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https://github.com/OpenFOAM/OpenFOAM-6.git
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7c301dbff4
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.
640 lines
17 KiB
C
640 lines
17 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 |
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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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foamToEnsight
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Description
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Translates OpenFOAM data to EnSight format.
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An Ensight part is created for the internalMesh and for each patch.
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Usage
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\b foamToEnsight [OPTION]
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Options:
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- \par -ascii
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Write Ensight data in ASCII format instead of "C Binary"
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- \par -patches patchList
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Specify particular patches to write.
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Specifying an empty list suppresses writing the internalMesh.
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- \par -noPatches
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Suppress writing any patches.
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- \par -faceZones zoneList
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Specify faceZones to write, with wildcards
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- \par -cellZone zoneName
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Specify single cellZone to write (not lagrangian)
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Note
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Parallel support for cloud data is not supported
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- writes to \a EnSight directory to avoid collisions with foamToEnsightParts
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\*---------------------------------------------------------------------------*/
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#include "argList.H"
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#include "timeSelector.H"
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#include "IOobjectList.H"
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#include "IOmanip.H"
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#include "OFstream.H"
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#include "volFields.H"
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#include "labelIOField.H"
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#include "scalarIOField.H"
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#include "tensorIOField.H"
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#include "ensightMesh.H"
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#include "ensightField.H"
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#include "ensightParticlePositions.H"
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#include "ensightCloudField.H"
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#include "fvc.H"
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#include "cellSet.H"
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#include "fvMeshSubset.H"
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using namespace Foam;
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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bool inFileNameList
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(
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const fileNameList& nameList,
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const word& name
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)
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{
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forAll(nameList, i)
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{
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if (nameList[i] == name)
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{
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return true;
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}
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}
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return false;
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}
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int main(int argc, char *argv[])
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{
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timeSelector::addOptions();
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#include "addRegionOption.H"
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argList::addBoolOption
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(
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"ascii",
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"write in ASCII format instead of 'C Binary'"
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);
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argList::addBoolOption
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(
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"nodeValues",
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"write values in nodes"
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);
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argList::addBoolOption
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(
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"noPatches",
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"suppress writing any patches"
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);
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argList::addOption
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(
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"patches",
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"wordReList",
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"specify particular patches to write - eg '(outlet \"inlet.*\")'. "
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"An empty list suppresses writing the internalMesh."
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);
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argList::addOption
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(
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"faceZones",
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"wordReList",
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"specify faceZones to write - eg '( slice \"mfp-.*\" )'."
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);
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argList::addOption
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(
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"fields",
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"wordReList",
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"specify fields to export (all by default) - eg '( \"U.*\" )'."
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);
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argList::addOption
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(
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"cellZone",
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"word",
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"specify cellZone to write"
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);
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#include "setRootCase.H"
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// Check options
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const bool binary = !args.optionFound("ascii");
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const bool nodeValues = args.optionFound("nodeValues");
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#include "createTime.H"
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instantList Times = timeSelector::select0(runTime, args);
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#include "createNamedMesh.H"
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// Mesh instance (region0 gets filtered out)
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fileName regionPrefix = "";
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if (regionName != polyMesh::defaultRegion)
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{
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regionPrefix = regionName;
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}
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const label nVolFieldTypes = 5;
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const word volFieldTypes[] =
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{
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volScalarField::typeName,
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volVectorField::typeName,
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volSphericalTensorField::typeName,
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volSymmTensorField::typeName,
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volTensorField::typeName
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};
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// Path to EnSight directory at case level only
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// - For parallel cases, data only written from master
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fileName ensightDir = args.rootPath()/args.globalCaseName()/"EnSight";
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if (Pstream::master())
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{
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if (isDir(ensightDir))
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{
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rmDir(ensightDir);
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}
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mkDir(ensightDir);
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}
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// Start of case file header output
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// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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const word prepend = args.globalCaseName() + '.';
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OFstream *ensightCaseFilePtr = nullptr;
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if (Pstream::master())
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{
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fileName caseFileName = prepend + "case";
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Info<< nl << "write case: " << caseFileName.c_str() << endl;
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// the case file is always ASCII
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ensightCaseFilePtr = new OFstream
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(
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ensightDir/caseFileName,
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IOstream::ASCII
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);
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*ensightCaseFilePtr
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<< "FORMAT" << nl
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<< "type: ensight gold" << nl << nl;
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}
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OFstream& ensightCaseFile = *ensightCaseFilePtr;
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// Construct the EnSight mesh
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const bool selectedPatches = args.optionFound("patches");
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wordReList patchPatterns;
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if (selectedPatches)
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{
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patchPatterns = wordReList(args.optionLookup("patches")());
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}
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const bool selectedZones = args.optionFound("faceZones");
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wordReList zonePatterns;
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if (selectedZones)
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{
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zonePatterns = wordReList(args.optionLookup("faceZones")());
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}
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const bool selectedFields = args.optionFound("fields");
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wordReList fieldPatterns;
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if (selectedFields)
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{
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fieldPatterns = wordReList(args.optionLookup("fields")());
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}
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word cellZoneName;
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const bool doCellZone = args.optionReadIfPresent("cellZone", cellZoneName);
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fvMeshSubset meshSubsetter(mesh);
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if (doCellZone)
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{
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Info<< "Converting cellZone " << cellZoneName
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<< " only (puts outside faces into patch "
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<< mesh.boundaryMesh()[0].name()
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<< ")" << endl;
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const cellZone& cz = mesh.cellZones()[cellZoneName];
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cellSet c0(mesh, "c0", labelHashSet(cz));
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meshSubsetter.setLargeCellSubset(c0, 0);
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}
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ensightMesh eMesh
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(
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(
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meshSubsetter.hasSubMesh()
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? meshSubsetter.subMesh()
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: meshSubsetter.baseMesh()
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),
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args.optionFound("noPatches"),
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selectedPatches,
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patchPatterns,
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selectedZones,
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zonePatterns,
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binary
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);
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// Set Time to the last time before looking for the lagrangian objects
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runTime.setTime(Times.last(), Times.size()-1);
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IOobjectList objects(mesh, runTime.timeName());
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#include "checkMeshMoving.H"
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if (meshMoving)
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{
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Info<< "Detected a moving mesh (multiple polyMesh/points files)."
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<< " Writing meshes for every timestep." << endl;
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}
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wordHashSet allCloudNames;
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if (Pstream::master())
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{
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word geomFileName = prepend + "0000";
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// test pre check variable if there is a moving mesh
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if (meshMoving)
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{
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geomFileName = prepend + "****";
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}
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ensightCaseFile
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<< "GEOMETRY" << nl
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<< "model: 1 "
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<< (geomFileName + ".mesh").c_str() << nl;
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}
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// Identify if lagrangian data exists at each time, and add clouds
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// to the 'allCloudNames' hash set
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forAll(Times, timeI)
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{
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runTime.setTime(Times[timeI], timeI);
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fileNameList cloudDirs = readDir
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(
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runTime.timePath()/regionPrefix/cloud::prefix,
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fileName::DIRECTORY
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);
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forAll(cloudDirs, cloudI)
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{
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IOobjectList cloudObjs
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(
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mesh,
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runTime.timeName(),
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cloud::prefix/cloudDirs[cloudI]
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);
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IOobject* positionsPtr = cloudObjs.lookup(word("positions"));
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if (positionsPtr)
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{
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allCloudNames.insert(cloudDirs[cloudI]);
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}
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}
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}
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HashTable<HashTable<word>> allCloudFields;
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forAllConstIter(wordHashSet, allCloudNames, cloudIter)
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{
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// Add the name of the cloud(s) to the case file header
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if (Pstream::master())
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{
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ensightCaseFile
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<< (
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"measured: 1 "
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+ prepend
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+ "****."
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+ cloudIter.key()
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).c_str()
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<< nl;
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}
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// Create a new hash table for each cloud
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allCloudFields.insert(cloudIter.key(), HashTable<word>());
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// Identify the new cloud in the hash table
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HashTable<HashTable<word>>::iterator newCloudIter =
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allCloudFields.find(cloudIter.key());
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// Loop over all times to build list of fields and field types
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// for each cloud
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forAll(Times, timeI)
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{
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runTime.setTime(Times[timeI], timeI);
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IOobjectList cloudObjs
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(
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mesh,
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runTime.timeName(),
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cloud::prefix/cloudIter.key()
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);
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forAllConstIter(IOobjectList, cloudObjs, fieldIter)
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{
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const IOobject obj = *fieldIter();
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if (obj.name() != "positions")
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{
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// Add field and field type
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newCloudIter().insert
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(
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obj.name(),
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obj.headerClassName()
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);
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}
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}
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}
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}
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label nTimeSteps = 0;
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forAll(Times, timeIndex)
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{
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nTimeSteps++;
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runTime.setTime(Times[timeIndex], timeIndex);
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word timeName = itoa(timeIndex);
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word timeFile = prepend + timeName;
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Info<< "Translating time = " << runTime.timeName() << nl;
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polyMesh::readUpdateState meshState = mesh.readUpdate();
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if (timeIndex != 0 && meshSubsetter.hasSubMesh())
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{
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Info<< "Converting cellZone " << cellZoneName
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<< " only (puts outside faces into patch "
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<< mesh.boundaryMesh()[0].name()
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<< ")" << endl;
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const cellZone& cz = mesh.cellZones()[cellZoneName];
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cellSet c0(mesh, "c0", labelHashSet(cz));
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meshSubsetter.setLargeCellSubset(c0, 0);
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}
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if (meshState != polyMesh::UNCHANGED)
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{
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eMesh.correct();
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}
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if (timeIndex == 0 || meshMoving)
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{
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eMesh.write
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(
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ensightDir,
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prepend,
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timeIndex,
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meshMoving,
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ensightCaseFile
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);
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}
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// Start of field data output
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// ~~~~~~~~~~~~~~~~~~~~~~~~~~
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if (timeIndex == 0 && Pstream::master())
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{
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ensightCaseFile<< nl << "VARIABLE" << nl;
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}
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// Cell field data output
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// ~~~~~~~~~~~~~~~~~~~~~~
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for (label i=0; i<nVolFieldTypes; i++)
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{
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wordList fieldNames = objects.names(volFieldTypes[i]);
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forAll(fieldNames, j)
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{
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const word& fieldName = fieldNames[j];
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// Check if the field has to be exported
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if (selectedFields)
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{
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if (!findStrings(fieldPatterns, fieldName))
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{
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continue;
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}
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}
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#include "checkData.H"
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if (!variableGood)
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{
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continue;
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}
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IOobject fieldObject
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(
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fieldName,
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mesh.time().timeName(),
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mesh,
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IOobject::MUST_READ,
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IOobject::NO_WRITE
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);
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if (volFieldTypes[i] == volScalarField::typeName)
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{
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volScalarField vf(fieldObject, mesh);
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ensightField<scalar>
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(
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volField(meshSubsetter, vf),
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eMesh,
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ensightDir,
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prepend,
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timeIndex,
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binary,
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nodeValues,
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ensightCaseFile
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);
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}
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else if (volFieldTypes[i] == volVectorField::typeName)
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{
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volVectorField vf(fieldObject, mesh);
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ensightField<vector>
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(
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volField(meshSubsetter, vf),
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eMesh,
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ensightDir,
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prepend,
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timeIndex,
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binary,
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nodeValues,
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ensightCaseFile
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);
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}
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else if (volFieldTypes[i] == volSphericalTensorField::typeName)
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{
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volSphericalTensorField vf(fieldObject, mesh);
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ensightField<sphericalTensor>
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(
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volField(meshSubsetter, vf),
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eMesh,
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ensightDir,
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prepend,
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timeIndex,
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binary,
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nodeValues,
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ensightCaseFile
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);
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}
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else if (volFieldTypes[i] == volSymmTensorField::typeName)
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{
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volSymmTensorField vf(fieldObject, mesh);
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ensightField<symmTensor>
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(
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volField(meshSubsetter, vf),
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eMesh,
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ensightDir,
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prepend,
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timeIndex,
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binary,
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nodeValues,
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ensightCaseFile
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);
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}
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else if (volFieldTypes[i] == volTensorField::typeName)
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{
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volTensorField vf(fieldObject, mesh);
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ensightField<tensor>
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(
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volField(meshSubsetter, vf),
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eMesh,
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ensightDir,
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prepend,
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timeIndex,
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binary,
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nodeValues,
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ensightCaseFile
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);
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}
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}
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}
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|
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// Cloud field data output
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// ~~~~~~~~~~~~~~~~~~~~~~~
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forAllConstIter(HashTable<HashTable<word>>, allCloudFields, cloudIter)
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{
|
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const word& cloudName = cloudIter.key();
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|
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fileNameList currentCloudDirs = readDir
|
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(
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runTime.timePath()/regionPrefix/cloud::prefix,
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fileName::DIRECTORY
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);
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|
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bool cloudExists = inFileNameList(currentCloudDirs, cloudName);
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|
ensightParticlePositions
|
|
(
|
|
mesh,
|
|
ensightDir,
|
|
timeFile,
|
|
cloudName,
|
|
cloudExists
|
|
);
|
|
|
|
forAllConstIter(HashTable<word>, cloudIter(), fieldIter)
|
|
{
|
|
const word& fieldName = fieldIter.key();
|
|
const word& fieldType = fieldIter();
|
|
|
|
IOobject fieldObject
|
|
(
|
|
fieldName,
|
|
mesh.time().timeName(),
|
|
cloud::prefix/cloudName,
|
|
mesh,
|
|
IOobject::MUST_READ
|
|
);
|
|
|
|
bool fieldExists = fieldObject.typeHeaderOk<IOField<scalar>>
|
|
(
|
|
false
|
|
);
|
|
if (fieldType == scalarIOField::typeName)
|
|
{
|
|
ensightCloudField<scalar>
|
|
(
|
|
fieldObject,
|
|
ensightDir,
|
|
prepend,
|
|
timeIndex,
|
|
cloudName,
|
|
ensightCaseFile,
|
|
fieldExists
|
|
);
|
|
}
|
|
else if (fieldType == vectorIOField::typeName)
|
|
{
|
|
ensightCloudField<vector>
|
|
(
|
|
fieldObject,
|
|
ensightDir,
|
|
prepend,
|
|
timeIndex,
|
|
cloudName,
|
|
ensightCaseFile,
|
|
fieldExists
|
|
);
|
|
}
|
|
else
|
|
{
|
|
Info<< "Unable to convert field type " << fieldType
|
|
<< " for field " << fieldName << endl;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
#include "ensightCaseTail.H"
|
|
|
|
if (Pstream::master())
|
|
{
|
|
delete ensightCaseFilePtr;
|
|
}
|
|
|
|
Info<< "End\n" << endl;
|
|
|
|
return 0;
|
|
}
|
|
|
|
|
|
// ************************************************************************* //
|