songtianlun/openfoam
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
d27457d41d
openfoam/applications/test/surfaceMeshConvert/Test-surfaceMeshConvert.C
Andrew Heather d8d6030ab6 INT: Integration of Mattijs' collocated parallel IO additions 
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.
2017-07-07 11:39:56 +01:00

610 lines
16 KiB
C
Raw Blame History

/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2016 OpenCFD Ltd.
-------------------------------------------------------------------------------
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
Test-surfaceMeshConvert
Group
grpSurfaceUtilities
Description
Test conversions from one surface mesh format to another.
Usage
\b Test-surfaceMeshConvert inputFile outputFile [OPTION]
Options:
- \par -clean
Perform some surface checking/cleanup on the input surface
- \par -orient
Check face orientation on the input surface
- \par -testModify
Test modification mechanism
- \par -scale \<scale\>
Specify a scaling factor for writing the files
- \par -triSurface
Use triSurface library for input/output
- \par -keyed
Use keyedSurface for input/output
Note
The filename extensions are used to determine the file format type.
\*---------------------------------------------------------------------------*/
#include "argList.H"
#include "Time.H"
#include "polyMesh.H"
#include "triSurface.H"
#include "surfMesh.H"
#include "surfFields.H"
#include "surfPointFields.H"
#include "PackedBoolList.H"
#include "MeshedSurfaces.H"
#include "ModifiableMeshedSurface.H"
#include "UnsortedMeshedSurfaces.H"
#include "StringStream.H"
using namespace Foam;
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
int main(int argc, char *argv[])
{
argList::addNote
(
"convert between surface formats, "
"but primarily for testing functionality\n"
"Normally use surfaceMeshConvert instead."
);
argList::noParallel();
argList::validArgs.append("inputFile");
argList::validArgs.append("outputFile");
argList::addBoolOption
(
"clean",
"perform some surface checking/cleanup on the input surface"
);
argList::addBoolOption
(
"orient",
"check surface orientation"
);
argList::addBoolOption
(
"testModify",
"Test modification mechanism (MeshedSurface)"
);
argList::addBoolOption
(
"surfMesh",
"test surfMesh output"
);
argList::addBoolOption
(
"triSurface",
"use triSurface for read/write"
);
argList::addBoolOption
(
"unsorted",
"use UnsortedMeshedSurface instead of MeshedSurface, "
"or unsorted output (with -triSurface option)"
);
argList::addBoolOption
(
"triFace",
"use triFace instead of face"
);
argList::addBoolOption
(
"stdout",
"ignore output filename and write to stdout"
);
argList::addOption
(
"scale",
"factor",
"geometry scaling factor - default is 1"
);
#include "setRootCase.H"
const bool optStdout = args.optionFound("stdout");
const scalar scaleFactor = args.optionLookupOrDefault("scale", 0.0);
const fileName importName = args[1];
const fileName exportName = optStdout ? "-stdout" : args[2];
if (importName == exportName)
{
FatalErrorInFunction
<< "Output file " << exportName << " would overwrite input file."
<< exit(FatalError);
}
if
(
!args.optionFound("triSurface")
&&
(
!MeshedSurface<face>::canRead(importName, true)
||
(
!optStdout
&& !MeshedSurface<face>::canWriteType(exportName.ext(), true)
)
)
)
{
return 1;
}
if (args.optionFound("triSurface"))
{
triSurface surf(importName);
Info<< "Read surface:" << endl;
surf.writeStats(Info);
Info<< "Area : " << sum(surf.magSf()) << nl
<< endl;
// check: output to ostream, construct from istream
{
OStringStream os;
os << surf;
IStringStream is(os.str());
// both work:
triSurface surf2(is);
// OR
// is.rewind();
// triSurface surf2;
// is >> surf2;
// surf2.read(is); // FAIL: private method
}
if (args.optionFound("orient"))
{
Info<< "Checking surface orientation" << endl;
PatchTools::checkOrientation(surf, true);
Info<< endl;
}
if (args.optionFound("clean"))
{
Info<< "Cleaning up surface" << endl;
surf.cleanup(true);
surf.writeStats(Info);
Info<< endl;
}
Info<< "writing " << exportName;
if (scaleFactor <= 0)
{
Info<< " without scaling" << endl;
}
else
{
Info<< " with scaling " << scaleFactor << endl;
surf.scalePoints(scaleFactor);
surf.writeStats(Info);
Info<< "Area : " << sum(surf.magSf()) << nl
<< endl;
}
if (optStdout)
{
Info<< surf;
}
else
{
// normally write sorted (looks nicer)
surf.write(exportName, !args.optionFound("unsorted"));
}
}
else if (args.optionFound("unsorted"))
{
UnsortedMeshedSurface<face> surf(importName);
Info<< "Read surface:" << endl;
surf.writeStats(Info);
Info<< "Area : " << sum(surf.magSf()) << nl
<< endl;
// check: output to ostream, construct from istream
{
OStringStream os;
os << surf;
IStringStream is(os.str());
// both work:
UnsortedMeshedSurface<face> surf2(is);
// OR
// is.rewind();
// UnsortedMeshedSurface<face> surf2;
// is >> surf2;
// surf2.read(is); // FAIL: private method
}
if (args.optionFound("orient"))
{
Info<< "Checking surface orientation" << endl;
PatchTools::checkOrientation(surf, true);
Info<< endl;
}
if (args.optionFound("clean"))
{
Info<< "Cleaning up surface" << endl;
surf.cleanup(true);
surf.writeStats(Info);
Info<< endl;
}
Info<< "writing " << exportName;
if (scaleFactor <= 0)
{
Info<< " without scaling" << endl;
}
else
{
Info<< " with scaling " << scaleFactor << endl;
surf.scalePoints(scaleFactor);
surf.writeStats(Info);
Info<< "Area : " << sum(surf.magSf()) << nl
<< endl;
}
if (optStdout)
{
Info<< surf;
}
else
{
surf.write(exportName);
}
}
else if (args.optionFound("triFace"))
{
MeshedSurface<triFace> surf(importName);
Info<< "Read surface:" << endl;
surf.writeStats(Info);
Info<< "Area : " << sum(surf.magSf()) << nl
<< endl;
// check: output to ostream, construct from istream
{
OStringStream os;
os << surf;
IStringStream is(os.str());
// both work:
MeshedSurface<face> surf2(is);
// OR
// is.rewind();
// MeshedSurface<face> surf2;
// is >> surf2;
// surf2.read(is); // FAIL: private method
}
if (args.optionFound("orient"))
{
Info<< "Checking surface orientation" << endl;
PatchTools::checkOrientation(surf, true);
Info<< endl;
}
if (args.optionFound("clean"))
{
Info<< "Cleaning up surface" << endl;
surf.cleanup(true);
surf.writeStats(Info);
Info<< endl;
}
Info<< "writing " << exportName;
if (scaleFactor <= 0)
{
Info<< " without scaling" << endl;
}
else
{
Info<< " with scaling " << scaleFactor << endl;
surf.scalePoints(scaleFactor);
surf.writeStats(Info);
Info<< "Area : " << sum(surf.magSf()) << nl
<< endl;
}
if (optStdout)
{
Info<< surf;
}
else
{
surf.write(exportName);
}
}
else
{
MeshedSurface<face> surf(importName);
Info<< "Read surface:" << endl;
surf.writeStats(Info);
Info<< "Area : " << sum(surf.magSf()) << nl
<< endl;
// check: output to ostream, construct from istream
{
OStringStream os;
os << surf;
IStringStream is(os.str());
// both work:
MeshedSurface<face> surf2(is);
// OR
// is.rewind();
// MeshedSurface<face> surf2;
// is >> surf2;
// surf2.read(is); // FAIL: private method
}
if (args.optionFound("orient"))
{
Info<< "Checking surface orientation" << endl;
PatchTools::checkOrientation(surf, true);
Info<< endl;
}
if (args.optionFound("clean"))
{
Info<< "Cleaning up surface" << endl;
surf.cleanup(true);
surf.writeStats(Info);
Info<< endl;
}
if (args.optionFound("testModify"))
{
Info<< "Use ModifiableMeshedSurface to shift (1, 0, 0)" << endl;
Info<< "original" << nl;
surf.writeStats(Info);
Info<< endl;
ModifiableMeshedSurface<face> tsurf(surf.xfer());
// ModifiableMeshedSurface<face> tsurf;
// tsurf.reset(surf.xfer());
Info<< "in-progress" << nl;
surf.writeStats(Info);
Info<< endl;
tsurf.storedPoints() += vector(1, 0, 0);
surf.transfer(tsurf);
Info<< "updated" << nl;
surf.writeStats(Info);
Info<< endl;
Info<< "modifier" << nl;
tsurf.writeStats(Info);
Info<< endl;
}
Info<< "writing " << exportName;
if (scaleFactor <= 0)
{
Info<< " without scaling" << endl;
}
else
{
Info<< " with scaling " << scaleFactor << endl;
surf.scalePoints(scaleFactor);
surf.writeStats(Info);
Info<< "Area : " << sum(surf.magSf()) << nl
<< endl;
}
if (optStdout)
{
Info<< surf;
}
else
{
surf.write(exportName);
}
if (args.optionFound("surfMesh"))
{
Foam::Time runTime
(
args.rootPath(),
args.caseName()
);
// start with "constant"
runTime.setTime(instant(0, runTime.constant()), 0);
Info<< "runTime.instance() = " << runTime.instance() << endl;
Info<< "runTime.timeName() = " << runTime.timeName() << endl;
Info<< "write MeshedSurface 'yetAnother' via proxy as surfMesh"
<< endl;
surf.write
(
runTime,
"yetAnother"
);
surfMesh surfIn
(
IOobject
(
"default",
runTime.timeName(),
runTime,
IOobject::MUST_READ,
IOobject::NO_WRITE
)
);
MeshedSurface<face> surfIn2(runTime, "foobar");
Info<<"surfIn2 = " << surfIn2.size() << endl;
Info<< "surfIn = " << surfIn.size() << endl;
Info<< "writing surfMesh as obj = oldSurfIn.obj" << endl;
using Foam::surfMesh;
surfIn.write(fileName("oldSurfIn.obj"));
Info<< "runTime.instance() = " << runTime.instance() << endl;
surfMesh surfOut
(
IOobject
(
"mySurf",
runTime.instance(),
runTime,
IOobject::NO_READ,
IOobject::NO_WRITE,
false
),
surf.xfer()
);
Info<< "writing surfMesh as well: " << surfOut.objectPath() << endl;
surfOut.write();
surfLabelField zoneIds
(
IOobject
(
"zoneIds",
surfOut.instance(),
surfOut,
IOobject::NO_READ,
IOobject::NO_WRITE
),
surfOut,
dimless
);
Info<<" surf name= " << surfOut.name() <<nl;
Info<< "rename to anotherSurf" << endl;
surfOut.rename("anotherSurf");
Info<<" surf name= " << surfOut.name() <<nl;
// advance time to 1
runTime.setTime(instant(1), 1);
surfOut.setInstance(runTime.timeName());
Info<< "writing surfMesh again well: " << surfOut.objectPath()
<< endl;
surfOut.write();
// write directly
surfOut.surfMesh::write(fileName("someName.ofs"));
#if 1
const surfZoneList& zones = surfOut.surfZones();
forAll(zones, zoneI)
{
SubList<label>
(
zoneIds,
zones[zoneI].size(),
zones[zoneI].start()
) = zoneI;
}
Info<< "write zoneIds (for testing only): "
<< zoneIds.objectPath() << endl;
zoneIds.write();
surfPointLabelField pointIds
(
IOobject
(
"zoneIds.",
// "pointIds",
surfOut.instance(),
// "pointFields",
surfOut,
IOobject::NO_READ,
IOobject::NO_WRITE
),
surfOut,
dimless
);
forAll(pointIds, i)
{
pointIds[i] = i;
}
Info<< "write pointIds (for testing only): "
<< pointIds.objectPath() << endl;
pointIds.write();
Info<<"surfMesh with these names: " << surfOut.names() << endl;
#endif
}
}
Info<< "\nEnd\n" << endl;
return 0;
}
// ************************************************************************* //
Reference in New Issue View Git Blame Copy Permalink