/************************************************************************************* Grid physics library, www.github.com/paboyle/Grid Source file: ./lib/parallelIO/BinaryIO.h Copyright (C) 2015 Author: Peter Boyle Author: Guido Cossu This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. See the full license in the file "LICENSE" in the top level distribution directory *************************************************************************************/ /* END LEGAL */ #ifndef GRID_BINARY_IO_H #define GRID_BINARY_IO_H #if defined(GRID_COMMS_MPI) || defined(GRID_COMMS_MPI3) || defined(GRID_COMMS_MPIT) #define USE_MPI_IO #else #undef USE_MPI_IO #endif #ifdef HAVE_ENDIAN_H #include #endif #include #include namespace Grid { ///////////////////////////////////////////////////////////////////////////////// // Byte reversal garbage ///////////////////////////////////////////////////////////////////////////////// inline uint32_t byte_reverse32(uint32_t f) { f = ((f&0xFF)<<24) | ((f&0xFF00)<<8) | ((f&0xFF0000)>>8) | ((f&0xFF000000UL)>>24) ; return f; } inline uint64_t byte_reverse64(uint64_t f) { uint64_t g; g = ((f&0xFF)<<24) | ((f&0xFF00)<<8) | ((f&0xFF0000)>>8) | ((f&0xFF000000UL)>>24) ; g = g << 32; f = f >> 32; g|= ((f&0xFF)<<24) | ((f&0xFF00)<<8) | ((f&0xFF0000)>>8) | ((f&0xFF000000UL)>>24) ; return g; } #if BYTE_ORDER == BIG_ENDIAN inline uint64_t Grid_ntohll(uint64_t A) { return A; } #else inline uint64_t Grid_ntohll(uint64_t A) { return byte_reverse64(A); } #endif // A little helper inline void removeWhitespace(std::string &key) { key.erase(std::remove_if(key.begin(), key.end(), ::isspace),key.end()); } /////////////////////////////////////////////////////////////////////////////////////////////////// // Static class holding the parallel IO code // Could just use a namespace /////////////////////////////////////////////////////////////////////////////////////////////////// class BinaryIO { public: ///////////////////////////////////////////////////////////////////////////// // more byte manipulation helpers ///////////////////////////////////////////////////////////////////////////// template static inline void Uint32Checksum(Lattice &lat,uint32_t &nersc_csum) { typedef typename vobj::scalar_object sobj; GridBase *grid = lat._grid; uint64_t lsites = grid->lSites(); std::vector scalardata(lsites); unvectorizeToLexOrdArray(scalardata,lat); NerscChecksum(grid,scalardata,nersc_csum); } template static inline void NerscChecksum(GridBase *grid, std::vector &fbuf, uint32_t &nersc_csum) { const uint64_t size32 = sizeof(fobj) / sizeof(uint32_t); uint64_t lsites = grid->lSites(); if (fbuf.size() == 1) { lsites = 1; } PARALLEL_REGION { uint32_t nersc_csum_thr = 0; PARALLEL_FOR_LOOP_INTERN for (uint64_t local_site = 0; local_site < lsites; local_site++) { uint32_t *site_buf = (uint32_t *)&fbuf[local_site]; for (uint64_t j = 0; j < size32; j++) { nersc_csum_thr = nersc_csum_thr + site_buf[j]; } } PARALLEL_CRITICAL { nersc_csum += nersc_csum_thr; } } } template static inline void ScidacChecksum(GridBase *grid,std::vector &fbuf,uint32_t &scidac_csuma,uint32_t &scidac_csumb) { const uint64_t size32 = sizeof(fobj)/sizeof(uint32_t); int nd = grid->_ndimension; uint64_t lsites =grid->lSites(); if (fbuf.size()==1) { lsites=1; } std::vector local_vol =grid->LocalDimensions(); std::vector local_start =grid->LocalStarts(); std::vector global_vol =grid->FullDimensions(); PARALLEL_REGION { std::vector coor(nd); uint32_t scidac_csuma_thr=0; uint32_t scidac_csumb_thr=0; uint32_t site_crc=0; PARALLEL_FOR_LOOP_INTERN for(uint64_t local_site=0;local_site>(32-gsite29); scidac_csumb_thr ^= site_crc<>(32-gsite31); } PARALLEL_CRITICAL { scidac_csuma^= scidac_csuma_thr; scidac_csumb^= scidac_csumb_thr; } } } // Network is big endian static inline void htobe32_v(void *file_object,uint32_t bytes){ be32toh_v(file_object,bytes);} static inline void htobe64_v(void *file_object,uint32_t bytes){ be64toh_v(file_object,bytes);} static inline void htole32_v(void *file_object,uint32_t bytes){ le32toh_v(file_object,bytes);} static inline void htole64_v(void *file_object,uint32_t bytes){ le64toh_v(file_object,bytes);} static inline void be32toh_v(void *file_object,uint64_t bytes) { uint32_t * f = (uint32_t *)file_object; uint64_t count = bytes/sizeof(uint32_t); parallel_for(uint64_t i=0;i>8) | ((f&0xFF000000UL)>>24) ; fp[i] = ntohl(f); } } // BE is same as network static inline void be64toh_v(void *file_object,uint64_t bytes) { uint64_t * f = (uint64_t *)file_object; uint64_t count = bytes/sizeof(uint64_t); parallel_for(uint64_t i=0;i>8) | ((f&0xFF000000UL)>>24) ; g = g << 32; f = f >> 32; g|= ((f&0xFF)<<24) | ((f&0xFF00)<<8) | ((f&0xFF0000)>>8) | ((f&0xFF000000UL)>>24) ; fp[i] = Grid_ntohll(g); } } ///////////////////////////////////////////////////////////////////////////// // Real action: // Read or Write distributed lexico array of ANY object to a specific location in file ////////////////////////////////////////////////////////////////////////////////////// static const int BINARYIO_MASTER_APPEND = 0x10; static const int BINARYIO_UNORDERED = 0x08; static const int BINARYIO_LEXICOGRAPHIC = 0x04; static const int BINARYIO_READ = 0x02; static const int BINARYIO_WRITE = 0x01; template static inline void IOobject(word w, GridBase *grid, std::vector &iodata, std::string file, uint64_t& offset, const std::string &format, int control, uint32_t &nersc_csum, uint32_t &scidac_csuma, uint32_t &scidac_csumb) { grid->Barrier(); GridStopWatch timer; GridStopWatch bstimer; nersc_csum=0; scidac_csuma=0; scidac_csumb=0; int ndim = grid->Dimensions(); int nrank = grid->ProcessorCount(); int myrank = grid->ThisRank(); std::vector psizes = grid->ProcessorGrid(); std::vector pcoor = grid->ThisProcessorCoor(); std::vector gLattice= grid->GlobalDimensions(); std::vector lLattice= grid->LocalDimensions(); std::vector lStart(ndim); std::vector gStart(ndim); // Flatten the file uint64_t lsites = grid->lSites(); if ( control & BINARYIO_MASTER_APPEND ) { assert(iodata.size()==1); } else { assert(lsites==iodata.size()); } for(int d=0;d distribs(ndim,MPI_DISTRIBUTE_BLOCK); std::vector dargs (ndim,MPI_DISTRIBUTE_DFLT_DARG); MPI_Datatype mpiObject; MPI_Datatype fileArray; MPI_Datatype localArray; MPI_Datatype mpiword; MPI_Offset disp = offset; MPI_File fh ; MPI_Status status; int numword; if ( sizeof( word ) == sizeof(float ) ) { numword = sizeof(fobj)/sizeof(float); mpiword = MPI_FLOAT; } else { numword = sizeof(fobj)/sizeof(double); mpiword = MPI_DOUBLE; } ////////////////////////////////////////////////////////////////////////////// // Sobj in MPI phrasing ////////////////////////////////////////////////////////////////////////////// int ierr; ierr = MPI_Type_contiguous(numword,mpiword,&mpiObject); assert(ierr==0); ierr = MPI_Type_commit(&mpiObject); ////////////////////////////////////////////////////////////////////////////// // File global array data type ////////////////////////////////////////////////////////////////////////////// ierr=MPI_Type_create_subarray(ndim,&gLattice[0],&lLattice[0],&gStart[0],MPI_ORDER_FORTRAN, mpiObject,&fileArray); assert(ierr==0); ierr=MPI_Type_commit(&fileArray); assert(ierr==0); ////////////////////////////////////////////////////////////////////////////// // local lattice array ////////////////////////////////////////////////////////////////////////////// ierr=MPI_Type_create_subarray(ndim,&lLattice[0],&lLattice[0],&lStart[0],MPI_ORDER_FORTRAN, mpiObject,&localArray); assert(ierr==0); ierr=MPI_Type_commit(&localArray); assert(ierr==0); #endif ////////////////////////////////////////////////////////////////////////////// // Byte order ////////////////////////////////////////////////////////////////////////////// int ieee32big = (format == std::string("IEEE32BIG")); int ieee32 = (format == std::string("IEEE32")); int ieee64big = (format == std::string("IEEE64BIG")); int ieee64 = (format == std::string("IEEE64")); ////////////////////////////////////////////////////////////////////////////// // Do the I/O ////////////////////////////////////////////////////////////////////////////// if ( control & BINARYIO_READ ) { timer.Start(); if ( (control & BINARYIO_LEXICOGRAPHIC) && (nrank > 1) ) { #ifdef USE_MPI_IO std::cout<< GridLogMessage<<"IOobject: MPI read I/O "<< file<< std::endl; ierr=MPI_File_open(grid->communicator,(char *) file.c_str(), MPI_MODE_RDONLY, MPI_INFO_NULL, &fh); assert(ierr==0); ierr=MPI_File_set_view(fh, disp, mpiObject, fileArray, "native", MPI_INFO_NULL); assert(ierr==0); ierr=MPI_File_read_all(fh, &iodata[0], 1, localArray, &status); assert(ierr==0); MPI_Offset os; MPI_File_get_position(fh, &os); MPI_File_get_byte_offset(fh, os, &disp); offset = disp; MPI_File_close(&fh); MPI_Type_free(&fileArray); MPI_Type_free(&localArray); #else assert(0); #endif } else { std::cout << GridLogMessage <<"IOobject: C++ read I/O " << file << " : " << iodata.size() * sizeof(fobj) << " bytes and offset " << offset << std::endl; std::ifstream fin; fin.open(file, std::ios::binary | std::ios::in); if (0)//control & BINARYIO_MASTER_APPEND) { // Note Guido. Crosscheck this for the RNG case // why the negative offset? fin.seekg(-sizeof(fobj), fin.end); } else { fin.seekg(offset + myrank * lsites * sizeof(fobj)); } fin.read((char *)&iodata[0], iodata.size() * sizeof(fobj)); offset = fin.tellg(); assert(fin.fail() == 0); fin.close(); } timer.Stop(); grid->Barrier(); bstimer.Start(); ScidacChecksum(grid,iodata,scidac_csuma,scidac_csumb); if (ieee32big) be32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size()); if (ieee32) le32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size()); if (ieee64big) be64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size()); if (ieee64) le64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size()); NerscChecksum(grid,iodata,nersc_csum); bstimer.Stop(); } if ( control & BINARYIO_WRITE ) { bstimer.Start(); NerscChecksum(grid,iodata,nersc_csum); if (ieee32big) htobe32_v((void *)&iodata[0], sizeof(fobj)*iodata.size()); if (ieee32) htole32_v((void *)&iodata[0], sizeof(fobj)*iodata.size()); if (ieee64big) htobe64_v((void *)&iodata[0], sizeof(fobj)*iodata.size()); if (ieee64) htole64_v((void *)&iodata[0], sizeof(fobj)*iodata.size()); ScidacChecksum(grid,iodata,scidac_csuma,scidac_csumb); bstimer.Stop(); grid->Barrier(); timer.Start(); if ( (control & BINARYIO_LEXICOGRAPHIC) && (nrank > 1) ) { #ifdef USE_MPI_IO std::cout << GridLogMessage <<"IOobject: MPI write I/O " << file << std::endl; ierr = MPI_File_open(grid->communicator, (char *)file.c_str(), MPI_MODE_RDWR | MPI_MODE_CREATE, MPI_INFO_NULL, &fh); // std::cout << GridLogMessage << "Checking for errors" << std::endl; if (ierr != MPI_SUCCESS) { char error_string[BUFSIZ]; int length_of_error_string, error_class; MPI_Error_class(ierr, &error_class); MPI_Error_string(error_class, error_string, &length_of_error_string); fprintf(stderr, "%3d: %s\n", myrank, error_string); MPI_Error_string(ierr, error_string, &length_of_error_string); fprintf(stderr, "%3d: %s\n", myrank, error_string); MPI_Abort(MPI_COMM_WORLD, 1); //assert(ierr == 0); } std::cout << GridLogDebug << "MPI write I/O set view " << file << std::endl; ierr = MPI_File_set_view(fh, disp, mpiObject, fileArray, "native", MPI_INFO_NULL); assert(ierr == 0); std::cout << GridLogDebug << "MPI write I/O write all " << file << std::endl; ierr = MPI_File_write_all(fh, &iodata[0], 1, localArray, &status); assert(ierr == 0); MPI_Offset os; MPI_File_get_position(fh, &os); MPI_File_get_byte_offset(fh, os, &disp); offset = disp; MPI_File_close(&fh); MPI_Type_free(&fileArray); MPI_Type_free(&localArray); #else assert(0); #endif } else { std::cout << GridLogMessage << "IOobject: C++ write I/O " << file << " : " << iodata.size() * sizeof(fobj) << " bytes and offset " << offset << std::endl; std::ofstream fout; fout.exceptions ( std::fstream::failbit | std::fstream::badbit ); try { if (offset) { // Must already exist and contain data fout.open(file,std::ios::binary|std::ios::out|std::ios::in); } else { // Allow create fout.open(file,std::ios::binary|std::ios::out); } } catch (const std::fstream::failure& exc) { std::cout << GridLogError << "Error in opening the file " << file << " for output" <Barrier(); grid->GlobalSum(nersc_csum); grid->GlobalXOR(scidac_csuma); grid->GlobalXOR(scidac_csumb); grid->Barrier(); } } ///////////////////////////////////////////////////////////////////////////// // Read a Lattice of object ////////////////////////////////////////////////////////////////////////////////////// template static inline void readLatticeObject(Lattice &Umu, std::string file, munger munge, uint64_t offset, const std::string &format, uint32_t &nersc_csum, uint32_t &scidac_csuma, uint32_t &scidac_csumb) { typedef typename vobj::scalar_object sobj; typedef typename vobj::Realified::scalar_type word; word w=0; GridBase *grid = Umu._grid; uint64_t lsites = grid->lSites(); std::vector scalardata(lsites); std::vector iodata(lsites); // Munge, checksum, byte order in here IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_LEXICOGRAPHIC, nersc_csum,scidac_csuma,scidac_csumb); GridStopWatch timer; timer.Start(); parallel_for(uint64_t x=0;xBarrier(); timer.Stop(); std::cout< static inline void writeLatticeObject(Lattice &Umu, std::string file, munger munge, uint64_t offset, const std::string &format, uint32_t &nersc_csum, uint32_t &scidac_csuma, uint32_t &scidac_csumb) { typedef typename vobj::scalar_object sobj; typedef typename vobj::Realified::scalar_type word; word w=0; GridBase *grid = Umu._grid; uint64_t lsites = grid->lSites(); std::vector scalardata(lsites); std::vector iodata(lsites); // Munge, checksum, byte order in here ////////////////////////////////////////////////////////////////////////////// // Munge [ .e.g 3rd row recon ] ////////////////////////////////////////////////////////////////////////////// GridStopWatch timer; timer.Start(); unvectorizeToLexOrdArray(scalardata,Umu); parallel_for(uint64_t x=0;xBarrier(); timer.Stop(); IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_LEXICOGRAPHIC, nersc_csum,scidac_csuma,scidac_csumb); std::cout< RNGstate; typedef RngStateType word; word w=0; std::string format = "IEEE32BIG"; GridBase *grid = parallel._grid; uint64_t gsites = grid->gSites(); uint64_t lsites = grid->lSites(); uint32_t nersc_csum_tmp = 0; uint32_t scidac_csuma_tmp = 0; uint32_t scidac_csumb_tmp = 0; GridStopWatch timer; std::cout << GridLogMessage << "RNG read I/O on file " << file << std::endl; std::vector iodata(lsites); IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_LEXICOGRAPHIC, nersc_csum,scidac_csuma,scidac_csumb); std::cout << GridLogMessage << "RNG file nersc_checksum " << std::hex << nersc_csum << std::dec << std::endl; std::cout << GridLogMessage << "RNG file scidac_checksuma " << std::hex << scidac_csuma << std::dec << std::endl; std::cout << GridLogMessage << "RNG file scidac_checksumb " << std::hex << scidac_csumb << std::dec << std::endl; timer.Start(); parallel_for(uint64_t lidx=0;lidx tmp(RngStateCount); std::copy(iodata[lidx].begin(),iodata[lidx].end(),tmp.begin()); parallel.SetState(tmp,lidx); } timer.Stop(); iodata.resize(1); IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_MASTER_APPEND, nersc_csum_tmp,scidac_csuma_tmp,scidac_csumb_tmp); { std::vector tmp(RngStateCount); std::copy(iodata[0].begin(),iodata[0].end(),tmp.begin()); serial.SetState(tmp,0); } std::cout << GridLogMessage << "RNG file checksum t " << std::hex << nersc_csum_tmp << std::dec << std::endl; std::cout << GridLogMessage << "RNG file checksuma t " << std::hex << scidac_csuma_tmp << std::dec << std::endl; std::cout << GridLogMessage << "RNG file checksumb t " << std::hex << scidac_csumb_tmp << std::dec << std::endl; nersc_csum = nersc_csum + nersc_csum_tmp; scidac_csuma = scidac_csuma ^ scidac_csuma_tmp; scidac_csumb = scidac_csumb ^ scidac_csumb_tmp; std::cout << GridLogMessage << "RNG file nersc_checksum " << std::hex << nersc_csum << std::dec << std::endl; std::cout << GridLogMessage << "RNG file scidac_checksuma " << std::hex << scidac_csuma << std::dec << std::endl; std::cout << GridLogMessage << "RNG file scidac_checksumb " << std::hex << scidac_csumb << std::dec << std::endl; std::cout << GridLogMessage << "RNG state overhead " << timer.Elapsed() << std::endl; } ///////////////////////////////////////////////////////////////////////////// // Write a RNG; lexico map to an array of state and use IOobject ////////////////////////////////////////////////////////////////////////////////////// static inline void writeRNG(GridSerialRNG &serial, GridParallelRNG ¶llel, std::string file, uint64_t offset, uint32_t &nersc_csum, uint32_t &scidac_csuma, uint32_t &scidac_csumb) { typedef typename GridSerialRNG::RngStateType RngStateType; typedef RngStateType word; word w=0; const int RngStateCount = GridSerialRNG::RngStateCount; typedef std::array RNGstate; GridBase *grid = parallel._grid; uint64_t gsites = grid->gSites(); uint64_t lsites = grid->lSites(); uint32_t nersc_csum_tmp; uint32_t scidac_csuma_tmp; uint32_t scidac_csumb_tmp; GridStopWatch timer; std::string format = "IEEE32BIG"; std::cout << GridLogMessage << "RNG write I/O on file " << file << std::endl; timer.Start(); std::vector iodata(lsites); parallel_for(uint64_t lidx=0;lidx tmp(RngStateCount); parallel.GetState(tmp,lidx); std::copy(tmp.begin(),tmp.end(),iodata[lidx].begin()); } timer.Stop(); IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_LEXICOGRAPHIC, nersc_csum,scidac_csuma,scidac_csumb); std::cout << GridLogMessage << "RNG file checksum " << std::hex << nersc_csum << std::dec << std::endl; std::cout << GridLogMessage << "RNG file checksuma " << std::hex << scidac_csuma << std::dec << std::endl; std::cout << GridLogMessage << "RNG file checksumb " << std::hex << scidac_csumb << std::dec << std::endl; iodata.resize(1); { std::vector tmp(RngStateCount); serial.GetState(tmp,0); std::copy(tmp.begin(),tmp.end(),iodata[0].begin()); } IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_MASTER_APPEND, nersc_csum_tmp,scidac_csuma_tmp,scidac_csumb_tmp); std::cout << GridLogMessage << "RNG file checksum t " << std::hex << nersc_csum_tmp << std::dec << std::endl; std::cout << GridLogMessage << "RNG file checksuma t " << std::hex << scidac_csuma_tmp << std::dec << std::endl; std::cout << GridLogMessage << "RNG file checksumb t " << std::hex << scidac_csumb_tmp << std::dec << std::endl; nersc_csum = nersc_csum + nersc_csum_tmp; scidac_csuma = scidac_csuma ^ scidac_csuma_tmp; scidac_csumb = scidac_csumb ^ scidac_csumb_tmp; std::cout << GridLogMessage << "RNG file checksum " << std::hex << nersc_csum << std::dec << std::endl; std::cout << GridLogMessage << "RNG file checksuma " << std::hex << scidac_csuma << std::dec << std::endl; std::cout << GridLogMessage << "RNG file checksumb " << std::hex << scidac_csumb << std::dec << std::endl; std::cout << GridLogMessage << "RNG state overhead " << timer.Elapsed() << std::endl; } }; } #endif