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Updates for SciDAC IO

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paboyle
2017-06-18 00:10:42 +01:00
parent d572170170
commit 8e9be9f84f
1 changed files with 59 additions and 76 deletions
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135
lib/parallelIO/BinaryIO.h
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@@ -69,46 +69,6 @@ inline uint64_t Grid_ntohll(uint64_t 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)
{
@@ -126,11 +86,7 @@ class BinaryIO {
// more byte manipulation helpers
/////////////////////////////////////////////////////////////////////////////
template<class vobj> static inline void Uint32Checksum(Lattice<vobj> &lat,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
template<class vobj> static inline void Uint32Checksum(Lattice<vobj> &lat,uint32_t &nersc_csum)
{
typedef typename vobj::scalar_object sobj;
@@ -140,15 +96,38 @@ class BinaryIO {
std::vector<sobj> scalardata(lsites);
unvectorizeToLexOrdArray(scalardata,lat);
Uint32Checksum(grid,scalardata,nersc_csum,scidac_csuma,scidac_csumb);
NerscChecksum(grid,scalardata,nersc_csum);
}
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)
template<class fobj> static inline void NerscChecksum(GridBase *grid,std::vector<fobj> &fbuf,uint32_t &nersc_csum)
{
const uint64_t size32 = sizeof(fobj)/sizeof(uint32_t);
uint64_t lsites =grid->lSites();
if (fbuf.size()==1) {
lsites=1;
}
#pragma omp parallel
{
uint32_t nersc_csum_thr=0;
#pragma omp for
for(uint64_t local_site=0;local_site<lsites;local_site++){
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];
}
}
#pragma omp critical
{
nersc_csum += nersc_csum_thr;
}
}
}
template<class fobj> static inline void ScidacChecksum(GridBase *grid,std::vector<fobj> &fbuf,uint32_t &scidac_csuma,uint32_t &scidac_csumb)
{
const uint64_t size32 = sizeof(fobj)/sizeof(uint32_t);
@@ -156,6 +135,9 @@ class BinaryIO {
int nd = grid->_ndimension;
uint64_t lsites =grid->lSites();
if (fbuf.size()==1) {
lsites=1;
}
std::vector<int> local_vol =grid->LocalDimensions();
std::vector<int> local_start =grid->LocalStarts();
std::vector<int> global_vol =grid->FullDimensions();
@@ -163,21 +145,15 @@ class BinaryIO {
#pragma omp parallel
{
std::vector<int> coor(nd);
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
for(uint64_t local_site=0;local_site<lsites;local_site++){
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
*/
@@ -185,23 +161,24 @@ class BinaryIO {
Lexicographic::CoorFromIndex(coor,local_site,local_vol);
for(int d=0;d<nd;d++)
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));
site_crc = crc32(0,(unsigned char *)site_buf,sizeof(fobj));
// std::cout << "Site "<<local_site << " crc "<<std::hex<<site_crc<<std::dec<<std::endl;
// std::cout << "Site "<<local_site << std::hex<<site_buf[0] <<site_buf[1]<<std::dec <<std::endl;
scidac_csuma_thr ^= site_crc<<gsite29 | site_crc>>(32-gsite29);
scidac_csumb_thr ^= site_crc<<gsite31 | site_crc>>(32-gsite31);
}
#pragma omp critical
{
nersc_csum += nersc_csum_thr;
scidac_csuma^= scidac_csuma_thr;
scidac_csumb^= scidac_csumb_thr;
}
@@ -386,7 +363,8 @@ class BinaryIO {
assert(0);
#endif
} else {
std::cout<< GridLogMessage<< "C++ read I/O "<< file<< std::endl;
std::cout<< GridLogMessage<< "C++ read I/O "<< file<<" : "
<< iodata.size()*sizeof(fobj)<<" bytes"<<std::endl;
std::ifstream fin;
fin.open(file,std::ios::binary|std::ios::in);
if ( control & BINARYIO_MASTER_APPEND ) {
@@ -402,22 +380,24 @@ class BinaryIO {
grid->Barrier();
bstimer.Start();
ScidacChecksum(grid,iodata,scidac_csuma,scidac_csumb);
if (ieee32big) be32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee32) le32toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee64big) be64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee64) le64toh_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
Uint32Checksum(grid,iodata,nersc_csum,scidac_csuma,scidac_csumb);
NerscChecksum(grid,iodata,nersc_csum);
bstimer.Stop();
}
if ( control & BINARYIO_WRITE ) {
bstimer.Start();
Uint32Checksum(grid,iodata,nersc_csum,scidac_csuma,scidac_csumb);
NerscChecksum(grid,iodata,nersc_csum);
if (ieee32big) htobe32_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee32) htole32_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee64big) htobe64_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
if (ieee64) htole64_v((void *)&iodata[0], sizeof(fobj)*iodata.size());
ScidacChecksum(grid,iodata,scidac_csuma,scidac_csumb);
bstimer.Stop();
grid->Barrier();
@@ -436,9 +416,9 @@ class BinaryIO {
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);
std::ofstream fout; fout.open(file,std::ios::binary|std::ios::out|std::ios::in);
std::cout<< GridLogMessage<< "C++ write I/O "<< file<<" : "
<< iodata.size()*sizeof(fobj)<<" bytes"<<std::endl;
if ( control & BINARYIO_MASTER_APPEND ) {
fout.seekp(0,fout.end);
} else {
@@ -467,9 +447,6 @@ class BinaryIO {
grid->GlobalXOR(scidac_csuma);
grid->GlobalXOR(scidac_csumb);
grid->Barrier();
// std::cout << "Binary IO NERSC checksum 0x"<<std::hex<<nersc_csum <<std::dec<<std::endl;
// 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;
}
/////////////////////////////////////////////////////////////////////////////
@@ -603,9 +580,9 @@ class BinaryIO {
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 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;
}
@@ -658,8 +635,14 @@ class BinaryIO {
}
IOobject(w,grid,iodata,file,offset,format,BINARYIO_WRITE|BINARYIO_MASTER_APPEND,
nersc_csum_tmp,scidac_csuma_tmp,scidac_csumb_tmp);
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 checksum " << std::hex << csum << std::dec << std::endl;
std::cout << GridLogMessage << "RNG file checksum " << std::hex << nersc_csum << std::dec << std::endl;
std::cout << GridLogMessage << "RNG file checksuma " << std::hex << scidac_csuma << std::dec << std::endl;
std::cout << GridLogMessage << "RNG file checksumb " << std::hex << scidac_csumb << std::dec << std::endl;
std::cout << GridLogMessage << "RNG state overhead " << timer.Elapsed() << std::endl;
}
};