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Got the NERSC IO working and fixed a bug in cshift.
This commit is contained in:
Peter Boyle
524
lib/parallelIO/GridNerscIO.h
Normal file
524
lib/parallelIO/GridNerscIO.h
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@@ -0,0 +1,524 @@
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#ifndef GRID_NERSC_IO_H
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#define GRID_NERSC_IO_H
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#include <algorithm>
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#include <iostream>
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#include <iomanip>
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#include <fstream>
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#include <arpa/inet.h>
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namespace Grid {
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using namespace QCD;
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////////////////////////////////////////////////////////////////////////////////
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// Some data types for intermediate storage
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////////////////////////////////////////////////////////////////////////////////
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template<typename vtype> using iLorentzColour2x3 = iVector<iVector<iVector<vtype, Nc>, 2>, 4 >;
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typedef iLorentzColour2x3<Complex> LorentzColour2x3;
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typedef iLorentzColour2x3<ComplexF> LorentzColour2x3F;
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typedef iLorentzColour2x3<ComplexD> LorentzColour2x3D;
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////////////////////////////////////////////////////////////////////////////////
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// header specification/interpretation
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////////////////////////////////////////////////////////////////////////////////
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class NerscField {
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public:
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// header strings (not in order)
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int dimension[4];
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std::string boundary[4];
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int data_start;
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std::string hdr_version;
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std::string storage_format;
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// Checks on data
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double link_trace;
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double plaquette;
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uint32_t checksum;
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unsigned int sequence_number;
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std::string data_type;
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std::string ensemble_id ;
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std::string ensemble_label ;
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std::string creator ;
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std::string creator_hardware ;
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std::string creation_date ;
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std::string archive_date ;
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std::string floating_point;
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};
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////////////////////////////////////////////////////////////////////////////////
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// Write and read from fstream; comput header offset for payload
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////////////////////////////////////////////////////////////////////////////////
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inline unsigned int writeNerscHeader(NerscField &field,std::string file)
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{
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std::ofstream fout(file,std::ios::out);
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fout.seekp(0,std::ios::beg);
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fout << "BEGIN_HEADER" << std::endl;
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fout << "HDR_VERSION = " << field.hdr_version << std::endl;
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fout << "DATATYPE = " << field.data_type << std::endl;
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fout << "STORAGE_FORMAT = " << field.storage_format << std::endl;
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for(int i=0;i<4;i++){
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fout << "DIMENSION_" << i+1 << " = " << field.dimension[i] << std::endl ;
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}
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// just to keep the space and write it later
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fout << "LINK_TRACE = " << std::setprecision(10) << field.link_trace << std::endl;
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fout << "PLAQUETTE = " << std::setprecision(10) << field.plaquette << std::endl;
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for(int i=0;i<4;i++){
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fout << "BOUNDARY_"<<i+1<<" = " << field.boundary[i] << std::endl;
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}
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fout << "CHECKSUM = "<< std::hex << std::setw(16) << 0 << field.checksum << std::endl;
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fout << "ENSEMBLE_ID = " << field.ensemble_id << std::endl;
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fout << "ENSEMBLE_LABEL = " << field.ensemble_label << std::endl;
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fout << "SEQUENCE_NUMBER = " << field.sequence_number << std::endl;
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fout << "CREATOR = " << field.creator << std::endl;
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fout << "CREATOR_HARDWARE = "<< field.creator_hardware << std::endl;
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fout << "CREATION_DATE = " << field.creation_date << std::endl;
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fout << "ARCHIVE_DATE = " << field.archive_date << std::endl;
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fout << "FLOATING_POINT = " << field.floating_point << std::endl;
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fout << "END_HEADER" << std::endl;
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field.data_start = fout.tellp();
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return field.data_start;
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}
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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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// for the header-reader
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inline int readNerscHeader(std::string file,GridBase *grid, NerscField &field)
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{
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int offset=0;
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std::map<std::string,std::string> header;
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std::string line;
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//////////////////////////////////////////////////
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// read the header
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//////////////////////////////////////////////////
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std::ifstream fin(file);
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getline(fin,line); // read one line and insist is
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removeWhitespace(line);
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assert(line==std::string("BEGIN_HEADER"));
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do {
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getline(fin,line); // read one line
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int eq = line.find("=");
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if(eq >0) {
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std::string key=line.substr(0,eq);
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std::string val=line.substr(eq+1);
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removeWhitespace(key);
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removeWhitespace(val);
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header[key] = val;
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}
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} while( line.find("END_HEADER") == std::string::npos );
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field.data_start = fin.tellg();
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//////////////////////////////////////////////////
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// chomp the values
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//////////////////////////////////////////////////
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field.hdr_version = header[std::string("HDR_VERSION")];
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field.data_type = header[std::string("DATATYPE")];
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field.storage_format = header[std::string("STORAGE_FORMAT")];
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field.dimension[0] = std::stol(header[std::string("DIMENSION_1")]);
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field.dimension[1] = std::stol(header[std::string("DIMENSION_2")]);
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field.dimension[2] = std::stol(header[std::string("DIMENSION_3")]);
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field.dimension[3] = std::stol(header[std::string("DIMENSION_4")]);
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assert(grid->_ndimension == 4);
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for(int d=0;d<4;d++){
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assert(grid->_fdimensions[d]==field.dimension[d]);
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}
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field.link_trace = std::stod(header[std::string("LINK_TRACE")]);
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field.plaquette = std::stod(header[std::string("PLAQUETTE")]);
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field.boundary[0] = header[std::string("BOUNDARY_1")];
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field.boundary[1] = header[std::string("BOUNDARY_2")];
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field.boundary[2] = header[std::string("BOUNDARY_3")];
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field.boundary[3] = header[std::string("BOUNDARY_4")];
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field.checksum = std::stoul(header[std::string("CHECKSUM")],0,16);
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field.ensemble_id = header[std::string("ENSEMBLE_ID")];
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field.ensemble_label = header[std::string("ENSEMBLE_LABEL")];
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field.sequence_number = std::stol(header[std::string("SEQUENCE_NUMBER")]);
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field.creator = header[std::string("CREATOR")];
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field.creator_hardware = header[std::string("CREATOR_HARDWARE")];
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field.creation_date = header[std::string("CREATION_DATE")];
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field.archive_date = header[std::string("ARCHIVE_DATE")];
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field.floating_point = header[std::string("FLOATING_POINT")];
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return field.data_start;
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}
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//////////////////////////////////////////////////////////////////////
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// Utilities
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//////////////////////////////////////////////////////////////////////
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inline void reconstruct3(LorentzColourMatrix & cm)
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{
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const int x=0;
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const int y=1;
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const int z=2;
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for(int mu=0;mu<4;mu++){
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cm(mu)()(2,x) = adj(cm(mu)()(0,y)*cm(mu)()(1,z)-cm(mu)()(0,z)*cm(mu)()(1,y)); //x= yz-zy
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cm(mu)()(2,y) = adj(cm(mu)()(0,z)*cm(mu)()(1,x)-cm(mu)()(0,x)*cm(mu)()(1,z)); //y= zx-xz
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cm(mu)()(2,z) = adj(cm(mu)()(0,x)*cm(mu)()(1,y)-cm(mu)()(0,y)*cm(mu)()(1,x)); //z= xy-yx
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}
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}
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void inline be32toh(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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void inline le32toh(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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void inline be64toh(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] = ntohll(f[i]);
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}
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}
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void inline le64toh(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] = ntohl(g);
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}
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}
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inline void NerscChecksum(uint32_t *buf,uint32_t buf_size,uint32_t &csum)
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{
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for(int i=0;i*sizeof(uint32_t)<buf_size;i++){
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csum=csum+buf[i];
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}
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}
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template<class fobj,class sobj>
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struct NerscSimpleMunger{
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void operator() (fobj &in,sobj &out,uint32_t &csum){
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for(int mu=0;mu<4;mu++){
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for(int i=0;i<3;i++){
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for(int j=0;j<3;j++){
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out(mu)()(i,j) = in(mu)()(i,j);
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}}}
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NerscChecksum((uint32_t *)&in,sizeof(in),csum);
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};
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};
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template<class fobj,class sobj>
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struct NerscSimpleUnmunger{
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void operator() (sobj &in,fobj &out,uint32_t &csum){
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for(int mu=0;mu<4;mu++){
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for(int i=0;i<3;i++){
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for(int j=0;j<3;j++){
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out(mu)()(i,j) = in(mu)()(i,j);
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}}}
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NerscChecksum((uint32_t *)&out,sizeof(out),csum);
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};
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};
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template<class fobj,class sobj>
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struct Nersc3x2munger{
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void operator() (fobj &in,sobj &out,uint32_t &csum){
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NerscChecksum((uint32_t *)&in,sizeof(in),csum);
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for(int mu=0;mu<4;mu++){
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for(int i=0;i<2;i++){
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for(int j=0;j<3;j++){
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out(mu)()(i,j) = in(mu)(i)(j);
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}}
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}
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reconstruct3(out);
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}
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};
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template<class fobj,class sobj>
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struct Nersc3x2unmunger{
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void operator() (sobj &in,fobj &out,uint32_t &csum){
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NerscChecksum((uint32_t *)&out,sizeof(out),csum);
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for(int mu=0;mu<4;mu++){
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for(int i=0;i<2;i++){
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for(int j=0;j<3;j++){
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out(mu)(i)(j) = in(mu)()(i,j);
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}}
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}
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}
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};
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////////////////////////////////////////////////////////////////////////////
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// Template wizardry to map types to strings for NERSC in an extensible way
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////////////////////////////////////////////////////////////////////////////
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template<class vobj> struct NerscDataType {
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static void DataType (std::string &str) { str = std::string("4D_BINARY_UNKNOWN"); };
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static void FloatingPoint(std::string &str) { str = std::string("IEEE64BIG"); };
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};
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template<> struct NerscDataType<iColourMatrix<ComplexD> > {
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static void DataType (std::string &str) { str = std::string("4D_SU3_GAUGE_3X3"); };
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static void FloatingPoint(std::string &str) { str = std::string("IEEE64BIG");};
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};
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template<> struct NerscDataType<iColourMatrix<ComplexF> > {
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static void DataType (std::string &str) { str = std::string("4D_SU3_GAUGE_3X3"); };
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static void FloatingPoint(std::string &str) { str = std::string("IEEE32BIG");};
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};
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//////////////////////////////////////////////////////////////////////
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// Bit and Physical Checksumming and QA of data
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//////////////////////////////////////////////////////////////////////
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/*
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template<class vobj> inline uint32_t NerscChecksum(Lattice<vobj> & data)
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{
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uint32_t sum;
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for(int ss=0;ss<data._grid->Osites();ss++){
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uint32_t *iptr = (uint32_t *)& data._odata[0] ;
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for(int i=0;i<sizeof(vobj);i+=sizeof(uint32_t)){
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sum=sum+iptr[i];
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}
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}
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data._grid->globalSum(sum);
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return sum;
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}
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*/
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template<class vobj> inline void NerscPhysicalCharacteristics(Lattice<vobj> & data,NerscField &header)
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{
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header.data_type = NerscDataType<vobj>::DataType;
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header.floating_point = NerscDataType<vobj>::FloatingPoint;
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return;
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}
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template<> inline void NerscPhysicalCharacteristics(LatticeGaugeField & data,NerscField &header)
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{
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NerscDataType<decltype(data._odata[0])>::DataType(header.data_type);
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NerscDataType<decltype(data._odata[0])>::FloatingPoint(header.floating_point);
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header.link_trace=1.0;
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header.plaquette =1.0;
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}
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template<class vobj> inline void NerscStatisics(Lattice<vobj> & data,NerscField &header)
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{
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assert(data._grid->_ndimension==4);
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for(int d=0;d<4;d++)
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header.dimension[d] = data._grid->_fdimensions[d];
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// compute checksum and any physical properties contained for this type
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// header.checksum = NerscChecksum(data);
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NerscPhysicalCharacteristics(data,header);
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}
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/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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// Now the meat: the object readers
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/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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template<class vobj,class sobj,class fobj,class munger>
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inline void readNerscObject(Lattice<vobj> &Umu,std::string file,munger munge,int offset,std::string &format)
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{
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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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// Find the location of each site and send to primary node
|
||||
// for(int site=0; site < Layout::vol(); ++site){
|
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// multi1d<int> coord = crtesn(site, Layout::lattSize());
|
||||
// for(int dd=0; dd<Nd; dd++){ /* dir */
|
||||
// cfg_in.readArray(su3_buffer, float_size, mat_size);
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//
|
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// Above from Chroma; defines loop order now that NERSC doc no longer
|
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// available (how short sighted is that?)
|
||||
{
|
||||
std::ifstream fin(file,std::ios::binary|std::ios::in);
|
||||
fin.seekg(offset);
|
||||
|
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Umu = zero;
|
||||
uint32_t csum=0;
|
||||
fobj file_object;
|
||||
sobj munged;
|
||||
|
||||
for(int t=0;t<grid->_fdimensions[3];t++){
|
||||
for(int z=0;z<grid->_fdimensions[2];z++){
|
||||
for(int y=0;y<grid->_fdimensions[1];y++){
|
||||
for(int x=0;x<grid->_fdimensions[0];x++){
|
||||
|
||||
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((void *)&file_object,sizeof(file_object));
|
||||
if(ieee32) le32toh((void *)&file_object,sizeof(file_object));
|
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if(ieee64big) be64toh((void *)&file_object,sizeof(file_object));
|
||||
if(ieee64) le64toh((void *)&file_object,sizeof(file_object));
|
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munge(file_object,munged,csum);
|
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}
|
||||
// The boss who read the file has their value poked
|
||||
pokeSite(munged,Umu,site);
|
||||
}}}}
|
||||
}
|
||||
}
|
||||
|
||||
template<class vobj,class sobj,class fobj,class munger>
|
||||
inline void writeNerscObject(Lattice<vobj> &Umu,std::string file,munger munge,int offset,
|
||||
int sequence,double lt,double pl)
|
||||
{
|
||||
GridBase *grid = Umu._grid;
|
||||
NerscField header;
|
||||
|
||||
//////////////////////////////////////////////////
|
||||
// First write the header; this is in wrong place
|
||||
//////////////////////////////////////////////////
|
||||
assert(grid->_ndimension == 4);
|
||||
for(int d=0;d<4;d++){
|
||||
header.dimension[d]=grid->_fdimensions[d];
|
||||
header.boundary [d]=std::string("PERIODIC");;
|
||||
}
|
||||
header.hdr_version=std::string("WHATDAHECK");
|
||||
// header.storage_format=storage_format<vobj>::string; // use template specialisation
|
||||
// header.data_type=data_type<vobj>::string;
|
||||
header.storage_format=std::string("debug");
|
||||
header.data_type =std::string("debug");
|
||||
|
||||
//FIXME; use template specialisation to fill these out
|
||||
header.link_trace =lt;
|
||||
header.plaquette =pl;
|
||||
header.checksum =0;
|
||||
|
||||
//
|
||||
header.sequence_number =sequence;
|
||||
header.ensemble_id =std::string("UKQCD");
|
||||
header.ensemble_label =std::string("UKQCD");
|
||||
header.creator =std::string("Tadahito");
|
||||
header.creator_hardware=std::string("BlueGene/Q");
|
||||
header.creation_date =std::string("AnnoDomini");
|
||||
header.archive_date =std::string("AnnoDomini");
|
||||
header.floating_point =std::string("IEEE64BIG");
|
||||
// header.data_start=;
|
||||
// unsigned int checksum;
|
||||
|
||||
//////////////////////////////////////////////////
|
||||
// Now write the body
|
||||
//////////////////////////////////////////////////
|
||||
{
|
||||
std::ofstream fout(file,std::ios::binary|std::ios::in);
|
||||
fout.seekp(offset);
|
||||
|
||||
Umu = zero;
|
||||
uint32_t csum=0;
|
||||
fobj file_object;
|
||||
sobj unmunged;
|
||||
for(int t=0;t<grid->_fdimensions[3];t++){
|
||||
for(int z=0;z<grid->_fdimensions[2];z++){
|
||||
for(int y=0;y<grid->_fdimensions[1];y++){
|
||||
for(int x=0;x<grid->_fdimensions[0];x++){
|
||||
std::vector<int> site({x,y,z,t});
|
||||
peekSite(unmunged,Umu,site);
|
||||
munge(unmunged,file_object,csum);
|
||||
// broadcast & insert
|
||||
fout.write((char *)&file_object,sizeof(file_object));
|
||||
}}}}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
inline void readNerscConfiguration(LatticeGaugeField &Umu,NerscField& header,std::string file)
|
||||
{
|
||||
GridBase *grid = Umu._grid;
|
||||
|
||||
int offset = readNerscHeader(file,Umu._grid,header);
|
||||
|
||||
std::string format(header.floating_point);
|
||||
|
||||
int ieee32big = (format == std::string("IEEE32BIG"));
|
||||
int ieee32 = (format == std::string("IEEE32"));
|
||||
int ieee64big = (format == std::string("IEEE64BIG"));
|
||||
int ieee64 = (format == std::string("IEEE64"));
|
||||
|
||||
// depending on datatype, set up munger;
|
||||
// munger is a function of <floating point, Real, data_type>
|
||||
if ( header.data_type == std::string("4D_SU3_GAUGE") ) {
|
||||
if ( ieee32 || ieee32big ) {
|
||||
readNerscObject<vLorentzColourMatrix, LorentzColourMatrix, LorentzColour2x3F>
|
||||
(Umu,file,
|
||||
Nersc3x2munger<LorentzColour2x3F,LorentzColourMatrix>(),
|
||||
offset,format);
|
||||
}
|
||||
if ( ieee64 || ieee64big ) {
|
||||
readNerscObject<vLorentzColourMatrix, LorentzColourMatrix, LorentzColour2x3D>
|
||||
(Umu,file,
|
||||
Nersc3x2munger<LorentzColour2x3D,LorentzColourMatrix>(),
|
||||
offset,format);
|
||||
}
|
||||
} else if ( header.data_type == std::string("4D_SU3_GAUGE_3X3") ) {
|
||||
if ( ieee32 || ieee32big ) {
|
||||
readNerscObject<vLorentzColourMatrix,LorentzColourMatrix,LorentzColourMatrixF>
|
||||
(Umu,file,NerscSimpleMunger<LorentzColourMatrixF,LorentzColourMatrix>(),offset,format);
|
||||
}
|
||||
if ( ieee64 || ieee64big ) {
|
||||
readNerscObject<vLorentzColourMatrix,LorentzColourMatrix,LorentzColourMatrixD>
|
||||
(Umu,file,NerscSimpleMunger<LorentzColourMatrixD,LorentzColourMatrix>(),offset,format);
|
||||
}
|
||||
} else {
|
||||
assert(0);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
template<class vobj>
|
||||
inline void writeNerscConfiguration(Lattice<vobj> &Umu,NerscField &header,std::string file)
|
||||
{
|
||||
GridBase &grid = Umu._grid;
|
||||
|
||||
NerscStatisics(Umu,header);
|
||||
|
||||
int offset = writeNerscHeader(header,file);
|
||||
|
||||
writeNerscObject(Umu,NerscSimpleMunger<vobj,vobj>(),offset);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
#endif
|
||||
Reference in New Issue
Block a user