mirror of
https://github.com/paboyle/Grid.git
synced 2024-09-20 09:15:38 +01:00
6aeaf6f568
turned up problems on the BlueWaters Cray. Gets 75MB/s from home filesystem on parallel configuration read. Need to make the RNG IO parallel, and also to look at aggregating bigger writes for the parallel write. Not sure what the home filesystem is.
652 lines
19 KiB
C++
652 lines
19 KiB
C++
/*************************************************************************************
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Grid physics library, www.github.com/paboyle/Grid
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Source file: ./lib/parallelIO/BinaryIO.h
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Copyright (C) 2015
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Author: Peter Boyle <paboyle@ph.ed.ac.uk>
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Author: paboyle <paboyle@ph.ed.ac.uk>
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation; either version 2 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License along
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with this program; if not, write to the Free Software Foundation, Inc.,
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51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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See the full license in the file "LICENSE" in the top level distribution directory
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*************************************************************************************/
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/* END LEGAL */
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#ifndef GRID_BINARY_IO_H
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#define GRID_BINARY_IO_H
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#ifdef HAVE_ENDIAN_H
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#include <endian.h>
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#endif
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#include <arpa/inet.h>
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#include <algorithm>
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// 64bit endian swap is a portability pain
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#ifndef __has_builtin // Optional of course.
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#define __has_builtin(x) 0 // Compatibility with non-clang compilers.
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#endif
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#if HAVE_DECL_BE64TOH
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#undef Grid_ntohll
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#define Grid_ntohll be64toh
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#endif
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#if HAVE_DECL_NTOHLL
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#undef Grid_ntohll
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#define Grid_ntohll ntohll
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#endif
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#ifndef Grid_ntohll
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#if BYTE_ORDER == BIG_ENDIAN
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#define Grid_ntohll(A) (A)
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#else
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#if __has_builtin(__builtin_bswap64)
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#define Grid_ntohll(A) __builtin_bswap64(A)
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#else
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#error
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#endif
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#endif
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#endif
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namespace Grid {
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// A little helper
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inline void removeWhitespace(std::string &key)
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{
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key.erase(std::remove_if(key.begin(), key.end(), ::isspace),key.end());
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}
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class BinaryIO {
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public:
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// Network is big endian
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static inline void htobe32_v(void *file_object,uint32_t bytes){ be32toh_v(file_object,bytes);}
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static inline void htobe64_v(void *file_object,uint32_t bytes){ be64toh_v(file_object,bytes);}
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static inline void htole32_v(void *file_object,uint32_t bytes){ le32toh_v(file_object,bytes);}
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static inline void htole64_v(void *file_object,uint32_t bytes){ le64toh_v(file_object,bytes);}
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static inline void be32toh_v(void *file_object,uint32_t bytes)
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{
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uint32_t * f = (uint32_t *)file_object;
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for(int i=0;i*sizeof(uint32_t)<bytes;i++){
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f[i] = ntohl(f[i]);
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}
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}
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// LE must Swap and switch to host
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static inline void le32toh_v(void *file_object,uint32_t bytes)
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{
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uint32_t *fp = (uint32_t *)file_object;
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uint32_t f;
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for(int i=0;i*sizeof(uint32_t)<bytes;i++){
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f = fp[i];
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// got network order and the network to host
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f = ((f&0xFF)<<24) | ((f&0xFF00)<<8) | ((f&0xFF0000)>>8) | ((f&0xFF000000UL)>>24) ;
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fp[i] = ntohl(f);
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}
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}
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// BE is same as network
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static inline void be64toh_v(void *file_object,uint32_t bytes)
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{
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uint64_t * f = (uint64_t *)file_object;
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for(int i=0;i*sizeof(uint64_t)<bytes;i++){
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f[i] = Grid_ntohll(f[i]);
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}
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}
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// LE must swap and switch;
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static inline void le64toh_v(void *file_object,uint32_t bytes)
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{
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uint64_t *fp = (uint64_t *)file_object;
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uint64_t f,g;
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for(int i=0;i*sizeof(uint64_t)<bytes;i++){
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f = fp[i];
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// got network order and the network to host
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g = ((f&0xFF)<<24) | ((f&0xFF00)<<8) | ((f&0xFF0000)>>8) | ((f&0xFF000000UL)>>24) ;
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g = g << 32;
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f = f >> 32;
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g|= ((f&0xFF)<<24) | ((f&0xFF00)<<8) | ((f&0xFF0000)>>8) | ((f&0xFF000000UL)>>24) ;
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fp[i] = Grid_ntohll(g);
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}
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}
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template<class vobj,class fobj,class munger> static inline void Uint32Checksum(Lattice<vobj> &lat,munger munge,uint32_t &csum)
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{
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typedef typename vobj::scalar_object sobj;
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GridBase *grid = lat._grid ;
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std::cout <<GridLogMessage<< "Uint32Checksum "<<norm2(lat)<<std::endl;
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sobj siteObj;
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fobj fileObj;
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csum = 0;
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std::vector<int> lcoor;
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for(int l=0;l<grid->lSites();l++){
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Lexicographic::CoorFromIndex(lcoor,l,grid->_ldimensions);
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peekLocalSite(siteObj,lat,lcoor);
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munge(siteObj,fileObj,csum);
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}
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grid->GlobalSum(csum);
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}
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static inline void Uint32Checksum(uint32_t *buf,uint32_t buf_size_bytes,uint32_t &csum)
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{
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for(int i=0;i*sizeof(uint32_t)<buf_size_bytes;i++){
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csum=csum+buf[i];
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}
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}
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template<class vobj,class fobj,class munger>
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static inline uint32_t readObjectSerial(Lattice<vobj> &Umu,std::string file,munger munge,int offset,const std::string &format)
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{
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typedef typename vobj::scalar_object sobj;
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GridBase *grid = Umu._grid;
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std::cout<< GridLogMessage<< "Serial read I/O "<< file<< std::endl;
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int ieee32big = (format == std::string("IEEE32BIG"));
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int ieee32 = (format == std::string("IEEE32"));
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int ieee64big = (format == std::string("IEEE64BIG"));
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int ieee64 = (format == std::string("IEEE64"));
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// Find the location of each site and send to primary node
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// Take loop order from Chroma; defines loop order now that NERSC doc no longer
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// available (how short sighted is that?)
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std::ifstream fin(file,std::ios::binary|std::ios::in);
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fin.seekg(offset);
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Umu = zero;
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uint32_t csum=0;
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fobj file_object;
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sobj munged;
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for(int t=0;t<grid->_fdimensions[3];t++){
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for(int z=0;z<grid->_fdimensions[2];z++){
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for(int y=0;y<grid->_fdimensions[1];y++){
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for(int x=0;x<grid->_fdimensions[0];x++){
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std::vector<int> site({x,y,z,t});
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if ( grid->IsBoss() ) {
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fin.read((char *)&file_object,sizeof(file_object));
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if(ieee32big) be32toh_v((void *)&file_object,sizeof(file_object));
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if(ieee32) le32toh_v((void *)&file_object,sizeof(file_object));
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if(ieee64big) be64toh_v((void *)&file_object,sizeof(file_object));
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if(ieee64) le64toh_v((void *)&file_object,sizeof(file_object));
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munge(file_object,munged,csum);
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}
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// The boss who read the file has their value poked
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pokeSite(munged,Umu,site);
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}}}}
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return csum;
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}
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template<class vobj,class fobj,class munger>
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static inline uint32_t writeObjectSerial(Lattice<vobj> &Umu,std::string file,munger munge,int offset,const std::string & format)
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{
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typedef typename vobj::scalar_object sobj;
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GridBase *grid = Umu._grid;
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int ieee32big = (format == std::string("IEEE32BIG"));
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int ieee32 = (format == std::string("IEEE32"));
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int ieee64big = (format == std::string("IEEE64BIG"));
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int ieee64 = (format == std::string("IEEE64"));
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//////////////////////////////////////////////////
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// Serialise through node zero
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//////////////////////////////////////////////////
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std::cout<< GridLogMessage<< "Serial write I/O "<< file<<std::endl;
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std::ofstream fout;
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if ( grid->IsBoss() ) {
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fout.open(file,std::ios::binary|std::ios::out|std::ios::in);
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fout.seekp(offset);
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}
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uint32_t csum=0;
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fobj file_object;
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sobj unmunged;
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for(int t=0;t<grid->_fdimensions[3];t++){
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for(int z=0;z<grid->_fdimensions[2];z++){
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for(int y=0;y<grid->_fdimensions[1];y++){
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for(int x=0;x<grid->_fdimensions[0];x++){
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std::vector<int> site({x,y,z,t});
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// peek & write
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peekSite(unmunged,Umu,site);
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munge(unmunged,file_object,csum);
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if ( grid->IsBoss() ) {
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if(ieee32big) htobe32_v((void *)&file_object,sizeof(file_object));
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if(ieee32) htole32_v((void *)&file_object,sizeof(file_object));
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if(ieee64big) htobe64_v((void *)&file_object,sizeof(file_object));
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if(ieee64) htole64_v((void *)&file_object,sizeof(file_object));
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fout.write((char *)&file_object,sizeof(file_object));
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}
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}}}}
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return csum;
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}
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static inline uint32_t writeRNGSerial(GridSerialRNG &serial,GridParallelRNG ¶llel,std::string file,int offset)
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{
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typedef typename GridSerialRNG::RngStateType RngStateType;
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const int RngStateCount = GridSerialRNG::RngStateCount;
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GridBase *grid = parallel._grid;
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int gsites = grid->_gsites;
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//////////////////////////////////////////////////
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// Serialise through node zero
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//////////////////////////////////////////////////
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std::cout<< GridLogMessage<< "Serial RNG write I/O "<< file<<std::endl;
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std::ofstream fout;
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if ( grid->IsBoss() ) {
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fout.open(file,std::ios::binary|std::ios::out|std::ios::in);
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fout.seekp(offset);
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}
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uint32_t csum=0;
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std::vector<RngStateType> saved(RngStateCount);
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int bytes = sizeof(RngStateType)*saved.size();
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std::vector<int> gcoor;
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for(int gidx=0;gidx<gsites;gidx++){
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int rank,o_idx,i_idx;
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grid->GlobalIndexToGlobalCoor(gidx,gcoor);
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grid->GlobalCoorToRankIndex(rank,o_idx,i_idx,gcoor);
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int l_idx=parallel.generator_idx(o_idx,i_idx);
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if( rank == grid->ThisRank() ){
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// std::cout << "rank" << rank<<" Getting state for index "<<l_idx<<std::endl;
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parallel.GetState(saved,l_idx);
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}
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grid->Broadcast(rank,(void *)&saved[0],bytes);
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if ( grid->IsBoss() ) {
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Uint32Checksum((uint32_t *)&saved[0],bytes,csum);
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fout.write((char *)&saved[0],bytes);
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}
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}
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if ( grid->IsBoss() ) {
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serial.GetState(saved,0);
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Uint32Checksum((uint32_t *)&saved[0],bytes,csum);
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fout.write((char *)&saved[0],bytes);
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}
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grid->Broadcast(0,(void *)&csum,sizeof(csum));
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return csum;
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}
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static inline uint32_t readRNGSerial(GridSerialRNG &serial,GridParallelRNG ¶llel,std::string file,int offset)
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{
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typedef typename GridSerialRNG::RngStateType RngStateType;
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const int RngStateCount = GridSerialRNG::RngStateCount;
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GridBase *grid = parallel._grid;
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int gsites = grid->_gsites;
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//////////////////////////////////////////////////
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// Serialise through node zero
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//////////////////////////////////////////////////
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std::cout<< GridLogMessage<< "Serial RNG read I/O "<< file<<std::endl;
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std::ifstream fin(file,std::ios::binary|std::ios::in);
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fin.seekg(offset);
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uint32_t csum=0;
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std::vector<RngStateType> saved(RngStateCount);
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int bytes = sizeof(RngStateType)*saved.size();
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std::vector<int> gcoor;
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for(int gidx=0;gidx<gsites;gidx++){
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int rank,o_idx,i_idx;
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grid->GlobalIndexToGlobalCoor(gidx,gcoor);
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grid->GlobalCoorToRankIndex(rank,o_idx,i_idx,gcoor);
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int l_idx=parallel.generator_idx(o_idx,i_idx);
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if ( grid->IsBoss() ) {
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fin.read((char *)&saved[0],bytes);
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Uint32Checksum((uint32_t *)&saved[0],bytes,csum);
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}
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grid->Broadcast(0,(void *)&saved[0],bytes);
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if( rank == grid->ThisRank() ){
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parallel.SetState(saved,l_idx);
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}
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}
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if ( grid->IsBoss() ) {
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fin.read((char *)&saved[0],bytes);
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serial.SetState(saved,0);
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Uint32Checksum((uint32_t *)&saved[0],bytes,csum);
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}
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grid->Broadcast(0,(void *)&csum,sizeof(csum));
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return csum;
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}
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template<class vobj,class fobj,class munger>
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static inline uint32_t readObjectParallel(Lattice<vobj> &Umu,std::string file,munger munge,int offset,const std::string &format)
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{
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typedef typename vobj::scalar_object sobj;
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GridBase *grid = Umu._grid;
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int ieee32big = (format == std::string("IEEE32BIG"));
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int ieee32 = (format == std::string("IEEE32"));
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int ieee64big = (format == std::string("IEEE64BIG"));
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int ieee64 = (format == std::string("IEEE64"));
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// Take into account block size of parallel file systems want about
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// 4-16MB chunks.
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// Ideally one reader/writer per xy plane and read these contiguously
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// with comms from nominated I/O nodes.
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std::ifstream fin;
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int nd = grid->_ndimension;
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std::vector<int> parallel(nd,1);
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std::vector<int> ioproc (nd);
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std::vector<int> start(nd);
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std::vector<int> range(nd);
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for(int d=0;d<nd;d++){
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assert(grid->CheckerBoarded(d) == 0);
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}
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uint64_t slice_vol = 1;
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int IOnode = 1;
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for(int d=0;d<grid->_ndimension;d++) {
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if ( d == 0 ) parallel[d] = 0;
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if (parallel[d]) {
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range[d] = grid->_ldimensions[d];
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start[d] = grid->_processor_coor[d]*range[d];
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ioproc[d]= grid->_processor_coor[d];
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} else {
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range[d] = grid->_gdimensions[d];
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start[d] = 0;
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ioproc[d]= 0;
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if ( grid->_processor_coor[d] != 0 ) IOnode = 0;
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}
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slice_vol = slice_vol * range[d];
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}
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{
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uint32_t tmp = IOnode;
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grid->GlobalSum(tmp);
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std::cout<< std::dec ;
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std::cout<< GridLogMessage<< "Parallel read I/O to "<< file << " with " <<tmp<< " IOnodes for subslice ";
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for(int d=0;d<grid->_ndimension;d++){
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std::cout<< range[d];
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if( d< grid->_ndimension-1 )
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std::cout<< " x ";
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}
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std::cout << std::endl;
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}
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int myrank = grid->ThisRank();
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int iorank = grid->RankFromProcessorCoor(ioproc);
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if ( IOnode ) {
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fin.open(file,std::ios::binary|std::ios::in);
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}
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//////////////////////////////////////////////////////////
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// Find the location of each site and send to primary node
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// Take loop order from Chroma; defines loop order now that NERSC doc no longer
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// available (how short sighted is that?)
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//////////////////////////////////////////////////////////
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Umu = zero;
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static uint32_t csum=0;
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fobj fileObj;
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static sobj siteObj; // Static to place in symmetric region for SHMEM
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// need to implement these loops in Nd independent way with a lexico conversion
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for(int tlex=0;tlex<slice_vol;tlex++){
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std::vector<int> tsite(nd); // temporary mixed up site
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std::vector<int> gsite(nd);
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std::vector<int> lsite(nd);
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std::vector<int> iosite(nd);
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Lexicographic::CoorFromIndex(tsite,tlex,range);
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for(int d=0;d<nd;d++){
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lsite[d] = tsite[d]%grid->_ldimensions[d]; // local site
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gsite[d] = tsite[d]+start[d]; // global site
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}
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/////////////////////////
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// Get the rank of owner of data
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/////////////////////////
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int rank, o_idx,i_idx, g_idx;
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grid->GlobalCoorToRankIndex(rank,o_idx,i_idx,gsite);
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grid->GlobalCoorToGlobalIndex(gsite,g_idx);
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////////////////////////////////
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// iorank reads from the seek
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////////////////////////////////
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if (myrank == iorank) {
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fin.seekg(offset+g_idx*sizeof(fileObj));
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fin.read((char *)&fileObj,sizeof(fileObj));
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if(ieee32big) be32toh_v((void *)&fileObj,sizeof(fileObj));
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if(ieee32) le32toh_v((void *)&fileObj,sizeof(fileObj));
|
|
if(ieee64big) be64toh_v((void *)&fileObj,sizeof(fileObj));
|
|
if(ieee64) le64toh_v((void *)&fileObj,sizeof(fileObj));
|
|
|
|
munge(fileObj,siteObj,csum);
|
|
|
|
}
|
|
|
|
// Possibly do transport through pt2pt
|
|
if ( rank != iorank ) {
|
|
if ( (myrank == rank) || (myrank==iorank) ) {
|
|
grid->SendRecvPacket((void *)&siteObj,(void *)&siteObj,iorank,rank,sizeof(siteObj));
|
|
}
|
|
}
|
|
// Poke at destination
|
|
if ( myrank == rank ) {
|
|
pokeLocalSite(siteObj,Umu,lsite);
|
|
}
|
|
grid->Barrier(); // necessary?
|
|
}
|
|
|
|
grid->GlobalSum(csum);
|
|
grid->Barrier();
|
|
|
|
return csum;
|
|
}
|
|
|
|
//////////////////////////////////////////////////////////
|
|
// Parallel writer
|
|
//////////////////////////////////////////////////////////
|
|
template<class vobj,class fobj,class munger>
|
|
static inline uint32_t writeObjectParallel(Lattice<vobj> &Umu,std::string file,munger munge,int offset,const std::string & format)
|
|
{
|
|
typedef typename vobj::scalar_object sobj;
|
|
GridBase *grid = Umu._grid;
|
|
|
|
int ieee32big = (format == std::string("IEEE32BIG"));
|
|
int ieee32 = (format == std::string("IEEE32"));
|
|
int ieee64big = (format == std::string("IEEE64BIG"));
|
|
int ieee64 = (format == std::string("IEEE64"));
|
|
|
|
int nd = grid->_ndimension;
|
|
for(int d=0;d<nd;d++){
|
|
assert(grid->CheckerBoarded(d) == 0);
|
|
}
|
|
|
|
std::vector<int> parallel(nd,1);
|
|
std::vector<int> ioproc (nd);
|
|
std::vector<int> start(nd);
|
|
std::vector<int> range(nd);
|
|
|
|
uint64_t slice_vol = 1;
|
|
|
|
int IOnode = 1;
|
|
|
|
for(int d=0;d<grid->_ndimension;d++) {
|
|
|
|
if ( d!= grid->_ndimension-1 ) parallel[d] = 0;
|
|
|
|
if (parallel[d]) {
|
|
range[d] = grid->_ldimensions[d];
|
|
start[d] = grid->_processor_coor[d]*range[d];
|
|
ioproc[d]= grid->_processor_coor[d];
|
|
} else {
|
|
range[d] = grid->_gdimensions[d];
|
|
start[d] = 0;
|
|
ioproc[d]= 0;
|
|
|
|
if ( grid->_processor_coor[d] != 0 ) IOnode = 0;
|
|
}
|
|
|
|
slice_vol = slice_vol * range[d];
|
|
}
|
|
|
|
{
|
|
uint32_t tmp = IOnode;
|
|
grid->GlobalSum(tmp);
|
|
std::cout<< GridLogMessage<< "Parallel write I/O from "<< file << " with " <<tmp<< " IOnodes for subslice ";
|
|
for(int d=0;d<grid->_ndimension;d++){
|
|
std::cout<< range[d];
|
|
if( d< grid->_ndimension-1 )
|
|
std::cout<< " x ";
|
|
}
|
|
std::cout << std::endl;
|
|
}
|
|
|
|
int myrank = grid->ThisRank();
|
|
int iorank = grid->RankFromProcessorCoor(ioproc);
|
|
|
|
// Take into account block size of parallel file systems want about
|
|
// 4-16MB chunks.
|
|
// Ideally one reader/writer per xy plane and read these contiguously
|
|
// with comms from nominated I/O nodes.
|
|
std::ofstream fout;
|
|
if ( IOnode ) fout.open(file,std::ios::binary|std::ios::in|std::ios::out);
|
|
|
|
//////////////////////////////////////////////////////////
|
|
// Find the location of each site and send to primary node
|
|
// Take loop order from Chroma; defines loop order now that NERSC doc no longer
|
|
// available (how short sighted is that?)
|
|
//////////////////////////////////////////////////////////
|
|
|
|
uint32_t csum=0;
|
|
fobj fileObj;
|
|
static sobj siteObj; // static for SHMEM target; otherwise dynamic allocate with AlignedAllocator
|
|
|
|
// should aggregate a whole chunk and then write.
|
|
// need to implement these loops in Nd independent way with a lexico conversion
|
|
for(int tlex=0;tlex<slice_vol;tlex++){
|
|
|
|
std::vector<int> tsite(nd); // temporary mixed up site
|
|
std::vector<int> gsite(nd);
|
|
std::vector<int> lsite(nd);
|
|
std::vector<int> iosite(nd);
|
|
|
|
Lexicographic::CoorFromIndex(tsite,tlex,range);
|
|
|
|
for(int d=0;d<nd;d++){
|
|
lsite[d] = tsite[d]%grid->_ldimensions[d]; // local site
|
|
gsite[d] = tsite[d]+start[d]; // global site
|
|
}
|
|
|
|
|
|
/////////////////////////
|
|
// Get the rank of owner of data
|
|
/////////////////////////
|
|
int rank, o_idx,i_idx, g_idx;
|
|
grid->GlobalCoorToRankIndex(rank,o_idx,i_idx,gsite);
|
|
grid->GlobalCoorToGlobalIndex(gsite,g_idx);
|
|
|
|
////////////////////////////////
|
|
// iorank writes from the seek
|
|
////////////////////////////////
|
|
|
|
// Owner of data peeks it
|
|
peekLocalSite(siteObj,Umu,lsite);
|
|
|
|
// Pair of nodes may need to do pt2pt send
|
|
if ( rank != iorank ) { // comms is necessary
|
|
if ( (myrank == rank) || (myrank==iorank) ) { // and we have to do it
|
|
// Send to IOrank
|
|
grid->SendRecvPacket((void *)&siteObj,(void *)&siteObj,rank,iorank,sizeof(siteObj));
|
|
}
|
|
}
|
|
|
|
grid->Barrier(); // necessary?
|
|
|
|
if (myrank == iorank) {
|
|
|
|
munge(siteObj,fileObj,csum);
|
|
|
|
if(ieee32big) htobe32_v((void *)&fileObj,sizeof(fileObj));
|
|
if(ieee32) htole32_v((void *)&fileObj,sizeof(fileObj));
|
|
if(ieee64big) htobe64_v((void *)&fileObj,sizeof(fileObj));
|
|
if(ieee64) htole64_v((void *)&fileObj,sizeof(fileObj));
|
|
|
|
fout.seekp(offset+g_idx*sizeof(fileObj));
|
|
fout.write((char *)&fileObj,sizeof(fileObj));
|
|
|
|
}
|
|
}
|
|
|
|
grid->GlobalSum(csum);
|
|
|
|
return csum;
|
|
}
|
|
|
|
};
|
|
|
|
}
|
|
|
|
#endif
|