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094c3d091a
Grid/lib/parallelIO/BinaryIO.h
paboyle 094c3d091a Improved and RNG's now survive checkpoint
2017-06-02 00:38:58 +01:00

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/*************************************************************************************
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
//////////////////////////////////////////////////////////////////////////////////////
static const int BINARYIO_MASTER_APPEND = 0x10;
static const int BINARYIO_UNORDERED = 0x08;
static const int BINARYIO_LEXICOGRAPHIC = 0x04;
static const int BINARYIO_READ = 0x02;
static const int BINARYIO_WRITE = 0x01;
template<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 control)
{
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> lStart(ndim);
std::vector<int> gStart(ndim);
// Flatten the file
uint64_t lsites = grid->lSites();
if ( control & BINARYIO_MASTER_APPEND ) {
assert(iodata.size()==1);
} else {
assert(lsites==iodata.size());
}
for(int d=0;d<ndim;d++){
gStart[d] = lLattice[d]*pcoor[d];
lStart[d] = 0;
}
#ifdef USE_MPI_IO
std::vector<int> distribs(ndim,MPI_DISTRIBUTE_BLOCK);
std::vector<int> dargs (ndim,MPI_DISTRIBUTE_DFLT_DARG);
MPI_Datatype mpiObject;
MPI_Datatype fileArray;
MPI_Datatype localArray;
MPI_Datatype mpiword;
MPI_Offset disp = offset;
MPI_File fh ;
MPI_Status status;
int numword;
if ( sizeof( word ) == sizeof(float ) ) {
numword = sizeof(fobj)/sizeof(float);
mpiword = MPI_FLOAT;
} else {
numword = sizeof(fobj)/sizeof(double);
mpiword = MPI_DOUBLE;
}
//////////////////////////////////////////////////////////////////////////////
// Sobj in MPI phrasing
//////////////////////////////////////////////////////////////////////////////
int ierr;
ierr = MPI_Type_contiguous(numword,mpiword,&mpiObject); assert(ierr==0);
ierr = MPI_Type_commit(&mpiObject);
//////////////////////////////////////////////////////////////////////////////
// File global array data type
//////////////////////////////////////////////////////////////////////////////
ierr=MPI_Type_create_subarray(ndim,&gLattice[0],&lLattice[0],&gStart[0],MPI_ORDER_FORTRAN, mpiObject,&fileArray); assert(ierr==0);
ierr=MPI_Type_commit(&fileArray); assert(ierr==0);
//////////////////////////////////////////////////////////////////////////////
// local lattice array
//////////////////////////////////////////////////////////////////////////////
ierr=MPI_Type_create_subarray(ndim,&lLattice[0],&lLattice[0],&lStart[0],MPI_ORDER_FORTRAN, mpiObject,&localArray); assert(ierr==0);
ierr=MPI_Type_commit(&localArray); assert(ierr==0);
#endif
//////////////////////////////////////////////////////////////////////////////
// Byte order
//////////////////////////////////////////////////////////////////////////////
int ieee32big = (format == std::string("IEEE32BIG"));
int ieee32 = (format == std::string("IEEE32"));
int ieee64big = (format == std::string("IEEE64BIG"));
int ieee64 = (format == std::string("IEEE64"));
//////////////////////////////////////////////////////////////////////////////
// Do the I/O
//////////////////////////////////////////////////////////////////////////////
if ( control & BINARYIO_READ ) {
timer.Start();
if ( (control & BINARYIO_LEXICOGRAPHIC) && (nrank > 1) ) {
#ifdef USE_MPI_IO
std::cout<< GridLogMessage<< "MPI read I/O "<< file<< std::endl;
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);
MPI_File_close(&fh);
MPI_Type_free(&fileArray);
MPI_Type_free(&localArray);
#else
assert(0);
#endif
} else {
std::cout<< GridLogMessage<< "C++ read I/O "<< file<< std::endl;
std::ifstream fin;
fin.open(file,std::ios::binary|std::ios::in);
if ( control & BINARYIO_MASTER_APPEND ) {
fin.seekg(-sizeof(fobj),fin.end);
} else {
fin.seekg(offset+myrank*lsites*sizeof(fobj));
}
fin.read((char *)&iodata[0],iodata.size()*sizeof(fobj));assert( fin.fail()==0);
fin.close();
}
timer.Stop();
grid->Barrier();
bstimer.Start();
if (ieee32big) be32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum);
if (ieee32) le32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum);
if (ieee64big) be64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum);
if (ieee64) le64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum);
bstimer.Stop();
}
if ( control & BINARYIO_WRITE ) {
bstimer.Start();
if (ieee32big) htobe32_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum);
if (ieee32) htole32_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum);
if (ieee64big) htobe64_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum);
if (ieee64) htole64_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum);
bstimer.Stop();
grid->Barrier();
timer.Start();
if ( (control & BINARYIO_LEXICOGRAPHIC) && (nrank > 1) ) {
#ifdef USE_MPI_IO
std::cout<< GridLogMessage<< "MPI write I/O "<< file<< std::endl;
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);
MPI_File_close(&fh);
MPI_Type_free(&fileArray);
MPI_Type_free(&localArray);
#else
assert(0);
#endif
} else {
std::cout<< GridLogMessage<< "C++ write I/O "<< file<< std::endl;
std::ofstream fout;
fout.open(file,std::ios::binary|std::ios::out|std::ios::in);
if ( control & BINARYIO_MASTER_APPEND ) {
fout.seekp(0,fout.end);
} else {
fout.seekp(offset+myrank*lsites*sizeof(fobj));
}
fout.write((char *)&iodata[0],iodata.size()*sizeof(fobj));assert( fout.fail()==0);
fout.close();
}
timer.Stop();
}
std::cout<<GridLogMessage<<"IOobject: ";
if ( control & BINARYIO_READ) std::cout << " read ";
else std::cout << " write ";
uint64_t bytes = sizeof(fobj)*iodata.size()*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
uint32_t csum= IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_LEXICOGRAPHIC);
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();
uint32_t csum= IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_LEXICOGRAPHIC);
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;
std::vector<RNGstate> iodata(lsites);
csum= IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_LEXICOGRAPHIC);
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();
iodata.resize(1);
csum+= IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_MASTER_APPEND);
{
std::vector<RngStateType> tmp(RngStateCount);
std::copy(iodata[0].begin(),iodata[0].end(),tmp.begin());
serial.SetState(tmp,0);
}
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();
csum= IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_LEXICOGRAPHIC);
iodata.resize(1);
{
std::vector<RngStateType> tmp(RngStateCount);
serial.GetState(tmp,0);
std::copy(tmp.begin(),tmp.end(),iodata[0].begin());
}
csum+= IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_MASTER_APPEND);
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
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