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IO improvements to fail on IO error

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This commit is contained in:
paboyle
2017-03-28 02:28:04 -04:00
parent d45cd7e677
commit 75112a632a
2 changed files with 126 additions and 135 deletions
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69
lib/parallelIO/BinaryIO.h
View File

@@ -35,37 +35,27 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
#endif #endif
#include <arpa/inet.h> #include <arpa/inet.h>
#include <algorithm> #include <algorithm>
// 64bit endian swap is a portability pain
#ifndef __has_builtin // Optional of course.
#define __has_builtin(x) 0 // Compatibility with non-clang compilers.
#endif
#if HAVE_DECL_BE64TOH
#undef Grid_ntohll
#define Grid_ntohll be64toh
#endif
#if HAVE_DECL_NTOHLL inline uint32_t byte_reverse32(uint32_t f) {
#undef Grid_ntohll f = ((f&0xFF)<<24) | ((f&0xFF00)<<8) | ((f&0xFF0000)>>8) | ((f&0xFF000000UL)>>24) ;
#define Grid_ntohll ntohll return f;
#endif }
inline uint64_t byte_reverse64(uint64_t f) {
#ifndef Grid_ntohll 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 #if BYTE_ORDER == BIG_ENDIAN
inline uint64_t Grid_ntohll(uint64_t A) { return A; }
#define Grid_ntohll(A) (A)
#else #else
inline uint64_t Grid_ntohll(uint64_t A) {
#if __has_builtin(__builtin_bswap64) return byte_reverse64(A);
#define Grid_ntohll(A) __builtin_bswap64(A) }
#else
#error
#endif
#endif
#endif #endif
namespace Grid { namespace Grid {
@@ -195,7 +185,7 @@ class BinaryIO {
std::vector<int> site({x,y,z,t}); std::vector<int> site({x,y,z,t});
if (grid->IsBoss()) { if (grid->IsBoss()) {
fin.read((char *)&file_object, sizeof(file_object)); fin.read((char *)&file_object, sizeof(file_object));assert( fin.fail()==0);
bytes += sizeof(file_object); bytes += sizeof(file_object);
if (ieee32big) be32toh_v((void *)&file_object, sizeof(file_object)); if (ieee32big) be32toh_v((void *)&file_object, sizeof(file_object));
if (ieee32) le32toh_v((void *)&file_object, sizeof(file_object)); if (ieee32) le32toh_v((void *)&file_object, sizeof(file_object));
@@ -211,11 +201,13 @@ class BinaryIO {
std::cout<<GridLogPerformance<<"readObjectSerial: read "<< bytes <<" bytes in "<<timer.Elapsed() <<" " std::cout<<GridLogPerformance<<"readObjectSerial: read "<< bytes <<" bytes in "<<timer.Elapsed() <<" "
<< (double)bytes/ (double)timer.useconds() <<" MB/s " <<std::endl; << (double)bytes/ (double)timer.useconds() <<" MB/s " <<std::endl;
grid->Broadcast(0,(void *)&csum,sizeof(csum));
return csum; return csum;
} }
template<class vobj,class fobj,class munger> template<class vobj,class fobj,class munger>
static inline uint32_t writeObjectSerial(Lattice<vobj> &Umu,std::string file,munger munge,int offset,const std::string & format) static inline uint32_t writeObjectSerial(Lattice<vobj> &Umu,std::string file,munger munge,int offset,
const std::string & format)
{ {
typedef typename vobj::scalar_object sobj; typedef typename vobj::scalar_object sobj;
@@ -261,7 +253,7 @@ class BinaryIO {
if(ieee64) htole64_v((void *)&file_object,sizeof(file_object)); if(ieee64) htole64_v((void *)&file_object,sizeof(file_object));
// NB could gather an xstrip as an optimisation. // NB could gather an xstrip as an optimisation.
fout.write((char *)&file_object,sizeof(file_object)); fout.write((char *)&file_object,sizeof(file_object));assert( fout.fail()==0);
bytes+=sizeof(file_object); bytes+=sizeof(file_object);
} }
}}}} }}}}
@@ -269,6 +261,7 @@ class BinaryIO {
std::cout<<GridLogPerformance<<"writeObjectSerial: wrote "<< bytes <<" bytes in "<<timer.Elapsed() <<" " std::cout<<GridLogPerformance<<"writeObjectSerial: wrote "<< bytes <<" bytes in "<<timer.Elapsed() <<" "
<< (double)bytes/timer.useconds() <<" MB/s " <<std::endl; << (double)bytes/timer.useconds() <<" MB/s " <<std::endl;
grid->Broadcast(0,(void *)&csum,sizeof(csum));
return csum; return csum;
} }
@@ -313,7 +306,7 @@ class BinaryIO {
if ( grid->IsBoss() ) { if ( grid->IsBoss() ) {
Uint32Checksum((uint32_t *)&saved[0],bytes,csum); Uint32Checksum((uint32_t *)&saved[0],bytes,csum);
fout.write((char *)&saved[0],bytes); fout.write((char *)&saved[0],bytes);assert( fout.fail()==0);
} }
} }
@@ -321,7 +314,7 @@ class BinaryIO {
if ( grid->IsBoss() ) { if ( grid->IsBoss() ) {
serial.GetState(saved,0); serial.GetState(saved,0);
Uint32Checksum((uint32_t *)&saved[0],bytes,csum); Uint32Checksum((uint32_t *)&saved[0],bytes,csum);
fout.write((char *)&saved[0],bytes); fout.write((char *)&saved[0],bytes);assert( fout.fail()==0);
} }
grid->Broadcast(0,(void *)&csum,sizeof(csum)); grid->Broadcast(0,(void *)&csum,sizeof(csum));
return csum; return csum;
@@ -355,7 +348,7 @@ class BinaryIO {
int l_idx=parallel.generator_idx(o_idx,i_idx); int l_idx=parallel.generator_idx(o_idx,i_idx);
if ( grid->IsBoss() ) { if ( grid->IsBoss() ) {
fin.read((char *)&saved[0],bytes); fin.read((char *)&saved[0],bytes);assert( fin.fail()==0);
Uint32Checksum((uint32_t *)&saved[0],bytes,csum); Uint32Checksum((uint32_t *)&saved[0],bytes,csum);
} }
@@ -368,7 +361,7 @@ class BinaryIO {
} }
if ( grid->IsBoss() ) { if ( grid->IsBoss() ) {
fin.read((char *)&saved[0],bytes); fin.read((char *)&saved[0],bytes);assert( fin.fail()==0);
serial.SetState(saved,0); serial.SetState(saved,0);
Uint32Checksum((uint32_t *)&saved[0],bytes,csum); Uint32Checksum((uint32_t *)&saved[0],bytes,csum);
} }
@@ -380,7 +373,8 @@ class BinaryIO {
template<class vobj,class fobj,class munger> template<class vobj,class fobj,class munger>
static inline uint32_t readObjectParallel(Lattice<vobj> &Umu,std::string file,munger munge,int offset,const std::string &format) static inline uint32_t readObjectParallel(Lattice<vobj> &Umu,std::string file,munger munge,int offset,
const std::string &format)
{ {
typedef typename vobj::scalar_object sobj; typedef typename vobj::scalar_object sobj;
@@ -489,7 +483,7 @@ class BinaryIO {
if (myrank == iorank) { if (myrank == iorank) {
fin.seekg(offset+g_idx*sizeof(fileObj)); fin.seekg(offset+g_idx*sizeof(fileObj));
fin.read((char *)&fileObj,sizeof(fileObj)); fin.read((char *)&fileObj,sizeof(fileObj));assert( fin.fail()==0);
bytes+=sizeof(fileObj); bytes+=sizeof(fileObj);
if(ieee32big) be32toh_v((void *)&fileObj,sizeof(fileObj)); if(ieee32big) be32toh_v((void *)&fileObj,sizeof(fileObj));
@@ -529,7 +523,8 @@ class BinaryIO {
// Parallel writer // Parallel writer
////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////
template<class vobj,class fobj,class munger> template<class vobj,class fobj,class munger>
static inline uint32_t writeObjectParallel(Lattice<vobj> &Umu,std::string file,munger munge,int offset,const std::string & format) static inline uint32_t writeObjectParallel(Lattice<vobj> &Umu,std::string file,munger munge,int offset,
const std::string & format)
{ {
typedef typename vobj::scalar_object sobj; typedef typename vobj::scalar_object sobj;
GridBase *grid = Umu._grid; GridBase *grid = Umu._grid;
@@ -658,7 +653,7 @@ class BinaryIO {
if(ieee64) htole64_v((void *)&fileObj,sizeof(fileObj)); if(ieee64) htole64_v((void *)&fileObj,sizeof(fileObj));
fout.seekp(offset+g_idx*sizeof(fileObj)); fout.seekp(offset+g_idx*sizeof(fileObj));
fout.write((char *)&fileObj,sizeof(fileObj)); fout.write((char *)&fileObj,sizeof(fileObj));assert( fout.fail()==0);
bytes+=sizeof(fileObj); bytes+=sizeof(fileObj);
} }
} }

44
lib/parallelIO/NerscIO.h
View File

@@ -242,7 +242,6 @@ class NerscIO : public BinaryIO {
static inline unsigned int writeHeader(NerscField &field,std::string file) 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_nersc_header(field, fout);
field.data_start = fout.tellp(); field.data_start = fout.tellp();
@@ -264,10 +263,13 @@ static inline int readHeader(std::string file,GridBase *grid, NerscField &field
getline(fin,line); // read one line and insist is getline(fin,line); // read one line and insist is
removeWhitespace(line); removeWhitespace(line);
std::cout << "* " << line << std::endl;
assert(line==std::string("BEGIN_HEADER")); assert(line==std::string("BEGIN_HEADER"));
do { do {
getline(fin,line); // read one line getline(fin,line); // read one line
std::cout << "* "<<line<< std::endl;
int eq = line.find("="); int eq = line.find("=");
if(eq >0) { if(eq >0) {
std::string key=line.substr(0,eq); std::string key=line.substr(0,eq);
@@ -345,24 +347,24 @@ static inline void readConfiguration(Lattice<iLorentzColourMatrix<vsimd> > &Umu,
// 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::readObjectSerial<iLorentzColourMatrix<vsimd>, LorentzColour2x3F> csum=BinaryIO::readObjectSerial<iLorentzColourMatrix<vsimd>, LorentzColour2x3F>
csum=BinaryIO::readObjectParallel<iLorentzColourMatrix<vsimd>, LorentzColour2x3F> // csum=BinaryIO::readObjectParallel<iLorentzColourMatrix<vsimd>, LorentzColour2x3F>
(Umu,file,Nersc3x2munger<LorentzColour2x3F,LorentzColourMatrix>(), offset,format); (Umu,file,Nersc3x2munger<LorentzColour2x3F,LorentzColourMatrix>(), offset,format);
} }
if ( ieee64 || ieee64big ) { if ( ieee64 || ieee64big ) {
//csum=BinaryIO::readObjectSerial<iLorentzColourMatrix<vsimd>, LorentzColour2x3D> csum=BinaryIO::readObjectSerial<iLorentzColourMatrix<vsimd>, LorentzColour2x3D>
csum=BinaryIO::readObjectParallel<iLorentzColourMatrix<vsimd>, LorentzColour2x3D> // csum=BinaryIO::readObjectParallel<iLorentzColourMatrix<vsimd>, LorentzColour2x3D>
(Umu,file,Nersc3x2munger<LorentzColour2x3D,LorentzColourMatrix>(),offset,format); (Umu,file,Nersc3x2munger<LorentzColour2x3D,LorentzColourMatrix>(),offset,format);
} }
} 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::readObjectSerial<iLorentzColourMatrix<vsimd>,LorentzColourMatrixF> csum=BinaryIO::readObjectSerial<iLorentzColourMatrix<vsimd>,LorentzColourMatrixF>
csum=BinaryIO::readObjectParallel<iLorentzColourMatrix<vsimd>,LorentzColourMatrixF> //csum=BinaryIO::readObjectParallel<iLorentzColourMatrix<vsimd>,LorentzColourMatrixF>
(Umu,file,NerscSimpleMunger<LorentzColourMatrixF,LorentzColourMatrix>(),offset,format); (Umu,file,NerscSimpleMunger<LorentzColourMatrixF,LorentzColourMatrix>(),offset,format);
} }
if ( ieee64 || ieee64big ) { if ( ieee64 || ieee64big ) {
// csum=BinaryIO::readObjectSerial<iLorentzColourMatrix<vsimd>,LorentzColourMatrixD> csum=BinaryIO::readObjectSerial<iLorentzColourMatrix<vsimd>,LorentzColourMatrixD>
csum=BinaryIO::readObjectParallel<iLorentzColourMatrix<vsimd>,LorentzColourMatrixD> // csum=BinaryIO::readObjectParallel<iLorentzColourMatrix<vsimd>,LorentzColourMatrixD>
(Umu,file,NerscSimpleMunger<LorentzColourMatrixD,LorentzColourMatrix>(),offset,format); (Umu,file,NerscSimpleMunger<LorentzColourMatrixD,LorentzColourMatrix>(),offset,format);
} }
} else { } else {
@@ -371,12 +373,17 @@ static inline void readConfiguration(Lattice<iLorentzColourMatrix<vsimd> > &Umu,
NerscStatistics<GaugeField>(Umu,clone); NerscStatistics<GaugeField>(Umu,clone);
std::cout<<GridLogMessage <<"NERSC Configuration "<<file<<" checksum "<<std::hex<< csum<< std::dec
<<" header "<<std::hex<<header.checksum<<std::dec <<std::endl;
std::cout<<GridLogMessage <<"NERSC Configuration "<<file<<" plaquette "<<clone.plaquette
<<" header "<<header.plaquette<<std::endl;
std::cout<<GridLogMessage <<"NERSC Configuration "<<file<<" link_trace "<<clone.link_trace
<<" header "<<header.link_trace<<std::endl;
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(csum == header.checksum );
std::cout<<GridLogMessage <<"Read 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>
@@ -416,19 +423,8 @@ static inline void writeConfiguration(Lattice<iLorentzColourMatrix<vsimd> > &Umu
Nersc3x2unmunger<fobj2D,sobj> munge; Nersc3x2unmunger<fobj2D,sobj> munge;
BinaryIO::Uint32Checksum<vobj,fobj2D>(Umu, munge,header.checksum); BinaryIO::Uint32Checksum<vobj,fobj2D>(Umu, munge,header.checksum);
offset = writeHeader(header,file); offset = writeHeader(header,file);
csum=BinaryIO::writeObjectSerial<vobj,fobj2D>(Umu,file,munge,offset,header.floating_point); // csum=BinaryIO::writeObjectSerial<vobj,fobj2D>(Umu,file,munge,offset,header.floating_point);
csum=BinaryIO::writeObjectParallel<vobj,fobj2D>(Umu,file,munge,offset,header.floating_point);
std::string file1 = file+"para";
int offset1 = writeHeader(header,file1);
int csum1=BinaryIO::writeObjectParallel<vobj,fobj2D>(Umu,file1,munge,offset,header.floating_point);
//int csum1=BinaryIO::writeObjectSerial<vobj,fobj2D>(Umu,file1,munge,offset,header.floating_point);
std::cout << GridLogMessage << " TESTING PARALLEL WRITE offsets " << offset1 << " "<< offset << std::endl;
std::cout << GridLogMessage << " TESTING PARALLEL WRITE csums " << csum1 << " "<<std::hex<< csum << std::dec<< std::endl;
assert(offset1==offset);
assert(csum1==csum);
} else { } else {
header.floating_point = std::string("IEEE64BIG"); header.floating_point = std::string("IEEE64BIG");