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Hadrons: meson field parallel IO

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This commit is contained in:
Antonin Portelli 2018-08-14 14:55:13 +01:00
parent 6e5a2b7922
commit cc2780bea3
1 changed files with 80 additions and 48 deletions
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128
extras/Hadrons/Modules/MContraction/A2AMesonField.hpp
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@ -37,6 +37,8 @@ See the full license in the file "LICENSE" in the top level distribution directo
#include <Grid/Hadrons/Modules/MSolver/A2AVectors.hpp>
#include <Grid/Hadrons/Modules/MContraction/A2AMesonFieldKernels.hpp>
#define MF_PARALLEL_IO
BEGIN_HADRONS_NAMESPACE
/******************************************************************************
@ -99,6 +101,7 @@ private:
std::string momphName_;
std::vector<Gamma::Algebra> gamma_;
std::vector<std::vector<double>> mom_;
std::vector<std::pair<unsigned int, unsigned int>> nodeFile_;
};
MODULE_REGISTER(A2AMesonField, ARG(TA2AMesonField<FIMPL>), MContraction);
@ -311,14 +314,30 @@ void TA2AMesonField<FImpl>::execute(void)
// IO
if (!par().output.empty())
{
double blockSize, ioTime;
double blockSize, ioTime;
unsigned int myRank = env().getGrid()->ThisRank(),
nRank = env().getGrid()->RankCount();
LOG(Message) << "Writing block to disk" << std::endl;
ioTime = -getDTimer("IO: write block");
startTimer("IO: total");
for(int m = 0; m < nmom; m++)
for(int g = 0; g < ngamma; g++)
makeFileDir(filename(0, 0), env().getGrid());
#ifdef MF_PARALLEL_IO
env().getGrid()->Barrier();
nodeFile_.clear();
for(int f = myRank; f < nmom*ngamma; f += nRank)
{
std::pair<unsigned int, unsigned int> file;
file.first = f/ngamma;
file.second = f % ngamma;
nodeFile_.push_back(file);
}
// parallel IO
for (auto &f: nodeFile_)
{
auto m = f.first, g = f.second;
if ((i == 0) and (j == 0))
{
startTimer("IO: file creation");
@ -329,6 +348,29 @@ void TA2AMesonField<FImpl>::execute(void)
saveBlock(mfBlock, m, g, i, j);
stopTimer("IO: write block");
}
env().getGrid()->Barrier();
#else
// serial IO
for(int m = 0; m < nmom; m++)
for(int g = 0; g < ngamma; g++)
{
if ((i == 0) and (j == 0))
{
startTimer("IO: file creation");
if (env().getGrid()->IsBoss())
{
initFile(m, g);
}
stopTimer("IO: file creation");
}
startTimer("IO: write block");
if (env().getGrid()->IsBoss())
{
saveBlock(mfBlock, m, g, i, j);
}
stopTimer("IO: write block");
}
#endif
stopTimer("IO: total");
blockSize = static_cast<double>(nmom*ngamma*nt*N_ii*N_jj*sizeof(Complex));
ioTime += getDTimer("IO: write block");
@ -372,30 +414,25 @@ void TA2AMesonField<FImpl>::initFile(unsigned int m, unsigned int g)
{
#ifdef HAVE_HDF5
std::string f = filename(m, g);
GridBase *grid = env().getGrid();
auto &v = envGet(std::vector<FermionField>, par().v);
auto &w = envGet(std::vector<FermionField>, par().w);
int nt = env().getDim().back();
int N_i = w.size();
int N_j = v.size();
makeFileDir(f, grid);
if (grid->IsBoss())
{
Hdf5Writer writer(f);
std::vector<hsize_t> dim = {static_cast<hsize_t>(nt),
static_cast<hsize_t>(N_i),
static_cast<hsize_t>(N_j)};
H5NS::DataSpace dataspace(dim.size(), dim.data());
H5NS::DataSet dataset;
push(writer, ioname(m, g));
write(writer, "momentum", mom_[m]);
write(writer, "gamma", gamma_[g]);
auto &group = writer.getGroup();
dataset = group.createDataSet("mesonField", Hdf5Type<Complex>::type(),
dataspace);
}
Hdf5Writer writer(f);
std::vector<hsize_t> dim = {static_cast<hsize_t>(nt),
static_cast<hsize_t>(N_i),
static_cast<hsize_t>(N_j)};
H5NS::DataSpace dataspace(dim.size(), dim.data());
H5NS::DataSet dataset;
push(writer, ioname(m, g));
write(writer, "momentum", mom_[m]);
write(writer, "gamma", gamma_[g]);
auto &group = writer.getGroup();
dataset = group.createDataSet("mesonField", Hdf5Type<Complex>::type(),
dataspace);
#else
HADRONS_ERROR(Implementation, "meson field I/O needs HDF5 library");
#endif
@ -407,34 +444,29 @@ void TA2AMesonField<FImpl>::saveBlock(const MesonField &mf,
unsigned int i, unsigned int j)
{
#ifdef HAVE_HDF5
std::string f = filename(m, g);
GridBase *grid = env().getGrid();
std::string f = filename(m, g);
Hdf5Reader reader(f);
hsize_t nt = mf.dimension(2),
Ni = mf.dimension(3),
Nj = mf.dimension(4);
std::vector<hsize_t> count = {nt, Ni, Nj},
offset = {0, static_cast<hsize_t>(i),
static_cast<hsize_t>(j)},
stride = {1, 1, 1},
block = {1, 1, 1};
H5NS::DataSpace memspace(count.size(), count.data()), dataspace;
H5NS::DataSet dataset;
size_t shift;
if (grid->IsBoss())
{
Hdf5Reader reader(f);
hsize_t nt = mf.dimension(2),
Ni = mf.dimension(3),
Nj = mf.dimension(4);
std::vector<hsize_t> count = {nt, Ni, Nj},
offset = {0, static_cast<hsize_t>(i),
static_cast<hsize_t>(j)},
stride = {1, 1, 1},
block = {1, 1, 1};
H5NS::DataSpace memspace(count.size(), count.data()), dataspace;
H5NS::DataSet dataset;
size_t shift;
push(reader, ioname(m, g));
auto &group = reader.getGroup();
dataset = group.openDataSet("mesonField");
dataspace = dataset.getSpace();
dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data(),
stride.data(), block.data());
shift = (m*mf.dimension(1) + g)*nt*Ni*Nj;
dataset.write(mf.data() + shift, Hdf5Type<Complex>::type(), memspace,
dataspace);
}
push(reader, ioname(m, g));
auto &group = reader.getGroup();
dataset = group.openDataSet("mesonField");
dataspace = dataset.getSpace();
dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data(),
stride.data(), block.data());
shift = (m*mf.dimension(1) + g)*nt*Ni*Nj;
dataset.write(mf.data() + shift, Hdf5Type<Complex>::type(), memspace,
dataspace);
#else
HADRONS_ERROR(Implementation, "meson field I/O needs HDF5 library");
#endif