Grid/lib/parallelIO/BinaryIO.h

    /*************************************************************************************

    Grid physics library, www.github.com/paboyle/Grid 

    Source file: ./lib/parallelIO/BinaryIO.h

    Copyright (C) 2015

    Author: Peter Boyle <paboyle@ph.ed.ac.uk>
    Author: Guido Cossu<guido.cossu@ed.ac.uk>

    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


#include "IldgIOtypes.h"

#ifdef HAVE_ENDIAN_H
#include <endian.h>
#endif
#include <arpa/inet.h>
#include <algorithm>

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

/////////////////////////////////////////////////////////////////////////////////
// Simple classes for precision conversion
/////////////////////////////////////////////////////////////////////////////////
template <class fobj, class sobj>
struct BinarySimpleUnmunger {
  typedef typename getPrecision<fobj>::real_scalar_type fobj_stype;
  typedef typename getPrecision<sobj>::real_scalar_type sobj_stype;
  
  void operator()(sobj &in, fobj &out) {
    // take word by word and transform accoding to the status
    fobj_stype *out_buffer = (fobj_stype *)&out;
    sobj_stype *in_buffer = (sobj_stype *)&in;
    size_t fobj_words = sizeof(out) / sizeof(fobj_stype);
    size_t sobj_words = sizeof(in) / sizeof(sobj_stype);
    assert(fobj_words == sobj_words);
    
    for (unsigned int word = 0; word < sobj_words; word++)
      out_buffer[word] = in_buffer[word];  // type conversion on the fly
    
  }
};

template <class fobj, class sobj>
struct BinarySimpleMunger {
  typedef typename getPrecision<fobj>::real_scalar_type fobj_stype;
  typedef typename getPrecision<sobj>::real_scalar_type sobj_stype;

  void operator()(fobj &in, sobj &out) {
    // take word by word and transform accoding to the status
    fobj_stype *in_buffer = (fobj_stype *)&in;
    sobj_stype *out_buffer = (sobj_stype *)&out;
    size_t fobj_words = sizeof(in) / sizeof(fobj_stype);
    size_t sobj_words = sizeof(out) / sizeof(sobj_stype);
    assert(fobj_words == sobj_words);
    
    for (unsigned int word = 0; word < sobj_words; word++)
      out_buffer[word] = in_buffer[word];  // type conversion on the fly
    
  }
};
// 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
  /////////////////////////////////////////////////////////////////////////////
  static inline void Uint32Checksum(uint32_t *buf,uint64_t buf_size_bytes,uint32_t &csum)
  {
#pragma omp parallel
    { 
      uint32_t csum_thr=0;
      uint64_t count = buf_size_bytes/sizeof(uint32_t);
#pragma omp for
      for(uint64_t i=0;i<count;i++){
	csum_thr=csum_thr+buf[i];
      }
#pragma omp critical
      csum = csum + csum_thr;

    }
  }
  // Network is big endian
  static inline void htobe32_v(void *file_object,uint64_t bytes,uint32_t &csum){ 
    Uint32Checksum((uint32_t *)file_object,bytes,csum); 
    htobe32_v(file_object,bytes); 
  }
  static inline void htobe64_v(void *file_object,uint64_t bytes,uint32_t &csum){
    Uint32Checksum((uint32_t *)file_object,bytes,csum); 
    htobe64_v(file_object,bytes);
  }
  static inline void htole32_v(void *file_object,uint64_t bytes,uint32_t &csum){ 
    Uint32Checksum((uint32_t *)file_object,bytes,csum);
    htole32_v(file_object,bytes);
  }
  static inline void htole64_v(void *file_object,uint64_t bytes,uint32_t &csum){ 
    Uint32Checksum((uint32_t *)file_object,bytes,csum);
    htole64_v(file_object,bytes);
  }
  static inline void be32toh_v(void *file_object,uint64_t bytes,uint32_t &csum){ 
    be32toh_v(file_object,bytes); 
    Uint32Checksum((uint32_t *)file_object,bytes,csum); 
  }
  static inline void be64toh_v(void *file_object,uint64_t bytes,uint32_t &csum){
    be64toh_v(file_object,bytes);
    Uint32Checksum((uint32_t *)file_object,bytes,csum); 
  }
  static inline void le32toh_v(void *file_object,uint64_t bytes,uint32_t &csum){ 
    le32toh_v(file_object,bytes);
    Uint32Checksum((uint32_t *)file_object,bytes,csum);
  }
  static inline void le64toh_v(void *file_object,uint64_t bytes,uint32_t &csum){ 
    le64toh_v(file_object,bytes);
    Uint32Checksum((uint32_t *)file_object,bytes,csum);
  }
  static inline void htobe32_v(void *file_object,uint64_t bytes){ be32toh_v(file_object,bytes);} 
  static inline void htobe64_v(void *file_object,uint64_t bytes){ be64toh_v(file_object,bytes);} 
  static inline void htole32_v(void *file_object,uint64_t bytes){ le32toh_v(file_object,bytes);} 
  static inline void htole64_v(void *file_object,uint64_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<count;i++){  
      f[i] = ntohl(f[i]);
    }
  }
  // LE must Swap and switch to host
  static inline void le32toh_v(void *file_object,uint64_t bytes)
  {
    uint32_t *fp = (uint32_t *)file_object;
    uint32_t f;

    uint64_t count = bytes/sizeof(uint32_t);
    parallel_for(uint64_t i=0;i<count;i++){  
      f = fp[i];
      // got network order and the network to host
      f = ((f&0xFF)<<24) | ((f&0xFF00)<<8) | ((f&0xFF0000)>>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<count;i++){  
      f[i] = Grid_ntohll(f[i]);
    }
  }
  
  // LE must swap and switch;
  static inline void le64toh_v(void *file_object,uint64_t bytes)
  {
    uint64_t *fp = (uint64_t *)file_object;
    uint64_t f,g;
    
    uint64_t count = bytes/sizeof(uint64_t);
    parallel_for(uint64_t i=0;i<count;i++){  
      f = fp[i];
      // got network order and the network to host
      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) ; 
      fp[i] = Grid_ntohll(g);
    }
  }
  /////////////////////////////////////////////////////////////////////////////
  // Real action:
  // Read or Write distributed lexico array of ANY object to a specific location in file 
  //////////////////////////////////////////////////////////////////////////////////////
  template<class word,class fobj>
    static inline uint32_t IOobject(word w,
				    GridBase *grid,
				    std::vector<fobj> &iodata,
				    std::string file,
				    int offset,
				    const std::string &format, int doread)
  {
    grid->Barrier();
    GridStopWatch timer; 
    GridStopWatch bstimer;

    uint32_t csum=0;

    int ndim                 = grid->Dimensions();
    int nrank                = grid->ProcessorCount();
    int myrank               = grid->ThisRank();

    std::vector<int>  psizes = grid->ProcessorGrid(); 
    std::vector<int>  pcoor  = grid->ThisProcessorCoor();
    std::vector<int> gLattice= grid->GlobalDimensions();
    std::vector<int> lLattice= grid->LocalDimensions();

    std::vector<int> distribs(ndim,MPI_DISTRIBUTE_BLOCK);
    std::vector<int> dargs   (ndim,MPI_DISTRIBUTE_DFLT_DARG);

    std::vector<int> lStart(ndim);
    std::vector<int> gStart(ndim);

    // Flatten the file
    uint64_t lsites = grid->lSites();
    iodata.resize(lsites);

    for(int d=0;d<ndim;d++){
      gStart[d] = lLattice[d]*pcoor[d];
      lStart[d] = 0;
    }

    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);

    //////////////////////////////////////////////////////////////////////////////
    // 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 MPI I/O read
    //////////////////////////////////////////////////////////////////////////////
    if ( doread ) { 
      std::cout<< GridLogMessage<< "MPI read I/O "<< file<< std::endl;
      timer.Start();
      ierr=MPI_File_open(grid->communicator, 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);
      timer.Stop();

      grid->Barrier();

      bstimer.Start();
      if (ieee32big) be32toh_v((void *)&iodata[0], sizeof(fobj)*lsites,csum);
      if (ieee32)    le32toh_v((void *)&iodata[0], sizeof(fobj)*lsites,csum);
      if (ieee64big) be64toh_v((void *)&iodata[0], sizeof(fobj)*lsites,csum);
      if (ieee64)    le64toh_v((void *)&iodata[0], sizeof(fobj)*lsites,csum);
      bstimer.Stop();

    } else { 
      std::cout<< GridLogMessage<< "MPI write I/O "<< file<< std::endl;
      bstimer.Start();
      if (ieee32big) htobe32_v((void *)&iodata[0], sizeof(fobj)*lsites,csum);
      if (ieee32)    htole32_v((void *)&iodata[0], sizeof(fobj)*lsites,csum);
      if (ieee64big) htobe64_v((void *)&iodata[0], sizeof(fobj)*lsites,csum);
      if (ieee64)    htole64_v((void *)&iodata[0], sizeof(fobj)*lsites,csum);
      bstimer.Stop();

      grid->Barrier();

      timer.Start();
      ierr=MPI_File_open(grid->communicator, file.c_str(), MPI_MODE_RDWR|MPI_MODE_CREATE,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_write_all(fh, &iodata[0], 1, localArray, &status);                                        assert(ierr==0);
      timer.Stop();
    
    }
   
    //////////////////////////////////////////////////////////////////////////////
    // Finish up MPI I/O
    //////////////////////////////////////////////////////////////////////////////
    MPI_File_close(&fh);
    MPI_Type_free(&fileArray);
    MPI_Type_free(&localArray);

    std::cout<<GridLogMessage<<"IOobject: ";
    if ( doread) std::cout << " read  ";
    else         std::cout << " write ";
    uint64_t bytes = sizeof(fobj)*lsites*nrank;
    std::cout<< bytes <<" bytes in "<<timer.Elapsed() <<" "
	     << (double)bytes/ (double)timer.useconds() <<" MB/s "<<std::endl;

    std::cout<<GridLogMessage<<"IOobject: endian and checksum overhead "<<bstimer.Elapsed()  <<std::endl;

    //////////////////////////////////////////////////////////////////////////////
    // Safety check
    //////////////////////////////////////////////////////////////////////////////
    grid->Barrier();
    grid->GlobalSum(csum);
    grid->Barrier();

    return csum;
  }

  /////////////////////////////////////////////////////////////////////////////
  // Read a Lattice of object
  //////////////////////////////////////////////////////////////////////////////////////
  template<class vobj,class fobj,class munger>
  static inline uint32_t readLatticeObject(Lattice<vobj> &Umu,std::string file,munger munge,int offset,const std::string &format)
  {
    typedef typename vobj::scalar_object sobj;
    typedef typename vobj::Realified::scalar_type word;    word w=0;

    GridBase *grid = Umu._grid;
    int lsites = grid->lSites();

    std::vector<sobj> scalardata(lsites); 
    std::vector<fobj>     iodata(lsites); // Munge, checksum, byte order in here
    
    int doread=1;
    uint32_t csum= IOobject(w,grid,iodata,file,offset,format,doread);

    GridStopWatch timer; 
    timer.Start();

    parallel_for(int x=0;x<lsites;x++) munge(iodata[x], scalardata[x]);

    vectorizeFromLexOrdArray(scalardata,Umu);    
    grid->Barrier();

    timer.Stop();
    std::cout<<GridLogMessage<<"readLatticeObject: vectorize overhead "<<timer.Elapsed()  <<std::endl;

    return csum;
  }

  /////////////////////////////////////////////////////////////////////////////
  // Write a Lattice of object
  //////////////////////////////////////////////////////////////////////////////////////
  template<class vobj,class fobj,class munger>
  static inline uint32_t writeLatticeObject(Lattice<vobj> &Umu,std::string file,munger munge,int offset,const std::string &format)
  {
    typedef typename vobj::scalar_object sobj;
    typedef typename vobj::Realified::scalar_type word;    word w=0;
    GridBase *grid = Umu._grid;
    int lsites = grid->lSites();

    std::vector<sobj> scalardata(lsites); 
    std::vector<fobj>     iodata(lsites); // Munge, checksum, byte order in here

    //////////////////////////////////////////////////////////////////////////////
    // Munge [ .e.g 3rd row recon ]
    //////////////////////////////////////////////////////////////////////////////
    GridStopWatch timer; timer.Start();
    unvectorizeToLexOrdArray(scalardata,Umu);    

    parallel_for(int x=0;x<lsites;x++) munge(scalardata[x],iodata[x]);

    grid->Barrier();
    timer.Stop();

    int dowrite=0;
    uint32_t csum= IOobject(w,grid,iodata,file,offset,format,dowrite);

    std::cout<<GridLogMessage<<"writeLatticeObject: unvectorize overhead "<<timer.Elapsed()  <<std::endl;

    return csum;
  }
  
  /////////////////////////////////////////////////////////////////////////////
  // Read a RNG;  use IOobject and lexico map to an array of state 
  //////////////////////////////////////////////////////////////////////////////////////
  static inline uint32_t readRNG(GridSerialRNG &serial,GridParallelRNG &parallel,std::string file,int offset)
  {
    typedef typename GridSerialRNG::RngStateType RngStateType;
    const int RngStateCount = GridSerialRNG::RngStateCount;
    typedef std::array<RngStateType,RngStateCount> RNGstate;
    typedef RngStateType word;    word w=0;

    uint32_t csum = 0;
    std::string format = "IEEE32BIG";

    GridBase *grid = parallel._grid;
    int gsites = grid->gSites();
    int lsites = grid->lSites();

    GridStopWatch timer;

    std::cout << GridLogMessage << "RNG read I/O on file " << file << std::endl;

    int doread=1;
    std::vector<RNGstate> iodata(lsites);
    csum= IOobject(w,grid,iodata,file,offset,format,doread);

    timer.Start();
    parallel_for(int lidx=0;lidx<lsites;lidx++){
      std::vector<RngStateType> tmp(RngStateCount);
      std::copy(iodata[lidx].begin(),iodata[lidx].end(),tmp.begin());
      parallel.SetState(tmp,lidx);
    }
    timer.Stop();

    std::cout << GridLogMessage << "RNG file checksum " << std::hex << csum << std::dec << std::endl;
    std::cout << GridLogMessage << "RNG state overhead " << timer.Elapsed() << std::endl;
    return csum;
  }
  /////////////////////////////////////////////////////////////////////////////
  // Write a RNG; lexico map to an array of state and use IOobject
  //////////////////////////////////////////////////////////////////////////////////////
  static inline uint32_t writeRNG(GridSerialRNG &serial,GridParallelRNG &parallel,std::string file,int offset)
  {
    typedef typename GridSerialRNG::RngStateType RngStateType;
    typedef RngStateType word; word w=0;
    const int RngStateCount = GridSerialRNG::RngStateCount;
    typedef std::array<RngStateType,RngStateCount> RNGstate;

    uint32_t csum = 0;

    GridBase *grid = parallel._grid;
    int gsites = grid->gSites();
    int lsites = grid->lSites();

    GridStopWatch timer;
    std::string format = "IEEE32BIG";

    std::cout << GridLogMessage << "RNG write I/O on file " << file << std::endl;

    timer.Start();
    std::vector<RNGstate> iodata(lsites);
    parallel_for(int lidx=0;lidx<lsites;lidx++){
      std::vector<RngStateType> tmp(RngStateCount);
      parallel.GetState(tmp,lidx);
      std::copy(tmp.begin(),tmp.end(),iodata[lidx].begin());
    }
    timer.Stop();

    int dowrite=0;
    csum= IOobject(w,grid,iodata,file,offset,format,dowrite);

    std::cout << GridLogMessage << "RNG file checksum " << std::hex << csum << std::dec << std::endl;
    std::cout << GridLogMessage << "RNG state overhead " << timer.Elapsed() << std::endl;
    return csum;
  }
};
}
#endif