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I/O improvements

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This commit is contained in:
paboyle 2017-06-11 23:14:10 +01:00
parent 092dcd4e04
commit 3bfd1f13e6
26 changed files with 779 additions and 579 deletions
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4
benchmarks/Benchmark_memory_bandwidth.cc
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@ -55,8 +55,8 @@ int main (int argc, char ** argv)
std::cout<<GridLogMessage << "===================================================================================================="<<std::endl; std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
std::cout<<GridLogMessage << " L "<<"\t\t"<<"bytes"<<"\t\t\t"<<"GB/s"<<"\t\t"<<"Gflop/s"<<"\t\t seconds"<<std::endl; std::cout<<GridLogMessage << " L "<<"\t\t"<<"bytes"<<"\t\t\t"<<"GB/s"<<"\t\t"<<"Gflop/s"<<"\t\t seconds"<<std::endl;
std::cout<<GridLogMessage << "----------------------------------------------------------"<<std::endl; std::cout<<GridLogMessage << "----------------------------------------------------------"<<std::endl;
uint64_t lmax=44; uint64_t lmax=64;
#define NLOOP (1*lmax*lmax*lmax*lmax/vol) #define NLOOP (100*lmax*lmax*lmax*lmax/vol)
for(int lat=4;lat<=lmax;lat+=4){ for(int lat=4;lat<=lmax;lat+=4){
std::vector<int> latt_size ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]}); std::vector<int> latt_size ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});

4
benchmarks/Benchmark_su3.cc
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@ -35,9 +35,9 @@ using namespace Grid::QCD;
int main (int argc, char ** argv) int main (int argc, char ** argv)
{ {
Grid_init(&argc,&argv); Grid_init(&argc,&argv);
#define LMAX (32) #define LMAX (64)
int Nloop=200; int Nloop=20;
std::vector<int> simd_layout = GridDefaultSimd(Nd,vComplex::Nsimd()); std::vector<int> simd_layout = GridDefaultSimd(Nd,vComplex::Nsimd());
std::vector<int> mpi_layout = GridDefaultMpi(); std::vector<int> mpi_layout = GridDefaultMpi();

2
configure.ac
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@ -27,7 +27,7 @@ AX_GXX_VERSION
AC_DEFINE_UNQUOTED([GXX_VERSION],["$GXX_VERSION"], AC_DEFINE_UNQUOTED([GXX_VERSION],["$GXX_VERSION"],
[version of g++ that will compile the code]) [version of g++ that will compile the code])
CXXFLAGS="-O3 $CXXFLAGS" CXXFLAGS="-g $CXXFLAGS"
############### Checks for typedefs, structures, and compiler characteristics ############### Checks for typedefs, structures, and compiler characteristics

4
extras/Hadrons/Modules/MGauge/Load.cc
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@ -65,7 +65,7 @@ void TLoad::setup(void)
// execution /////////////////////////////////////////////////////////////////// // execution ///////////////////////////////////////////////////////////////////
void TLoad::execute(void) void TLoad::execute(void)
{ {
NerscField header; FieldMetaData header;
std::string fileName = par().file + "." std::string fileName = par().file + "."
+ std::to_string(env().getTrajectory()); + std::to_string(env().getTrajectory());
@ -74,5 +74,5 @@ void TLoad::execute(void)
LatticeGaugeField &U = *env().createLattice<LatticeGaugeField>(getName()); LatticeGaugeField &U = *env().createLattice<LatticeGaugeField>(getName());
NerscIO::readConfiguration(U, header, fileName); NerscIO::readConfiguration(U, header, fileName);
LOG(Message) << "NERSC header:" << std::endl; LOG(Message) << "NERSC header:" << std::endl;
dump_nersc_header(header, LOG(Message)); dump_meta_data(header, LOG(Message));
} }

1
lib/Grid.h
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@ -42,6 +42,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
#include <Grid/GridQCDcore.h> #include <Grid/GridQCDcore.h>
#include <Grid/qcd/action/Action.h> #include <Grid/qcd/action/Action.h>
#include <Grid/qcd/smearing/Smearing.h> #include <Grid/qcd/smearing/Smearing.h>
#include <Grid/parallelIO/MetaData.h>
#include <Grid/qcd/hmc/HMC_aggregate.h> #include <Grid/qcd/hmc/HMC_aggregate.h>
#endif #endif

1
lib/GridStd.h
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@ -18,6 +18,7 @@
#include <ctime> #include <ctime>
#include <sys/time.h> #include <sys/time.h>
#include <chrono> #include <chrono>
#include <zlib.h>
/////////////////// ///////////////////
// Grid config // Grid config

9
lib/cartesian/Cartesian_base.h
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@ -50,7 +50,6 @@ public:
GridBase(const std::vector<int> & processor_grid) : CartesianCommunicator(processor_grid) {}; GridBase(const std::vector<int> & processor_grid) : CartesianCommunicator(processor_grid) {};
// Physics Grid information. // Physics Grid information.
std::vector<int> _simd_layout;// Which dimensions get relayed out over simd lanes. std::vector<int> _simd_layout;// Which dimensions get relayed out over simd lanes.
std::vector<int> _fdimensions;// (full) Global dimensions of array prior to cb removal std::vector<int> _fdimensions;// (full) Global dimensions of array prior to cb removal
@ -63,13 +62,12 @@ public:
int _isites; int _isites;
int _fsites; // _isites*_osites = product(dimensions). int _fsites; // _isites*_osites = product(dimensions).
int _gsites; int _gsites;
std::vector<int> _slice_block; // subslice information std::vector<int> _slice_block;// subslice information
std::vector<int> _slice_stride; std::vector<int> _slice_stride;
std::vector<int> _slice_nblock; std::vector<int> _slice_nblock;
// Might need these at some point std::vector<int> _lstart; // local start of array in gcoors _processor_coor[d]*_ldimensions[d]
// std::vector<int> _lstart; // local start of array in gcoors. _processor_coor[d]*_ldimensions[d] std::vector<int> _lend ; // local end of array in gcoors _processor_coor[d]*_ldimensions[d]+_ldimensions_[d]-1
// std::vector<int> _lend; // local end of array in gcoors _processor_coor[d]*_ldimensions[d]+_ldimensions_[d]-1
public: public:
@ -176,6 +174,7 @@ public:
inline int gSites(void) const { return _isites*_osites*_Nprocessors; }; inline int gSites(void) const { return _isites*_osites*_Nprocessors; };
inline int Nd (void) const { return _ndimension;}; inline int Nd (void) const { return _ndimension;};
inline const std::vector<int> LocalStarts(void) { return _lstart; };
inline const std::vector<int> &FullDimensions(void) { return _fdimensions;}; inline const std::vector<int> &FullDimensions(void) { return _fdimensions;};
inline const std::vector<int> &GlobalDimensions(void) { return _gdimensions;}; inline const std::vector<int> &GlobalDimensions(void) { return _gdimensions;};
inline const std::vector<int> &LocalDimensions(void) { return _ldimensions;}; inline const std::vector<int> &LocalDimensions(void) { return _ldimensions;};

8
lib/cartesian/Cartesian_full.h
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@ -76,6 +76,8 @@ public:
_ldimensions.resize(_ndimension); _ldimensions.resize(_ndimension);
_rdimensions.resize(_ndimension); _rdimensions.resize(_ndimension);
_simd_layout.resize(_ndimension); _simd_layout.resize(_ndimension);
_lstart.resize(_ndimension);
_lend.resize(_ndimension);
_ostride.resize(_ndimension); _ostride.resize(_ndimension);
_istride.resize(_ndimension); _istride.resize(_ndimension);
@ -94,8 +96,10 @@ public:
// Use a reduced simd grid // Use a reduced simd grid
_ldimensions[d]= _gdimensions[d]/_processors[d]; //local dimensions _ldimensions[d]= _gdimensions[d]/_processors[d]; //local dimensions
_rdimensions[d]= _ldimensions[d]/_simd_layout[d]; //overdecomposition _rdimensions[d]= _ldimensions[d]/_simd_layout[d]; //overdecomposition
_osites *= _rdimensions[d]; _lstart[d] = _processor_coor[d]*_ldimensions[d];
_isites *= _simd_layout[d]; _lend[d] = _processor_coor[d]*_ldimensions[d]+_ldimensions[d]-1;
_osites *= _rdimensions[d];
_isites *= _simd_layout[d];
// Addressing support // Addressing support
if ( d==0 ) { if ( d==0 ) {

4
lib/cartesian/Cartesian_red_black.h
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@ -151,6 +151,8 @@ public:
_ldimensions.resize(_ndimension); _ldimensions.resize(_ndimension);
_rdimensions.resize(_ndimension); _rdimensions.resize(_ndimension);
_simd_layout.resize(_ndimension); _simd_layout.resize(_ndimension);
_lstart.resize(_ndimension);
_lend.resize(_ndimension);
_ostride.resize(_ndimension); _ostride.resize(_ndimension);
_istride.resize(_ndimension); _istride.resize(_ndimension);
@ -169,6 +171,8 @@ public:
_gdimensions[d] = _gdimensions[d]/2; // Remove a checkerboard _gdimensions[d] = _gdimensions[d]/2; // Remove a checkerboard
} }
_ldimensions[d] = _gdimensions[d]/_processors[d]; _ldimensions[d] = _gdimensions[d]/_processors[d];
_lstart[d] = _processor_coor[d]*_ldimensions[d];
_lend[d] = _processor_coor[d]*_ldimensions[d]+_ldimensions[d]-1;
// Use a reduced simd grid // Use a reduced simd grid
_simd_layout[d] = simd_layout[d]; _simd_layout[d] = simd_layout[d];

2
lib/communicator/Communicator_base.h
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@ -177,6 +177,8 @@ class CartesianCommunicator {
void GlobalSumVector(ComplexF *c,int N); void GlobalSumVector(ComplexF *c,int N);
void GlobalSum(ComplexD &c); void GlobalSum(ComplexD &c);
void GlobalSumVector(ComplexD *c,int N); void GlobalSumVector(ComplexD *c,int N);
void GlobalXOR(uint32_t &);
void GlobalXOR(uint64_t &);
template<class obj> void GlobalSum(obj &o){ template<class obj> void GlobalSum(obj &o){
typedef typename obj::scalar_type scalar_type; typedef typename obj::scalar_type scalar_type;

8
lib/communicator/Communicator_mpi.cc
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@ -83,6 +83,14 @@ void CartesianCommunicator::GlobalSum(uint64_t &u){
int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT64_T,MPI_SUM,communicator); int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT64_T,MPI_SUM,communicator);
assert(ierr==0); assert(ierr==0);
} }
void CartesianCommunicator::GlobalXOR(uint32_t &u){
int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT32_T,MPI_BXOR,communicator);
assert(ierr==0);
}
void CartesianCommunicator::GlobalXOR(uint64_t &u){
int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT64_T,MPI_BXOR,communicator);
assert(ierr==0);
}
void CartesianCommunicator::GlobalSum(float &f){ void CartesianCommunicator::GlobalSum(float &f){
int ierr=MPI_Allreduce(MPI_IN_PLACE,&f,1,MPI_FLOAT,MPI_SUM,communicator); int ierr=MPI_Allreduce(MPI_IN_PLACE,&f,1,MPI_FLOAT,MPI_SUM,communicator);
assert(ierr==0); assert(ierr==0);

8
lib/communicator/Communicator_mpi3.cc
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@ -510,6 +510,14 @@ void CartesianCommunicator::GlobalSum(uint64_t &u){
int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT64_T,MPI_SUM,communicator); int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT64_T,MPI_SUM,communicator);
assert(ierr==0); assert(ierr==0);
} }
void CartesianCommunicator::GlobalXOR(uint32_t &u){
int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT32_T,MPI_BXOR,communicator);
assert(ierr==0);
}
void CartesianCommunicator::GlobalXOR(uint64_t &u){
int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT64_T,MPI_BXOR,communicator);
assert(ierr==0);
}
void CartesianCommunicator::GlobalSum(float &f){ void CartesianCommunicator::GlobalSum(float &f){
int ierr=MPI_Allreduce(MPI_IN_PLACE,&f,1,MPI_FLOAT,MPI_SUM,communicator); int ierr=MPI_Allreduce(MPI_IN_PLACE,&f,1,MPI_FLOAT,MPI_SUM,communicator);
assert(ierr==0); assert(ierr==0);

2
lib/communicator/Communicator_none.cc
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@ -59,6 +59,8 @@ void CartesianCommunicator::GlobalSum(double &){}
void CartesianCommunicator::GlobalSum(uint32_t &){} void CartesianCommunicator::GlobalSum(uint32_t &){}
void CartesianCommunicator::GlobalSum(uint64_t &){} void CartesianCommunicator::GlobalSum(uint64_t &){}
void CartesianCommunicator::GlobalSumVector(double *,int N){} void CartesianCommunicator::GlobalSumVector(double *,int N){}
void CartesianCommunicator::GlobalXOR(uint32_t &){}
void CartesianCommunicator::GlobalXOR(uint64_t &){}
void CartesianCommunicator::SendRecvPacket(void *xmit, void CartesianCommunicator::SendRecvPacket(void *xmit,
void *recv, void *recv,

249
lib/parallelIO/BinaryIO.h
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@ -125,57 +125,94 @@ class BinaryIO {
///////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////
// more byte manipulation helpers // more byte manipulation helpers
///////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////
static inline void Uint32Checksum(uint32_t *buf,uint64_t buf_size_bytes,uint32_t &csum)
template<class vobj> static inline void Uint32Checksum(Lattice<vobj> &lat,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
{ {
typedef typename vobj::scalar_object sobj;
GridBase *grid = lat._grid;
int lsites = grid->lSites();
std::vector<sobj> scalardata(lsites);
unvectorizeToLexOrdArray(scalardata,lat);
Uint32Checksum(grid,scalardata,nersc_csum,scidac_csuma,scidac_csumb);
}
template<class fobj>
static inline void Uint32Checksum(GridBase *grid,
std::vector<fobj> &fbuf,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
{
const uint64_t size32 = sizeof(fobj)/sizeof(uint32_t);
int nd = grid->_ndimension;
uint64_t lsites =grid->lSites();
std::vector<int> local_vol =grid->LocalDimensions();
std::vector<int> local_start =grid->LocalStarts();
std::vector<int> global_vol =grid->FullDimensions();
#pragma omp parallel #pragma omp parallel
{ {
uint32_t csum_thr=0; std::vector<int> coor(nd);
uint64_t count = buf_size_bytes/sizeof(uint32_t); uint32_t nersc_csum_thr=0;
uint32_t scidac_csuma_thr=0;
uint32_t scidac_csumb_thr=0;
uint32_t site_crc=0;
uint32_t zcrc = crc32(0L, Z_NULL, 0);
#pragma omp for #pragma omp for
for(uint64_t i=0;i<count;i++){ for(uint64_t local_site=0;local_site<lsites;local_site++){
csum_thr=csum_thr+buf[i];
uint32_t * site_buf = (uint32_t *)&fbuf[local_site];
for(uint64_t j=0;j<size32;j++){
nersc_csum_thr=nersc_csum_thr+site_buf[j];
}
/*
* Scidac csum is rather more heavyweight
*/
int global_site;
Lexicographic::CoorFromIndex(coor,local_site,local_vol);
for(int d=0;d<nd;d++)
coor[d] = coor[d]+local_start[d];
Lexicographic::IndexFromCoor(coor,global_site,global_vol);
uint32_t gsite29 = global_site%29;
uint32_t gsite31 = global_site%31;
site_crc = crc32(zcrc,(unsigned char *)site_buf,sizeof(fobj));
scidac_csuma_thr ^= site_crc<<gsite29 | site_crc>>(32-gsite29);
scidac_csumb_thr ^= site_crc<<gsite31 | site_crc>>(32-gsite31);
} }
#pragma omp critical #pragma omp critical
csum = csum + csum_thr; {
nersc_csum += nersc_csum_thr;
scidac_csuma^= scidac_csuma_thr;
scidac_csumb^= scidac_csumb_thr;
}
} }
} }
// Network is big endian // Network is big endian
static inline void htobe32_v(void *file_object,uint64_t bytes,uint32_t &csum){ static inline void htobe32_v(void *file_object,uint32_t bytes){ be32toh_v(file_object,bytes);}
Uint32Checksum((uint32_t *)file_object,bytes,csum); static inline void htobe64_v(void *file_object,uint32_t bytes){ be64toh_v(file_object,bytes);}
htobe32_v(file_object,bytes); static inline void htole32_v(void *file_object,uint32_t bytes){ le32toh_v(file_object,bytes);}
} static inline void htole64_v(void *file_object,uint32_t bytes){ le64toh_v(file_object,bytes);}
static inline void 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) static inline void be32toh_v(void *file_object,uint64_t bytes)
{ {
@ -199,6 +236,7 @@ class BinaryIO {
fp[i] = ntohl(f); fp[i] = ntohl(f);
} }
} }
// BE is same as network // BE is same as network
static inline void be64toh_v(void *file_object,uint64_t bytes) static inline void be64toh_v(void *file_object,uint64_t bytes)
{ {
@ -238,18 +276,23 @@ class BinaryIO {
static const int BINARYIO_WRITE = 0x01; static const int BINARYIO_WRITE = 0x01;
template<class word,class fobj> template<class word,class fobj>
static inline uint32_t IOobject(word w, static inline void IOobject(word w,
GridBase *grid, GridBase *grid,
std::vector<fobj> &iodata, std::vector<fobj> &iodata,
std::string file, std::string file,
int offset, int offset,
const std::string &format, int control) const std::string &format, int control,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
{ {
grid->Barrier(); grid->Barrier();
GridStopWatch timer; GridStopWatch timer;
GridStopWatch bstimer; GridStopWatch bstimer;
uint32_t csum=0; nersc_csum=0;
scidac_csuma=0;
scidac_csumb=0;
int ndim = grid->Dimensions(); int ndim = grid->Dimensions();
int nrank = grid->ProcessorCount(); int nrank = grid->ProcessorCount();
@ -359,20 +402,22 @@ class BinaryIO {
grid->Barrier(); grid->Barrier();
bstimer.Start(); bstimer.Start();
if (ieee32big) be32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum); if (ieee32big) be32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee32) le32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum); if (ieee32) le32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee64big) be64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum); if (ieee64big) be64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee64) le64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum); if (ieee64) le64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
Uint32Checksum(grid,iodata,nersc_csum,scidac_csuma,scidac_csumb);
bstimer.Stop(); bstimer.Stop();
} }
if ( control & BINARYIO_WRITE ) { if ( control & BINARYIO_WRITE ) {
bstimer.Start(); bstimer.Start();
if (ieee32big) htobe32_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum); Uint32Checksum(grid,iodata,nersc_csum,scidac_csuma,scidac_csumb);
if (ieee32) htole32_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum); if (ieee32big) htobe32_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee64big) htobe64_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum); if (ieee32) htole32_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee64) htole64_v((void *)&iodata[0], sizeof(fobj)*iodata.size(),csum); if (ieee64big) htobe64_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee64) htole64_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
bstimer.Stop(); bstimer.Stop();
grid->Barrier(); grid->Barrier();
@ -418,17 +463,27 @@ class BinaryIO {
// Safety check // Safety check
////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////
grid->Barrier(); grid->Barrier();
grid->GlobalSum(csum); grid->GlobalSum(nersc_csum);
grid->GlobalXOR(scidac_csuma);
grid->GlobalXOR(scidac_csumb);
grid->Barrier(); grid->Barrier();
// std::cout << "Binary IO NERSC checksum 0x"<<std::hex<<nersc_csum <<std::dec<<std::endl;
return csum; // std::cout << "Binary IO SCIDAC checksuma 0x"<<std::hex<<scidac_csuma<<std::dec<<std::endl;
// std::cout << "Binary IO SCIDAC checksumb 0x"<<std::hex<<scidac_csumb<<std::dec<<std::endl;
} }
///////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////
// Read a Lattice of object // Read a Lattice of object
////////////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////////////
template<class vobj,class fobj,class munger> 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) static inline void readLatticeObject(Lattice<vobj> &Umu,
std::string file,
munger munge,
int offset,
const std::string &format,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
{ {
typedef typename vobj::scalar_object sobj; typedef typename vobj::scalar_object sobj;
typedef typename vobj::Realified::scalar_type word; word w=0; typedef typename vobj::Realified::scalar_type word; word w=0;
@ -439,7 +494,8 @@ class BinaryIO {
std::vector<sobj> scalardata(lsites); std::vector<sobj> scalardata(lsites);
std::vector<fobj> iodata(lsites); // Munge, checksum, byte order in here 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); IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_LEXICOGRAPHIC,
nersc_csum,scidac_csuma,scidac_csumb);
GridStopWatch timer; GridStopWatch timer;
timer.Start(); timer.Start();
@ -451,15 +507,20 @@ class BinaryIO {
timer.Stop(); timer.Stop();
std::cout<<GridLogMessage<<"readLatticeObject: vectorize overhead "<<timer.Elapsed() <<std::endl; std::cout<<GridLogMessage<<"readLatticeObject: vectorize overhead "<<timer.Elapsed() <<std::endl;
return csum;
} }
///////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////
// Write a Lattice of object // Write a Lattice of object
////////////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////////////
template<class vobj,class fobj,class munger> 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) static inline void writeLatticeObject(Lattice<vobj> &Umu,
std::string file,
munger munge,
int offset,
const std::string &format,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
{ {
typedef typename vobj::scalar_object sobj; typedef typename vobj::scalar_object sobj;
typedef typename vobj::Realified::scalar_type word; word w=0; typedef typename vobj::Realified::scalar_type word; word w=0;
@ -480,36 +541,45 @@ class BinaryIO {
grid->Barrier(); grid->Barrier();
timer.Stop(); timer.Stop();
uint32_t csum= IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_LEXICOGRAPHIC); IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_LEXICOGRAPHIC,
nersc_csum,scidac_csuma,scidac_csumb);
std::cout<<GridLogMessage<<"writeLatticeObject: unvectorize overhead "<<timer.Elapsed() <<std::endl; 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 // 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) static inline void readRNG(GridSerialRNG &serial,
GridParallelRNG &parallel,
std::string file,
int offset,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
{ {
typedef typename GridSerialRNG::RngStateType RngStateType; typedef typename GridSerialRNG::RngStateType RngStateType;
const int RngStateCount = GridSerialRNG::RngStateCount; const int RngStateCount = GridSerialRNG::RngStateCount;
typedef std::array<RngStateType,RngStateCount> RNGstate; typedef std::array<RngStateType,RngStateCount> RNGstate;
typedef RngStateType word; word w=0; typedef RngStateType word; word w=0;
uint32_t csum = 0;
std::string format = "IEEE32BIG"; std::string format = "IEEE32BIG";
GridBase *grid = parallel._grid; GridBase *grid = parallel._grid;
int gsites = grid->gSites(); int gsites = grid->gSites();
int lsites = grid->lSites(); int lsites = grid->lSites();
uint32_t nersc_csum_tmp;
uint32_t scidac_csuma_tmp;
uint32_t scidac_csumb_tmp;
GridStopWatch timer; GridStopWatch timer;
std::cout << GridLogMessage << "RNG read I/O on file " << file << std::endl; std::cout << GridLogMessage << "RNG read I/O on file " << file << std::endl;
std::vector<RNGstate> iodata(lsites); std::vector<RNGstate> iodata(lsites);
csum= IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_LEXICOGRAPHIC); IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_LEXICOGRAPHIC,
nersc_csum,scidac_csuma,scidac_csumb);
timer.Start(); timer.Start();
parallel_for(int lidx=0;lidx<lsites;lidx++){ parallel_for(int lidx=0;lidx<lsites;lidx++){
@ -520,33 +590,49 @@ class BinaryIO {
timer.Stop(); timer.Stop();
iodata.resize(1); iodata.resize(1);
csum+= IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_MASTER_APPEND); IOobject(w,grid,iodata,file,offset,format,BINARYIO_READ|BINARYIO_MASTER_APPEND,
nersc_csum_tmp,scidac_csuma_tmp,scidac_csumb_tmp);
{ {
std::vector<RngStateType> tmp(RngStateCount); std::vector<RngStateType> tmp(RngStateCount);
std::copy(iodata[0].begin(),iodata[0].end(),tmp.begin()); std::copy(iodata[0].begin(),iodata[0].end(),tmp.begin());
serial.SetState(tmp,0); serial.SetState(tmp,0);
} }
std::cout << GridLogMessage << "RNG file checksum " << std::hex << csum << std::dec << std::endl; nersc_csum = nersc_csum + nersc_csum_tmp;
scidac_csuma = scidac_csuma ^ scidac_csuma_tmp;
scidac_csumb = scidac_csumb ^ scidac_csumb_tmp;
// std::cout << GridLogMessage << "RNG file nersc_checksum " << std::hex << nersc_csum << std::dec << std::endl;
// std::cout << GridLogMessage << "RNG file scidac_checksuma " << std::hex << scidac_csuma << std::dec << std::endl;
// std::cout << GridLogMessage << "RNG file scidac_checksumb " << std::hex << scidac_csumb << std::dec << std::endl;
std::cout << GridLogMessage << "RNG state overhead " << timer.Elapsed() << std::endl; 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 // 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) static inline void writeRNG(GridSerialRNG &serial,
GridParallelRNG &parallel,
std::string file,
int offset,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
{ {
typedef typename GridSerialRNG::RngStateType RngStateType; typedef typename GridSerialRNG::RngStateType RngStateType;
typedef RngStateType word; word w=0; typedef RngStateType word; word w=0;
const int RngStateCount = GridSerialRNG::RngStateCount; const int RngStateCount = GridSerialRNG::RngStateCount;
typedef std::array<RngStateType,RngStateCount> RNGstate; typedef std::array<RngStateType,RngStateCount> RNGstate;
uint32_t csum = 0;
GridBase *grid = parallel._grid; GridBase *grid = parallel._grid;
int gsites = grid->gSites(); int gsites = grid->gSites();
int lsites = grid->lSites(); int lsites = grid->lSites();
uint32_t nersc_csum_tmp;
uint32_t scidac_csuma_tmp;
uint32_t scidac_csumb_tmp;
GridStopWatch timer; GridStopWatch timer;
std::string format = "IEEE32BIG"; std::string format = "IEEE32BIG";
@ -561,7 +647,8 @@ class BinaryIO {
} }
timer.Stop(); timer.Stop();
csum= IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_LEXICOGRAPHIC); IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_LEXICOGRAPHIC,
nersc_csum,scidac_csuma,scidac_csumb);
iodata.resize(1); iodata.resize(1);
{ {
@ -569,11 +656,11 @@ class BinaryIO {
serial.GetState(tmp,0); serial.GetState(tmp,0);
std::copy(tmp.begin(),tmp.end(),iodata[0].begin()); std::copy(tmp.begin(),tmp.end(),iodata[0].begin());
} }
csum+= IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_MASTER_APPEND); IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_MASTER_APPEND,
nersc_csum_tmp,scidac_csuma_tmp,scidac_csumb_tmp);
std::cout << GridLogMessage << "RNG file checksum " << std::hex << csum << std::dec << std::endl; // std::cout << GridLogMessage << "RNG file checksum " << std::hex << csum << std::dec << std::endl;
std::cout << GridLogMessage << "RNG state overhead " << timer.Elapsed() << std::endl; std::cout << GridLogMessage << "RNG state overhead " << timer.Elapsed() << std::endl;
return csum;
} }
}; };
} }

472
lib/parallelIO/IldgIO.h
View File

@ -43,201 +43,351 @@ extern "C" { // for linkage
#include "lime.h" #include "lime.h"
} }
// Unused SCIDAC records names
// SCIDAC_PRIVATE_FILE_XML "scidac-private-file-xml"
// SCIDAC_SITELIST "scidac-sitelist"
// SCIDAC_FILE_XML "scidac-file-xml"
// SCIDAC_RIVATE_RECORD_XML "scidac-private-record-xml"
// SCIDAC_RECORD_XML "scidac-record-xml"
// SCIDAC_BINARY_DATA "scidac-binary-data"
//
// Scidac checksum: CRC32 every site, xor reduce some hash of this.
// https://github.com/usqcd-software/qio/blob/master/lib/dml/DML_utils.c
namespace Grid { namespace Grid {
namespace QCD { namespace QCD {
inline void ILDGGrid(GridBase *grid, ILDGField &header) { class IldgIO : public BinaryIO {
assert(grid->_ndimension == 4); // emit error if not
header.dimension.resize(4);
header.boundary.resize(4);
for (int d = 0; d < 4; d++) {
header.dimension[d] = grid->_fdimensions[d];
// Read boundary conditions from ... ?
header.boundary[d] = std::string("periodic");
}
}
inline void ILDGChecksum(uint32_t *buf, uint32_t buf_size_bytes,
uint32_t &csum) {
BinaryIO::Uint32Checksum(buf, buf_size_bytes, csum);
}
//////////////////////////////////////////////////////////////////////
// Utilities ; these are QCD aware
//////////////////////////////////////////////////////////////////////
template <class GaugeField>
inline void ILDGStatistics(GaugeField &data, ILDGField &header) {
// How to convert data precision etc...
header.link_trace = Grid::QCD::WilsonLoops<PeriodicGimplR>::linkTrace(data);
header.plaquette = Grid::QCD::WilsonLoops<PeriodicGimplR>::avgPlaquette(data);
// header.polyakov =
}
// Forcing QCD here
template <class fobj, class sobj>
struct ILDGMunger {
void operator()(fobj &in, sobj &out, uint32_t &csum) {
for (int mu = 0; mu < 4; mu++) {
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
out(mu)()(i, j) = in(mu)()(i, j);
}
}
}
ILDGChecksum((uint32_t *)&in, sizeof(in), csum);
};
};
template <class fobj, class sobj>
struct ILDGUnmunger {
void operator()(sobj &in, fobj &out, uint32_t &csum) {
for (int mu = 0; mu < 4; mu++) {
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
out(mu)()(i, j) = in(mu)()(i, j);
}
}
}
ILDGChecksum((uint32_t *)&out, sizeof(out), csum);
};
};
////////////////////////////////////////////////////////////////////////////////
// Write and read from fstream; compute header offset for payload
////////////////////////////////////////////////////////////////////////////////
enum ILDGstate {ILDGread, ILDGwrite};
class ILDGIO : public BinaryIO {
FILE *File;
LimeWriter *LimeW;
LimeRecordHeader *LimeHeader;
LimeReader *LimeR;
std::string filename;
public: public:
ILDGIO(std::string file, ILDGstate RW) {
filename = file;
if (RW == ILDGwrite){
File = fopen(file.c_str(), "w");
// check if opened correctly
LimeW = limeCreateWriter(File); static int createHeader(std::string message, int MB, int ME, size_t PayloadSize, LimeWriter* L)
} else { {
File = fopen(file.c_str(), "r");
// check if opened correctly
LimeR = limeCreateReader(File);
}
}
~ILDGIO() { fclose(File); }
int createHeader(std::string message, int MB, int ME, size_t PayloadSize, LimeWriter* L){
LimeRecordHeader *h; LimeRecordHeader *h;
h = limeCreateHeader(MB, ME, const_cast<char *>(message.c_str()), PayloadSize); h = limeCreateHeader(MB, ME, const_cast<char *>(message.c_str()), PayloadSize);
int status = limeWriteRecordHeader(h, L); assert(limeWriteRecordHeader(h, L) >= 0);
if (status < 0) {
std::cerr << "ILDG Header error\n";
return status;
}
limeDestroyHeader(h); limeDestroyHeader(h);
return LIME_SUCCESS; return LIME_SUCCESS;
} }
unsigned int writeHeader(ILDGField &header) { template<class serialisable_object>
// write header in LIME static void writeLimeObject(int MB,int ME,serialisable_object &object,std::string object_name,std::string record_name, LimeWriter *LimeW)
n_uint64_t nbytes; {
int MB_flag = 1, ME_flag = 0; std::string xmlstring;
{
char message[] = "ildg-format"; XmlWriter WR("","");
nbytes = strlen(message); write(WR,object_name,object);
LimeHeader = limeCreateHeader(MB_flag, ME_flag, message, nbytes); xmlstring = WR.XmlString();
limeWriteRecordHeader(LimeHeader, LimeW); }
limeDestroyHeader(LimeHeader); uint64_t nbytes = xmlstring.size();
// save the xml header here LimeRecordHeader *h = limeCreateHeader(MB, ME,(char *)record_name.c_str(), nbytes);
// use the xml_writer to c++ streams in pugixml assert(limeWriteRecordHeader(h, LimeW)>=0);
// and convert to char message assert(limeWriteRecordData(&xmlstring[0], &nbytes, LimeW)>=0);
limeWriteRecordData(message, &nbytes, LimeW);
limeWriterCloseRecord(LimeW); limeWriterCloseRecord(LimeW);
limeDestroyHeader(h);
return 0;
} }
unsigned int readHeader(ILDGField &header) { static unsigned int writeHeader(FieldMetaData &header, LimeWriter *LimeW) {
uint64_t nbytes;
ildgFormat ildgfmt ;
usqcdInfo info;
//////////////////////////////////////////////////////
// Fill ILDG header data struct
//////////////////////////////////////////////////////
ildgfmt.field = std::string("su3gauge");
ildgfmt.precision = 64;
ildgfmt.version = 1.0;
ildgfmt.lx = header.dimension[0];
ildgfmt.ly = header.dimension[1];
ildgfmt.lz = header.dimension[2];
ildgfmt.lt = header.dimension[3];
assert(header.nd==4);
assert(header.nd==header.dimension.size());
info.version=1.0;
info.plaq = header.plaquette;
info.linktr = header.link_trace;
// Following scidac file downloaded from NERSC under MILC
// Begin message, keep open on successive records
//Message 1
// Type: scidac-private-file-xml <scidacFile><version>1.1</version><spacetime>4</spacetime><dims>16 16 16 48 </dims><volfmt>0</volfmt></scidacFile>
// Type: scidac-file-xml <title>MILC ILDG archival gauge configuration</title>
//Message 2
// Type: scidac-private-record-xml <scidacRecord><version>1.0</version><date>Thu May 11 00:11:33 2006 UTC</date><globaldata>0</globaldata>
// <datatype>QDP_F3_ColorMatrix</datatype><precision>F</precision><colors>3</colors><typesize>72</typesize><datacount>4</datacount></scidacRecord>
// Type: scidac-record-xml
// Type: ildg-format
// Type: ildg-data-lfn
// Type: ildg-binary-data
// Type: scidac-checksum
writeLimeObject(1,0,header ,std::string("FieldMetaData"),std::string(GRID_FORMAT),LimeW);
writeLimeObject(0,0,info ,std::string("usqcdInfo" ),std::string(USQCD_INFO ),LimeW);
writeLimeObject(0,0,ildgfmt,std::string("ildgFormat") ,std::string(ILDG_FORMAT),LimeW);
// LFN is not a serializable object
{
std::string LFN = header.ildg_lfn;
uint64_t PayloadSize = LFN.size();
createHeader(ILDG_DATA_LFN, 0 , 0, PayloadSize, LimeW);
limeWriteRecordData(const_cast<char*>(LFN.c_str()), &PayloadSize, LimeW);
limeWriterCloseRecord(LimeW);
}
return 0; return 0;
} }
template <class vsimd> template <class vsimd>
uint32_t readConfiguration(Lattice<iLorentzColourMatrix<vsimd> > &Umu) { static void writeConfiguration(std::string filename,Lattice<iLorentzColourMatrix<vsimd> > &Umu, std::string format) {
typedef Lattice<iLorentzColourMatrix<vsimd> > GaugeField;
typedef LorentzColourMatrixD sobjd;
typedef LorentzColourMatrixF sobjf;
typedef iLorentzColourMatrix<vsimd> itype;
typedef LorentzColourMatrix sobj;
GridBase *grid = Umu._grid;
ILDGField header; FILE *File = fopen(filename.c_str(), "w");
readHeader(header); LimeWriter *LimeW = limeCreateWriter(File);
// now just the conf, ignore the header
std::string format = std::string("IEEE64BIG");
do {limeReaderNextRecord(LimeR);}
while (strncmp(limeReaderType(LimeR), "ildg-binary-data",16));
n_uint64_t nbytes = limeReaderBytes(LimeR);//size of this record (configuration)
ILDGtype ILDGt(true, LimeR);
// this is special for double prec data, just for the moment
uint32_t csum = BinaryIO::readObjectParallel< itype, sobjd >(
Umu, filename, ILDGMunger<sobjd, sobj>(), 0, format, ILDGt);
// Check configuration
// todo
return csum;
}
template <class vsimd>
uint32_t writeConfiguration(Lattice<iLorentzColourMatrix<vsimd> > &Umu, std::string format) {
typedef Lattice<iLorentzColourMatrix<vsimd> > GaugeField; typedef Lattice<iLorentzColourMatrix<vsimd> > GaugeField;
typedef iLorentzColourMatrix<vsimd> vobj; typedef iLorentzColourMatrix<vsimd> vobj;
typedef typename vobj::scalar_object sobj; typedef typename vobj::scalar_object sobj;
typedef LorentzColourMatrixD fobj; typedef LorentzColourMatrixD fobj;
ILDGField header; GridBase * grid = Umu._grid;
// fill the header
////////////////////////////////////////
// fill the headers
////////////////////////////////////////
FieldMetaData header;
GridMetaData(grid,header);
GaugeStatistics<GaugeField>(Umu,header);
MachineCharacteristics(header);
assert( (format=="IEEE64BIG") || (format=="IEEE32BIG"));
header.floating_point = format; header.floating_point = format;
header.checksum = 0x0; // unused in ILDG
writeHeader(header,LimeW);
ILDGUnmunger<fobj, sobj> munge; ////////////////////////////////////////
unsigned int offset = writeHeader(header);
BinaryIO::Uint32Checksum<vobj, fobj>(Umu, munge, header.checksum);
// Write data record header // Write data record header
n_uint64_t PayloadSize = sizeof(fobj) * Umu._grid->_gsites; ////////////////////////////////////////
createHeader("ildg-binary-data", 0, 1, PayloadSize, LimeW); uint64_t PayloadSize = sizeof(fobj) * Umu._grid->_gsites;
createHeader(ILDG_BINARY_DATA, 0, 0, PayloadSize, LimeW);
ILDGtype ILDGt(true, LimeW);
uint32_t csum = BinaryIO::writeObjectParallel<vobj, fobj>( off_t offset = ftell(File);
Umu, filename, munge, 0, header.floating_point, ILDGt); uint32_t nersc_csum,scidac_csuma,scidac_csumb;
GaugeSimpleMunger<sobj, fobj> munge;
BinaryIO::writeLatticeObject<vobj, fobj >(Umu, filename, munge, offset, header.floating_point,
nersc_csum,scidac_csuma,scidac_csumb);
limeWriterCloseRecord(LimeW); limeWriterCloseRecord(LimeW);
// Last record ////////////////////////////////////////
// the logical file name LNF // Write checksum element, propagaing forward from the BinaryIO
// look into documentation on how to generate this string ////////////////////////////////////////
std::string LNF = "empty"; scidacChecksum checksum;
checksum.suma= scidac_csuma;
checksum.sumb= scidac_csumb;
// std::cout << " writing scidac checksums "<<std::hex<<scidac_csuma<<"/"<<scidac_csumb<<std::dec<<std::endl;
writeLimeObject(0,1,checksum,std::string("scidacChecksum" ),std::string(SCIDAC_CHECKSUM),LimeW);
fclose(File);
}
template <class vsimd>
static void readConfiguration(std::string filename,Lattice<iLorentzColourMatrix<vsimd> > &Umu, FieldMetaData &FieldMetaData_) {
typedef Lattice<iLorentzColourMatrix<vsimd> > GaugeField;
typedef LorentzColourMatrixD sobjd;
typedef LorentzColourMatrixF sobjf;
typedef iLorentzColourMatrix<vsimd> itype;
typedef LorentzColourMatrix sobj;
GridBase *grid = Umu._grid;
std::vector<int> dims = Umu._grid->FullDimensions();
assert(dims.size()==4);
FILE *File = fopen(filename.c_str(), "r");
LimeReader *LimeR = limeCreateReader(File);
PayloadSize = sizeof(LNF); // Metadata holders
createHeader("ildg-binary-lfn", 1 , 1, PayloadSize, LimeW); ildgFormat ildgFormat_ ;
limeWriteRecordData(const_cast<char*>(LNF.c_str()), &PayloadSize, LimeW); std::string ildgLFN_ ;
scidacChecksum scidacChecksum_;
usqcdInfo usqcdInfo_ ;
limeWriterCloseRecord(LimeW); // track what we read from file
int found_ildgFormat =0;
int found_ildgLFN =0;
int found_scidacChecksum=0;
int found_usqcdInfo =0;
int found_ildgBinary =0;
int found_FieldMetaData =0;
return csum; uint32_t nersc_csum;
uint32_t scidac_csuma;
uint32_t scidac_csumb;
// Binary format
std::string format;
//////////////////////////////////////////////////////////////////////////
// Loop over all records
// -- Order is poorly guaranteed except ILDG header preceeds binary section.
// -- Run like an event loop.
// -- Impose trust hierarchy. Grid takes precedence & look for ILDG, and failing
// that Scidac.
// -- Insist on Scidac checksum record.
//////////////////////////////////////////////////////////////////////////
while ( limeReaderNextRecord(LimeR) == LIME_SUCCESS ) {
uint64_t nbytes = limeReaderBytes(LimeR);//size of this record (configuration)
//////////////////////////////////////////////////////////////////
// If not BINARY_DATA read a string and parse
//////////////////////////////////////////////////////////////////
if ( strncmp(limeReaderType(LimeR), ILDG_BINARY_DATA,strlen(ILDG_BINARY_DATA) ) ) {
// Copy out the string
std::vector<char> xmlc(nbytes+1,'\0');
limeReaderReadData((void *)&xmlc[0], &nbytes, LimeR);
std::cout << GridLogMessage<< "Non binary record :" <<limeReaderType(LimeR) <<std::endl; //<<"\n"<<(&xmlc[0])<<std::endl;
//////////////////////////////////
// ILDG format record
if ( !strncmp(limeReaderType(LimeR), ILDG_FORMAT,strlen(ILDG_FORMAT)) ) {
XmlReader RD(&xmlc[0],"");
read(RD,"ildgFormat",ildgFormat_);
if ( ildgFormat_.precision == 64 ) format = std::string("IEEE64BIG");
if ( ildgFormat_.precision == 32 ) format = std::string("IEEE32BIG");
// std::cout << "This is an ILDG format record : "<<format<<std::endl;
assert( ildgFormat_.lx == dims[0]);
assert( ildgFormat_.ly == dims[1]);
assert( ildgFormat_.lz == dims[2]);
assert( ildgFormat_.lt == dims[3]);
found_ildgFormat = 1;
}
if ( !strncmp(limeReaderType(LimeR), ILDG_DATA_LFN,strlen(ILDG_DATA_LFN)) ) {
FieldMetaData_.ildg_lfn = std::string(&xmlc[0]);
// std::cout << "ILDG logical file name "<< FieldMetaData_.ildg_lfn << std::endl;
found_ildgLFN = 1;
}
if ( !strncmp(limeReaderType(LimeR), GRID_FORMAT,strlen(ILDG_FORMAT)) ) {
XmlReader RD(&xmlc[0],"");
read(RD,"FieldMetaData",FieldMetaData_);
// std::cout << "Grid header found : format is "<<FieldMetaData_.floating_point<<std::endl;
format = FieldMetaData_.floating_point;
assert(FieldMetaData_.dimension[0] == dims[0]);
assert(FieldMetaData_.dimension[1] == dims[1]);
assert(FieldMetaData_.dimension[2] == dims[2]);
assert(FieldMetaData_.dimension[3] == dims[3]);
found_FieldMetaData = 1;
}
if ( !strncmp(limeReaderType(LimeR), USQCD_INFO,strlen(USQCD_INFO)) ) {
XmlReader RD(&xmlc[0],"");
read(RD,USQCD_INFO,usqcdInfo_);
// std::cout << "USQCD info record found " <<std::endl;
found_usqcdInfo = 1;
}
if ( !strncmp(limeReaderType(LimeR), SCIDAC_CHECKSUM,strlen(SCIDAC_CHECKSUM)) ) {
XmlReader RD(&xmlc[0],"");
read(RD,"scidacChecksum",scidacChecksum_);
FieldMetaData_.scidac_checksuma = scidacChecksum_.suma;
FieldMetaData_.scidac_checksumb = scidacChecksum_.sumb;
//std::cout << " Read Out "<<scidacChecksum_.version<<"/"<< scidacChecksum_.suma<<"/"<<scidacChecksum_.sumb<<std::endl;
found_scidacChecksum = 1;
}
} else {
/////////////////////////////////
// Binary data
/////////////////////////////////
std::cout << GridLogMessage << ILDG_BINARY_DATA << std::endl;
off_t offset= ftell(File);
GaugeSimpleMunger<sobjd, sobj> munge;
BinaryIO::readLatticeObject< itype, sobjd >(Umu, filename, munge, offset, format,
nersc_csum,scidac_csuma,scidac_csumb);
found_ildgBinary = 1;
}
}
//////////////////////////////////////////////////////
// Minimally must find binary segment and checksum
//////////////////////////////////////////////////////
assert(found_ildgBinary);
assert(found_scidacChecksum);
// Must find something with the lattice dimensions
assert(found_FieldMetaData||found_ildgFormat);
if ( found_FieldMetaData ) {
std::cout << GridLogMessage<<"a Grid MetaData was record found: configuration was probably written by Grid ! Yay ! "<<std::endl;
// std::cout << "Read Grid Plaqette "<<FieldMetaData_.plaquette<<std::endl;
// std::cout << "Read Grid LinkTrace "<<FieldMetaData_.link_trace<<std::endl;
} else {
assert(found_ildgFormat);
assert ( ildgFormat_.field == std::string("su3gauge") );
///////////////////////////////////////////////////////////////////////////////////////
// Populate our Grid metadata as best we can
///////////////////////////////////////////////////////////////////////////////////////
std::ostringstream vers; vers << ildgFormat_.version;
FieldMetaData_.hdr_version = vers.str();
FieldMetaData_.data_type = std::string("4D_SU3_GAUGE_3X3");
assert(FieldMetaData_.nd==4);
assert(FieldMetaData_.dimension.size()==4);
FieldMetaData_.dimension[0] = ildgFormat_.lx ;
FieldMetaData_.dimension[1] = ildgFormat_.ly ;
FieldMetaData_.dimension[2] = ildgFormat_.lz ;
FieldMetaData_.dimension[3] = ildgFormat_.lt ;
if ( found_usqcdInfo ) {
FieldMetaData_.plaquette = usqcdInfo_.plaq;
FieldMetaData_.link_trace= usqcdInfo_.linktr;
// std::cout << "This configuration was probably written by USQCD and not Grid "<<std::endl;
// std::cout << "Read USQCD Plaquette "<<FieldMetaData_.plaquette<<std::endl;
// std::cout << "Read USQCD LinkTrace "<<FieldMetaData_.link_trace<<std::endl;
} else {
FieldMetaData_.plaquette = 0.0;
FieldMetaData_.link_trace= 0.0;
std::cout << "Uhoh... This configuration is unsafe and contains no recognised checksum or physics records that can verify it !!! "<<std::endl;
}
}
if ( found_scidacChecksum ) {
assert( scidac_csuma ==FieldMetaData_.scidac_checksuma);
assert( scidac_csumb ==FieldMetaData_.scidac_checksumb);
std::cout << GridLogMessage<<"SciDAC checksums match " << std::endl;
}
if ( found_FieldMetaData || found_usqcdInfo ) {
FieldMetaData checker;
GaugeStatistics<GaugeField>(Umu,checker);
assert(fabs(checker.plaquette - FieldMetaData_.plaquette )<1.0e-5);
assert(fabs(checker.link_trace - FieldMetaData_.link_trace)<1.0e-5);
std::cout << GridLogMessage<<"Plaquette and link trace match " << std::endl;
}
} }
// format for RNG? Now just binary out // format for RNG? Now just binary out

110
lib/parallelIO/IldgIOtypes.h
View File

@ -34,47 +34,83 @@ extern "C" { // for linkage
namespace Grid { namespace Grid {
struct ILDGtype { #define GRID_FORMAT "grid-format"
bool is_ILDG; #define ILDG_FORMAT "ildg-format"
LimeWriter* LW; #define ILDG_BINARY_DATA "ildg-binary-data"
LimeReader* LR; #define ILDG_DATA_LFN "ildg-data-lfn"
#define USQCD_INFO "usqcdInfo"
#define SCIDAC_CHECKSUM "scidac-checksum"
ILDGtype(bool is, LimeWriter* L) : is_ILDG(is), LW(L), LR(NULL) {} /////////////////////////////////////////////////////////////////////////////////
ILDGtype(bool is, LimeReader* L) : is_ILDG(is), LW(NULL), LR(L) {} // Data representation of records that enter ILDG and SciDac formats
ILDGtype() : is_ILDG(false), LW(NULL), LR(NULL) {} /////////////////////////////////////////////////////////////////////////////////
struct ildgFormat : Serializable {
public:
GRID_SERIALIZABLE_CLASS_MEMBERS(ildgFormat,
double, version,
std::string, field,
int, precision,
int, lx,
int, ly,
int, lz,
int, lt);
ildgFormat() {
version=1.0;
};
}; };
struct usqcdInfo : Serializable {
class ILDGField {
public: public:
// header strings (not in order) GRID_SERIALIZABLE_CLASS_MEMBERS(usqcdInfo,
std::vector<int> dimension; double, version,
std::vector<std::string> boundary; double, plaq,
int data_start; double, linktr,
std::string hdr_version; std::string, info);
std::string storage_format; usqcdInfo() {
// Checks on data version=1.0;
double link_trace; };
double plaquette; };
uint32_t checksum;
unsigned int sequence_number; struct usqcdPropFile : Serializable {
std::string data_type; public:
std::string ensemble_id; GRID_SERIALIZABLE_CLASS_MEMBERS(usqcdPropFile,
std::string ensemble_label; double, version,
std::string creator; std::string, type,
std::string creator_hardware; std::string, info);
std::string creation_date; usqcdPropFile() {
std::string archive_date; version=1.0;
std::string floating_point; };
};
struct usqcdSourceInfo : Serializable {
public:
GRID_SERIALIZABLE_CLASS_MEMBERS(usqcdSourceInfo,
double, version,
std::string, info);
usqcdSourceInfo() {
version=1.0;
};
};
struct usqcdPropInfo : Serializable {
public:
GRID_SERIALIZABLE_CLASS_MEMBERS(usqcdPropInfo,
double, version,
int, spin,
int, color,
std::string, info);
usqcdPropInfo() {
version=1.0;
};
};
struct scidacChecksum : Serializable {
public:
GRID_SERIALIZABLE_CLASS_MEMBERS(scidacChecksum,
double, version,
uint32_t, suma,
uint32_t, sumb);
scidacChecksum() {
version=1.0;
suma=sumb=0;
};
}; };
} }
#else
namespace Grid {
struct ILDGtype {
bool is_ILDG;
ILDGtype() : is_ILDG(false) {}
};
}
#endif #endif
#endif #endif

301
lib/parallelIO/NerscIO.h
View File

@ -30,168 +30,11 @@
#ifndef GRID_NERSC_IO_H #ifndef GRID_NERSC_IO_H
#define GRID_NERSC_IO_H #define GRID_NERSC_IO_H
#include <algorithm>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <map>
#include <unistd.h>
#include <sys/utsname.h>
#include <pwd.h>
namespace Grid { namespace Grid {
namespace QCD { namespace QCD {
using namespace Grid; using namespace Grid;
////////////////////////////////////////////////////////////////////////////////
// Some data types for intermediate storage
////////////////////////////////////////////////////////////////////////////////
template<typename vtype> using iLorentzColour2x3 = iVector<iVector<iVector<vtype, Nc>, 2>, 4 >;
typedef iLorentzColour2x3<Complex> LorentzColour2x3;
typedef iLorentzColour2x3<ComplexF> LorentzColour2x3F;
typedef iLorentzColour2x3<ComplexD> LorentzColour2x3D;
////////////////////////////////////////////////////////////////////////////////
// header specification/interpretation
////////////////////////////////////////////////////////////////////////////////
class NerscField {
public:
// header strings (not in order)
int dimension[4];
std::string boundary[4];
int data_start;
std::string hdr_version;
std::string storage_format;
// Checks on data
double link_trace;
double plaquette;
uint32_t checksum;
unsigned int sequence_number;
std::string data_type;
std::string ensemble_id ;
std::string ensemble_label ;
std::string creator ;
std::string creator_hardware ;
std::string creation_date ;
std::string archive_date ;
std::string floating_point;
};
//////////////////////////////////////////////////////////////////////
// Bit and Physical Checksumming and QA of data
//////////////////////////////////////////////////////////////////////
inline void NerscGrid(GridBase *grid,NerscField &header)
{
assert(grid->_ndimension==4);
for(int d=0;d<4;d++) {
header.dimension[d] = grid->_fdimensions[d];
}
for(int d=0;d<4;d++) {
header.boundary[d] = std::string("PERIODIC");
}
}
template<class GaugeField>
inline void NerscStatistics(GaugeField & data,NerscField &header)
{
// How to convert data precision etc...
header.link_trace=Grid::QCD::WilsonLoops<PeriodicGimplR>::linkTrace(data);
header.plaquette =Grid::QCD::WilsonLoops<PeriodicGimplR>::avgPlaquette(data);
}
inline void NerscMachineCharacteristics(NerscField &header)
{
// Who
struct passwd *pw = getpwuid (getuid());
if (pw) header.creator = std::string(pw->pw_name);
// When
std::time_t t = std::time(nullptr);
std::tm tm = *std::localtime(&t);
std::ostringstream oss;
// oss << std::put_time(&tm, "%c %Z");
header.creation_date = oss.str();
header.archive_date = header.creation_date;
// What
struct utsname name; uname(&name);
header.creator_hardware = std::string(name.nodename)+"-";
header.creator_hardware+= std::string(name.machine)+"-";
header.creator_hardware+= std::string(name.sysname)+"-";
header.creator_hardware+= std::string(name.release);
}
//////////////////////////////////////////////////////////////////////
// Utilities ; these are QCD aware
//////////////////////////////////////////////////////////////////////
inline void reconstruct3(LorentzColourMatrix & cm)
{
const int x=0;
const int y=1;
const int z=2;
for(int mu=0;mu<4;mu++){
cm(mu)()(2,x) = adj(cm(mu)()(0,y)*cm(mu)()(1,z)-cm(mu)()(0,z)*cm(mu)()(1,y)); //x= yz-zy
cm(mu)()(2,y) = adj(cm(mu)()(0,z)*cm(mu)()(1,x)-cm(mu)()(0,x)*cm(mu)()(1,z)); //y= zx-xz
cm(mu)()(2,z) = adj(cm(mu)()(0,x)*cm(mu)()(1,y)-cm(mu)()(0,y)*cm(mu)()(1,x)); //z= xy-yx
}
}
template<class fobj,class sobj>
struct NerscSimpleMunger{
void operator()(fobj &in, sobj &out) {
for (int mu = 0; mu < Nd; mu++) {
for (int i = 0; i < Nc; i++) {
for (int j = 0; j < Nc; j++) {
out(mu)()(i, j) = in(mu)()(i, j);
}}
}
};
};
template <class fobj, class sobj>
struct NerscSimpleUnmunger {
void operator()(sobj &in, fobj &out) {
for (int mu = 0; mu < Nd; mu++) {
for (int i = 0; i < Nc; i++) {
for (int j = 0; j < Nc; j++) {
out(mu)()(i, j) = in(mu)()(i, j);
}}
}
};
};
template<class fobj,class sobj>
struct Nersc3x2munger{
void operator() (fobj &in,sobj &out){
for(int mu=0;mu<4;mu++){
for(int i=0;i<2;i++){
for(int j=0;j<3;j++){
out(mu)()(i,j) = in(mu)(i)(j);
}}
}
reconstruct3(out);
}
};
template<class fobj,class sobj>
struct Nersc3x2unmunger{
void operator() (sobj &in,fobj &out){
for(int mu=0;mu<4;mu++){
for(int i=0;i<2;i++){
for(int j=0;j<3;j++){
out(mu)(i)(j) = in(mu)()(i,j);
}}
}
}
};
//////////////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////////////////
// Write and read from fstream; comput header offset for payload // Write and read from fstream; comput header offset for payload
//////////////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////////////////
@ -202,42 +45,17 @@ namespace Grid {
std::ofstream fout(file,std::ios::out); std::ofstream fout(file,std::ios::out);
} }
#define dump_nersc_header(field, s) \ static inline unsigned int writeHeader(FieldMetaData &field,std::string file)
s << "BEGIN_HEADER" << std::endl; \
s << "HDR_VERSION = " << field.hdr_version << std::endl; \
s << "DATATYPE = " << field.data_type << std::endl; \
s << "STORAGE_FORMAT = " << field.storage_format << std::endl; \
for(int i=0;i<4;i++){ \
s << "DIMENSION_" << i+1 << " = " << field.dimension[i] << std::endl ; \
} \
s << "LINK_TRACE = " << std::setprecision(10) << field.link_trace << std::endl; \
s << "PLAQUETTE = " << std::setprecision(10) << field.plaquette << std::endl; \
for(int i=0;i<4;i++){ \
s << "BOUNDARY_"<<i+1<<" = " << field.boundary[i] << std::endl; \
} \
\
s << "CHECKSUM = "<< std::hex << std::setw(10) << field.checksum << std::dec<<std::endl; \
s << "ENSEMBLE_ID = " << field.ensemble_id << std::endl; \
s << "ENSEMBLE_LABEL = " << field.ensemble_label << std::endl; \
s << "SEQUENCE_NUMBER = " << field.sequence_number << std::endl; \
s << "CREATOR = " << field.creator << std::endl; \
s << "CREATOR_HARDWARE = "<< field.creator_hardware << std::endl; \
s << "CREATION_DATE = " << field.creation_date << std::endl; \
s << "ARCHIVE_DATE = " << field.archive_date << std::endl; \
s << "FLOATING_POINT = " << field.floating_point << std::endl; \
s << "END_HEADER" << std::endl;
static inline unsigned int writeHeader(NerscField &field,std::string file)
{ {
std::ofstream fout(file,std::ios::out|std::ios::in); std::ofstream fout(file,std::ios::out|std::ios::in);
fout.seekp(0,std::ios::beg); fout.seekp(0,std::ios::beg);
dump_nersc_header(field, fout); dump_meta_data(field, fout);
field.data_start = fout.tellp(); field.data_start = fout.tellp();
return field.data_start; return field.data_start;
} }
// for the header-reader // for the header-reader
static inline int readHeader(std::string file,GridBase *grid, NerscField &field) static inline int readHeader(std::string file,GridBase *grid, FieldMetaData &field)
{ {
int offset=0; int offset=0;
std::map<std::string,std::string> header; std::map<std::string,std::string> header;
@ -309,19 +127,21 @@ namespace Grid {
return field.data_start; return field.data_start;
} }
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Now the meat: the object readers // Now the meat: the object readers
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template<class vsimd> template<class vsimd>
static inline void readConfiguration(Lattice<iLorentzColourMatrix<vsimd> > &Umu,NerscField& header,std::string file) static inline void readConfiguration(Lattice<iLorentzColourMatrix<vsimd> > &Umu,
FieldMetaData& header,
std::string file)
{ {
typedef Lattice<iLorentzColourMatrix<vsimd> > GaugeField; typedef Lattice<iLorentzColourMatrix<vsimd> > GaugeField;
GridBase *grid = Umu._grid; GridBase *grid = Umu._grid;
int offset = readHeader(file,Umu._grid,header); int offset = readHeader(file,Umu._grid,header);
NerscField clone(header); FieldMetaData clone(header);
std::string format(header.floating_point); std::string format(header.floating_point);
@ -330,34 +150,38 @@ namespace Grid {
int ieee64big = (format == std::string("IEEE64BIG")); int ieee64big = (format == std::string("IEEE64BIG"));
int ieee64 = (format == std::string("IEEE64")); int ieee64 = (format == std::string("IEEE64"));
uint32_t csum; uint32_t nersc_csum,scidac_csuma,scidac_csumb;
// depending on datatype, set up munger; // depending on datatype, set up munger;
// munger is a function of <floating point, Real, data_type> // munger is a function of <floating point, Real, data_type>
if ( header.data_type == std::string("4D_SU3_GAUGE") ) { if ( header.data_type == std::string("4D_SU3_GAUGE") ) {
if ( ieee32 || ieee32big ) { if ( ieee32 || ieee32big ) {
csum=BinaryIO::readLatticeObject<iLorentzColourMatrix<vsimd>, LorentzColour2x3F> BinaryIO::readLatticeObject<iLorentzColourMatrix<vsimd>, LorentzColour2x3F>
(Umu,file,Nersc3x2munger<LorentzColour2x3F,LorentzColourMatrix>(), offset,format); (Umu,file,Gauge3x2munger<LorentzColour2x3F,LorentzColourMatrix>(), offset,format,
nersc_csum,scidac_csuma,scidac_csumb);
} }
if ( ieee64 || ieee64big ) { if ( ieee64 || ieee64big ) {
csum=BinaryIO::readLatticeObject<iLorentzColourMatrix<vsimd>, LorentzColour2x3D> BinaryIO::readLatticeObject<iLorentzColourMatrix<vsimd>, LorentzColour2x3D>
(Umu,file,Nersc3x2munger<LorentzColour2x3D,LorentzColourMatrix>(),offset,format); (Umu,file,Gauge3x2munger<LorentzColour2x3D,LorentzColourMatrix>(),offset,format,
nersc_csum,scidac_csuma,scidac_csumb);
} }
} else if ( header.data_type == std::string("4D_SU3_GAUGE_3x3") ) { } else if ( header.data_type == std::string("4D_SU3_GAUGE_3x3") ) {
if ( ieee32 || ieee32big ) { if ( ieee32 || ieee32big ) {
csum=BinaryIO::readLatticeObject<iLorentzColourMatrix<vsimd>,LorentzColourMatrixF> BinaryIO::readLatticeObject<iLorentzColourMatrix<vsimd>,LorentzColourMatrixF>
(Umu,file,NerscSimpleMunger<LorentzColourMatrixF,LorentzColourMatrix>(),offset,format); (Umu,file,GaugeSimpleMunger<LorentzColourMatrixF,LorentzColourMatrix>(),offset,format,
nersc_csum,scidac_csuma,scidac_csumb);
} }
if ( ieee64 || ieee64big ) { if ( ieee64 || ieee64big ) {
csum=BinaryIO::readLatticeObject<iLorentzColourMatrix<vsimd>,LorentzColourMatrixD> BinaryIO::readLatticeObject<iLorentzColourMatrix<vsimd>,LorentzColourMatrixD>
(Umu,file,NerscSimpleMunger<LorentzColourMatrixD,LorentzColourMatrix>(),offset,format); (Umu,file,GaugeSimpleMunger<LorentzColourMatrixD,LorentzColourMatrix>(),offset,format,
nersc_csum,scidac_csuma,scidac_csumb);
} }
} else { } else {
assert(0); assert(0);
} }
NerscStatistics<GaugeField>(Umu,clone); GaugeStatistics<GaugeField>(Umu,clone);
std::cout<<GridLogMessage <<"NERSC Configuration "<<file<<" checksum "<<std::hex<< csum<< std::dec std::cout<<GridLogMessage <<"NERSC Configuration "<<file<<" checksum "<<std::hex<<nersc_csum<< std::dec
<<" header "<<std::hex<<header.checksum<<std::dec <<std::endl; <<" header "<<std::hex<<header.checksum<<std::dec <<std::endl;
std::cout<<GridLogMessage <<"NERSC Configuration "<<file<<" plaquette "<<clone.plaquette std::cout<<GridLogMessage <<"NERSC Configuration "<<file<<" plaquette "<<clone.plaquette
<<" header "<<header.plaquette<<std::endl; <<" header "<<header.plaquette<<std::endl;
@ -369,30 +193,35 @@ namespace Grid {
std::cout << Umu[0]<<std::endl; std::cout << Umu[0]<<std::endl;
std::cout << Umu[1]<<std::endl; std::cout << Umu[1]<<std::endl;
} }
if ( csum != header.checksum ) { if ( nersc_csum != header.checksum ) {
std::cerr << " checksum mismatch " << std::endl; std::cerr << " checksum mismatch " << std::endl;
std::cerr << " plaqs " << clone.plaquette << " " << header.plaquette << std::endl; std::cerr << " plaqs " << clone.plaquette << " " << header.plaquette << std::endl;
std::cerr << " trace " << clone.link_trace<< " " << header.link_trace<< std::endl; std::cerr << " trace " << clone.link_trace<< " " << header.link_trace<< std::endl;
std::cerr << " csum " <<std::hex<< csum << " " << header.checksum<< std::dec<< std::endl; std::cerr << " nersc_csum " <<std::hex<< nersc_csum << " " << header.checksum<< std::dec<< std::endl;
exit(0); exit(0);
} }
assert(fabs(clone.plaquette -header.plaquette ) < 1.0e-5 ); assert(fabs(clone.plaquette -header.plaquette ) < 1.0e-5 );
assert(fabs(clone.link_trace-header.link_trace) < 1.0e-6 ); assert(fabs(clone.link_trace-header.link_trace) < 1.0e-6 );
assert(csum == header.checksum ); assert(nersc_csum == header.checksum );
std::cout<<GridLogMessage <<"NERSC Configuration "<<file<< " and plaquette, link trace, and checksum agree"<<std::endl; std::cout<<GridLogMessage <<"NERSC Configuration "<<file<< " and plaquette, link trace, and checksum agree"<<std::endl;
} }
template<class vsimd> template<class vsimd>
static inline void writeConfiguration(Lattice<iLorentzColourMatrix<vsimd> > &Umu,std::string file, int two_row,int bits32) static inline void writeConfiguration(Lattice<iLorentzColourMatrix<vsimd> > &Umu,
std::string file,
int two_row,
int bits32)
{ {
typedef Lattice<iLorentzColourMatrix<vsimd> > GaugeField; typedef Lattice<iLorentzColourMatrix<vsimd> > GaugeField;
typedef iLorentzColourMatrix<vsimd> vobj; typedef iLorentzColourMatrix<vsimd> vobj;
typedef typename vobj::scalar_object sobj; typedef typename vobj::scalar_object sobj;
FieldMetaData header;
///////////////////////////////////////////
// Following should become arguments // Following should become arguments
NerscField header; ///////////////////////////////////////////
header.sequence_number = 1; header.sequence_number = 1;
header.ensemble_id = "UKQCD"; header.ensemble_id = "UKQCD";
header.ensemble_label = "DWF"; header.ensemble_label = "DWF";
@ -402,32 +231,31 @@ namespace Grid {
GridBase *grid = Umu._grid; GridBase *grid = Umu._grid;
NerscGrid(grid,header); GridMetaData(grid,header);
NerscStatistics<GaugeField>(Umu,header); assert(header.nd==4);
NerscMachineCharacteristics(header); GaugeStatistics<GaugeField>(Umu,header);
MachineCharacteristics(header);
int offset; int offset;
truncate(file); truncate(file);
if ( two_row ) { // Sod it -- always write 3x3 double
header.floating_point = std::string("IEEE64BIG"); header.floating_point = std::string("IEEE64BIG");
header.data_type = std::string("4D_SU3_GAUGE"); header.data_type = std::string("4D_SU3_GAUGE_3x3");
Nersc3x2unmunger<fobj2D,sobj> munge; GaugeSimpleUnmunger<fobj3D,sobj> munge;
offset = writeHeader(header,file); offset = writeHeader(header,file);
header.checksum=BinaryIO::writeLatticeObject<vobj,fobj2D>(Umu,file,munge,offset,header.floating_point);
writeHeader(header,file); uint32_t nersc_csum,scidac_csuma,scidac_csumb;
} else { BinaryIO::writeLatticeObject<vobj,fobj3D>(Umu,file,munge,offset,header.floating_point,
header.floating_point = std::string("IEEE64BIG"); nersc_csum,scidac_csuma,scidac_csumb);
header.data_type = std::string("4D_SU3_GAUGE_3x3"); header.checksum = nersc_csum;
NerscSimpleUnmunger<fobj3D,sobj> munge; writeHeader(header,file);
offset = writeHeader(header,file);
header.checksum=BinaryIO::writeLatticeObject<vobj,fobj3D>(Umu,file,munge,offset,header.floating_point);
writeHeader(header,file);
}
std::cout<<GridLogMessage <<"Written NERSC Configuration on "<< file << " checksum " std::cout<<GridLogMessage <<"Written NERSC Configuration on "<< file << " checksum "
<<std::hex<<header.checksum <<std::hex<<header.checksum
<<std::dec<<" plaq "<< header.plaquette <<std::endl; <<std::dec<<" plaq "<< header.plaquette <<std::endl;
} }
/////////////////////////////// ///////////////////////////////
// RNG state // RNG state
@ -437,17 +265,18 @@ namespace Grid {
typedef typename GridParallelRNG::RngStateType RngStateType; typedef typename GridParallelRNG::RngStateType RngStateType;
// Following should become arguments // Following should become arguments
NerscField header; FieldMetaData header;
header.sequence_number = 1; header.sequence_number = 1;
header.ensemble_id = "UKQCD"; header.ensemble_id = "UKQCD";
header.ensemble_label = "DWF"; header.ensemble_label = "DWF";
GridBase *grid = parallel._grid; GridBase *grid = parallel._grid;
NerscGrid(grid,header); GridMetaData(grid,header);
assert(header.nd==4);
header.link_trace=0.0; header.link_trace=0.0;
header.plaquette=0.0; header.plaquette=0.0;
NerscMachineCharacteristics(header); MachineCharacteristics(header);
int offset; int offset;
@ -466,7 +295,9 @@ namespace Grid {
truncate(file); truncate(file);
offset = writeHeader(header,file); offset = writeHeader(header,file);
header.checksum = BinaryIO::writeRNG(serial,parallel,file,offset); uint32_t nersc_csum,scidac_csuma,scidac_csumb;
BinaryIO::writeRNG(serial,parallel,file,offset,nersc_csum,scidac_csuma,scidac_csumb);
header.checksum = nersc_csum;
offset = writeHeader(header,file); offset = writeHeader(header,file);
std::cout<<GridLogMessage std::cout<<GridLogMessage
@ -476,7 +307,7 @@ namespace Grid {
} }
static inline void readRNGState(GridSerialRNG &serial,GridParallelRNG & parallel,NerscField& header,std::string file) static inline void readRNGState(GridSerialRNG &serial,GridParallelRNG & parallel,FieldMetaData& header,std::string file)
{ {
typedef typename GridParallelRNG::RngStateType RngStateType; typedef typename GridParallelRNG::RngStateType RngStateType;
@ -484,7 +315,7 @@ namespace Grid {
int offset = readHeader(file,grid,header); int offset = readHeader(file,grid,header);
NerscField clone(header); FieldMetaData clone(header);
std::string format(header.floating_point); std::string format(header.floating_point);
std::string data_type(header.data_type); std::string data_type(header.data_type);
@ -504,19 +335,19 @@ namespace Grid {
// depending on datatype, set up munger; // depending on datatype, set up munger;
// munger is a function of <floating point, Real, data_type> // munger is a function of <floating point, Real, data_type>
uint32_t csum=BinaryIO::readRNG(serial,parallel,file,offset); uint32_t nersc_csum,scidac_csuma,scidac_csumb;
BinaryIO::readRNG(serial,parallel,file,offset,nersc_csum,scidac_csuma,scidac_csumb);
if ( csum != header.checksum ) { if ( nersc_csum != header.checksum ) {
std::cerr << "checksum mismatch "<<std::hex<< csum <<" "<<header.checksum<<std::dec<<std::endl; std::cerr << "checksum mismatch "<<std::hex<< nersc_csum <<" "<<header.checksum<<std::dec<<std::endl;
exit(0); exit(0);
} }
assert(csum == header.checksum ); assert(nersc_csum == header.checksum );
std::cout<<GridLogMessage <<"Read NERSC RNG file "<<file<< " format "<< data_type <<std::endl; std::cout<<GridLogMessage <<"Read NERSC RNG file "<<file<< " format "<< data_type <<std::endl;
} }
}; };
}} }}
#endif #endif

38
lib/qcd/hmc/checkpointers/BinaryCheckpointer.h
View File

@ -62,36 +62,50 @@ class BinaryHmcCheckpointer : public BaseHmcCheckpointer<Impl> {
fout.close(); fout.close();
} }
void TrajectoryComplete(int traj, Field &U, GridSerialRNG &sRNG, void TrajectoryComplete(int traj, Field &U, GridSerialRNG &sRNG, GridParallelRNG &pRNG) {
GridParallelRNG &pRNG) {
if ((traj % Params.saveInterval) == 0) { if ((traj % Params.saveInterval) == 0) {
std::string config, rng; std::string config, rng;
this->build_filenames(traj, Params, config, rng); this->build_filenames(traj, Params, config, rng);
uint32_t nersc_csum;
uint32_t scidac_csuma;
uint32_t scidac_csumb;
BinarySimpleUnmunger<sobj_double, sobj> munge; BinarySimpleUnmunger<sobj_double, sobj> munge;
truncate(rng); truncate(rng);
BinaryIO::writeRNG(sRNG, pRNG, rng, 0); BinaryIO::writeRNG(sRNG, pRNG, rng, 0,nersc_csum,scidac_csuma,scidac_csumb);
truncate(config); truncate(config);
uint32_t csum = BinaryIO::writeLatticeObject<vobj, sobj_double>(
U, config, munge, 0, Params.format); BinaryIO::writeLatticeObject<vobj, sobj_double>(U, config, munge, 0, Params.format,
nersc_csum,scidac_csuma,scidac_csumb);
std::cout << GridLogMessage << "Written Binary Configuration " << config std::cout << GridLogMessage << "Written Binary Configuration " << config
<< " checksum " << std::hex << csum << std::dec << std::endl; << " checksum " << std::hex
<< nersc_csum <<"/"
<< scidac_csuma <<"/"
<< scidac_csumb
<< std::dec << std::endl;
} }
}; };
void CheckpointRestore(int traj, Field &U, GridSerialRNG &sRNG, void CheckpointRestore(int traj, Field &U, GridSerialRNG &sRNG, GridParallelRNG &pRNG) {
GridParallelRNG &pRNG) {
std::string config, rng; std::string config, rng;
this->build_filenames(traj, Params, config, rng); this->build_filenames(traj, Params, config, rng);
BinarySimpleMunger<sobj_double, sobj> munge; BinarySimpleMunger<sobj_double, sobj> munge;
BinaryIO::readRNG(sRNG, pRNG, rng, 0);
uint32_t csum = BinaryIO::readLatticeObject<vobj, sobj_double>(
U, config, munge, 0, Params.format);
uint32_t nersc_csum;
uint32_t scidac_csuma;
uint32_t scidac_csumb;
BinaryIO::readRNG(sRNG, pRNG, rng, 0,nersc_csum,scidac_csuma,scidac_csumb);
BinaryIO::readLatticeObject<vobj, sobj_double>(U, config, munge, 0, Params.format,
nersc_csum,scidac_csuma,scidac_csumb);
std::cout << GridLogMessage << "Read Binary Configuration " << config std::cout << GridLogMessage << "Read Binary Configuration " << config
<< " checksum " << std::hex << csum << std::dec << std::endl; << " checksums " << std::hex << nersc_csum<<"/"<<scidac_csuma<<"/"<<scidac_csumb
<< std::dec << std::endl;
}; };
}; };
} }

32
lib/qcd/hmc/checkpointers/ILDGCheckpointer.h
View File

@ -54,9 +54,9 @@ class ILDGHmcCheckpointer : public BaseHmcCheckpointer<Implementation> {
// check here that the format is valid // check here that the format is valid
int ieee32big = (Params.format == std::string("IEEE32BIG")); int ieee32big = (Params.format == std::string("IEEE32BIG"));
int ieee32 = (Params.format == std::string("IEEE32")); int ieee32 = (Params.format == std::string("IEEE32"));
int ieee64big = (Params.format == std::string("IEEE64BIG")); int ieee64big = (Params.format == std::string("IEEE64BIG"));
int ieee64 = (Params.format == std::string("IEEE64")); int ieee64 = (Params.format == std::string("IEEE64"));
if (!(ieee64big || ieee32 || ieee32big || ieee64)) { if (!(ieee64big || ieee32 || ieee32big || ieee64)) {
std::cout << GridLogError << "Unrecognized file format " << Params.format std::cout << GridLogError << "Unrecognized file format " << Params.format
@ -74,13 +74,17 @@ class ILDGHmcCheckpointer : public BaseHmcCheckpointer<Implementation> {
if ((traj % Params.saveInterval) == 0) { if ((traj % Params.saveInterval) == 0) {
std::string config, rng; std::string config, rng;
this->build_filenames(traj, Params, config, rng); this->build_filenames(traj, Params, config, rng);
ILDGIO IO(config, ILDGwrite); uint32_t nersc_csum,scidac_csuma,scidac_csumb;
BinaryIO::writeRNGSerial(sRNG, pRNG, rng, 0); BinaryIO::writeRNG(sRNG, pRNG, rng, 0,nersc_csum,scidac_csuma,scidac_csumb);
uint32_t csum = IO.writeConfiguration(U, Params.format); IldgIO::writeConfiguration(config,U, Params.format);
std::cout << GridLogMessage << "Written ILDG Configuration on " << config std::cout << GridLogMessage << "Written ILDG Configuration on " << config
<< " checksum " << std::hex << csum << std::dec << std::endl; << " checksum " << std::hex
<< nersc_csum<<"/"
<< scidac_csuma<<"/"
<< scidac_csumb
<< std::dec << std::endl;
} }
}; };
@ -89,12 +93,18 @@ class ILDGHmcCheckpointer : public BaseHmcCheckpointer<Implementation> {
std::string config, rng; std::string config, rng;
this->build_filenames(traj, Params, config, rng); this->build_filenames(traj, Params, config, rng);
ILDGIO IO(config, ILDGread); uint32_t nersc_csum,scidac_csuma,scidac_csumb;
BinaryIO::readRNGSerial(sRNG, pRNG, rng, 0); BinaryIO::readRNG(sRNG, pRNG, rng, 0,nersc_csum,scidac_csuma,scidac_csumb);
uint32_t csum = IO.readConfiguration(U); // format from the header
FieldMetaData header;
IldgIO::readConfiguration(config,U,header); // format from the header
std::cout << GridLogMessage << "Read ILDG Configuration from " << config std::cout << GridLogMessage << "Read ILDG Configuration from " << config
<< " checksum " << std::hex << csum << std::dec << std::endl; << " checksum " << std::hex
<< nersc_csum<<"/"
<< scidac_csuma<<"/"
<< scidac_csumb
<< std::dec << std::endl;
}; };
}; };
} }

2
lib/qcd/hmc/checkpointers/NerscCheckpointer.h
View File

@ -70,7 +70,7 @@ class NerscHmcCheckpointer : public BaseHmcCheckpointer<Gimpl> {
std::string config, rng; std::string config, rng;
this->build_filenames(traj, Params, config, rng); this->build_filenames(traj, Params, config, rng);
NerscField header; FieldMetaData header;
NerscIO::readRNGState(sRNG, pRNG, header, rng); NerscIO::readRNGState(sRNG, pRNG, header, rng);
NerscIO::readConfiguration(U, header, config); NerscIO::readConfiguration(U, header, config);
}; };

3
lib/qcd/utils/Utils.h
View File

@ -12,7 +12,4 @@
#include <Grid/qcd/utils/SUnAdjoint.h> #include <Grid/qcd/utils/SUnAdjoint.h>
#include <Grid/qcd/utils/SUnTwoIndex.h> #include <Grid/qcd/utils/SUnTwoIndex.h>
#endif #endif

58
lib/serialisation/XmlIO.cc
View File

@ -32,16 +32,21 @@ using namespace Grid;
using namespace std; using namespace std;
// Writer implementation /////////////////////////////////////////////////////// // Writer implementation ///////////////////////////////////////////////////////
XmlWriter::XmlWriter(const string &fileName) XmlWriter::XmlWriter(const string &fileName, string toplev) : fileName_(fileName)
: fileName_(fileName)
{ {
node_ = doc_.append_child(); if ( toplev == std::string("") ) {
node_.set_name("grid"); node_=doc_;
} else {
node_=doc_.append_child();
node_.set_name(toplev.c_str());
}
} }
XmlWriter::~XmlWriter(void) XmlWriter::~XmlWriter(void)
{ {
doc_.save_file(fileName_.c_str(), " "); if ( fileName_ != std::string("") ) {
doc_.save_file(fileName_.c_str(), " ");
}
} }
void XmlWriter::push(const string &s) void XmlWriter::push(const string &s)
@ -53,21 +58,44 @@ void XmlWriter::pop(void)
{ {
node_ = node_.parent(); node_ = node_.parent();
} }
std::string XmlWriter::XmlString(void)
// Reader implementation ///////////////////////////////////////////////////////
XmlReader::XmlReader(const string &fileName)
: fileName_(fileName)
{ {
pugi::xml_parse_result result = doc_.load_file(fileName_.c_str()); std::ostringstream oss;
doc_.save(oss);
if ( !result ) return oss.str();
{ }
XmlReader::XmlReader(const char *xmlstring,string toplev) : fileName_("")
{
pugi::xml_parse_result result;
result = doc_.load_string(xmlstring);
if ( !result ) {
cerr << "XML error description: " << result.description() << "\n"; cerr << "XML error description: " << result.description() << "\n";
cerr << "XML error offset : " << result.offset << "\n"; cerr << "XML error offset : " << result.offset << "\n";
abort(); abort();
} }
if ( toplev == std::string("") ) {
node_ = doc_.child("grid"); node_ = doc_;
} else {
node_ = doc_.child(toplev.c_str());
}
}
// Reader implementation ///////////////////////////////////////////////////////
XmlReader::XmlReader(const string &fileName,string toplev) : fileName_(fileName)
{
pugi::xml_parse_result result;
result = doc_.load_file(fileName_.c_str());
if ( !result ) {
cerr << "XML error description: " << result.description() << "\n";
cerr << "XML error offset : " << result.offset << "\n";
abort();
}
if ( toplev == std::string("") ) {
node_ = doc_;
} else {
node_ = doc_.child(toplev.c_str());
}
} }
bool XmlReader::push(const string &s) bool XmlReader::push(const string &s)

11
lib/serialisation/XmlIO.h
View File

@ -44,10 +44,9 @@ namespace Grid
{ {
class XmlWriter: public Writer<XmlWriter> class XmlWriter: public Writer<XmlWriter>
{ {
public: public:
XmlWriter(const std::string &fileName); XmlWriter(const std::string &fileName,std::string toplev = std::string("grid") );
virtual ~XmlWriter(void); virtual ~XmlWriter(void);
void push(const std::string &s); void push(const std::string &s);
void pop(void); void pop(void);
@ -55,6 +54,7 @@ namespace Grid
void writeDefault(const std::string &s, const U &x); void writeDefault(const std::string &s, const U &x);
template <typename U> template <typename U>
void writeDefault(const std::string &s, const std::vector<U> &x); void writeDefault(const std::string &s, const std::vector<U> &x);
std::string XmlString(void);
private: private:
pugi::xml_document doc_; pugi::xml_document doc_;
pugi::xml_node node_; pugi::xml_node node_;
@ -64,7 +64,8 @@ namespace Grid
class XmlReader: public Reader<XmlReader> class XmlReader: public Reader<XmlReader>
{ {
public: public:
XmlReader(const std::string &fileName); XmlReader(const char *xmlstring,std::string toplev = std::string("grid") );
XmlReader(const std::string &fileName,std::string toplev = std::string("grid") );
virtual ~XmlReader(void) = default; virtual ~XmlReader(void) = default;
bool push(const std::string &s); bool push(const std::string &s);
void pop(void); void pop(void);
@ -118,7 +119,7 @@ namespace Grid
std::string buf; std::string buf;
readDefault(s, buf); readDefault(s, buf);
std::cout << s << " " << buf << std::endl; // std::cout << s << " " << buf << std::endl;
fromString(output, buf); fromString(output, buf);
} }

4
tests/IO/Test_nersc_io.cc
View File

@ -64,8 +64,8 @@ int main (int argc, char ** argv)
std::cout <<GridLogMessage<< " ...done "<<std::endl; std::cout <<GridLogMessage<< " ...done "<<std::endl;
std::string rfile("./ckpoint_rng.4000"); std::string rfile("./ckpoint_rng.4000");
FieldMetaData rngheader;
NerscIO::writeRNGState(sRNGa,pRNGa,rfile); NerscIO::writeRNGState(sRNGa,pRNGa,rfile);
NerscField rngheader;
NerscIO::readRNGState (sRNGb,pRNGb,rngheader,rfile); NerscIO::readRNGState (sRNGb,pRNGb,rngheader,rfile);
LatticeComplex tmpa(&Fine); random(pRNGa,tmpa); LatticeComplex tmpa(&Fine); random(pRNGa,tmpa);
@ -87,7 +87,7 @@ int main (int argc, char ** argv)
SU3::HotConfiguration(pRNGa,Umu); SU3::HotConfiguration(pRNGa,Umu);
NerscField header; FieldMetaData header;
std::string file("./ckpoint_lat.4000"); std::string file("./ckpoint_lat.4000");
int precision32 = 0; int precision32 = 0;

2
tests/IO/Test_nersc_read.cc
View File

@ -50,7 +50,7 @@ int main (int argc, char ** argv)
LatticeGaugeField Umu(&Fine); LatticeGaugeField Umu(&Fine);
std::vector<LatticeColourMatrix> U(4,&Fine); std::vector<LatticeColourMatrix> U(4,&Fine);
NerscField header; FieldMetaData header;
std::string file("./ckpoint_lat"); std::string file("./ckpoint_lat");
NerscIO::readConfiguration(Umu,header,file); NerscIO::readConfiguration(Umu,header,file);

19
tests/IO/Test_serialisation.cc
View File

@ -31,6 +31,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
using namespace Grid; using namespace Grid;
using namespace Grid::QCD;
GRID_SERIALIZABLE_ENUM(myenum, undef, red, 1, blue, 2, green, 3); GRID_SERIALIZABLE_ENUM(myenum, undef, red, 1, blue, 2, green, 3);
@ -62,6 +63,7 @@ public:
} }
}; };
int16_t i16 = 1; int16_t i16 = 1;
uint16_t u16 = 2; uint16_t u16 = 2;
int32_t i32 = 3; int32_t i32 = 3;
@ -237,7 +239,22 @@ int main(int argc,char **argv)
std::cout << "Loaded (JSON) -----------------" << std::endl; std::cout << "Loaded (JSON) -----------------" << std::endl;
std::cout << jcopy1 << std::endl << jveccopy1 << std::endl; std::cout << jcopy1 << std::endl << jveccopy1 << std::endl;
} }
{
ildgFormat format;
format.version =1.0;
format.field =std::string("su3gauge");
format.precision =32;
format.lx =24;
format.ly =24;
format.lz =24;
format.lt =48;
XmlWriter WR("ildg-format.xml","");
XmlWriter WRs("","");
write(WR,"ildgFormat",format);
write(WRs,"ildgFormat",format);
std::cout << " XmlString: " <<WRs.XmlString()<<std::endl;
}
/* /*
// This is still work in progress // This is still work in progress
{ {