Original commit message: ------------------------ Parallel IO: New collated file format When an OpenFOAM simulation runs in parallel, the data for decomposed fields and mesh(es) has historically been stored in multiple files within separate directories for each processor. Processor directories are named 'processorN', where N is the processor number. This commit introduces an alternative "collated" file format where the data for each decomposed field (and mesh) is collated into a single file, which is written and read on the master processor. The files are stored in a single directory named 'processors'. The new format produces significantly fewer files - one per field, instead of N per field. For large parallel cases, this avoids the restriction on the number of open files imposed by the operating system limits. The file writing can be threaded allowing the simulation to continue running while the data is being written to file. NFS (Network File System) is not needed when using the the collated format and additionally, there is an option to run without NFS with the original uncollated approach, known as "masterUncollated". The controls for the file handling are in the OptimisationSwitches of etc/controlDict: OptimisationSwitches { ... //- Parallel IO file handler // uncollated (default), collated or masterUncollated fileHandler uncollated; //- collated: thread buffer size for queued file writes. // If set to 0 or not sufficient for the file size threading is not used. // Default: 2e9 maxThreadFileBufferSize 2e9; //- masterUncollated: non-blocking buffer size. // If the file exceeds this buffer size scheduled transfer is used. // Default: 2e9 maxMasterFileBufferSize 2e9; } When using the collated file handling, memory is allocated for the data in the thread. maxThreadFileBufferSize sets the maximum size of memory in bytes that is allocated. If the data exceeds this size, the write does not use threading. When using the masterUncollated file handling, non-blocking MPI communication requires a sufficiently large memory buffer on the master node. maxMasterFileBufferSize sets the maximum size in bytes of the buffer. If the data exceeds this size, the system uses scheduled communication. The installation defaults for the fileHandler choice, maxThreadFileBufferSize and maxMasterFileBufferSize (set in etc/controlDict) can be over-ridden within the case controlDict file, like other parameters. Additionally the fileHandler can be set by: - the "-fileHandler" command line argument; - a FOAM_FILEHANDLER environment variable. A foamFormatConvert utility allows users to convert files between the collated and uncollated formats, e.g. mpirun -np 2 foamFormatConvert -parallel -fileHandler uncollated An example case demonstrating the file handling methods is provided in: $FOAM_TUTORIALS/IO/fileHandling The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
411 lines
11 KiB
C
411 lines
11 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) 2012-2017 OpenFOAM Foundation
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\\/ M anipulation | Copyright (C) 2015 OpenCFD Ltd.
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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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\*---------------------------------------------------------------------------*/
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#include "loadOrCreateMesh.H"
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#include "processorPolyPatch.H"
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#include "processorCyclicPolyPatch.H"
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#include "Time.H"
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//#include "IOPtrList.H"
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#include "polyBoundaryMeshEntries.H"
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// * * * * * * * * * * * * * * * Global Functions * * * * * * * * * * * * * //
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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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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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// Read mesh if available. Otherwise create empty mesh with same non-proc
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// patches as proc0 mesh. Requires all processors to have all patches
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// (and in same order).
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Foam::autoPtr<Foam::fvMesh> Foam::loadOrCreateMesh
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(
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const IOobject& io
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)
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{
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// Region name
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// ~~~~~~~~~~~
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fileName meshSubDir;
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if (io.name() == polyMesh::defaultRegion)
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{
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meshSubDir = polyMesh::meshSubDir;
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}
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else
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{
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meshSubDir = io.name()/polyMesh::meshSubDir;
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}
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// Patch types
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// ~~~~~~~~~~~
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// Read and scatter master patches (without reading master mesh!)
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PtrList<entry> patchEntries;
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if (Pstream::master())
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{
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//// Read PtrList of dictionary as 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> dictList
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//(
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// IOobject
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// (
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// "boundary",
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// io.time().findInstance
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// (
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// meshSubDir,
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// "boundary",
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// IOobject::MUST_READ
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// ),
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// meshSubDir,
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// io.db(),
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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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//);
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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&>(dictList.type()) = dictList.headerClassName();
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//
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//patchEntries.transfer(dictList);
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const fileName facesInstance = io.time().findInstance
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(
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meshSubDir,
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"faces",
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IOobject::MUST_READ
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);
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patchEntries = polyBoundaryMeshEntries
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(
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IOobject
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(
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"boundary",
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facesInstance,
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meshSubDir,
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io.db(),
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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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);
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// Send patches
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for
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(
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int slave=Pstream::firstSlave();
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slave<=Pstream::lastSlave();
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slave++
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)
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{
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OPstream toSlave(Pstream::commsTypes::scheduled, slave);
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toSlave << patchEntries;
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}
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}
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else
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{
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// Receive patches
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IPstream fromMaster
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(
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Pstream::commsTypes::scheduled,
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Pstream::masterNo()
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);
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fromMaster >> patchEntries;
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}
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// Dummy meshes
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// ~~~~~~~~~~~~
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// Check who has a mesh
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const bool haveMesh = fileHandler().isFile
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(
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fileHandler().filePath
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(
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io.time().path()/io.instance()/meshSubDir/"faces"
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)
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);
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if (!haveMesh)
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{
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bool oldParRun = Pstream::parRun();
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Pstream::parRun() = false;
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// Create dummy mesh. Only used on procs that don't have mesh.
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IOobject noReadIO(io);
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noReadIO.readOpt() = IOobject::NO_READ;
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fvMesh dummyMesh
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(
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noReadIO,
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xferCopy(pointField()),
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xferCopy(faceList()),
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xferCopy(labelList()),
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xferCopy(labelList()),
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false
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);
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// Add patches
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List<polyPatch*> patches(patchEntries.size());
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label nPatches = 0;
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forAll(patchEntries, patchi)
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{
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const entry& e = patchEntries[patchi];
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const word type(e.dict().lookup("type"));
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const word& name = e.keyword();
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if
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(
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type != processorPolyPatch::typeName
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&& type != processorCyclicPolyPatch::typeName
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)
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{
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dictionary patchDict(e.dict());
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patchDict.set("nFaces", 0);
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patchDict.set("startFace", 0);
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patches[patchi] = polyPatch::New
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(
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name,
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patchDict,
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nPatches++,
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dummyMesh.boundaryMesh()
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).ptr();
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}
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}
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patches.setSize(nPatches);
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dummyMesh.addFvPatches(patches, false); // no parallel comms
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// Add some dummy zones so upon reading it does not read them
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// from the undecomposed case. Should be done as extra argument to
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// regIOobject::readStream?
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List<pointZone*> pz
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(
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1,
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new pointZone
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(
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"dummyPointZone",
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labelList(0),
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0,
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dummyMesh.pointZones()
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)
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);
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List<faceZone*> fz
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(
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1,
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new faceZone
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(
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"dummyFaceZone",
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labelList(0),
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boolList(0),
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0,
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dummyMesh.faceZones()
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)
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);
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List<cellZone*> cz
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(
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1,
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new cellZone
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(
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"dummyCellZone",
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labelList(0),
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0,
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dummyMesh.cellZones()
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)
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);
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dummyMesh.addZones(pz, fz, cz);
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dummyMesh.pointZones().clear();
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dummyMesh.faceZones().clear();
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dummyMesh.cellZones().clear();
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//Pout<< "Writing dummy mesh to " << dummyMesh.polyMesh::objectPath()
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// << endl;
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dummyMesh.write();
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Pstream::parRun() = oldParRun;
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}
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// Read mesh
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// ~~~~~~~~~
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// Now all processors have a (possibly zero size) mesh so read in
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// parallel
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//Pout<< "Reading mesh from " << io.objectPath() << endl;
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autoPtr<fvMesh> meshPtr(new fvMesh(io));
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fvMesh& mesh = meshPtr();
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// Sync patches
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// ~~~~~~~~~~~~
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if (!Pstream::master() && haveMesh)
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{
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// Check master names against mine
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const polyBoundaryMesh& patches = mesh.boundaryMesh();
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forAll(patchEntries, patchi)
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{
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const entry& e = patchEntries[patchi];
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const word type(e.dict().lookup("type"));
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const word& name = e.keyword();
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if (type == processorPolyPatch::typeName)
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{
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break;
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}
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if (patchi >= patches.size())
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{
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FatalErrorInFunction
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<< "Non-processor patches not synchronised."
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<< endl
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<< "Processor " << Pstream::myProcNo()
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<< " has only " << patches.size()
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<< " patches, master has "
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<< patchi
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<< exit(FatalError);
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}
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if
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(
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type != patches[patchi].type()
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|| name != patches[patchi].name()
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)
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{
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FatalErrorInFunction
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<< "Non-processor patches not synchronised."
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<< endl
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<< "Master patch " << patchi
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<< " name:" << type
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<< " type:" << type << endl
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<< "Processor " << Pstream::myProcNo()
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<< " patch " << patchi
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<< " has name:" << patches[patchi].name()
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<< " type:" << patches[patchi].type()
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<< exit(FatalError);
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}
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}
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}
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// Determine zones
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// ~~~~~~~~~~~~~~~
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wordList pointZoneNames(mesh.pointZones().names());
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Pstream::scatter(pointZoneNames);
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wordList faceZoneNames(mesh.faceZones().names());
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Pstream::scatter(faceZoneNames);
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wordList cellZoneNames(mesh.cellZones().names());
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Pstream::scatter(cellZoneNames);
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if (!haveMesh)
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{
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// Add the zones. Make sure to remove the old dummy ones first
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mesh.pointZones().clear();
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mesh.faceZones().clear();
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mesh.cellZones().clear();
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List<pointZone*> pz(pointZoneNames.size());
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forAll(pointZoneNames, i)
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{
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pz[i] = new pointZone
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(
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pointZoneNames[i],
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labelList(0),
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i,
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mesh.pointZones()
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);
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}
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List<faceZone*> fz(faceZoneNames.size());
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forAll(faceZoneNames, i)
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{
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fz[i] = new faceZone
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(
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faceZoneNames[i],
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labelList(0),
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boolList(0),
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i,
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mesh.faceZones()
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);
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}
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List<cellZone*> cz(cellZoneNames.size());
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forAll(cellZoneNames, i)
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{
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cz[i] = new cellZone
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(
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cellZoneNames[i],
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labelList(0),
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i,
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mesh.cellZones()
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);
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}
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mesh.addZones(pz, fz, cz);
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}
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// if (!haveMesh)
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// {
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// // We created a dummy mesh file above. Delete it.
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// const fileName meshFiles = io.time().path()/io.instance()/meshSubDir;
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// //Pout<< "Removing dummy mesh " << meshFiles << endl;
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// mesh.removeFiles();
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// rmDir(meshFiles);
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// }
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//
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// Force recreation of globalMeshData.
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// mesh.clearOut();
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mesh.globalData();
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// Do some checks.
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// Check if the boundary definition is unique
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mesh.boundaryMesh().checkDefinition(true);
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// Check if the boundary processor patches are correct
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mesh.boundaryMesh().checkParallelSync(true);
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// Check names of zones are equal
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mesh.cellZones().checkDefinition(true);
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mesh.cellZones().checkParallelSync(true);
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mesh.faceZones().checkDefinition(true);
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mesh.faceZones().checkParallelSync(true);
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mesh.pointZones().checkDefinition(true);
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mesh.pointZones().checkParallelSync(true);
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return meshPtr;
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}
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// ************************************************************************* //
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