mirror of
https://github.com/OpenFOAM/OpenFOAM-6.git
synced 2025-12-08 06:57:46 +00:00
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.
649 lines
17 KiB
C
649 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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foamUpgradeCyclics
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Description
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Tool to upgrade mesh and fields for split cyclics.
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Usage
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\b foamUpgradeCyclics [OPTION]
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Options:
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- \par -test
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Suppress writing the updated files with split cyclics
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- \par -enableFunctionEntries
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By default all dictionary preprocessing of fields is disabled
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\*---------------------------------------------------------------------------*/
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#include "argList.H"
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#include "Time.H"
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#include "timeSelector.H"
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#include "IOdictionary.H"
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#include "polyMesh.H"
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#include "entry.H"
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#include "IOPtrList.H"
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#include "cyclicPolyPatch.H"
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#include "dictionaryEntry.H"
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#include "IOobjectList.H"
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#include "volFields.H"
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#include "pointFields.H"
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#include "surfaceFields.H"
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#include "string.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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// Read boundary file without reading mesh
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void rewriteBoundary
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(
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const bool isTestRun,
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const IOobject& io,
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const fileName& regionPrefix,
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HashTable<word>& thisNames,
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HashTable<word>& nbrNames
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)
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{
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Info<< "Reading boundary from " << typeFilePath<IOPtrList<entry>>(io)
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<< endl;
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// Read PtrList of dictionary.
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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> patches(io);
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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&>(patches.type()) = patches.headerClassName();
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// Replace any 'cyclic'
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label nOldCyclics = 0;
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forAll(patches, patchi)
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{
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const dictionary& patchDict = patches[patchi].dict();
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if (word(patchDict["type"]) == cyclicPolyPatch::typeName)
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{
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if (!patchDict.found("neighbourPatch"))
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{
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Info<< "Patch " << patches[patchi].keyword()
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<< " does not have 'neighbourPatch' entry; assuming it"
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<< " is of the old type." << endl;
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nOldCyclics++;
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}
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}
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}
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Info<< "Detected " << nOldCyclics << " old cyclics." << nl << endl;
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// Save old patches.
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PtrList<entry> oldPatches(patches);
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// Extend
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label nOldPatches = patches.size();
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patches.setSize(nOldPatches+nOldCyclics);
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// Create reordering map
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labelList oldToNew(patches.size());
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// Add new entries
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label addedPatchi = nOldPatches;
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label newPatchi = 0;
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forAll(oldPatches, patchi)
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{
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const dictionary& patchDict = oldPatches[patchi].dict();
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if
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(
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word(patchDict["type"]) == cyclicPolyPatch::typeName
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)
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{
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const word& name = oldPatches[patchi].keyword();
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if (patchDict.found("neighbourPatch"))
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{
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patches.set(patchi, oldPatches.set(patchi, nullptr));
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oldToNew[patchi] = newPatchi++;
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// Check if patches come from automatic conversion
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word oldName;
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string::size_type i = name.rfind("_half0");
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if (i != string::npos)
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{
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oldName = name.substr(0, i);
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thisNames.insert(oldName, name);
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Info<< "Detected converted cyclic patch " << name
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<< " ; assuming it originates from " << oldName
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<< endl;
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}
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else
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{
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i = name.rfind("_half1");
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if (i != string::npos)
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{
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oldName = name.substr(0, i);
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nbrNames.insert(oldName, name);
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Info<< "Detected converted cyclic patch " << name
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<< " ; assuming it originates from " << oldName
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<< endl;
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}
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}
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}
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else
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{
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label nFaces = readLabel(patchDict["nFaces"]);
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label startFace = readLabel(patchDict["startFace"]);
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Info<< "Detected old style " << word(patchDict["type"])
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<< " patch " << name << " with" << nl
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<< " nFaces : " << nFaces << nl
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<< " startFace : " << startFace << endl;
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word thisName = name + "_half0";
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word nbrName = name + "_half1";
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thisNames.insert(name, thisName);
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nbrNames.insert(name, nbrName);
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// Save current dictionary
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const dictionary patchDict(patches[patchi].dict());
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// Change entry on this side
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patches.set(patchi, oldPatches.set(patchi, nullptr));
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oldToNew[patchi] = newPatchi++;
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dictionary& thisPatchDict = patches[patchi].dict();
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thisPatchDict.add("neighbourPatch", nbrName);
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thisPatchDict.set("nFaces", nFaces/2);
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patches[patchi].keyword() = thisName;
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// Add entry on other side
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patches.set
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(
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addedPatchi,
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new dictionaryEntry
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(
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nbrName,
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dictionary::null,
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patchDict
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)
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);
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oldToNew[addedPatchi] = newPatchi++;
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dictionary& nbrPatchDict = patches[addedPatchi].dict();
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nbrPatchDict.set("neighbourPatch", thisName);
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nbrPatchDict.set("nFaces", nFaces/2);
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nbrPatchDict.set("startFace", startFace+nFaces/2);
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patches[addedPatchi].keyword() = nbrName;
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Info<< "Replaced with patches" << nl
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<< patches[patchi].keyword() << " with" << nl
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<< " nFaces : "
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<< readLabel(thisPatchDict.lookup("nFaces"))
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<< nl
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<< " startFace : "
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<< readLabel(thisPatchDict.lookup("startFace")) << nl
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<< patches[addedPatchi].keyword() << " with" << nl
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<< " nFaces : "
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<< readLabel(nbrPatchDict.lookup("nFaces"))
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<< nl
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<< " startFace : "
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<< readLabel(nbrPatchDict.lookup("startFace"))
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<< nl << endl;
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addedPatchi++;
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}
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}
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else
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{
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patches.set(patchi, oldPatches.set(patchi, nullptr));
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oldToNew[patchi] = newPatchi++;
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}
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}
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patches.reorder(oldToNew);
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if (returnReduce(nOldCyclics, sumOp<label>()) > 0)
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{
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if (isTestRun)
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{
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//Info<< "-test option: no changes made" << nl << endl;
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}
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else
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{
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if (mvBak(patches.objectPath(), "old"))
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{
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Info<< "Backup to "
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<< (patches.objectPath() + ".old") << nl;
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}
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Info<< "Write to "
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<< patches.objectPath() << nl << endl;
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patches.write();
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}
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}
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else
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{
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Info<< "No changes made to boundary file." << nl << endl;
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}
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}
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void rewriteField
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(
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const bool isTestRun,
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const Time& runTime,
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const word& fieldName,
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const HashTable<word>& thisNames,
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const HashTable<word>& nbrNames
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)
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{
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// Read dictionary. (disable class type checking so we can load
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// field)
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Info<< "Loading field " << fieldName << endl;
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const word oldTypeName = IOdictionary::typeName;
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const_cast<word&>(IOdictionary::typeName) = word::null;
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IOdictionary fieldDict
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(
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IOobject
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(
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fieldName,
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runTime.timeName(),
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runTime,
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IOobject::MUST_READ_IF_MODIFIED,
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IOobject::NO_WRITE,
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false
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)
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);
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const_cast<word&>(IOdictionary::typeName) = oldTypeName;
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// Fake type back to what was in field
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const_cast<word&>(fieldDict.type()) = fieldDict.headerClassName();
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dictionary& boundaryField = fieldDict.subDict("boundaryField");
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label nChanged = 0;
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forAllConstIter(HashTable<word>, thisNames, iter)
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{
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const word& patchName = iter.key();
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const word& newName = iter();
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Info<< "Looking for entry for patch " << patchName << endl;
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// Find old patch name either direct or through wildcards
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// Find new patch name direct only
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if
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(
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boundaryField.found(patchName)
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&& !boundaryField.found(newName, false, false)
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)
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{
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Info<< " Changing entry " << patchName << " to " << newName
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<< endl;
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dictionary& patchDict = boundaryField.subDict(patchName);
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if (patchDict.found("value"))
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{
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// Remove any value field since wrong size.
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patchDict.remove("value");
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}
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boundaryField.changeKeyword(patchName, newName);
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boundaryField.add
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(
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nbrNames[patchName],
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patchDict
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);
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Info<< " Adding entry " << nbrNames[patchName] << endl;
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nChanged++;
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}
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}
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//Info<< "New boundaryField:" << boundaryField << endl;
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if (returnReduce(nChanged, sumOp<label>()) > 0)
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{
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if (isTestRun)
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{
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//Info<< "-test option: no changes made" << endl;
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}
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else
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{
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if (mvBak(fieldDict.objectPath(), "old"))
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{
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Info<< "Backup to "
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<< (fieldDict.objectPath() + ".old") << nl;
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}
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Info<< "Write to "
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<< fieldDict.objectPath() << endl;
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fieldDict.regIOobject::write();
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}
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}
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else
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{
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Info<< "No changes made to field " << fieldName << endl;
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}
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Info<< endl;
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}
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void rewriteFields
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(
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const bool isTestRun,
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const Time& runTime,
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const wordList& fieldNames,
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const HashTable<word>& thisNames,
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const HashTable<word>& nbrNames
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)
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{
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forAll(fieldNames, i)
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{
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rewriteField
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(
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isTestRun,
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runTime,
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fieldNames[i],
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thisNames,
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nbrNames
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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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timeSelector::addOptions();
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argList::addBoolOption("test", "test only; do not change any files");
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argList::addBoolOption
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(
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"enableFunctionEntries",
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"enable expansion of dictionary directives - #include, #codeStream etc"
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);
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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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// 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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instantList timeDirs = timeSelector::select0(runTime, args);
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const bool isTestRun = args.optionFound("test");
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if (isTestRun)
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{
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Info<< "-test option: no changes made" << nl << endl;
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}
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const bool enableEntries = args.optionFound("enableFunctionEntries");
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Foam::word regionName = polyMesh::defaultRegion;
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args.optionReadIfPresent("region", regionName);
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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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// Per cyclic patch the new name for this side and the other side
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HashTable<word> thisNames;
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HashTable<word> nbrNames;
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// Rewrite constant boundary file. Return any patches that have been split.
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IOobject io
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(
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"boundary",
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runTime.constant(),
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polyMesh::meshSubDir,
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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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if (io.typeHeaderOk<IOPtrList<entry>>(false))
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{
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rewriteBoundary
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(
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isTestRun,
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io,
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regionPrefix,
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thisNames,
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nbrNames
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);
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}
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// Convert any fields
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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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// See if mesh in time directory
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IOobject io
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(
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"boundary",
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runTime.timeName(),
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polyMesh::meshSubDir,
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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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if (io.typeHeaderOk<IOPtrList<entry>>(false))
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{
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rewriteBoundary
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(
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isTestRun,
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io,
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regionPrefix,
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thisNames,
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nbrNames
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);
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}
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IOobjectList objects(runTime, runTime.timeName());
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int oldFlag = entry::disableFunctionEntries;
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if (!enableEntries)
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{
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// By default disable dictionary expansion for fields
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entry::disableFunctionEntries = 1;
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}
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// volFields
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// ~~~~~~~~~
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rewriteFields
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(
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isTestRun,
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runTime,
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objects.names(volScalarField::typeName),
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thisNames,
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nbrNames
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);
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rewriteFields
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(
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isTestRun,
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runTime,
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objects.names(volVectorField::typeName),
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thisNames,
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nbrNames
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);
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rewriteFields
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(
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isTestRun,
|
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runTime,
|
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objects.names(volSphericalTensorField::typeName),
|
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thisNames,
|
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nbrNames
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);
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rewriteFields
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(
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isTestRun,
|
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runTime,
|
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objects.names(volSymmTensorField::typeName),
|
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thisNames,
|
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nbrNames
|
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);
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rewriteFields
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|
(
|
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isTestRun,
|
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runTime,
|
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objects.names(volTensorField::typeName),
|
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thisNames,
|
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nbrNames
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);
|
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|
|
|
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// pointFields
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// ~~~~~~~~~~~
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|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(pointScalarField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(pointVectorField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(pointSphericalTensorField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(pointSymmTensorField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(pointTensorField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
|
|
|
|
// surfaceFields
|
|
// ~~~~~~~~~~~
|
|
|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(surfaceScalarField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(surfaceVectorField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(surfaceSphericalTensorField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(surfaceSymmTensorField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
rewriteFields
|
|
(
|
|
isTestRun,
|
|
runTime,
|
|
objects.names(surfaceTensorField::typeName),
|
|
thisNames,
|
|
nbrNames
|
|
);
|
|
|
|
entry::disableFunctionEntries = oldFlag;
|
|
}
|
|
|
|
return 0;
|
|
}
|
|
|
|
|
|
// ************************************************************************* //
|