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WIP: rdataset: new read function

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This commit is contained in:
Christian Zimmermann 2025-03-16 23:51:58 -07:00
parent 70358e4233
commit ca207d4013
1 changed files with 111 additions and 0 deletions

111
src/opt/hdf5_mpi/lib/h5_rdataset.cc
View file

@ -89,6 +89,117 @@ namespace CNORXZ
return *this;
}
void RDataset::readbase(void* dest, Sptr<YIndex> mbeg, Sptr<YIndex> mend,
Sptr<YIndex> fbeg) const
{
const SizeT D = mFileRange->dim();
const bool todo = mbeg != nullptr;
Vector<hsize_t> offset(D);
Vector<hsize_t> dims(D);
if(todo){
RangePtr dr = mbeg->range();
//const bool parallel = true;
CXZ_ASSERT(mend != nullptr, "no end edge given");
CXZ_ASSERT(beg->range()->dim() == D, "dimension of file index ("
<< dr->dim() << ") different from dimension of file range ("
<< mFileRange->dim() << ")");
CXZ_ASSERT(mbeg->range()->dim() == D, "dimension of data index ("
<< dr->dim() << ") different from dimension of file range ("
<< mFileRange->dim() << ")");
CXZ_ASSERT(mend->range()->dim() == D, "dimension of data index ("
<< dr->dim() << ") different from dimension of file range ("
<< mFileRange->dim() << ")");
for(SizeT i = 0; i != D; ++i){
const SizeT bi = mbeg->pack().get(i)->lex();
const SizeT ei = mend->pack().get(i)->lex();
const SizeT fgebi = fbeg->pack().get(i)->lex();
dims[i] = ei - bi + 1; // inclusive!
offset[i] = fbegi;
}
}
else {
for(SizeT i = 0; i != D; ++i){
dims[i] = 0;
offset[i] = 0;
}
}
H5Sselect_hyperslab(mFilespace, H5S_SELECT_SET, offset.data(), NULL, dims.data(), NULL);
const hid_t mem_space_id = H5Screate_simple(static_cast<hsize_t>(dims.size()),
dims.data(), nullptr);
const hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(xfer_plist_id, H5FD_MPIO_COLLECTIVE);
const herr_t err = H5Dread(mId, mType, mem_space_id, mFilespace, xfer_plist_id, dest);
CXZ_ASSERT(err >= 0, "error while reading dataset '" << mName
<< "', errorcode :" << err);
H5Pclose(xfer_plist_id);
H5Sclose(mem_space_id);
MPI_Barrier(MPI_COMM_WORLD);
}
void RDataset::readbase(void* dest, Sptr<mpi::RIndex<YIndex,YIndex>> mbeg,
Sptr<mpi::RIndex<YIndex,YIndex>> mend, Sptr<YIndex> fbeg) const
{
const SizeT D = mFileRange->dim()
CXZ_ASSERT(beg->range()->dim() == D, "dimension of file index ("
<< dr->dim() << ") different from dimension of file range ("
<< mFileRange->dim() << ")");
CXZ_ASSERT(mbeg->range()->dim() == D, "dimension of data index ("
<< dr->dim() << ") different from dimension of file range ("
<< mFileRange->dim() << ")");
CXZ_ASSERT(mend->range()->dim() == D, "dimension of data index ("
<< dr->dim() << ") different from dimension of file range ("
<< mFileRange->dim() << ")");
Sptr<YIndex> mbegl = std::make_shared<YIndex>(mbeg->local());
Sptr<YIndex> mendl = std::make_shared<YIndex>(mend->local());
Sptr<YIndex> fbegl = std::make_shared<YIndex>(fbeg);
mbeg->localize();
mend->localize();
auto mbeg2 = std::make_shared<mpi::RIndex<YIndex,YIndex>>(mbeg->range());
mbeg2->synchronize();
auto rmy = mbeg2->rankI();
auto rb = mbeg->rankI();
auto re = mend->rankI();
auto lb = mbeg->local();
auto le = mend->local();
bool skip = false;
for(SizeT i = 0; i != offset.size(); ++i){
const SizeT rmyi = rmy->pack().get(i)->lex();
const SizeT rbi = rb->pack().get(i)->lex();
const SizeT rei = re->pack().get(i)->lex();
const SizeT lbi = lb->pack().get(i)->lex();
const SizeT lei = le->pack().get(i)->lex();
const SizeT Li = lb->pack().get(i)->range()->size();
const SizeT fgebi = fbeg->pack().get(i)->lex();
if(rei < rmyi or rbi > rmyi){
skip = true;
}
const SizeT lbegi = (rbi < rmyi) ? 0 : ( (rbi > rmyi) ? Li-1 : lbi );
const SizeT lendi = (rei < rmyi) ? 0 : ( (rei > rmyi) ? Li-1 : lei );
const SizeT offxi = Li - fbegi % Li + ( rmyi - rbi ) * Li;
*mbegl->pack().get(i) = lbegi;
*mendl->pack().get(i) = lendi;
*fbegl->pack().get(i) = (rbi == rmyi) ? fbegi : ( (rbi > rmyi) ? Li-1 : offxi );
}
(*mbegl)();
(*mendl)();
(*fbegl)();
if(skip){
// synchronous MPI read -> have to call this functio on all ranks
readbase(dest, nullptr, nullptr, fbegl);
}
else {
readbase(dest, mbegl, mendl, fbegl);
}
}
void RDataset::readbase(void* dest, RangePtr readRange, Sptr<YIndex> beg) const
{
RangePtr dr = readRange;