add hdf5-mpi test; works but there are hdf5 identifiers left open...

src/opt/hdf5-mpi/CMakeLists.txt

@@ -23,7 +23,7 @@ if(HDF5_IS_PARALLEL)
   include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include)
 
   add_subdirectory(lib)
-  #add_subdirectory(tests)
+  add_subdirectory(tests)
 
   install(CODE "execute_process(COMMAND sed -i \"s|CXZ_H5_MPI_BUILD_MODE 1|CXZ_H5_MPI_BUILD_MODE 0|g;\" ${CMAKE_CURRENT_SOURCE_DIR}/include/h5_mpi_base.h)")
   install(DIRECTORY include/ DESTINATION ${INSTALL_PATH}/include/cnorxz/hdf5-mpi)

src/opt/hdf5-mpi/include/cnorxz_hdf5_mpi.cc.h

@@ -0,0 +1,12 @@
+// -*- C++ -*-
+/**
+
+   @file opt/hdf5-mpi/include/cnorxz_hdf5_mpi.cc.h
+   @brief CNORXZ HDF5 MPI template sources header
+
+   Copyright (c) 2024 Christian Zimmermann. All rights reserved.
+   Mail: chizeta@f3l.de
+
+ **/
+
+#include "h5_rdataset.cc.h"

src/opt/hdf5-mpi/include/cnorxz_hdf5_mpi.h

@@ -0,0 +1,15 @@
+// -*- C++ -*-
+/**
+
+   @file opt/hdf5-mpi/include/cnorxz_hdf5_mpi.h
+   @brief CNORXZ HDF5 MPI main header
+
+   Copyright (c) 2024 Christian Zimmermann. All rights reserved.
+   Mail: chizeta@f3l.de
+
+ **/
+
+#include "h5_rfile.h"
+#include "h5_rdataset.h"
+
+#include "cnorxz_hdf5_mpi.cc.h"

src/opt/hdf5-mpi/include/h5_rdataset.cc.h

@@ -23,7 +23,7 @@ namespace CNORXZ
 	{
 	    const hid_t tid = getTypeId(*data.data());
 	    if(data.begin().formatIsTrivial()){
-		init(data.range(), tid, data.data());
+		dynamic_cast<Dataset*>(this)->initbase(data.range(), tid, data.data());
 	    }
 	    else {
 		CXZ_ERROR("Got array type with non-trivial format; non-contiguous data formats are not supported yet!");
@@ -39,7 +39,7 @@ namespace CNORXZ
 	template <typename T>
 	mpi::RArray<T> SRDataset<T>::read(const RangePtr& geom) const
 	{
-	    RangePtr rr = mpi::rrange(mFileRange, geom);
+	    auto rr = rangeCast<mpi::RRange<YRange,YRange>>( mpi::rrange(mFileRange, geom) );
 	    mpi::RArray<T> out(rr);
 	    readbase(out.data(), rr, nullptr);
 	    return out;
@@ -48,3 +48,4 @@ namespace CNORXZ
     }
 }
     
+#endif

src/opt/hdf5-mpi/include/h5_rdataset.h

@@ -36,6 +36,7 @@ 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,
@@ -46,7 +47,7 @@ namespace CNORXZ
 		@param data Array containing the dataset.
 	    */
 	    template <typename T>
-	    Dataset& init(const mpi::RArray<T>& data);
+	    RDataset& init(const mpi::RArray<T>& data);
 
 	private:
 	    bool checkHaveParallel() const;

src/opt/hdf5-mpi/lib/h5_rdataset.cc

@@ -26,6 +26,11 @@ namespace CNORXZ
 	    }
 	}
 
+	RDataset::~RDataset()
+	{
+	    this->close();
+	}
+
 	RDataset& RDataset::initbase(const RangePtr& fileRange, hid_t type)
 	{
 	    RangePtr fr = fileRange;
@@ -42,6 +47,7 @@ namespace CNORXZ
 		fr = yrange(rs);
 	    }
 	    Dataset::initbase(fr, type);
+	    MPI_Barrier(MPI_COMM_WORLD);
 	    return *this;
 	}
 	    
@@ -49,14 +55,15 @@ namespace CNORXZ
 	{
 	    //bool todo = true;
 	    RangePtr dr = writeRange;
-	    if(dr->stype() == "R"){
+	    bool parallel = dr->stype() == "R";
+	    if(parallel){
 		dr = writeRange->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(dr->stype() == "R"){
+	    if(parallel){
 		mpi::RIndex<YIndex,YIndex> idx(writeRange);
 		idx.localize();
 		const SizeT rat = mpi::getNumRanks() / idx.rankI()->lmax().val();
@@ -79,6 +86,7 @@ namespace CNORXZ
 	    for(SizeT i = 0; i != dims.size(); ++i){
 		dims[i] = dr->sub(i)->size();
 	    }
+	    VCHECK(toString(offset));
 	    H5Sselect_hyperslab(mFilespace, H5S_SELECT_SET, offset.data(), NULL, dims.data(), NULL);
 	    const hid_t memspace = H5Screate_simple(dims.size(), dims.data(), NULL);
 	    const hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);
@@ -86,23 +94,25 @@ namespace CNORXZ
 	    H5Dwrite(mId, mType, memspace, mFilespace, xfer_plist_id, data);
 	    H5Pclose(xfer_plist_id);
 	    H5Sclose(memspace);
+	    MPI_Barrier(MPI_COMM_WORLD);
 	    return *this;
 	}
 
-	void Dataset::readbase(void* dest, RangePtr readRange, Sptr<YIndex> beg) const
+	void RDataset::readbase(void* dest, RangePtr readRange, Sptr<YIndex> beg) const
 	{
 	    RangePtr dr = readRange;
+	    bool parallel = dr->stype() == "R";
 	    if(not dr){
 		dr = mFileRange;
 	    }
-	    if(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(dr->stype() == "R"){
+	    if(parallel){
 		mpi::RIndex<YIndex,YIndex> idx(readRange);
 		idx.localize();
 		const SizeT rat = mpi::getNumRanks() / idx.rankI()->lmax().val();
@@ -123,7 +133,7 @@ namespace CNORXZ
 
 	    Vector<hsize_t> dims(mFileRange->dim());
 	    for(SizeT i = 0; i != dims.size(); ++i){
-		dims[i] = readRange->sub(i)->size();
+		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()),
@@ -136,6 +146,7 @@ namespace CNORXZ
 		       << "', errorcode :" << err);
 	    H5Pclose(xfer_plist_id);
 	    H5Sclose(mem_space_id);
+	    MPI_Barrier(MPI_COMM_WORLD);
 	}
 
 	bool RDataset::checkHaveParallel() const

src/opt/hdf5-mpi/lib/h5_rfile.cc

@@ -25,6 +25,7 @@ namespace CNORXZ
 
 	RFile::~RFile()
 	{
+	    this->close();
 	    if(mFAPL_id){
 		H5Pclose(mFAPL_id);
 	    }

src/opt/hdf5-mpi/tests/CMakeLists.txt

@@ -0,0 +1,9 @@
+
+add_definitions(-DTEST_NUMBER_FILE="${CMAKE_SOURCE_DIR}/src/tests/numbers.txt")
+include_directories(${CMAKE_SOURCE_DIR}/src/tests)
+include_directories(${CMAKE_SOURCE_DIR}/src/opt/mpi/tests)
+add_executable(h5mpibasic h5_mpi_basic_unit_test.cc)
+add_dependencies(h5mpibasic cnorxz cnorxzhdf5 test_lib)
+target_link_libraries(h5mpibasic ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${HDF5_LIBS} ${MPI_LIBS} cnorxz cnorxzhdf5 cnorxzmpi cnorxzhdf5mpi test_lib)
+set(MPI_TEST_COMMAND mpirun -n 4 h5mpibasic)
+add_test(NAME h5mpibasic COMMAND ${MPI_TEST_COMMAND})

src/opt/hdf5-mpi/tests/h5_mpi_basic_unit_test.cc

@@ -0,0 +1,122 @@
+// -*- C++ -*-
+/**
+   
+   @file opt/hdf5-mpi/tests/h5_mpi_basic_unit_test.cc
+   @brief cnorxz hdf5 mpi basic unit tests.
+
+   Copyright (c) 2024 Christian Zimmermann. All rights reserved.
+   Mail: chizeta@f3l.de
+   
+**/
+
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <cstdio>
+
+#include "gtest/gtest.h"
+
+#include "cnorxz_hdf5.h"
+#include "cnorxz_hdf5_mpi.h"
+#include "test_numbers.h"
+#include "mpi_env.h"
+
+namespace
+{
+    using namespace CNORXZ;
+    using namespace CNORXZ::hdf5;
+    using namespace CNORXZ::mpi;
+    using Test::Numbers;
+
+    typedef MIndex<CIndex,CIndex,CIndex,CIndex> C4;
+    
+    class RDataset_test : public ::testing::Test
+    {
+    protected:
+
+	RDataset_test()
+	{
+	    mFilename = "parallel_test_file.h5";
+	    Vector<RangePtr> grv(4);
+	    grv[0] = CRangeFactory(5).create();
+	    grv[1] = CRangeFactory(14).create();
+	    grv[2] = CRangeFactory(10).create();
+	    grv[3] = CRangeFactory(3).create();
+	    const RangePtr g1 = CRangeFactory(1).create();
+	    const RangePtr g2 = CRangeFactory(2).create();
+	    mGeom = yrange(Vector<RangePtr>{g1,g2,g2,g1});
+	    const RangePtr gr = yrange(grv);
+	    const RangePtr rr = rrange(gr,mGeom);
+	    mLR = rr->sub(1);
+	    Vector<Double> vec = Numbers::get(14,gr->size()+10);
+	    Vector<Double> loc(mLR->size());
+	    for(auto k = CIndex(mGeom); k.lex() != k.lmax().val(); ++k){
+		if(k.lex() == getRankNumber()){
+		    std::copy(vec.begin()+k.lex()*mLR->size(), vec.begin()+(k.lex()+1)*mLR->size(), loc.begin());
+		}
+	    }
+	    auto locarr = MArray<Double>( mLR, loc );
+	    mA = RArray<Double>( locarr, mGeom );
+	}
+	
+	RArray<Double> mA;
+	RangePtr mGeom;
+	RangePtr mLR;
+	String mFilename;
+    };
+
+    TEST_F(RDataset_test, Write)
+    {
+	if(getRankNumber() == 0){
+	    std::remove(mFilename.c_str());
+	}
+	MPI_Barrier(MPI_COMM_WORLD);
+	RFile h5f(mFilename, false);
+	h5f.open();
+	h5f.addGroup("dir");
+	auto dir = h5f.getGroup("dir");
+	dir->add("dat", [](const String& name, const ContentBase* par, const RArray<Double>& d)
+	{ auto o = std::make_shared<SRDataset<Double>>( name, par ); o->init(d); return o; }, mA );
+	h5f.close();
+    }
+
+    TEST_F(RDataset_test, Read)
+    {
+	RFile h5f(mFilename, false);
+	h5f.open();
+	//h5f.addGroup("dir");
+	auto dir = h5f.getGroup("dir");
+	CHECK;
+	MPI_Barrier(MPI_COMM_WORLD);
+	dir->open();
+	CHECK;
+	MPI_Barrier(MPI_COMM_WORLD);
+	auto dat = dir->get("dat", [](const String& name, const ContentBase* par, auto& i)
+	{ i->close(); auto dset = std::make_shared<SRDataset<Double>>(name, par); i = dset;
+	    return dset; } );
+	CHECK;
+	MPI_Barrier(MPI_COMM_WORLD);
+	auto a = dat->read(mGeom);
+	CHECK;
+	MPI_Barrier(MPI_COMM_WORLD);
+	dat->close();
+	CHECK;
+	MPI_Barrier(MPI_COMM_WORLD);
+	dir->close();
+	CHECK;
+	MPI_Barrier(MPI_COMM_WORLD);
+	h5f.close();
+	CHECK;
+	MPI_Barrier(MPI_COMM_WORLD);
+
+	auto i = std::make_shared<CIndex>(mLR);
+	i->ifor( operation( [](Double a, Double b) { EXPECT_EQ(a,b); }, mA(i), a(i) ), NoF{} )();
+    }
+}
+
+int main(int argc, char** argv)
+{
+    ::testing::InitGoogleTest(&argc, argv);
+    ::testing::AddGlobalTestEnvironment( new MPIEnv(argc, argv) );
+    return RUN_ALL_TESTS();
+}

src/opt/hdf5/include/h5_group.cc.h

@@ -43,7 +43,7 @@ namespace CNORXZ
 	decltype(auto) Group::get(const String& name, F&& f)
 	{
 	    auto i = this->getIndexTo(name);
-	    return f(*i);
+	    return f(name,this,*i);
 	}
 	
 	template <typename... Ts>
@@ -122,7 +122,7 @@ namespace CNORXZ
 	    Vector<String> nvec({name});
 	    mCont.extend( URangeFactory<String>( nvec ).create() );
 	    auto ii = getIndexTo(name);
-	    *ii = f(args...);
+	    *ii = f(name, this, args...);
 	    return *this;
 	}
 

src/opt/hdf5/lib/h5_group.cc

@@ -56,6 +56,13 @@ namespace CNORXZ
 	
 	Group& Group::close()
 	{
+	    if(mCont.range() != nullptr){
+		for(auto& x: mCont){
+		    if(x != nullptr){
+			x->close();
+		    }
+		}
+	    }
 	    if(mId != 0){
 		H5Gclose(mId);
 	    }