mirror of
https://develop.openfoam.com/Development/openfoam.git
synced 2025-11-28 03:28:01 +00:00
INT: Integration of Mattijs' collocated parallel IO additions
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.
This commit is contained in:
Andrew Heather
@ -443,255 +443,274 @@ int main(int argc, char *argv[])
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FatalErrorInFunction
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<< "No times selected." << exit(FatalError);
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}
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runTime.setTime(times[0], 0);
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word instance = args.optionLookupOrDefault("instance", runTime.timeName());
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#include "createNamedMesh.H"
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const bool literalRE = args.optionFound("literalRE");
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if (literalRE)
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forAll(times, timei)
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{
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Info<< "Not interpreting any regular expressions (RE)"
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<< " in the changeDictionaryDict." << endl
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<< "Instead they are handled as any other entry, i.e. added if"
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<< " not present." << endl;
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}
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const bool enableEntries = args.optionFound("enableFunctionEntries");
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if (enableEntries)
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{
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Info<< "Allowing dictionary preprocessing ('#include', '#codeStream')."
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<< endl;
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}
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const 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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const bool disablePatchGroups = args.optionFound("disablePatchGroups");
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if (disablePatchGroups)
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{
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Info<< "Not interpreting any keys in the changeDictionary"
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<< " as patchGroups"
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<< endl;
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}
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fileName regionPrefix = "";
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if (regionName != fvMesh::defaultRegion)
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{
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regionPrefix = regionName;
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}
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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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// Get the replacement rules from a dictionary
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const word dictName("changeDictionaryDict");
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#include "setSystemMeshDictionaryIO.H"
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IOdictionary dict(dictIO);
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const dictionary* replaceDictsPtr = &dict;
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if (args.optionFound("subDict"))
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{
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word subDictName(args.optionLookup("subDict")());
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replaceDictsPtr = &dict.subDict(subDictName);
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}
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const dictionary& replaceDicts = *replaceDictsPtr;
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Info<< "Read dictionary " << dict.name()
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<< " with replacements for dictionaries "
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<< replaceDicts.toc() << endl;
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// Always read boundary to get patch groups
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// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Info<< "Reading polyMesh/boundary file to extract patch names"
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<< endl;
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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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runTime.findInstance
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(
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regionPrefix/polyMesh::meshSubDir,
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"boundary",
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IOobject::READ_IF_PRESENT
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),
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polyMesh::meshSubDir,
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mesh,
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IOobject::READ_IF_PRESENT,
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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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// Temporary convert to dictionary
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dictionary fieldDict;
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forAll(dictList, i)
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{
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fieldDict.add(dictList[i].keyword(), dictList[i].dict());
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}
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if (dictList.size())
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{
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Info<< "Loaded dictionary " << dictList.name()
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<< " with entries " << fieldDict.toc() << endl;
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}
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// Extract any patchGroups information (= shortcut for set of
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// patches)
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HashTable<wordList, word> patchGroups;
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if (!disablePatchGroups)
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{
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patchGroups = extractPatchGroups(fieldDict);
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if (patchGroups.size())
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word instance;
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if (args.optionFound("instance"))
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{
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Info<< "Extracted patch groups:" << endl;
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wordList groups(patchGroups.sortedToc());
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forAll(groups, i)
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if (times.size() > 1)
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{
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Info<< " group " << groups[i] << " with patches "
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<< patchGroups[groups[i]] << endl;
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}
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}
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}
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// Every replacement is a dictionary name and a keyword in this
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forAllConstIter(dictionary, replaceDicts, fieldIter)
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{
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const word& fieldName = fieldIter().keyword();
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Info<< "Replacing entries in dictionary " << fieldName << endl;
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// Handle 'boundary' specially:
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// - is PtrList of dictionaries
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// - is in polyMesh/
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if (fieldName == "boundary")
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{
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Info<< "Special handling of " << fieldName
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<< " as polyMesh/boundary file." << endl;
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// Get the replacement dictionary for the field
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const dictionary& replaceDict = fieldIter().dict();
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Info<< "Merging entries from " << replaceDict.toc() << endl;
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// Merge the replacements in. Do not add non-existing entries.
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merge(false, fieldDict, replaceDict, literalRE, patchGroups);
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Info<< "fieldDict:" << fieldDict << endl;
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// Convert back into dictList
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wordList doneKeys(dictList.size());
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label nEntries = fieldDict.size();
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forAll(dictList, i)
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{
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doneKeys[i] = dictList[i].keyword();
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dictList.set
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(
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i,
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fieldDict.lookupEntry
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(
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doneKeys[i],
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false,
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true
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).clone()
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);
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fieldDict.remove(doneKeys[i]);
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FatalErrorInFunction
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<< "Multiple times selected with 'instance' option"
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<< exit(FatalError);
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}
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// Add remaining entries
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label sz = dictList.size();
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dictList.setSize(nEntries);
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forAllConstIter(dictionary, fieldDict, iter)
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{
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dictList.set(sz++, iter().clone());
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}
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Info<< "Writing modified " << fieldName << endl;
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dictList.writeObject
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(
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runTime.writeFormat(),
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runTime.writeFormat(),
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IOstream::UNCOMPRESSED
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);
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args.optionLookup("instance")() >> instance;
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}
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else
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{
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// Read dictionary
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// Note: disable class type checking so we can load field
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Info<< "Loading dictionary " << 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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runTime.setTime(times[timei], timei);
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instance = runTime.timeName();
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}
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IOobject fieldHeader
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#include "createNamedMesh.H"
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const bool literalRE = args.optionFound("literalRE");
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if (literalRE)
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{
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Info<< "Not interpreting any regular expressions (RE)"
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<< " in the changeDictionaryDict." << endl
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<< "Instead they are handled as any other entry, i.e. added if"
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<< " not present." << endl;
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}
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const bool enableEntries = args.optionFound("enableFunctionEntries");
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if (enableEntries)
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{
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Info<< "Allowing dictionary preprocessing ('#include', '#codeStream')."
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<< endl;
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}
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const 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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const bool disablePatchGroups = args.optionFound("disablePatchGroups");
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if (disablePatchGroups)
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{
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Info<< "Not interpreting any keys in the changeDictionary"
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<< " as patchGroups"
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<< endl;
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}
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fileName regionPrefix = "";
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if (regionName != fvMesh::defaultRegion)
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{
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regionPrefix = regionName;
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}
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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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// Get the replacement rules from a dictionary
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const word dictName("changeDictionaryDict");
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#include "setSystemMeshDictionaryIO.H"
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IOdictionary dict(dictIO);
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const dictionary* replaceDictsPtr = &dict;
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if (args.optionFound("subDict"))
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{
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word subDictName(args.optionLookup("subDict")());
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replaceDictsPtr = &dict.subDict(subDictName);
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}
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const dictionary& replaceDicts = *replaceDictsPtr;
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Info<< "Read dictionary " << dict.name()
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<< " with replacements for dictionaries "
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<< replaceDicts.toc() << endl;
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// Always read boundary to get patch groups
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// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Info<< "Reading polyMesh/boundary file to extract patch names"
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<< endl;
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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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fieldName,
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instance,
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"boundary",
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runTime.findInstance
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(
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regionPrefix/polyMesh::meshSubDir,
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"boundary",
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IOobject::READ_IF_PRESENT
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),
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polyMesh::meshSubDir,
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mesh,
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IOobject::MUST_READ_IF_MODIFIED,
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IOobject::READ_IF_PRESENT,
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IOobject::NO_WRITE,
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false
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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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if (fieldHeader.typeHeaderOk<IOdictionary>(false))
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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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// Temporary convert to dictionary
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dictionary fieldDict;
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forAll(dictList, i)
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{
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fieldDict.add(dictList[i].keyword(), dictList[i].dict());
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}
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if (dictList.size())
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{
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Info<< "Loaded dictionary " << dictList.name()
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<< " with entries " << fieldDict.toc() << endl;
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}
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// Extract any patchGroups information (= shortcut for set of
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// patches)
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HashTable<wordList, word> patchGroups;
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if (!disablePatchGroups)
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{
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patchGroups = extractPatchGroups(fieldDict);
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if (patchGroups.size())
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{
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IOdictionary fieldDict(fieldHeader);
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Info<< "Extracted patch groups:" << endl;
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wordList groups(patchGroups.sortedToc());
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forAll(groups, i)
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{
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Info<< " group " << groups[i] << " with patches "
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<< patchGroups[groups[i]] << endl;
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}
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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()) =
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fieldDict.headerClassName();
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// Every replacement is a dictionary name and a keyword in this
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Info<< "Loaded dictionary " << fieldName
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<< " with entries " << fieldDict.toc() << endl;
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forAllConstIter(dictionary, replaceDicts, fieldIter)
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{
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const word& fieldName = fieldIter().keyword();
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Info<< "Replacing entries in dictionary " << fieldName << endl;
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// Handle 'boundary' specially:
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// - is PtrList of dictionaries
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// - is in polyMesh/
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if (fieldName == "boundary")
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{
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Info<< "Special handling of " << fieldName
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<< " as polyMesh/boundary file." << endl;
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// Get the replacement dictionary for the field
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const dictionary& replaceDict = fieldIter().dict();
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Info<< "Merging entries from " << replaceDict.toc() << endl;
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// Merge the replacements in (allow adding)
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merge(true, fieldDict, replaceDict, literalRE, patchGroups);
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// Merge the replacements in. Do not add non-existing entries.
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merge(false, fieldDict, replaceDict, literalRE, patchGroups);
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Info<< "Writing modified fieldDict " << fieldName << endl;
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fieldDict.regIOobject::write();
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Info<< "fieldDict:" << fieldDict << endl;
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// Convert back into dictList
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wordList doneKeys(dictList.size());
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label nEntries = fieldDict.size();
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forAll(dictList, i)
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{
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doneKeys[i] = dictList[i].keyword();
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dictList.set
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(
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i,
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fieldDict.lookupEntry
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(
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doneKeys[i],
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false,
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true
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).clone()
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);
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fieldDict.remove(doneKeys[i]);
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}
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// Add remaining entries
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label sz = dictList.size();
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dictList.setSize(nEntries);
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forAllConstIter(dictionary, fieldDict, iter)
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{
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dictList.set(sz++, iter().clone());
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}
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Info<< "Writing modified " << fieldName << endl;
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dictList.writeObject
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(
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runTime.writeFormat(),
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runTime.writeFormat(),
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IOstream::UNCOMPRESSED,
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true
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);
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}
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else
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{
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WarningInFunction
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<< "Requested field to change " << fieldName
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<< " does not exist in " << fieldHeader.path() << endl;
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// Read dictionary
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// Note: disable class type checking so we can load field
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Info<< "Loading dictionary " << 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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IOobject fieldHeader
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(
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fieldName,
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instance,
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mesh,
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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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if (fieldHeader.typeHeaderOk<IOdictionary>(false))
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{
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IOdictionary fieldDict(fieldHeader);
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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()) =
|
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fieldDict.headerClassName();
|
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|
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Info<< "Loaded dictionary " << fieldName
|
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<< " with entries " << fieldDict.toc() << endl;
|
||||
|
||||
// Get the replacement dictionary for the field
|
||||
const dictionary& replaceDict = fieldIter().dict();
|
||||
Info<< "Merging entries from " << replaceDict.toc() << endl;
|
||||
|
||||
// Merge the replacements in (allow adding)
|
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merge(true, fieldDict, replaceDict, literalRE, patchGroups);
|
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|
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Info<< "Writing modified fieldDict " << fieldName << endl;
|
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fieldDict.regIOobject::write();
|
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}
|
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else
|
||||
{
|
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WarningInFunction
|
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<< "Requested field to change " << fieldName
|
||||
<< " does not exist in " << fieldHeader.path() << endl;
|
||||
}
|
||||
}
|
||||
|
||||
entry::disableFunctionEntries = oldFlag;
|
||||
}
|
||||
}
|
||||
|
||||
entry::disableFunctionEntries = oldFlag;
|
||||
|
||||
Info<< "\nEnd\n" << endl;
|
||||
|
||||
return 0;
|
||||
|
||||
Reference in New Issue
Block a user