From 97473157f24e6e22aa77e45b4bfb0d9468a58721 Mon Sep 17 00:00:00 2001
From: Christian Zimmermann <chizeta@f3l.de>
Date: Tue, 18 Mar 2025 15:37:42 -0700
Subject: [PATCH] hdf5 + hdf5 mpi: clean up
---
src/opt/hdf5/include/h5_dataset.h | 9 +---
src/opt/hdf5/lib/h5_dataset.cc | 40 ++----------------
src/opt/hdf5/tests/h5_basic_unit_test.cc | 8 ++--
src/opt/hdf5_mpi/include/h5_rdataset.cc.h | 7 +++-
src/opt/hdf5_mpi/include/h5_rdataset.h | 4 --
src/opt/hdf5_mpi/lib/h5_rdataset.cc | 51 +----------------------
6 files changed, 14 insertions(+), 105 deletions(-)
diff --git a/src/opt/hdf5/include/h5_dataset.h b/src/opt/hdf5/include/h5_dataset.h
index 3c58cd3..ca0ad60 100644
--- a/src/opt/hdf5/include/h5_dataset.h
+++ b/src/opt/hdf5/include/h5_dataset.h
@@ -64,13 +64,6 @@ namespace CNORXZ
*/
virtual Dataset& writebase(const RangePtr& dataRange, Sptr<YIndex> pos, const void* data);
- /** Read the dataset.
- @param dest Pointer to destination.
- @param readrange Range of the destination data.
- @param beg Position within the file space.
- */
- virtual void readbase(void* dest, RangePtr readrange, Sptr<YIndex> beg) const;
-
/** Read the dataset.
@param dest Pointer to destination.
@param tsize Size of dest data type.
@@ -91,7 +84,7 @@ namespace CNORXZ
/** Get the data range.
@return Pointer to the range.
*/
- const RangePtr& dataRange() const;
+ const RangePtr& fileRange() const;
protected:
Vector<hsize_t> mkOff(const Sptr<YIndex>& beg) const;
diff --git a/src/opt/hdf5/lib/h5_dataset.cc b/src/opt/hdf5/lib/h5_dataset.cc
index 6e2a468..b1a5294 100644
--- a/src/opt/hdf5/lib/h5_dataset.cc
+++ b/src/opt/hdf5/lib/h5_dataset.cc
@@ -136,38 +136,6 @@ namespace CNORXZ
H5Sclose(memspace);
return *this;
}
-
- void Dataset::readbase(void* dest, RangePtr readRange, Sptr<YIndex> beg) const
- {
- // TODO: Check if readRange is compatible with mFileRange!!!
- if(not readRange){
- readRange = mFileRange;
- }
- else {
- CXZ_ASSERT(readRange->dim() == mFileRange->dim(), "dimension of data range ("
- << readRange->dim() << ") different from dimension of file range ("
- << mFileRange->dim() << ")");
- }
- Vector<hsize_t> dims(readRange->dim());
- for(SizeT i = 0; i != dims.size(); ++i){
- dims[i] = readRange->sub(i)->size();
- }
- if(beg){
- CXZ_ASSERT(beg->range()->dim() == mFileRange->dim(), "dimension of position index ("
- << beg->range()->dim() << ") different from dimension of file range ("
- << mFileRange->dim() << ")");
- const Vector<hsize_t> fpos = mkOff(beg);
- H5Sselect_hyperslab(mFilespace, H5S_SELECT_SET, fpos.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 = this->mkdxpl();
- 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);
- }
void Dataset::readbase(void* dest, SizeT tsize, Sptr<YIndex> mbeg, Sptr<YIndex> mend,
Sptr<YIndex> fbeg) const
@@ -175,12 +143,10 @@ namespace CNORXZ
const SizeT D = mFileRange->dim();
const bool todo = mbeg != nullptr;
Vector<hsize_t> offset(D);
- Vector<hsize_t> moffset(D);//!!!
+ Vector<hsize_t> moffset(D);
Vector<hsize_t> dims(D);
- Vector<hsize_t> mdims(D);//!!!
+ Vector<hsize_t> mdims(D);
if(todo){
- //RangePtr dr = mbeg->range();
- //const bool parallel = true;
CXZ_ASSERT(mend != nullptr, "no end edge given");
CXZ_ASSERT(fbeg->range()->dim() == D, "dimension of file index ("
<< fbeg->range()->dim() << ") different from dimension of file range ("
@@ -229,7 +195,7 @@ namespace CNORXZ
return xfer_plist_id;
}
- const RangePtr& Dataset::dataRange() const
+ const RangePtr& Dataset::fileRange() const
{
return mFileRange;
}
diff --git a/src/opt/hdf5/tests/h5_basic_unit_test.cc b/src/opt/hdf5/tests/h5_basic_unit_test.cc
index afad1eb..c8210c0 100644
--- a/src/opt/hdf5/tests/h5_basic_unit_test.cc
+++ b/src/opt/hdf5/tests/h5_basic_unit_test.cc
@@ -231,7 +231,7 @@ namespace
File h5f(mFileName, true);
h5f.open();
auto dset = h5f.getGroup("gr2")->open().getDataset("dat1", Double{});
- YIndex beg(dset->dataRange());
+ YIndex beg(dset->fileRange());
beg.setSub(0,2);
YIndex end = beg - 1;
end.setSub(0,2);
@@ -252,12 +252,12 @@ namespace
File h5f(mFileName, true);
h5f.open();
auto dset = h5f.getGroup("gr2")->open().getDataset("dat1", Double{});
- //YIndex beg(dset->dataRange());
+ //YIndex beg(dset->fileRange());
//beg.setSub(0,2);
//YIndex end = beg - 1;
//end.setSub(0,2);
//auto data = dset->read(beg,end);
- Vector<RangePtr> dranges(dset->dataRange()->dim());
+ Vector<RangePtr> dranges(dset->fileRange()->dim());
EXPECT_EQ(dranges.size(), 5u);
dranges[0] = CRangeFactory(5).create();
dranges[1] = CRangeFactory(2).create();
@@ -268,7 +268,7 @@ namespace
MArray<Double> data(drange);
auto mbeg = data.begin();
auto mend = data.begin();
- YIndex fbeg(dset->dataRange());
+ YIndex fbeg(dset->fileRange());
Arr<SizeT,5> mbegpos = { 1,0,0,2,0 };
Arr<SizeT,5> mendpos = { 3,1,3,4,1 };
Arr<SizeT,5> fbegpos = { 3,1,4,2,0 };
diff --git a/src/opt/hdf5_mpi/include/h5_rdataset.cc.h b/src/opt/hdf5_mpi/include/h5_rdataset.cc.h
index 265cb83..16bbc2e 100644
--- a/src/opt/hdf5_mpi/include/h5_rdataset.cc.h
+++ b/src/opt/hdf5_mpi/include/h5_rdataset.cc.h
@@ -40,8 +40,12 @@ namespace CNORXZ
mpi::RArray<T> SRDataset<T>::read(const RangePtr& geom) const
{
auto rr = rangeCast<mpi::RRange<YRange,YRange>>( mpi::rrange(mFileRange, geom) );
+ auto mbeg = std::make_shared<mpi::RIndex<YIndex,YIndex>>(rr);
+ auto mend = std::make_shared<mpi::RIndex<YIndex,YIndex>>(rr);
+ *mend = mend->lmax().val()-1;
+ auto fbeg = std::make_shared<YIndex>(mFileRange);
mpi::RArray<T> out(rr);
- readbase(out.data(), rr, nullptr);
+ rreadbase(out.data(), sizeof(T), mbeg, mend, fbeg);
return out;
}
@@ -60,7 +64,6 @@ namespace CNORXZ
auto mend = std::make_shared<mpi::RIndex<YIndex,YIndex>>(outrange);
*mend = mend->lmax().val()-1;
auto fbeg = std::make_shared<YIndex>(mFileRange);
- //readbase(out.data(), outrange, nullptr);
rreadbase(out.data(), sizeof(T), mbeg, mend, fbeg);
return out;
}
diff --git a/src/opt/hdf5_mpi/include/h5_rdataset.h b/src/opt/hdf5_mpi/include/h5_rdataset.h
index 30122f5..8b61397 100644
--- a/src/opt/hdf5_mpi/include/h5_rdataset.h
+++ b/src/opt/hdf5_mpi/include/h5_rdataset.h
@@ -36,14 +36,10 @@ namespace CNORXZ
@param _parent Parent content object.
*/
RDataset(const String& name, const ContentBase* _parent);
- //virtual ~RDataset();
virtual RDataset& initbase(const RangePtr& fileRange, hid_t type) override;
virtual RDataset& writebase(const RangePtr& writeRange, Sptr<YIndex> pos,
const void* data) override;
- virtual void readbase(void* dest, RangePtr readrange, Sptr<YIndex> beg) const override;
- //virtual void readbase(void* dest, Sptr<YIndex> mbeg, Sptr<YIndex> mend,
- // Sptr<YIndex> fbeg) const override;
virtual hid_t mkdxpl() const override;
diff --git a/src/opt/hdf5_mpi/lib/h5_rdataset.cc b/src/opt/hdf5_mpi/lib/h5_rdataset.cc
index 9c5ded1..00bcb15 100644
--- a/src/opt/hdf5_mpi/lib/h5_rdataset.cc
+++ b/src/opt/hdf5_mpi/lib/h5_rdataset.cc
@@ -153,56 +153,7 @@ namespace CNORXZ
Dataset::readbase(dest, tsize, mbegl, mendl, fbegl);
}
}
-
- void RDataset::readbase(void* dest, RangePtr readRange, Sptr<YIndex> beg) const
- {
- RangePtr dr = readRange;
- if(not dr){
- dr = mFileRange;
- }
- bool parallel = dr->stype() == "R";
- if(parallel){
- dr = readRange->sub(1);
- }
- CXZ_ASSERT(dr->dim() == mFileRange->dim(), "dimension of data range ("
- << dr->dim() << ") different from dimension of file range ("
- << mFileRange->dim() << ")");
- Vector<hsize_t> offset(mFileRange->dim());
- if(parallel){
- mpi::RIndex<YIndex,YIndex> idx(readRange);
- idx.localize();
- const SizeT rat = mpi::getNumRanks() / idx.rankI()->lmax().val();
- assert(rat == 1); // for now...
- assert(mpi::getRankNumber() == idx.rankI()->lex());
- for(SizeT i = 0; i != offset.size(); ++i){
- offset[i] = idx.rankI()->pack().get(i)->lex() * dr->savesub(i)->size();
- }
- }
- if(beg){
- CXZ_ASSERT(beg->range()->dim() == mFileRange->dim(), "dimension of position index ("
- << beg->range()->dim() << ") different from dimension of file range ("
- << mFileRange->dim() << ")");
- for(SizeT i = 0; i != offset.size(); ++i){
- offset[i] += beg->pack().get(i)->lex();
- }
- }
-
- Vector<hsize_t> dims(mFileRange->dim());
- for(SizeT i = 0; i != dims.size(); ++i){
- dims[i] = dr->sub(i)->size();
- }
- 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 = this->mkdxpl();
- 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);
- }
-
+
hid_t RDataset::mkdxpl() const
{
const hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);