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reworked-c
Author | SHA1 | Date | |
---|---|---|---|
|
f94fa7004a | ||
|
90d8f45298 | ||
|
f1ece719b0 |
File diff suppressed because it is too large
Load Diff
@ -135,23 +135,15 @@ protected:
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// Protected Member Functions
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//- Helper: determine number of processors whose recvSizes fits
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//- into maxBufferSize
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static label calcNumProcs
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(
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const label comm,
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const off_t maxBufferSize,
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const labelUList& recvSizes,
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const label startProci
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);
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//- Read data into *this. ISstream is only valid on master.
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//- Read data (on master) and transmit.
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static bool readBlocks
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(
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const label comm,
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// [in] The input stream (only valid on master)
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autoPtr<ISstream>& isPtr,
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List<char>& contentChars,
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const UPstream::commsTypes commsType
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// [out] The processor local data
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List<char>& localData,
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const UPstream::commsTypes commsType /* unused */
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);
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//- Helper: skip a block of (binary) character data
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@ -277,6 +269,19 @@ public:
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}
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//- Helper: write block of (binary) character content
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// Housekeeping
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static std::streamoff writeBlockEntry
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(
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OSstream& os,
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const label blocki,
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const stdFoam::span<char>& s
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)
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{
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return writeBlockEntry(os, blocki, s.data(), s.size());
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}
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//- Helper: write block of (binary) character content
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// Housekeeping
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static std::streamoff writeBlockEntry
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(
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OSstream& os,
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@ -307,41 +312,37 @@ public:
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);
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//- Read master header information (into headerIO) and return
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//- data in stream. Note: isPtr is only valid on master.
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//- data in stream.
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static autoPtr<ISstream> readBlocks
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(
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const label comm,
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const fileName& fName,
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//! [in] The input stream (only valid on master)
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autoPtr<ISstream>& isPtr,
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//! [out] header information
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IOobject& headerIO,
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const UPstream::commsTypes commsType
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const UPstream::commsTypes commsType /* unused */
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);
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//- Helper: gather single label. Note: using native Pstream.
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// datas sized with num procs but undefined contents on
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// slaves
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static void gather
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(
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const label comm,
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const label data,
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labelList& datas
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);
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//- Helper: gather data from (subset of) slaves.
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//- Helper: gather data from (subset of) sub-ranks.
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// In non-blocking mode it sets up send/recv for non-empty content.
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// In blocking/scheduled mode it uses MPI_Gatherv to collect data.
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//
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// Returns:
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// - recvData : received data
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// - recvData : the received data
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// - recvOffsets : offset in data. recvOffsets is nProcs+1
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static void gatherSlaveData
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static void gatherProcData
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(
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const label comm,
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const UList<char>& data,
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const labelUList& recvSizes,
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const UList<char>& localData, //!< [in] required on all procs
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const labelUList& recvSizes, //!< [in] only required on master
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const labelRange& fromProcs,
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const labelRange& whichProcs, //!< [in] required on all procs
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List<int>& recvOffsets,
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DynamicList<char>& recvData
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List<int>& recvOffsets, //!< [out] only relevant on master
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DynamicList<char>& recvData, //!< [out] only relevant on master
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const UPstream::commsTypes commsType
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);
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//- Write *this. Ostream only valid on master.
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@ -349,19 +350,98 @@ public:
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static bool writeBlocks
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(
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const label comm,
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//! [in] output stream (relevant on master)
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autoPtr<OSstream>& osPtr,
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//! [out] start offsets to each block (relevant on master),
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//! ignored if List::null() type
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List<std::streamoff>& blockOffset,
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const UList<char>& masterData,
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const UList<char>& localData, //!< [in] required on all procs
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const labelUList& recvSizes, //!< [in] only required on master
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const labelUList& recvSizes,
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// Optional slave data (on master)
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const UPtrList<SubList<char>>& slaveData,
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//! Optional proc data (only written on master)
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//! but \b must also be symmetrically defined (empty/non-empty)
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//! on all ranks
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const UList<stdFoam::span<char>>& procData,
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const UPstream::commsTypes commsType,
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const bool syncReturnState = true
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);
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// Housekeeping
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//- Write *this. Ostream only valid on master.
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// Returns offsets of processor blocks in blockOffset
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FOAM_DEPRECATED_FOR(2023-09, "write with char span instead")
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static bool writeBlocks
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(
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const label comm,
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autoPtr<OSstream>& osPtr,
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List<std::streamoff>& blockOffset,
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const UList<char>& localData, // [in] required on all procs
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const labelUList& recvSizes, // [in] only required on master
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// Optional proc data (only written on master)
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// but \b must also be symmetrically defined (empty/non-empty)
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// on all ranks
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const UPtrList<SubList<char>>& procData,
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const UPstream::commsTypes commsType,
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const bool syncReturnState = true
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)
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{
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// Transcribe to span<char>
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List<stdFoam::span<char>> spans(procData.size());
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forAll(procData, proci)
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{
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if (procData.test(proci))
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{
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spans[proci] = stdFoam::span<char>
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(
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const_cast<char*>(procData[proci].cdata()),
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procData[proci].size()
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);
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}
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}
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return decomposedBlockData::writeBlocks
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(
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comm,
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osPtr,
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blockOffset,
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localData,
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recvSizes,
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spans,
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commsType,
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syncReturnState
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);
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}
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//- Deprecated(2023-09) - consider UPstream::listGatherValue
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// The only difference is that this gather also resizes the output
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// on the non-master procs
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// \deprecated(2023-09) - consider UPstream::listGatherValue
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FOAM_DEPRECATED_FOR(2023-09, "consider UPstream::listGatherValue()")
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static void gather
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(
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const label comm,
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const label localValue,
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labelList& allValues
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)
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{
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allValues.resize_nocopy(UPstream::nProcs(comm));
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UPstream::mpiGather
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(
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reinterpret_cast<const char*>(&localValue),
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allValues.data_bytes(),
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sizeof(label), // The send/recv size per rank
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comm
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);
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}
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};
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@ -29,7 +29,7 @@ License
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#include "masterOFstream.H"
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#include "OFstream.H"
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#include "OSspecific.H"
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#include "PstreamBuffers.H"
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#include "Pstream.H"
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#include "masterUncollatedFileOperation.H"
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// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
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@ -38,10 +38,10 @@ void Foam::masterOFstream::checkWrite
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(
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const fileName& fName,
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const char* str,
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std::streamsize len
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const std::streamsize len
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)
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{
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if (!len)
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if (!str || !len)
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{
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// Can probably skip all of this if there is nothing to write
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return;
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@ -63,9 +63,7 @@ void Foam::masterOFstream::checkWrite
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<< exit(FatalIOError);
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}
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// Use writeRaw() instead of writeQuoted(string,false) to output
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// characters directly.
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// Write characters directly to std::ostream
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os.writeRaw(str, len);
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if (!os.good())
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@ -77,97 +75,159 @@ void Foam::masterOFstream::checkWrite
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}
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void Foam::masterOFstream::checkWrite
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(
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const fileName& fName,
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const std::string& s
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)
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{
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checkWrite(fName, s.data(), s.length());
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}
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void Foam::masterOFstream::commit()
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{
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// Take ownership of serialized content, without copying or reallocation
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DynamicList<char> charData(OCharStream::release());
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if (UPstream::parRun())
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{
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// Ignore content if not writing (reduces communication)
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if (!writeOnProc_)
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{
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charData.clear();
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}
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List<fileName> filePaths(UPstream::nProcs(comm_));
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filePaths[UPstream::myProcNo(comm_)] = pathName_;
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Pstream::gatherList(filePaths, UPstream::msgType(), comm_);
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// Test for identical output paths
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bool uniform =
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(
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UPstream::master(comm_)
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&& fileOperation::uniformFile(filePaths)
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? fileOperation::uniformFile(filePaths)
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: true
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);
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Pstream::broadcast(uniform, comm_);
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if (uniform)
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{
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// Identical file paths - write on master
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if (UPstream::master(comm_) && writeOnProc_)
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{
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checkWrite(pathName_, this->str());
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checkWrite(pathName_, charData);
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}
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this->reset();
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return;
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}
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// Different files
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PstreamBuffers pBufs(comm_);
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// ---------------
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// Current strategy is to setup all non-blocking send/recv
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// using the probed message size to establish the recv size
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// (to avoid an additional communication of the sizes).
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//
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// For ranks with writeOnProc=false, the message size is 0.
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if (!UPstream::master(comm_))
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// An alternative approach would be to gather recv sizes
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// to avoid zero-sized messages and/or use double buffering
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// to recv into a buffer and write.
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//
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// const labelList recvSizes
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// (
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// UPstream::listGatherValues<label>
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// (
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// (UPstream::is_subrank(comm_) ? charData.size() : label(0)),
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// comm_
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// )
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// );
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const label startOfRequests = UPstream::nRequests();
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// Some unique tag for this read/write/probe grouping
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const int messageTag = UPstream::msgType() + 256;
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if (UPstream::is_subrank(comm_))
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{
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if (writeOnProc_)
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{
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// Send buffer to master
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string s(this->str());
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UOPstream os(UPstream::masterNo(), pBufs);
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os.write(s.data(), s.length());
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}
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this->reset(); // Done with contents
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// Send to master. When (!writeOnProc_) it is zero-sized.
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UOPstream::write
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(
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UPstream::commsTypes::nonBlocking,
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UPstream::masterNo(),
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charData.cdata_bytes(),
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charData.size_bytes(),
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messageTag,
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comm_
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);
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}
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pBufs.finishedGathers();
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if (UPstream::master(comm_))
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else if (UPstream::master(comm_))
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{
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// The receive slots
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List<List<char>> procBuffers(UPstream::nProcs(comm_));
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const auto recvProcs = UPstream::subProcs(comm_);
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for (const int proci : recvProcs)
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{
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auto& procSlice = procBuffers[proci];
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// Probe the message size
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std::pair<int, int64_t> probed =
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UPstream::probeMessage
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(
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UPstream::commsTypes::scheduled, // blocking call
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proci,
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messageTag,
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comm_
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);
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procSlice.resize_nocopy(probed.second);
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// Receive content (can also be zero-sized)
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UIPstream::read
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(
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UPstream::commsTypes::nonBlocking,
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proci,
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procSlice.data_bytes(),
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procSlice.size_bytes(),
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messageTag,
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comm_
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);
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}
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if (writeOnProc_)
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{
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// Write master data
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checkWrite(filePaths[UPstream::masterNo()], this->str());
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// Write non-empty master data
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checkWrite(pathName_, charData);
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}
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this->reset(); // Done with contents
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// Allocate large enough to read without resizing
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List<char> buf(pBufs.maxRecvCount());
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|
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for (const int proci : UPstream::subProcs(comm_))
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// Poll for completed receive requests and dispatch
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DynamicList<int> indices(recvProcs.size());
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while
|
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(
|
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UPstream::waitSomeRequests
|
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(
|
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startOfRequests,
|
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recvProcs.size(),
|
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&indices
|
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)
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)
|
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{
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const std::streamsize count(pBufs.recvDataCount(proci));
|
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|
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if (count)
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for (const int idx : indices)
|
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{
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UIPstream is(proci, pBufs);
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const int proci = recvProcs[idx];
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auto& procSlice = procBuffers[proci];
|
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|
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is.read(buf.data(), count);
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checkWrite(filePaths[proci], buf.cdata(), count);
|
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if (!procSlice.empty())
|
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{
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// Write non-empty sub-proc data
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checkWrite(filePaths[proci], procSlice);
|
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}
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|
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// Eager cleanup?
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// TBD: procSlice.clear();
|
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}
|
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}
|
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}
|
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|
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UPstream::waitRequests(startOfRequests);
|
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}
|
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else
|
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{
|
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checkWrite(pathName_, this->str());
|
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this->reset();
|
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// Write (non-empty) data
|
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checkWrite(pathName_, charData);
|
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}
|
||||
|
||||
// This method is only called once (internally)
|
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// so no need to clear/flush old buffered data
|
||||
}
|
||||
|
||||
|
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@ -183,7 +243,7 @@ Foam::masterOFstream::masterOFstream
|
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const bool writeOnProc
|
||||
)
|
||||
:
|
||||
OStringStream(streamOpt),
|
||||
OCharStream(streamOpt),
|
||||
pathName_(pathName),
|
||||
atomic_(atomic),
|
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compression_(streamOpt.compression()),
|
||||
|
@ -41,7 +41,7 @@ SourceFiles
|
||||
#ifndef Foam_masterOFstream_H
|
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#define Foam_masterOFstream_H
|
||||
|
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#include "StringStream.H"
|
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#include "SpanStream.H"
|
||||
#include "UPstream.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
@ -55,7 +55,7 @@ namespace Foam
|
||||
|
||||
class masterOFstream
|
||||
:
|
||||
public OStringStream
|
||||
public OCharStream
|
||||
{
|
||||
// Private Data
|
||||
|
||||
@ -85,13 +85,20 @@ class masterOFstream
|
||||
(
|
||||
const fileName& fName,
|
||||
const char* str,
|
||||
std::streamsize len
|
||||
const std::streamsize len
|
||||
);
|
||||
|
||||
//- Open file with checking and write append contents
|
||||
void checkWrite(const fileName& fName, const std::string& s);
|
||||
void checkWrite
|
||||
(
|
||||
const fileName& fName,
|
||||
const UList<char>& charData
|
||||
)
|
||||
{
|
||||
checkWrite(fName, charData.cdata(), charData.size_bytes());
|
||||
}
|
||||
|
||||
//- Commit buffered information, including parallel gather as required
|
||||
//- Commit buffered information, including communication as required
|
||||
void commit();
|
||||
|
||||
|
||||
|
@ -47,9 +47,9 @@ bool Foam::OFstreamCollator::writeFile
|
||||
const label comm,
|
||||
const word& objectType,
|
||||
const fileName& fName,
|
||||
const string& masterData,
|
||||
const UList<char>& localData,
|
||||
const labelUList& recvSizes,
|
||||
const UPtrList<SubList<char>>& slaveData, // optional slave data
|
||||
const UList<stdFoam::span<char>>& procData, // optional proc data
|
||||
IOstreamOption streamOpt,
|
||||
IOstreamOption::atomicType atomic,
|
||||
IOstreamOption::appendType append,
|
||||
@ -58,18 +58,14 @@ bool Foam::OFstreamCollator::writeFile
|
||||
{
|
||||
if (debug)
|
||||
{
|
||||
Pout<< "OFstreamCollator : Writing master " << label(masterData.size())
|
||||
Pout<< "OFstreamCollator : Writing local " << localData.size()
|
||||
<< " bytes to " << fName << " using comm " << comm
|
||||
<< " and " << slaveData.size() << " sub-ranks" << endl;
|
||||
<< " and " << procData.size() << " sub-ranks" << endl;
|
||||
|
||||
forAll(slaveData, proci)
|
||||
forAll(procData, proci)
|
||||
{
|
||||
if (slaveData.set(proci))
|
||||
{
|
||||
Pout<< " " << proci
|
||||
<< " size:" << slaveData[proci].size()
|
||||
<< endl;
|
||||
}
|
||||
Pout<< " " << proci << " size:"
|
||||
<< label(procData[proci].size()) << nl;
|
||||
}
|
||||
}
|
||||
|
||||
@ -91,7 +87,7 @@ bool Foam::OFstreamCollator::writeFile
|
||||
streamOpt, // streamOpt for container
|
||||
objectType,
|
||||
"", // note
|
||||
"", // location (leave empty instead inaccurate)
|
||||
"", // location (leave empty, otherwise inaccurate)
|
||||
fName.name(), // object name
|
||||
headerEntries
|
||||
);
|
||||
@ -104,32 +100,27 @@ bool Foam::OFstreamCollator::writeFile
|
||||
// for some mpi so default is non-blocking.
|
||||
const UPstream::commsTypes myCommsType
|
||||
(
|
||||
mag
|
||||
(
|
||||
fileOperations::masterUncollatedFileOperation::
|
||||
maxMasterFileBufferSize == 0
|
||||
)
|
||||
maxMasterFileBufferSize
|
||||
) < 1
|
||||
? UPstream::commsTypes::scheduled
|
||||
: UPstream::commsTypes::nonBlocking
|
||||
);
|
||||
|
||||
|
||||
UList<char> slice
|
||||
(
|
||||
const_cast<char*>(masterData.data()),
|
||||
label(masterData.size())
|
||||
);
|
||||
|
||||
List<std::streamoff> blockOffset;
|
||||
List<std::streamoff> blockOffsets; // Optional
|
||||
decomposedBlockData::writeBlocks
|
||||
(
|
||||
comm,
|
||||
osPtr,
|
||||
blockOffset,
|
||||
slice,
|
||||
blockOffsets, // or List<std::streamoff>::null()
|
||||
localData,
|
||||
recvSizes,
|
||||
slaveData,
|
||||
procData,
|
||||
myCommsType,
|
||||
false // do not reduce return state
|
||||
false // do not sync return state
|
||||
);
|
||||
|
||||
if (osPtr && !osPtr->good())
|
||||
@ -140,17 +131,18 @@ bool Foam::OFstreamCollator::writeFile
|
||||
|
||||
if (debug)
|
||||
{
|
||||
Pout<< "OFstreamCollator : Finished writing " << masterData.size()
|
||||
<< " bytes";
|
||||
Pout<< "OFstreamCollator : Finished writing "
|
||||
<< localData.size() << " bytes";
|
||||
|
||||
if (UPstream::master(comm))
|
||||
{
|
||||
off_t sum = 0;
|
||||
off_t total = 0;
|
||||
for (const label recv : recvSizes)
|
||||
{
|
||||
sum += recv;
|
||||
total += recv;
|
||||
}
|
||||
// Use std::to_string to display long int
|
||||
Pout<< " (overall " << std::to_string(sum) << ')';
|
||||
Pout<< " (overall " << std::to_string(total) << ')';
|
||||
}
|
||||
Pout<< " to " << fName
|
||||
<< " using comm " << comm << endl;
|
||||
@ -167,13 +159,16 @@ void* Foam::OFstreamCollator::writeAll(void *threadarg)
|
||||
// Consume stack
|
||||
while (true)
|
||||
{
|
||||
writeData* ptr = nullptr;
|
||||
std::unique_ptr<writeData> ptr;
|
||||
|
||||
{
|
||||
std::lock_guard<std::mutex> guard(handler.mutex_);
|
||||
|
||||
if (handler.objects_.size())
|
||||
{
|
||||
ptr = handler.objects_.pop();
|
||||
// FIFO
|
||||
ptr.reset(handler.objects_.front());
|
||||
handler.objects_.pop_front();
|
||||
}
|
||||
}
|
||||
|
||||
@ -181,51 +176,39 @@ void* Foam::OFstreamCollator::writeAll(void *threadarg)
|
||||
{
|
||||
break;
|
||||
}
|
||||
else
|
||||
|
||||
writeData& obj = *ptr;
|
||||
|
||||
// Obtain spans from storage
|
||||
List<stdFoam::span<char>> procData(obj.procData_.size());
|
||||
forAll(procData, proci)
|
||||
{
|
||||
// Convert storage to pointers
|
||||
PtrList<SubList<char>> slaveData;
|
||||
if (ptr->slaveData_.size())
|
||||
{
|
||||
slaveData.resize(ptr->slaveData_.size());
|
||||
forAll(slaveData, proci)
|
||||
{
|
||||
if (ptr->slaveData_.set(proci))
|
||||
{
|
||||
slaveData.set
|
||||
(
|
||||
proci,
|
||||
new SubList<char>
|
||||
(
|
||||
ptr->slaveData_[proci],
|
||||
ptr->sizes_[proci]
|
||||
)
|
||||
);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
bool ok = writeFile
|
||||
procData[proci] = stdFoam::span<char>
|
||||
(
|
||||
ptr->comm_,
|
||||
ptr->objectType_,
|
||||
ptr->pathName_,
|
||||
ptr->data_,
|
||||
ptr->sizes_,
|
||||
slaveData,
|
||||
ptr->streamOpt_,
|
||||
ptr->atomic_,
|
||||
ptr->append_,
|
||||
ptr->headerEntries_
|
||||
const_cast<char*>(obj.procData_[proci].cdata()),
|
||||
obj.procData_[proci].size()
|
||||
);
|
||||
if (!ok)
|
||||
{
|
||||
FatalIOErrorInFunction(ptr->pathName_)
|
||||
<< "Failed writing " << ptr->pathName_
|
||||
<< exit(FatalIOError);
|
||||
}
|
||||
}
|
||||
|
||||
delete ptr;
|
||||
bool ok = writeFile
|
||||
(
|
||||
obj.comm_,
|
||||
obj.objectType_,
|
||||
obj.pathName_,
|
||||
obj.localData_,
|
||||
obj.sizes_,
|
||||
procData,
|
||||
obj.streamOpt_,
|
||||
obj.atomic_,
|
||||
obj.append_,
|
||||
obj.headerEntries_
|
||||
);
|
||||
|
||||
if (!ok)
|
||||
{
|
||||
FatalIOErrorInFunction(obj.pathName_)
|
||||
<< "Failed writing " << obj.pathName_
|
||||
<< exit(FatalIOError);
|
||||
}
|
||||
//sleep(1);
|
||||
}
|
||||
@ -248,14 +231,14 @@ void Foam::OFstreamCollator::waitForBufferSpace(const off_t wantedSize) const
|
||||
{
|
||||
while (true)
|
||||
{
|
||||
// Count files to be written
|
||||
// The pending output size(s)
|
||||
off_t totalSize = 0;
|
||||
|
||||
{
|
||||
std::lock_guard<std::mutex> guard(mutex_);
|
||||
forAllConstIters(objects_, iter)
|
||||
for (const writeData* ptr : objects_)
|
||||
{
|
||||
totalSize += iter()->size();
|
||||
if (ptr) totalSize += ptr->size();
|
||||
}
|
||||
}
|
||||
|
||||
@ -287,17 +270,7 @@ void Foam::OFstreamCollator::waitForBufferSpace(const off_t wantedSize) const
|
||||
|
||||
Foam::OFstreamCollator::OFstreamCollator(const off_t maxBufferSize)
|
||||
:
|
||||
maxBufferSize_(maxBufferSize),
|
||||
threadRunning_(false),
|
||||
localComm_(UPstream::worldComm),
|
||||
threadComm_
|
||||
(
|
||||
UPstream::allocateCommunicator
|
||||
(
|
||||
localComm_,
|
||||
labelRange(UPstream::nProcs(localComm_))
|
||||
)
|
||||
)
|
||||
OFstreamCollator(maxBufferSize, UPstream::worldComm)
|
||||
{}
|
||||
|
||||
|
||||
@ -312,6 +285,7 @@ Foam::OFstreamCollator::OFstreamCollator
|
||||
localComm_(comm),
|
||||
threadComm_
|
||||
(
|
||||
// dupComm
|
||||
UPstream::allocateCommunicator
|
||||
(
|
||||
localComm_,
|
||||
@ -345,7 +319,7 @@ bool Foam::OFstreamCollator::write
|
||||
(
|
||||
const word& objectType,
|
||||
const fileName& fName,
|
||||
const string& data,
|
||||
DynamicList<char>&& localData,
|
||||
IOstreamOption streamOpt,
|
||||
IOstreamOption::atomicType atomic,
|
||||
IOstreamOption::appendType append,
|
||||
@ -355,78 +329,112 @@ bool Foam::OFstreamCollator::write
|
||||
{
|
||||
// Determine (on master) sizes to receive. Note: do NOT use thread
|
||||
// communicator
|
||||
labelList recvSizes;
|
||||
decomposedBlockData::gather(localComm_, label(data.size()), recvSizes);
|
||||
const labelList recvSizes
|
||||
(
|
||||
UPstream::listGatherValues<label>(localData.size(), localComm_)
|
||||
);
|
||||
|
||||
off_t totalSize = 0;
|
||||
label maxLocalSize = 0;
|
||||
|
||||
if (UPstream::master(localComm_))
|
||||
{
|
||||
if (UPstream::master(localComm_))
|
||||
for (const label recvSize : recvSizes)
|
||||
{
|
||||
for (const label recvSize : recvSizes)
|
||||
{
|
||||
totalSize += recvSize;
|
||||
maxLocalSize = max(maxLocalSize, recvSize);
|
||||
}
|
||||
totalSize += recvSize;
|
||||
maxLocalSize = max(maxLocalSize, recvSize);
|
||||
}
|
||||
Pstream::broadcasts(localComm_, totalSize, maxLocalSize);
|
||||
}
|
||||
Pstream::broadcasts(localComm_, totalSize, maxLocalSize);
|
||||
|
||||
|
||||
// Determine how things will be gathered and written...
|
||||
|
||||
enum class dispatchModes { DIRECT_WRITE, THREADED_WRITE, FULL_THREADED };
|
||||
|
||||
dispatchModes dispatch(dispatchModes::DIRECT_WRITE);
|
||||
|
||||
if (!useThread || maxBufferSize_ == 0 || maxLocalSize > maxBufferSize_)
|
||||
{
|
||||
dispatch = dispatchModes::DIRECT_WRITE;
|
||||
}
|
||||
else if (totalSize <= maxBufferSize_)
|
||||
{
|
||||
// Total size can be stored locally
|
||||
// - gather all data now and only do the writing in the thread
|
||||
|
||||
dispatch = dispatchModes::THREADED_WRITE;
|
||||
}
|
||||
else
|
||||
{
|
||||
// Gather data and write in the thread
|
||||
|
||||
dispatch = dispatchModes::FULL_THREADED;
|
||||
|
||||
if (!UPstream::haveThreads())
|
||||
{
|
||||
WarningInFunction
|
||||
<< "MPI not initialized with thread support." << nl
|
||||
<< " maxThreadFileBufferSize = 0 to disable threading" << nl
|
||||
<< " or maxThreadFileBufferSize > " << totalSize
|
||||
<< " to collate before threaded writing." << nl << nl;
|
||||
|
||||
dispatch = dispatchModes::DIRECT_WRITE;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// -----------
|
||||
// Dispatching
|
||||
// -----------
|
||||
|
||||
if (dispatch == dispatchModes::DIRECT_WRITE)
|
||||
{
|
||||
if (debug)
|
||||
{
|
||||
Pout<< "OFstreamCollator : non-thread gather and write of " << fName
|
||||
<< " using local comm " << localComm_ << endl;
|
||||
Pout<< "OFstreamCollator : non-thread gather "
|
||||
<< "(local comm: " << localComm_
|
||||
<< "); non-thread write of "
|
||||
<< fName << endl;
|
||||
}
|
||||
|
||||
// Direct collating and writing (so master blocks until all written!)
|
||||
const PtrList<SubList<char>> dummySlaveData;
|
||||
return writeFile
|
||||
(
|
||||
localComm_,
|
||||
objectType,
|
||||
fName,
|
||||
data,
|
||||
localData,
|
||||
recvSizes,
|
||||
dummySlaveData,
|
||||
UList<stdFoam::span<char>>::null(), // dummy proc data
|
||||
streamOpt,
|
||||
atomic,
|
||||
append,
|
||||
headerEntries
|
||||
);
|
||||
}
|
||||
else if (totalSize <= maxBufferSize_)
|
||||
else if (dispatch == dispatchModes::THREADED_WRITE)
|
||||
{
|
||||
// Total size can be stored locally so receive all data now and only
|
||||
// do the writing in the thread
|
||||
|
||||
if (debug)
|
||||
{
|
||||
Pout<< "OFstreamCollator : non-thread gather; thread write of "
|
||||
Pout<< "OFstreamCollator : non-thread gather "
|
||||
<< "(local comm: " << localComm_
|
||||
<< "); thread write of "
|
||||
<< fName << endl;
|
||||
}
|
||||
|
||||
if (Pstream::master(localComm_))
|
||||
if (UPstream::master(localComm_))
|
||||
{
|
||||
waitForBufferSpace(totalSize);
|
||||
}
|
||||
|
||||
|
||||
// Receive in chunks of labelMax (2^31-1) since this is the maximum
|
||||
// size that a List can be
|
||||
|
||||
autoPtr<writeData> fileAndDataPtr
|
||||
std::unique_ptr<writeData> fileAndDataPtr
|
||||
(
|
||||
new writeData
|
||||
(
|
||||
threadComm_, // Note: comm not actually used anymore
|
||||
threadComm_,
|
||||
objectType,
|
||||
fName,
|
||||
(
|
||||
Pstream::master(localComm_)
|
||||
? data // Only used on master
|
||||
: string::null
|
||||
),
|
||||
recvSizes,
|
||||
streamOpt,
|
||||
atomic,
|
||||
@ -434,63 +442,86 @@ bool Foam::OFstreamCollator::write
|
||||
headerEntries
|
||||
)
|
||||
);
|
||||
writeData& fileAndData = fileAndDataPtr();
|
||||
auto& fileAndData = *fileAndDataPtr;
|
||||
|
||||
PtrList<List<char>>& slaveData = fileAndData.slaveData_;
|
||||
List<List<char>>& procData = fileAndData.procData_;
|
||||
if (UPstream::master(localComm_))
|
||||
{
|
||||
// Move in local data (master only!)
|
||||
fileAndData.transfer(localData);
|
||||
|
||||
UList<char> slice(const_cast<char*>(data.data()), label(data.size()));
|
||||
// Storage for receive data
|
||||
procData.resize(UPstream::nProcs(localComm_));
|
||||
|
||||
for (const int proci : UPstream::subProcs(localComm_))
|
||||
{
|
||||
procData[proci].resize(recvSizes[proci]);
|
||||
}
|
||||
}
|
||||
else if (UPstream::is_subrank(localComm_))
|
||||
{
|
||||
// Requires a size for decomposedBlockData::writeBlocks() logic
|
||||
procData.resize(UPstream::nProcs(localComm_));
|
||||
}
|
||||
|
||||
slaveData.setSize(recvSizes.size());
|
||||
|
||||
// Gather all data onto master. Is done in local communicator since
|
||||
// not in write thread. Note that we do not store in contiguous
|
||||
// buffer since that would limit to 2G chars.
|
||||
// not in write thread.
|
||||
const label startOfRequests = UPstream::nRequests();
|
||||
if (Pstream::master(localComm_))
|
||||
|
||||
const int messageTag = UPstream::msgType();
|
||||
|
||||
if (UPstream::master(localComm_))
|
||||
{
|
||||
for (label proci = 1; proci < slaveData.size(); proci++)
|
||||
for (const int proci : UPstream::subProcs(localComm_))
|
||||
{
|
||||
slaveData.set(proci, new List<char>(recvSizes[proci]));
|
||||
List<char>& procSlice = procData[proci];
|
||||
if (procSlice.empty()) continue;
|
||||
|
||||
UIPstream::read
|
||||
(
|
||||
UPstream::commsTypes::nonBlocking,
|
||||
proci,
|
||||
slaveData[proci].data(),
|
||||
slaveData[proci].size_bytes(),
|
||||
Pstream::msgType(),
|
||||
procSlice.data_bytes(),
|
||||
procSlice.size_bytes(),
|
||||
messageTag,
|
||||
localComm_
|
||||
);
|
||||
}
|
||||
}
|
||||
else
|
||||
else if (UPstream::is_subrank(localComm_) && !localData.empty())
|
||||
{
|
||||
if
|
||||
(
|
||||
!UOPstream::write
|
||||
(
|
||||
UPstream::commsTypes::nonBlocking,
|
||||
0,
|
||||
slice.cdata(),
|
||||
slice.size_bytes(),
|
||||
Pstream::msgType(),
|
||||
UPstream::masterNo(),
|
||||
localData.cdata_bytes(),
|
||||
localData.size_bytes(),
|
||||
messageTag,
|
||||
localComm_
|
||||
)
|
||||
)
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Cannot send outgoing message. "
|
||||
<< "to:" << 0 << " nBytes:"
|
||||
<< label(slice.size_bytes())
|
||||
<< "Failure to send message (size: "
|
||||
<< localData.size() << ") to master" << nl
|
||||
<< Foam::abort(FatalError);
|
||||
}
|
||||
}
|
||||
UPstream::waitRequests(startOfRequests);
|
||||
|
||||
// The localData has been moved (master) or communicated
|
||||
localData.clearStorage();
|
||||
|
||||
|
||||
// Queue up for threading
|
||||
{
|
||||
std::lock_guard<std::mutex> guard(mutex_);
|
||||
|
||||
// Append to thread buffer
|
||||
objects_.push(fileAndDataPtr.ptr());
|
||||
// Add to thread buffer (as FIFO), take ownership
|
||||
objects_.push_back(fileAndDataPtr.release());
|
||||
|
||||
// Start thread if not running
|
||||
if (!threadRunning_)
|
||||
@ -517,49 +548,48 @@ bool Foam::OFstreamCollator::write
|
||||
|
||||
return true;
|
||||
}
|
||||
else
|
||||
else if (dispatch == dispatchModes::FULL_THREADED)
|
||||
{
|
||||
if (debug)
|
||||
{
|
||||
Pout<< "OFstreamCollator : thread gather and write of " << fName
|
||||
<< " using communicator " << threadComm_ << endl;
|
||||
Pout<< "OFstreamCollator : thread gather; thread write "
|
||||
<< "(thread comm: " << threadComm_
|
||||
<< ") of " << fName << endl;
|
||||
}
|
||||
|
||||
if (!UPstream::haveThreads())
|
||||
if (UPstream::master(localComm_))
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "mpi does not seem to have thread support."
|
||||
<< " Make sure to set buffer size 'maxThreadFileBufferSize'"
|
||||
<< " to at least " << totalSize
|
||||
<< " to be able to do the collating before threading."
|
||||
<< exit(FatalError);
|
||||
waitForBufferSpace(localData.size());
|
||||
}
|
||||
|
||||
if (Pstream::master(localComm_))
|
||||
{
|
||||
waitForBufferSpace(data.size());
|
||||
}
|
||||
std::unique_ptr<writeData> fileAndDataPtr
|
||||
(
|
||||
new writeData
|
||||
(
|
||||
threadComm_,
|
||||
objectType,
|
||||
fName,
|
||||
recvSizes,
|
||||
streamOpt,
|
||||
atomic,
|
||||
append,
|
||||
headerEntries
|
||||
)
|
||||
);
|
||||
|
||||
// Move in local data (all procs)
|
||||
fileAndDataPtr->transfer(localData);
|
||||
|
||||
|
||||
// Queue up for threading
|
||||
{
|
||||
std::lock_guard<std::mutex> guard(mutex_);
|
||||
|
||||
// Push all file info on buffer. Note that no slave data provided
|
||||
// so it will trigger communication inside the thread
|
||||
objects_.push
|
||||
(
|
||||
new writeData
|
||||
(
|
||||
threadComm_,
|
||||
objectType,
|
||||
fName,
|
||||
data,
|
||||
recvSizes,
|
||||
streamOpt,
|
||||
atomic,
|
||||
append,
|
||||
headerEntries
|
||||
)
|
||||
);
|
||||
// Add to thread buffer (as FIFO), take ownership
|
||||
objects_.push_back(fileAndDataPtr.release());
|
||||
|
||||
// Note: no proc data provided
|
||||
// so it will trigger communication inside the thread!!!
|
||||
|
||||
if (!threadRunning_)
|
||||
{
|
||||
@ -584,14 +614,21 @@ bool Foam::OFstreamCollator::write
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
FatalErrorInFunction
|
||||
<< "Unknown dispatch mode: " << int(dispatch)
|
||||
<< " - programming error?" << abort(FatalError);
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
void Foam::OFstreamCollator::waitAll()
|
||||
{
|
||||
// Wait for all buffer space to be available i.e. wait for all jobs
|
||||
// to finish
|
||||
if (Pstream::master(localComm_))
|
||||
// Wait for all buffer space to be available
|
||||
// - ie, wait for all jobs to finish
|
||||
|
||||
if (UPstream::master(localComm_))
|
||||
{
|
||||
if (debug)
|
||||
{
|
||||
|
@ -6,7 +6,7 @@
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
Copyright (C) 2017-2018 OpenFOAM Foundation
|
||||
Copyright (C) 2021-2022 OpenCFD Ltd.
|
||||
Copyright (C) 2019-2023 OpenCFD Ltd.
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
@ -51,14 +51,14 @@ SourceFiles
|
||||
#ifndef Foam_OFstreamCollator_H
|
||||
#define Foam_OFstreamCollator_H
|
||||
|
||||
#include <thread>
|
||||
#include <mutex>
|
||||
#include "IOstream.H"
|
||||
#include "labelList.H"
|
||||
#include "FIFOStack.H"
|
||||
#include "SubList.H"
|
||||
#include "List.H"
|
||||
#include "CircularBuffer.H" // As FIFO
|
||||
#include "dictionary.H"
|
||||
|
||||
#include <mutex>
|
||||
#include <thread>
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
namespace Foam
|
||||
@ -72,26 +72,33 @@ class OFstreamCollator
|
||||
{
|
||||
// Private Class
|
||||
|
||||
//- Holds data to be written
|
||||
struct writeData
|
||||
{
|
||||
const label comm_;
|
||||
const word objectType_;
|
||||
const fileName pathName_;
|
||||
const string data_;
|
||||
DynamicList<char> localData_;
|
||||
const labelList sizes_;
|
||||
PtrList<List<char>> slaveData_;
|
||||
List<List<char>> procData_;
|
||||
const IOstreamOption streamOpt_;
|
||||
IOstreamOption::atomicType atomic_;
|
||||
IOstreamOption::appendType append_;
|
||||
const dictionary headerEntries_;
|
||||
|
||||
writeData() = delete; // No default construct
|
||||
writeData(const writeData&) = delete; // No copy construct
|
||||
writeData(writeData&&) = delete; // No move construct
|
||||
void operator=(const writeData&) = delete; // No copy assign
|
||||
void operator=(writeData&&) = delete; // No move assign
|
||||
|
||||
//- Construct without local data
|
||||
writeData
|
||||
(
|
||||
const label comm,
|
||||
const word& objectType,
|
||||
const fileName& pathName,
|
||||
const string& data,
|
||||
const labelList& sizes,
|
||||
const labelUList& sizes,
|
||||
IOstreamOption streamOpt,
|
||||
IOstreamOption::atomicType atomic,
|
||||
IOstreamOption::appendType append,
|
||||
@ -101,27 +108,30 @@ class OFstreamCollator
|
||||
comm_(comm),
|
||||
objectType_(objectType),
|
||||
pathName_(pathName),
|
||||
data_(data),
|
||||
localData_(),
|
||||
sizes_(sizes),
|
||||
slaveData_(),
|
||||
procData_(),
|
||||
streamOpt_(streamOpt),
|
||||
atomic_(atomic),
|
||||
append_(append),
|
||||
headerEntries_(headerEntries)
|
||||
{}
|
||||
|
||||
//- The (approximate) size of master + any optional slave data
|
||||
//- Move reset local data
|
||||
void transfer(DynamicList<char>& localData)
|
||||
{
|
||||
localData_.transfer(localData);
|
||||
}
|
||||
|
||||
//- The (approximate) size of local + any optional proc data
|
||||
off_t size() const
|
||||
{
|
||||
off_t totalSize = data_.size();
|
||||
forAll(slaveData_, i)
|
||||
off_t total = localData_.size();
|
||||
for (const auto& data : procData_)
|
||||
{
|
||||
if (slaveData_.set(i))
|
||||
{
|
||||
totalSize += slaveData_[i].size();
|
||||
}
|
||||
total += data.size();
|
||||
}
|
||||
return totalSize;
|
||||
return total;
|
||||
}
|
||||
};
|
||||
|
||||
@ -135,8 +145,8 @@ class OFstreamCollator
|
||||
|
||||
std::unique_ptr<std::thread> thread_;
|
||||
|
||||
//- Stack of files to write + contents
|
||||
FIFOStack<writeData*> objects_;
|
||||
//- FIFO of files to write and their contents
|
||||
CircularBuffer<writeData*> objects_;
|
||||
|
||||
//- Whether thread is running (and not exited)
|
||||
bool threadRunning_;
|
||||
@ -156,9 +166,9 @@ class OFstreamCollator
|
||||
const label comm,
|
||||
const word& objectType,
|
||||
const fileName& fName,
|
||||
const string& masterData,
|
||||
const UList<char>& localData,
|
||||
const labelUList& recvSizes,
|
||||
const UPtrList<SubList<char>>& slaveData,
|
||||
const UList<stdFoam::span<char>>& procData,
|
||||
IOstreamOption streamOpt,
|
||||
IOstreamOption::atomicType atomic,
|
||||
IOstreamOption::appendType append,
|
||||
@ -181,7 +191,8 @@ public:
|
||||
|
||||
// Constructors
|
||||
|
||||
//- Construct from buffer size. 0 = do not use thread
|
||||
//- Construct from buffer size (0 = do not use thread)
|
||||
//- and with worldComm
|
||||
explicit OFstreamCollator(const off_t maxBufferSize);
|
||||
|
||||
//- Construct from buffer size (0 = do not use thread)
|
||||
@ -195,14 +206,15 @@ public:
|
||||
|
||||
// Member Functions
|
||||
|
||||
//- Write file with contents.
|
||||
// Blocks until writethread has space available
|
||||
//- Write file with contents, possibly taking ownership of the
|
||||
//- content.
|
||||
// Blocks until write-thread has space available
|
||||
// (total file sizes < maxBufferSize)
|
||||
bool write
|
||||
(
|
||||
const word& objectType,
|
||||
const fileName&,
|
||||
const string& data,
|
||||
const fileName& fName,
|
||||
DynamicList<char>&& localData,
|
||||
IOstreamOption streamOpt,
|
||||
IOstreamOption::atomicType atomic,
|
||||
IOstreamOption::appendType append,
|
||||
@ -210,6 +222,37 @@ public:
|
||||
const dictionary& headerEntries = dictionary::null
|
||||
);
|
||||
|
||||
//- Write file with contents.
|
||||
FOAM_DEPRECATED_FOR(2023-09, "use write with movable content")
|
||||
bool write
|
||||
(
|
||||
const word& objectType,
|
||||
const fileName& fName,
|
||||
const std::string& s,
|
||||
IOstreamOption streamOpt,
|
||||
IOstreamOption::atomicType atomic,
|
||||
IOstreamOption::appendType append,
|
||||
const bool useThread = true,
|
||||
const dictionary& headerEntries = dictionary::null
|
||||
)
|
||||
{
|
||||
DynamicList<char> charData;
|
||||
charData.setCapacity(s.size());
|
||||
std::copy(s.begin(), s.end(), charData.begin());
|
||||
|
||||
return write
|
||||
(
|
||||
objectType,
|
||||
fName,
|
||||
std::move(charData),
|
||||
streamOpt,
|
||||
atomic,
|
||||
append,
|
||||
useThread,
|
||||
headerEntries
|
||||
);
|
||||
}
|
||||
|
||||
//- Wait for all thread actions to have finished
|
||||
void waitAll();
|
||||
};
|
||||
|
@ -6,7 +6,7 @@
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
Copyright (C) 2017-2018 OpenFOAM Foundation
|
||||
Copyright (C) 2020-2022 OpenCFD Ltd.
|
||||
Copyright (C) 2020-2023 OpenCFD Ltd.
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
@ -41,7 +41,7 @@ Foam::threadedCollatedOFstream::threadedCollatedOFstream
|
||||
const bool useThread
|
||||
)
|
||||
:
|
||||
OStringStream(streamOpt),
|
||||
OCharStream(streamOpt),
|
||||
writer_(writer),
|
||||
pathName_(pathName),
|
||||
atomic_(atomic),
|
||||
@ -74,11 +74,22 @@ Foam::threadedCollatedOFstream::threadedCollatedOFstream
|
||||
|
||||
Foam::threadedCollatedOFstream::~threadedCollatedOFstream()
|
||||
{
|
||||
commit();
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
void Foam::threadedCollatedOFstream::commit()
|
||||
{
|
||||
// Take ownership of serialized content, without copying or reallocation
|
||||
DynamicList<char> charData(OCharStream::release());
|
||||
|
||||
writer_.write
|
||||
(
|
||||
decomposedBlockData::typeName,
|
||||
pathName_,
|
||||
str(),
|
||||
std::move(charData),
|
||||
IOstreamOption(IOstreamOption::BINARY, version(), compression_),
|
||||
atomic_,
|
||||
IOstreamOption::NO_APPEND,
|
||||
|
@ -6,7 +6,7 @@
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
Copyright (C) 2017-2018 OpenFOAM Foundation
|
||||
Copyright (C) 2021-2022 OpenCFD Ltd.
|
||||
Copyright (C) 2021-2023 OpenCFD Ltd.
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
@ -39,7 +39,7 @@ SourceFiles
|
||||
#define Foam_threadedCollatedOFstream_H
|
||||
|
||||
#include "dictionary.H"
|
||||
#include "StringStream.H"
|
||||
#include "SpanStream.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
@ -55,7 +55,7 @@ class OFstreamCollator;
|
||||
|
||||
class threadedCollatedOFstream
|
||||
:
|
||||
public OStringStream
|
||||
public OCharStream
|
||||
{
|
||||
// Private Data
|
||||
|
||||
@ -78,6 +78,11 @@ class threadedCollatedOFstream
|
||||
dictionary headerEntries_;
|
||||
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
//- Commit buffered information
|
||||
void commit();
|
||||
|
||||
public:
|
||||
|
||||
// Constructors
|
||||
@ -102,12 +107,14 @@ public:
|
||||
);
|
||||
|
||||
|
||||
//- Destructor
|
||||
//- Destructor - commits buffered information to file
|
||||
~threadedCollatedOFstream();
|
||||
|
||||
|
||||
// Member Functions
|
||||
|
||||
// -> using OCharStream::rewind
|
||||
|
||||
//- Define the header entries for the data block(s)
|
||||
void setHeaderEntries(const dictionary& dict);
|
||||
};
|
||||
|
Loading…
Reference in New Issue
Block a user