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.
469 lines
12 KiB
C
469 lines
12 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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Description
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Set values on a selected set of cells/patchfaces through a dictionary.
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\*---------------------------------------------------------------------------*/
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#include "argList.H"
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#include "Time.H"
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#include "fvMesh.H"
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#include "topoSetSource.H"
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#include "cellSet.H"
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#include "faceSet.H"
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#include "volFields.H"
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using namespace Foam;
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template<class Type>
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bool setCellFieldType
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(
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const word& fieldTypeDesc,
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const fvMesh& mesh,
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const labelList& selectedCells,
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Istream& fieldValueStream
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)
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{
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typedef GeometricField<Type, fvPatchField, volMesh> fieldType;
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if (fieldTypeDesc != fieldType::typeName + "Value")
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{
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return false;
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}
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word fieldName(fieldValueStream);
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// Check the current time directory
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IOobject fieldHeader
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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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);
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// Check the "constant" directory
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if (!fieldHeader.typeHeaderOk<fieldType>(true))
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{
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fieldHeader = IOobject
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(
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fieldName,
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mesh.time().constant(),
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mesh,
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IOobject::MUST_READ
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);
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}
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// Check field exists
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if (fieldHeader.typeHeaderOk<fieldType>(true))
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{
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Info<< " Setting internal values of "
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<< fieldHeader.headerClassName()
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<< " " << fieldName << endl;
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fieldType field(fieldHeader, mesh);
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const Type& value = pTraits<Type>(fieldValueStream);
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if (selectedCells.size() == field.size())
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{
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field.primitiveFieldRef() = value;
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}
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else
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{
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forAll(selectedCells, celli)
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{
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field[selectedCells[celli]] = value;
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}
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}
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typename GeometricField<Type, fvPatchField, volMesh>::
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Boundary& fieldBf = field.boundaryFieldRef();
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forAll(field.boundaryField(), patchi)
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{
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fieldBf[patchi] = fieldBf[patchi].patchInternalField();
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}
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if (!field.write())
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{
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FatalErrorInFunction
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<< "Failed writing field " << fieldName << endl;
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}
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}
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else
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{
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WarningInFunction
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<< "Field " << fieldName << " not found" << endl;
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// Consume value
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(void)pTraits<Type>(fieldValueStream);
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}
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return true;
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}
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class setCellField
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{
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public:
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setCellField()
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{}
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autoPtr<setCellField> clone() const
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{
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return autoPtr<setCellField>(new setCellField());
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}
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class iNew
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{
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const fvMesh& mesh_;
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const labelList& selectedCells_;
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public:
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iNew(const fvMesh& mesh, const labelList& selectedCells)
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:
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mesh_(mesh),
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selectedCells_(selectedCells)
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{}
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autoPtr<setCellField> operator()(Istream& fieldValues) const
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{
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word fieldType(fieldValues);
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if
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(
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!(
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setCellFieldType<scalar>
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(fieldType, mesh_, selectedCells_, fieldValues)
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|| setCellFieldType<vector>
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(fieldType, mesh_, selectedCells_, fieldValues)
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|| setCellFieldType<sphericalTensor>
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(fieldType, mesh_, selectedCells_, fieldValues)
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|| setCellFieldType<symmTensor>
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(fieldType, mesh_, selectedCells_, fieldValues)
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|| setCellFieldType<tensor>
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(fieldType, mesh_, selectedCells_, fieldValues)
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)
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)
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{
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WarningInFunction
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<< "field type " << fieldType << " not currently supported"
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<< endl;
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}
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return autoPtr<setCellField>(new setCellField());
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}
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};
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};
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template<class Type>
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bool setFaceFieldType
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(
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const word& fieldTypeDesc,
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const fvMesh& mesh,
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const labelList& selectedFaces,
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Istream& fieldValueStream
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)
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{
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typedef GeometricField<Type, fvPatchField, volMesh> fieldType;
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if (fieldTypeDesc != fieldType::typeName + "Value")
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{
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return false;
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}
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word fieldName(fieldValueStream);
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// Check the current time directory
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IOobject fieldHeader
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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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);
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// Check the "constant" directory
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if (!fieldHeader.typeHeaderOk<fieldType>(true))
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{
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fieldHeader = IOobject
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(
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fieldName,
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mesh.time().constant(),
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mesh,
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IOobject::MUST_READ
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);
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}
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// Check field exists
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if (fieldHeader.typeHeaderOk<fieldType>(true))
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{
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Info<< " Setting patchField values of "
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<< fieldHeader.headerClassName()
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<< " " << fieldName << endl;
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fieldType field(fieldHeader, mesh);
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const Type& value = pTraits<Type>(fieldValueStream);
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// Create flat list of selected faces and their value.
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Field<Type> allBoundaryValues(mesh.nFaces()-mesh.nInternalFaces());
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forAll(field.boundaryField(), patchi)
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{
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SubField<Type>
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(
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allBoundaryValues,
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field.boundaryField()[patchi].size(),
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field.boundaryField()[patchi].patch().start()
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- mesh.nInternalFaces()
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) = field.boundaryField()[patchi];
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}
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// Override
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bool hasWarned = false;
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labelList nChanged
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(
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returnReduce(field.boundaryField().size(), maxOp<label>()),
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0
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);
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forAll(selectedFaces, i)
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{
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label facei = selectedFaces[i];
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if (mesh.isInternalFace(facei))
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{
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if (!hasWarned)
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{
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hasWarned = true;
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WarningInFunction
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<< "Ignoring internal face " << facei
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<< ". Suppressing further warnings." << endl;
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}
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}
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else
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{
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label bFacei = facei-mesh.nInternalFaces();
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allBoundaryValues[bFacei] = value;
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nChanged[mesh.boundaryMesh().patchID()[bFacei]]++;
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}
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}
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Pstream::listCombineGather(nChanged, plusEqOp<label>());
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Pstream::listCombineScatter(nChanged);
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typename GeometricField<Type, fvPatchField, volMesh>::
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Boundary& fieldBf = field.boundaryFieldRef();
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// Reassign.
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forAll(field.boundaryField(), patchi)
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{
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if (nChanged[patchi] > 0)
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{
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Info<< " On patch "
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<< field.boundaryField()[patchi].patch().name()
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<< " set " << nChanged[patchi] << " values" << endl;
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fieldBf[patchi] == SubField<Type>
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(
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allBoundaryValues,
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fieldBf[patchi].size(),
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fieldBf[patchi].patch().start()
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- mesh.nInternalFaces()
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);
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}
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}
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if (!field.write())
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{
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FatalErrorInFunction
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<< "Failed writing field " << field.name() << exit(FatalError);
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}
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}
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else
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{
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WarningInFunction
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<< "Field " << fieldName << " not found" << endl;
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// Consume value
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(void)pTraits<Type>(fieldValueStream);
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}
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return true;
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}
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class setFaceField
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{
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public:
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setFaceField()
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{}
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autoPtr<setFaceField> clone() const
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{
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return autoPtr<setFaceField>(new setFaceField());
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}
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class iNew
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{
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const fvMesh& mesh_;
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const labelList& selectedFaces_;
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public:
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iNew(const fvMesh& mesh, const labelList& selectedFaces)
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:
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mesh_(mesh),
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selectedFaces_(selectedFaces)
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{}
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autoPtr<setFaceField> operator()(Istream& fieldValues) const
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{
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word fieldType(fieldValues);
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if
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(
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!(
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setFaceFieldType<scalar>
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(fieldType, mesh_, selectedFaces_, fieldValues)
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|| setFaceFieldType<vector>
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(fieldType, mesh_, selectedFaces_, fieldValues)
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|| setFaceFieldType<sphericalTensor>
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(fieldType, mesh_, selectedFaces_, fieldValues)
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|| setFaceFieldType<symmTensor>
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(fieldType, mesh_, selectedFaces_, fieldValues)
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|| setFaceFieldType<tensor>
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(fieldType, mesh_, selectedFaces_, fieldValues)
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)
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)
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{
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WarningInFunction
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<< "field type " << fieldType << " not currently supported"
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<< endl;
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}
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return autoPtr<setFaceField>(new setFaceField());
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}
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};
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};
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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int main(int argc, char *argv[])
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{
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#include "addDictOption.H"
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#include "addRegionOption.H"
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#include "setRootCase.H"
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#include "createTime.H"
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#include "createNamedMesh.H"
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const word dictName("setFieldsDict");
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#include "setSystemMeshDictionaryIO.H"
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Info<< "Reading " << dictName << "\n" << endl;
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IOdictionary setFieldsDict(dictIO);
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if (setFieldsDict.found("defaultFieldValues"))
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{
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Info<< "Setting field default values" << endl;
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PtrList<setCellField> defaultFieldValues
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(
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setFieldsDict.lookup("defaultFieldValues"),
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setCellField::iNew(mesh, labelList(mesh.nCells()))
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);
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Info<< endl;
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}
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Info<< "Setting field region values" << endl;
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PtrList<entry> regions(setFieldsDict.lookup("regions"));
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forAll(regions, regionI)
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{
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const entry& region = regions[regionI];
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autoPtr<topoSetSource> source =
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topoSetSource::New(region.keyword(), mesh, region.dict());
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if (source().setType() == topoSetSource::CELLSETSOURCE)
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{
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cellSet selectedCellSet
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(
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mesh,
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"cellSet",
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mesh.nCells()/10+1 // Reasonable size estimate.
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);
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source->applyToSet
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(
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topoSetSource::NEW,
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selectedCellSet
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);
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PtrList<setCellField> fieldValues
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(
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region.dict().lookup("fieldValues"),
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setCellField::iNew(mesh, selectedCellSet.toc())
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);
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}
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else if (source().setType() == topoSetSource::FACESETSOURCE)
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{
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faceSet selectedFaceSet
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(
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mesh,
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"faceSet",
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(mesh.nFaces()-mesh.nInternalFaces())/10+1
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);
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source->applyToSet
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(
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topoSetSource::NEW,
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selectedFaceSet
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);
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PtrList<setFaceField> fieldValues
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(
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region.dict().lookup("fieldValues"),
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setFaceField::iNew(mesh, selectedFaceSet.toc())
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);
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}
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}
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Info<< "\nEnd\n" << endl;
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return 0;
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}
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// ************************************************************************* //
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