Files
OpenFOAM-6/applications/utilities/surface/surfaceMeshExport/surfaceMeshExport.C
Henry Weller 7c301dbff4 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

294 lines
7.7 KiB
C

/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2017 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
surfaceMeshExport
Description
Export from surfMesh to various third-party surface formats with
optional scaling or transformations (rotate/translate) on a
coordinateSystem.
Usage
\b surfaceMeshExport outputFile [OPTION]
Options:
- \par -clean
Perform some surface checking/cleanup on the input surface.
- \par -name \<name\>
Specify an alternative surface name when writing.
- \par -scaleIn \<scale\>
Specify a scaling factor when reading files.
- \par -scaleOut \<scale\>
Specify a scaling factor when writing files.
- \par -dict \<dictionary\>
Specify an alternative dictionary for constant/coordinateSystems.
- \par -from \<coordinateSystem\>
Specify a coordinate system when reading files.
- \par -to \<coordinateSystem\>
Specify a coordinate system when writing files.
Note
The filename extensions are used to determine the file format type.
\*---------------------------------------------------------------------------*/
#include "argList.H"
#include "Time.H"
#include "MeshedSurfaces.H"
#include "coordinateSystems.H"
using namespace Foam;
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
int main(int argc, char *argv[])
{
argList::addNote
(
"export from surfMesh to various third-party surface formats"
);
argList::noParallel();
argList::validArgs.append("output surface file");
argList::addBoolOption
(
"clean",
"perform some surface checking/cleanup on the input surface"
);
argList::addOption
(
"name",
"name",
"specify an alternative surface name when reading - "
"default is 'default'"
);
argList::addOption
(
"scaleIn",
"factor",
"geometry scaling factor on input - default is 1"
);
argList::addOption
(
"scaleOut",
"factor",
"geometry scaling factor on output - default is 1"
);
#include "addDictOption.H"
argList::addOption
(
"from",
"coordinateSystem",
"specify the source coordinate system, applied after '-scaleIn'"
);
argList::addOption
(
"to",
"coordinateSystem",
"specify the target coordinate system, applied before '-scaleOut'"
);
argList args(argc, argv);
Time runTime(args.rootPath(), args.caseName());
const fileName exportName = args[1];
const word importName = args.optionLookupOrDefault<word>("name", "default");
// check that writing is supported
if (!MeshedSurface<face>::canWriteType(exportName.ext(), true))
{
return 1;
}
// get the coordinate transformations
autoPtr<coordinateSystem> fromCsys;
autoPtr<coordinateSystem> toCsys;
if (args.optionFound("from") || args.optionFound("to"))
{
autoPtr<IOobject> ioPtr;
if (args.optionFound("dict"))
{
const fileName dictPath = args["dict"];
ioPtr.set
(
new IOobject
(
(
isDir(dictPath)
? dictPath/coordinateSystems::typeName
: dictPath
),
runTime,
IOobject::MUST_READ,
IOobject::NO_WRITE,
false
)
);
}
else
{
ioPtr.set
(
new IOobject
(
coordinateSystems::typeName,
runTime.constant(),
runTime,
IOobject::MUST_READ,
IOobject::NO_WRITE,
false
)
);
}
if (!ioPtr->typeHeaderOk<coordinateSystems>(false))
{
FatalErrorInFunction
<< ioPtr->objectPath() << nl
<< exit(FatalError);
}
coordinateSystems csLst(ioPtr());
if (args.optionFound("from"))
{
const word csName = args["from"];
const label csIndex = csLst.findIndex(csName);
if (csIndex < 0)
{
FatalErrorInFunction
<< "Cannot find -from " << csName << nl
<< "available coordinateSystems: " << csLst.toc() << nl
<< exit(FatalError);
}
fromCsys.reset(new coordinateSystem(csLst[csIndex]));
}
if (args.optionFound("to"))
{
const word csName = args["to"];
const label csIndex = csLst.findIndex(csName);
if (csIndex < 0)
{
FatalErrorInFunction
<< "Cannot find -to " << csName << nl
<< "available coordinateSystems: " << csLst.toc() << nl
<< exit(FatalError);
}
toCsys.reset(new coordinateSystem(csLst[csIndex]));
}
// maybe fix this later
if (fromCsys.valid() && toCsys.valid())
{
FatalErrorInFunction
<< exit(FatalError);
}
}
surfMesh smesh
(
IOobject
(
importName,
runTime.constant(),
runTime,
IOobject::MUST_READ_IF_MODIFIED,
IOobject::NO_WRITE
)
);
Info<< "read surfMesh:\n " << smesh.objectPath() << endl;
// Simply copy for now, but really should have a separate write method
MeshedSurface<face> surf(smesh);
if (args.optionFound("clean"))
{
surf.cleanup(true);
}
scalar scaleIn = 0;
if (args.optionReadIfPresent("scaleIn", scaleIn) && scaleIn > 0)
{
Info<< " -scaleIn " << scaleIn << endl;
surf.scalePoints(scaleIn);
}
if (fromCsys.valid())
{
Info<< " -from " << fromCsys().name() << endl;
tmp<pointField> tpf = fromCsys().localPosition(surf.points());
surf.movePoints(tpf());
}
if (toCsys.valid())
{
Info<< " -to " << toCsys().name() << endl;
tmp<pointField> tpf = toCsys().globalPosition(surf.points());
surf.movePoints(tpf());
}
scalar scaleOut = 0;
if (args.optionReadIfPresent("scaleOut", scaleOut) && scaleOut > 0)
{
Info<< " -scaleOut " << scaleOut << endl;
surf.scalePoints(scaleOut);
}
surf.writeStats(Info);
Info<< endl;
Info<< "writing " << exportName << endl;
surf.write(exportName);
Info<< "\nEnd\n" << endl;
return 0;
}
// ************************************************************************* //