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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.
546 lines
16 KiB
C
546 lines
16 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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foamFormatConvert
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Description
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Converts all IOobjects associated with a case into the format specified
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in the controlDict.
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Mainly used to convert binary mesh/field files to ASCII.
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Problem: any zero-size List written binary gets written as '0'. When
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reading the file as a dictionary this is interpreted as a label. This
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is (usually) not a problem when doing patch fields since these get the
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'uniform', 'nonuniform' prefix. However zone contents are labelLists
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not labelFields and these go wrong. For now hacked a solution where
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we detect the keywords in zones and redo the dictionary entries
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to be labelLists.
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\*---------------------------------------------------------------------------*/
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#include "argList.H"
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#include "timeSelector.H"
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#include "Time.H"
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#include "volFields.H"
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#include "surfaceFields.H"
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#include "pointFields.H"
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#include "cellIOList.H"
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#include "IOobjectList.H"
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#include "IOPtrList.H"
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#include "cloud.H"
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#include "labelIOField.H"
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#include "scalarIOField.H"
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#include "sphericalTensorIOField.H"
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#include "symmTensorIOField.H"
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#include "tensorIOField.H"
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#include "labelFieldIOField.H"
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#include "vectorFieldIOField.H"
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#include "Cloud.H"
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#include "passiveParticle.H"
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#include "fieldDictionary.H"
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#include "writeMeshObject.H"
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using namespace Foam;
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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namespace Foam
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{
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defineTemplateTypeNameAndDebug(IOPtrList<entry>, 0);
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}
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// Hack to do zones which have Lists in them. See above.
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bool writeZones(const word& name, const fileName& meshDir, Time& runTime)
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{
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IOobject io
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(
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name,
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runTime.timeName(),
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meshDir,
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runTime,
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IOobject::MUST_READ,
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IOobject::NO_WRITE,
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false
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);
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bool writeOk = false;
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if (io.typeHeaderOk<cellZoneMesh>(false))
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{
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Info<< " Reading " << io.headerClassName()
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<< " : " << name << endl;
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// Switch off type checking (for reading e.g. faceZones as
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// generic list of dictionaries).
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const word oldTypeName = IOPtrList<entry>::typeName;
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const_cast<word&>(IOPtrList<entry>::typeName) = word::null;
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IOPtrList<entry> meshObject(io);
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forAll(meshObject, i)
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{
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if (meshObject[i].isDict())
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{
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dictionary& d = meshObject[i].dict();
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if (d.found("faceLabels"))
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{
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d.set("faceLabels", labelList(d.lookup("faceLabels")));
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}
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if (d.found("flipMap"))
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{
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d.set("flipMap", boolList(d.lookup("flipMap")));
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}
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if (d.found("cellLabels"))
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{
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d.set("cellLabels", labelList(d.lookup("cellLabels")));
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}
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if (d.found("pointLabels"))
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{
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d.set("pointLabels", labelList(d.lookup("pointLabels")));
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}
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}
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}
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const_cast<word&>(IOPtrList<entry>::typeName) = oldTypeName;
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// Fake type back to what was in field
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const_cast<word&>(meshObject.type()) = io.headerClassName();
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Info<< " Writing " << name << endl;
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// Force writing as ascii
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writeOk = meshObject.regIOobject::writeObject
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(
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IOstream::ASCII,
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IOstream::currentVersion,
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runTime.writeCompression(),
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true
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);
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}
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return writeOk;
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}
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// Reduction for non-empty strings
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class uniqueEqOp
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{
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public:
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void operator()(stringList& x, const stringList& y) const
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{
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stringList newX(x.size()+y.size());
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label n = 0;
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forAll(x, i)
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{
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if (!x[i].empty())
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{
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newX[n++] = x[i];
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}
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}
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forAll(y, i)
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{
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if (!y[i].empty() && findIndex(x, y[i]) == -1)
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{
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newX[n++] = y[i];
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}
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}
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newX.setSize(n);
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x.transfer(newX);
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}
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};
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template<class T>
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bool writeOptionalMeshObject
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(
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const word& name,
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const fileName& meshDir,
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Time& runTime,
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const bool valid
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)
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{
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IOobject io
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(
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name,
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runTime.timeName(),
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meshDir,
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runTime,
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IOobject::MUST_READ,
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IOobject::NO_WRITE,
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false
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);
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bool writeOk = false;
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bool haveFile = io.typeHeaderOk<IOField<label>>(false);
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// Make sure all know if there is a valid class name
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stringList classNames(1, io.headerClassName());
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combineReduce(classNames, uniqueEqOp());
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// Check for correct type
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if (classNames[0] == T::typeName)
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{
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Info<< " Reading " << classNames[0]
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<< " : " << name << endl;
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T meshObject(io, valid && haveFile);
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Info<< " Writing " << name << endl;
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writeOk = meshObject.regIOobject::write(valid && haveFile);
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}
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return writeOk;
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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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argList::addBoolOption
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(
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"noConstant",
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"exclude the 'constant/' dir in the times list"
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);
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#include "addRegionOption.H"
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#include "setRootCase.H"
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// enable noConstant by switching
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if (!args.optionFound("noConstant"))
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{
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args.setOption("constant", "");
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}
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else
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{
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args.unsetOption("constant");
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Info<< "Excluding the constant directory." << nl << endl;
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}
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#include "createTime.H"
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// Optional mesh (used to read Clouds)
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autoPtr<polyMesh> meshPtr;
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// Make sure we do not use the master-only reading since we read
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// fields (different per processor) as dictionaries.
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regIOobject::fileModificationChecking = regIOobject::timeStamp;
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fileName meshDir = polyMesh::meshSubDir;
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fileName regionPrefix = "";
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word regionName = polyMesh::defaultRegion;
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if (args.optionReadIfPresent("region", regionName))
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{
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Info<< "Using region " << regionName << nl << endl;
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regionPrefix = regionName;
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meshDir = regionName/polyMesh::meshSubDir;
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}
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Foam::instantList timeDirs = Foam::timeSelector::select0(runTime, args);
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forAll(timeDirs, timeI)
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{
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runTime.setTime(timeDirs[timeI], timeI);
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Info<< "Time = " << runTime.timeName() << endl;
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// Convert all the standard mesh files
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writeMeshObject<cellCompactIOList, cellIOList>
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(
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"cells",
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meshDir,
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runTime
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);
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writeMeshObject<labelIOList>("owner", meshDir, runTime);
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writeMeshObject<labelIOList>("neighbour", meshDir, runTime);
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writeMeshObject<faceCompactIOList, faceIOList>
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(
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"faces",
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meshDir,
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runTime
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);
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writeMeshObject<pointIOField>("points", meshDir, runTime);
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// Write boundary in ascii. This is only needed for fileHandler to
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// kick in. Should not give problems since always writing ascii.
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writeZones("boundary", meshDir, runTime);
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writeMeshObject<labelIOList>("pointProcAddressing", meshDir, runTime);
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writeMeshObject<labelIOList>("faceProcAddressing", meshDir, runTime);
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writeMeshObject<labelIOList>("cellProcAddressing", meshDir, runTime);
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writeMeshObject<labelIOList>
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(
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"boundaryProcAddressing",
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meshDir,
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runTime
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);
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// foamyHexMesh vertices
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writeMeshObject<pointIOField>
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(
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"internalDelaunayVertices",
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regionPrefix,
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runTime
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);
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if (runTime.writeFormat() == IOstream::ASCII)
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{
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// Only do zones when converting from binary to ascii
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// The other way gives problems since working on dictionary level.
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writeZones("cellZones", meshDir, runTime);
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writeZones("faceZones", meshDir, runTime);
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writeZones("pointZones", meshDir, runTime);
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}
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// Get list of objects from the database
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IOobjectList objects(runTime, runTime.timeName(), regionPrefix);
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forAllConstIter(IOobjectList, objects, iter)
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{
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const word& headerClassName = iter()->headerClassName();
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if
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(
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headerClassName == volScalarField::typeName
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|| headerClassName == volVectorField::typeName
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|| headerClassName == volSphericalTensorField::typeName
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|| headerClassName == volSymmTensorField::typeName
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|| headerClassName == volTensorField::typeName
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|| headerClassName == surfaceScalarField::typeName
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|| headerClassName == surfaceVectorField::typeName
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|| headerClassName == surfaceSphericalTensorField::typeName
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|| headerClassName == surfaceSymmTensorField::typeName
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|| headerClassName == surfaceTensorField::typeName
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|| headerClassName == pointScalarField::typeName
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|| headerClassName == pointVectorField::typeName
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|| headerClassName == pointSphericalTensorField::typeName
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|| headerClassName == pointSymmTensorField::typeName
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|| headerClassName == pointTensorField::typeName
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|| headerClassName == volScalarField::Internal::typeName
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|| headerClassName == volVectorField::Internal::typeName
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|| headerClassName == volSphericalTensorField::Internal::typeName
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|| headerClassName == volSymmTensorField::Internal::typeName
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|| headerClassName == volTensorField::Internal::typeName
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)
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{
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Info<< " Reading " << headerClassName
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<< " : " << iter()->name() << endl;
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fieldDictionary fDict(*iter(), headerClassName);
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Info<< " Writing " << iter()->name() << endl;
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fDict.regIOobject::write();
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}
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}
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// Check for lagrangian
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stringList lagrangianDirs
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(
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1,
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fileHandler().filePath
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(
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runTime.timePath()
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/ regionPrefix
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/ cloud::prefix
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)
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);
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combineReduce(lagrangianDirs, uniqueEqOp());
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if (!lagrangianDirs.empty())
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{
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if (meshPtr.valid())
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{
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meshPtr().readUpdate();
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}
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else
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{
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Info<< " Create polyMesh for time = "
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<< runTime.timeName() << endl;
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meshPtr.reset
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(
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new polyMesh
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(
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IOobject
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(
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polyMesh::defaultRegion,
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runTime.timeName(),
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runTime,
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Foam::IOobject::MUST_READ
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)
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)
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);
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}
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stringList cloudDirs
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(
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fileHandler().readDir
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(
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lagrangianDirs[0],
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fileName::DIRECTORY
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)
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);
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combineReduce(cloudDirs, uniqueEqOp());
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forAll(cloudDirs, i)
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{
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fileName dir(cloud::prefix/cloudDirs[i]);
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Cloud<passiveParticle> parcels(meshPtr(), cloudDirs[i], false);
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parcels.writeObject
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(
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runTime.writeFormat(),
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IOstream::currentVersion,
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runTime.writeCompression(),
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parcels.size()
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);
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// Do local scan for valid cloud objects
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IOobjectList sprayObjs(runTime, runTime.timeName(), dir);
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// Combine with all other cloud objects
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stringList sprayFields(sprayObjs.sortedToc());
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combineReduce(sprayFields, uniqueEqOp());
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forAll(sprayFields, fieldi)
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{
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const word& name = sprayFields[fieldi];
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// Note: try the various field types. Make sure to
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// exit once sucessful conversion to avoid re-read
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// converted file.
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if
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(
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name == "positions"
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|| name == "origProcId"
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|| name == "origId"
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)
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{
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continue;
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}
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bool writeOk = writeOptionalMeshObject<labelIOField>
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(
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name,
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dir,
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runTime,
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parcels.size() > 0
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);
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if (writeOk) continue;
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writeOk = writeOptionalMeshObject<scalarIOField>
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(
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name,
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dir,
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runTime,
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parcels.size() > 0
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);
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if (writeOk) continue;
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writeOk = writeOptionalMeshObject<vectorIOField>
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(
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name,
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dir,
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runTime,
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parcels.size() > 0
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);
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if (writeOk) continue;
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writeOk = writeOptionalMeshObject<sphericalTensorIOField>
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(
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name,
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dir,
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runTime,
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parcels.size() > 0
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);
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if (writeOk) continue;
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writeOk = writeOptionalMeshObject<symmTensorIOField>
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(
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name,
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dir,
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runTime,
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parcels.size() > 0
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);
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if (writeOk) continue;
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writeOk = writeOptionalMeshObject<tensorIOField>
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(
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name,
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dir,
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runTime,
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parcels.size() > 0
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);
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if (writeOk) continue;
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writeOk = writeOptionalMeshObject<labelFieldIOField>
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(
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name,
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dir,
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runTime,
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parcels.size() > 0
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);
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if (writeOk) continue;
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writeOk = writeOptionalMeshObject<vectorFieldIOField>
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(
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name,
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dir,
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runTime,
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parcels.size() > 0
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);
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if (!writeOk)
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{
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Info<< " Failed converting " << name << endl;
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}
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}
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}
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}
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Info<< endl;
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}
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Info<< "End\n" << endl;
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return 0;
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}
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// ************************************************************************* //
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