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Merge branch 'develop' into feature/hadrons

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This commit is contained in:
Antonin Portelli 2018-03-19 13:30:21 +00:00
commit 41d6cab033
5 changed files with 97 additions and 41 deletions
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44
lib/communicator/SharedMemoryMPI.cc
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@ -226,6 +226,48 @@ void GlobalSharedMemory::SharedMemoryAllocate(uint64_t bytes, int flags)
};
#endif // MMAP
#ifdef GRID_MPI3_SHM_NONE
void GlobalSharedMemory::SharedMemoryAllocate(uint64_t bytes, int flags)
{
std::cout << "SharedMemoryAllocate "<< bytes<< " MMAP anonymous implementation "<<std::endl;
assert(_ShmSetup==1);
assert(_ShmAlloc==0);
//////////////////////////////////////////////////////////////////////////////////////////////////////////
// allocate the shared windows for our group
//////////////////////////////////////////////////////////////////////////////////////////////////////////
MPI_Barrier(WorldShmComm);
WorldShmCommBufs.resize(WorldShmSize);
////////////////////////////////////////////////////////////////////////////////////////////
// Hugetlbf and others map filesystems as mappable huge pages
////////////////////////////////////////////////////////////////////////////////////////////
char shm_name [NAME_MAX];
assert(WorldShmSize == 1);
for(int r=0;r<WorldShmSize;r++){
int fd=-1;
int mmap_flag = MAP_SHARED |MAP_ANONYMOUS ;
#ifdef MAP_POPULATE
mmap_flag|=MAP_POPULATE;
#endif
#ifdef MAP_HUGETLB
if ( flags ) mmap_flag |= MAP_HUGETLB;
#endif
void *ptr = (void *) mmap(NULL, bytes, PROT_READ | PROT_WRITE, mmap_flag,fd, 0);
if ( ptr == (void *)MAP_FAILED ) {
printf("mmap %s failed\n",shm_name);
perror("failed mmap"); assert(0);
}
assert(((uint64_t)ptr&0x3F)==0);
close(fd);
WorldShmCommBufs[r] =ptr;
std::cout << "Set WorldShmCommBufs["<<r<<"]="<<ptr<< "("<< bytes<< "bytes)"<<std::endl;
}
_ShmAlloc=1;
_ShmAllocBytes = bytes;
};
#endif // MMAP
#ifdef GRID_MPI3_SHMOPEN
////////////////////////////////////////////////////////////////////////////////////////////
// POSIX SHMOPEN ; as far as I know Linux does not allow EXPLICIT HugePages with this case
@ -246,7 +288,7 @@ void GlobalSharedMemory::SharedMemoryAllocate(uint64_t bytes, int flags)
size_t size = bytes;
sprintf(shm_name,"/Grid_mpi3_shm_%d_%d",WorldNode,r);
sprintf(shm_name,"/myGrid_mpi3_shm_%d_%d",WorldNode,r);
shm_unlink(shm_name);
int fd=shm_open(shm_name,O_RDWR|O_CREAT,0666);

34
lib/parallelIO/BinaryIO.h
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@ -91,7 +91,7 @@ class BinaryIO {
typedef typename vobj::scalar_object sobj;
GridBase *grid = lat._grid;
int lsites = grid->lSites();
uint64_t lsites = grid->lSites();
std::vector<sobj> scalardata(lsites);
unvectorizeToLexOrdArray(scalardata,lat);
@ -160,7 +160,9 @@ class BinaryIO {
/*
* Scidac csum is rather more heavyweight
* FIXME -- 128^3 x 256 x 16 will overflow.
*/
int global_site;
Lexicographic::CoorFromIndex(coor,local_site,local_vol);
@ -261,7 +263,7 @@ class BinaryIO {
GridBase *grid,
std::vector<fobj> &iodata,
std::string file,
Integer offset,
uint64_t offset,
const std::string &format, int control,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
@ -523,7 +525,7 @@ class BinaryIO {
static inline void readLatticeObject(Lattice<vobj> &Umu,
std::string file,
munger munge,
Integer offset,
uint64_t offset,
const std::string &format,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
@ -533,7 +535,7 @@ class BinaryIO {
typedef typename vobj::Realified::scalar_type word; word w=0;
GridBase *grid = Umu._grid;
int lsites = grid->lSites();
uint64_t lsites = grid->lSites();
std::vector<sobj> scalardata(lsites);
std::vector<fobj> iodata(lsites); // Munge, checksum, byte order in here
@ -544,7 +546,7 @@ class BinaryIO {
GridStopWatch timer;
timer.Start();
parallel_for(int x=0;x<lsites;x++) munge(iodata[x], scalardata[x]);
parallel_for(uint64_t x=0;x<lsites;x++) munge(iodata[x], scalardata[x]);
vectorizeFromLexOrdArray(scalardata,Umu);
grid->Barrier();
@ -560,7 +562,7 @@ class BinaryIO {
static inline void writeLatticeObject(Lattice<vobj> &Umu,
std::string file,
munger munge,
Integer offset,
uint64_t offset,
const std::string &format,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
@ -569,7 +571,7 @@ class BinaryIO {
typedef typename vobj::scalar_object sobj;
typedef typename vobj::Realified::scalar_type word; word w=0;
GridBase *grid = Umu._grid;
int lsites = grid->lSites();
uint64_t lsites = grid->lSites();
std::vector<sobj> scalardata(lsites);
std::vector<fobj> iodata(lsites); // Munge, checksum, byte order in here
@ -580,7 +582,7 @@ class BinaryIO {
GridStopWatch timer; timer.Start();
unvectorizeToLexOrdArray(scalardata,Umu);
parallel_for(int x=0;x<lsites;x++) munge(scalardata[x],iodata[x]);
parallel_for(uint64_t x=0;x<lsites;x++) munge(scalardata[x],iodata[x]);
grid->Barrier();
timer.Stop();
@ -597,7 +599,7 @@ class BinaryIO {
static inline void readRNG(GridSerialRNG &serial,
GridParallelRNG &parallel,
std::string file,
Integer offset,
uint64_t offset,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
@ -610,8 +612,8 @@ class BinaryIO {
std::string format = "IEEE32BIG";
GridBase *grid = parallel._grid;
int gsites = grid->gSites();
int lsites = grid->lSites();
uint64_t gsites = grid->gSites();
uint64_t lsites = grid->lSites();
uint32_t nersc_csum_tmp = 0;
uint32_t scidac_csuma_tmp = 0;
@ -626,7 +628,7 @@ class BinaryIO {
nersc_csum,scidac_csuma,scidac_csumb);
timer.Start();
parallel_for(int lidx=0;lidx<lsites;lidx++){
parallel_for(uint64_t lidx=0;lidx<lsites;lidx++){
std::vector<RngStateType> tmp(RngStateCount);
std::copy(iodata[lidx].begin(),iodata[lidx].end(),tmp.begin());
parallel.SetState(tmp,lidx);
@ -659,7 +661,7 @@ class BinaryIO {
static inline void writeRNG(GridSerialRNG &serial,
GridParallelRNG &parallel,
std::string file,
Integer offset,
uint64_t offset,
uint32_t &nersc_csum,
uint32_t &scidac_csuma,
uint32_t &scidac_csumb)
@ -670,8 +672,8 @@ class BinaryIO {
typedef std::array<RngStateType,RngStateCount> RNGstate;
GridBase *grid = parallel._grid;
int gsites = grid->gSites();
int lsites = grid->lSites();
uint64_t gsites = grid->gSites();
uint64_t lsites = grid->lSites();
uint32_t nersc_csum_tmp;
uint32_t scidac_csuma_tmp;
@ -684,7 +686,7 @@ class BinaryIO {
timer.Start();
std::vector<RNGstate> iodata(lsites);
parallel_for(int lidx=0;lidx<lsites;lidx++){
parallel_for(uint64_t lidx=0;lidx<lsites;lidx++){
std::vector<RngStateType> tmp(RngStateCount);
parallel.GetState(tmp,lidx);
std::copy(tmp.begin(),tmp.end(),iodata[lidx].begin());

47
lib/parallelIO/IldgIO.h
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@ -337,6 +337,20 @@ class GridLimeWriter : public BinaryIO {
template<class vobj>
void writeLimeLatticeBinaryObject(Lattice<vobj> &field,std::string record_name)
{
////////////////////////////////////////////////////////////////////
// NB: FILE and iostream are jointly writing disjoint sequences in the
// the same file through different file handles (integer units).
//
// These are both buffered, so why I think this code is right is as follows.
//
// i) write record header to FILE *File, telegraphing the size; flush
// ii) ftello reads the offset from FILE *File .
// iii) iostream / MPI Open independently seek this offset. Write sequence direct to disk.
// Closes iostream and flushes.
// iv) fseek on FILE * to end of this disjoint section.
// v) Continue writing scidac record.
////////////////////////////////////////////////////////////////////
////////////////////////////////////////////
// Create record header
////////////////////////////////////////////
@ -350,25 +364,24 @@ class GridLimeWriter : public BinaryIO {
// std::cout << "W Gsites " <<field._grid->_gsites<<std::endl;
// std::cout << "W Payload expected " <<PayloadSize<<std::endl;
////////////////////////////////////////////////////////////////////
// NB: FILE and iostream are jointly writing disjoint sequences in the
// the same file through different file handles (integer units).
//
// These are both buffered, so why I think this code is right is as follows.
//
// i) write record header to FILE *File, telegraphing the size.
// ii) ftello reads the offset from FILE *File .
// iii) iostream / MPI Open independently seek this offset. Write sequence direct to disk.
// Closes iostream and flushes.
// iv) fseek on FILE * to end of this disjoint section.
// v) Continue writing scidac record.
////////////////////////////////////////////////////////////////////
uint64_t offset = ftello(File);
// std::cout << " Writing to offset "<<offset << std::endl;
fflush(File);
///////////////////////////////////////////
// Write by other means into the binary record
///////////////////////////////////////////
uint64_t offset1 = ftello(File); // std::cout << " Writing to offset "<<offset1 << std::endl;
std::string format = getFormatString<vobj>();
BinarySimpleMunger<sobj,sobj> munge;
BinaryIO::writeLatticeObject<vobj,sobj>(field, filename, munge, offset, format,nersc_csum,scidac_csuma,scidac_csumb);
// fseek(File,0,SEEK_END); offset = ftello(File);std::cout << " offset now "<<offset << std::endl;
BinaryIO::writeLatticeObject<vobj,sobj>(field, filename, munge, offset1, format,nersc_csum,scidac_csuma,scidac_csumb);
///////////////////////////////////////////
// Wind forward and close the record
///////////////////////////////////////////
fseek(File,0,SEEK_END);
uint64_t offset2 = ftello(File); // std::cout << " now at offset "<<offset2 << std::endl;
assert((offset2-offset1) == PayloadSize);
err=limeWriterCloseRecord(LimeW); assert(err>=0);
////////////////////////////////////////

10
lib/parallelIO/NerscIO.h
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@ -57,7 +57,7 @@ namespace Grid {
// for the header-reader
static inline int readHeader(std::string file,GridBase *grid, FieldMetaData &field)
{
int offset=0;
uint64_t offset=0;
std::map<std::string,std::string> header;
std::string line;
@ -139,7 +139,7 @@ namespace Grid {
typedef Lattice<iLorentzColourMatrix<vsimd> > GaugeField;
GridBase *grid = Umu._grid;
int offset = readHeader(file,Umu._grid,header);
uint64_t offset = readHeader(file,Umu._grid,header);
FieldMetaData clone(header);
@ -236,7 +236,7 @@ namespace Grid {
GaugeStatistics(Umu,header);
MachineCharacteristics(header);
int offset;
uint64_t offset;
truncate(file);
@ -278,7 +278,7 @@ namespace Grid {
header.plaquette=0.0;
MachineCharacteristics(header);
int offset;
uint64_t offset;
#ifdef RNG_RANLUX
header.floating_point = std::string("UINT64");
@ -313,7 +313,7 @@ namespace Grid {
GridBase *grid = parallel._grid;
int offset = readHeader(file,grid,header);
uint64_t offset = readHeader(file,grid,header);
FieldMetaData clone(header);

3
tests/lanczos/Test_dwf_compressed_lanczos_reorg.cc
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@ -180,7 +180,6 @@ int main (int argc, char ** argv) {
GridCartesian * CoarseGrid4 = SpaceTimeGrid::makeFourDimGrid(coarseLatt, GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
GridRedBlackCartesian * CoarseGrid4rb = SpaceTimeGrid::makeFourDimRedBlackGrid(CoarseGrid4);
GridCartesian * CoarseGrid5 = SpaceTimeGrid::makeFiveDimGrid(cLs,CoarseGrid4);
GridRedBlackCartesian * CoarseGrid5rb = SpaceTimeGrid::makeFourDimRedBlackGrid(CoarseGrid5);
// Gauge field
LatticeGaugeField Umu(UGrid);
@ -206,7 +205,7 @@ int main (int argc, char ** argv) {
const int nbasis= 60;
assert(nbasis==Ns1);
LocalCoherenceLanczosScidac<vSpinColourVector,vTComplex,nbasis> _LocalCoherenceLanczos(FrbGrid,CoarseGrid5rb,HermOp,Odd);
LocalCoherenceLanczosScidac<vSpinColourVector,vTComplex,nbasis> _LocalCoherenceLanczos(FrbGrid,CoarseGrid5,HermOp,Odd);
std::cout << GridLogMessage << "Constructed LocalCoherenceLanczos" << std::endl;
assert( (Params.doFine)||(Params.doFineRead));