @@ void Foam::mergeAndWrite
mesh.points()
);
const fileName outputDir
fileName outputDir
(
set.time().path()
/ (Pstream::parRun() ? ".." : "")
@ -382,6 +383,7 @@ void Foam::mergeAndWrite
/ mesh.pointsInstance()
/ set.name()
);
outputDir.clean();
mergeAndWrite(mesh, writer, set.name(), setPatch, outputDir);
}
@ -477,7 +479,7 @@ void Foam::mergeAndWrite
// Output e.g. pointSet p0 to
// postProcessing/<time>/p0.vtk
const fileName outputDir
fileName outputDir
(
set.time().path()
/ (Pstream::parRun() ? ".." : "")
@ -485,6 +487,7 @@ void Foam::mergeAndWrite
/ mesh.pointsInstance()
// set.name()
);
outputDir.clean();
mkDir(outputDir);
fileName outputFile(outputDir/writer.getFileName(points, wordList()));

1
applications/utilities/mesh/manipulation/createPatch/createPatch.C
View File

@ -53,6 +53,7 @@ Description
#include "polyModifyFace.H"
#include "wordReList.H"
#include "processorMeshes.H"
#include "IOdictionary.H"
using namespace Foam;

3
applications/utilities/mesh/manipulation/refineMesh/refineMesh.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -54,6 +54,7 @@ Description
#include "wedgePolyPatch.H"
#include "plane.H"
#include "SubField.H"
#include "IOdictionary.H"
using namespace Foam;

8
applications/utilities/mesh/manipulation/setSet/setSet.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2017 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
@ -52,6 +52,7 @@ Description
#include "faceZoneSet.H"
#include "pointZoneSet.H"
#include "timeSelector.H"
#include "collatedFileOperation.H"
#include <stdio.h>
@ -743,6 +744,11 @@ commandStatus parseAction(const word& actionName)
int main(int argc, char *argv[])
{
// Specific to topoSet/setSet: quite often we want to block upon writing
// a set so we can immediately re-read it. So avoid use of threading
// for set writing.
fileOperations::collatedFileOperation::maxThreadFileBufferSize = 0;
timeSelector::addOptions(true, false);
#include "addRegionOption.H"
argList::addBoolOption("noVTK", "do not write VTK files");

5
applications/utilities/mesh/manipulation/stitchMesh/stitchMesh.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -487,7 +487,8 @@ int main(int argc, char *argv[])
(
runTime.writeFormat(),
IOstream::currentVersion,
runTime.writeCompression()
runTime.writeCompression(),
true
)
)
{

9
applications/utilities/mesh/manipulation/topoSet/topoSet.C
View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -42,6 +42,8 @@ Description
#include "cellZoneSet.H"
#include "faceZoneSet.H"
#include "pointZoneSet.H"
#include "IOdictionary.H"
#include "collatedFileOperation.H"
using namespace Foam;
@ -194,6 +196,11 @@ polyMesh::readUpdateState meshReadUpdate(polyMesh& mesh)
int main(int argc, char *argv[])
{
// Specific to topoSet/setSet: quite often we want to block upon writing
// a set so we can immediately re-read it. So avoid use of threading
// for set writing.
fileOperations::collatedFileOperation::maxThreadFileBufferSize = 0;
timeSelector::addOptions(true, false);
#include "addDictOption.H"
#include "addRegionOption.H"