hdf5: fix bug + hdf5-mpi: test works

src/opt/hdf5-mpi/CMakeLists.txt

@@ -25,9 +25,8 @@ if(HDF5_IS_PARALLEL)
   add_subdirectory(lib)
   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)
-  install(CODE "execute_process(COMMAND sed -i \"s|CXZ_H5_MPI_BUILD_MODE 0|CXZ_H5_MPI_BUILD_MODE 1|g;\" ${CMAKE_CURRENT_SOURCE_DIR}/include/h5_mpi_base.h)")
+  install(CODE "execute_process(COMMAND sed -i \"s|CXZ_H5_MPI_BUILD_MODE 1|CXZ_H5_MPI_BUILD_MODE 0|g;\" ${INSTALL_PATH}/include/cnorxz/hdf5-mpi/h5_mpi_base.h)")
 else()
   message(WARNING "no parallel support in available HDF5 library")
 endif()

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

@@ -36,7 +36,7 @@ namespace CNORXZ
 		@param _parent Parent content object.
 	     */
 	    RDataset(const String& name, const ContentBase* _parent);
-	    virtual ~RDataset();
+	    //virtual ~RDataset();
 
 	    virtual RDataset& initbase(const RangePtr& fileRange, hid_t type) override;
 	    virtual RDataset& writebase(const RangePtr& writeRange, Sptr<YIndex> pos,

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

@@ -21,14 +21,6 @@ namespace CNORXZ
 	{
 	    CXZ_ASSERT( checkHaveParallel(), "tried to open dataset in parallel mode while file"
 			<< parent()->filename() << " was opened in serial mode");
-	    if(exists()){
-		open();
-	    }
-	}
-
-	RDataset::~RDataset()
-	{
-	    this->close();
 	}
 
 	RDataset& RDataset::initbase(const RangePtr& fileRange, hid_t type)
@@ -86,7 +78,6 @@ 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);

src/opt/hdf5-mpi/tests/diag_utils.h

@@ -0,0 +1,84 @@
+
+#ifndef __cxz_hdf5_mpi_diag_utils_h__
+#define __cxz_hdf5_mpi_diag_utils_h__
+
+inline String getStringObjType(hid_t obj_id)
+{
+    const H5I_type_t t = H5Iget_type(obj_id);
+    switch(t){
+    case H5I_UNINIT:
+	return "uninitialized";
+    case H5I_BADID:
+	return "bad";
+    case H5I_FILE:
+	return "file";
+    case H5I_GROUP:
+	return "group";
+    case H5I_DATATYPE:
+	return "datatype";
+    case H5I_DATASPACE:
+	return "dataspace";
+    case H5I_DATASET:
+	return "dataset";
+    case H5I_MAP:
+	return "map";
+    case H5I_ATTR:
+	return "attr";
+    case H5I_VFL:
+	return "vfl";
+    case H5I_VOL:
+	return "vol";
+    case H5I_GENPROP_CLS:
+	return "gen prop list class";
+    case H5I_GENPROP_LST:
+	return "gen prop list";
+    case H5I_ERROR_CLASS:
+	return "err class";
+    case H5I_ERROR_MSG:
+	return "err msg";
+    case H5I_ERROR_STACK:
+	return "err stack";
+    case H5I_SPACE_SEL_ITER:
+	return "space sel iter";
+    case H5I_EVENTSET:
+	return "eventset";
+    case H5I_NTYPES:
+	return "ntypes";
+    default:
+	return "unknonw";
+    }
+}
+    
+void list_objects(hid_t file_id, const String& desc)
+{
+    constexpr SizeT maxnamesize = 256;
+    MPI_Barrier(MPI_COMM_WORLD);
+    if(getRankNumber() == 0){
+	std::cout << " ======= " << desc << " ======= " << std::endl;
+    }
+    const ssize_t num = H5Fget_obj_count(file_id, H5F_OBJ_ALL);
+    CXZ_ASSERT(num >= 0, "error while counting objects: " << num);
+    Vector<hid_t> list(num);
+    H5Fget_obj_ids(file_id, H5F_OBJ_ALL, num, list.data());
+    const SizeT nranks = getNumRanks();
+    for(SizeT n = 0; n != nranks; ++n){
+	MPI_Barrier(MPI_COMM_WORLD);
+	if(n == getRankNumber()){
+	    std::cout << "have " << num << " objects on rank " << n << ":" << std::endl;
+	    for(SizeT i = 0; i != static_cast<SizeT>(num); ++i){
+		char iname[maxnamesize];
+		H5Iget_name(list[i], iname, maxnamesize);
+		const String itype = getStringObjType(list[i]);
+		std::cout << " - " << list[i] << " [" << itype << "]: " << iname << std::endl;
+	    }
+	}
+	MPI_Barrier(MPI_COMM_WORLD);
+    }
+    if(getRankNumber() == 0){
+	std::cout << " ==================== " << std::endl;
+	std::cout << std::endl;
+    }
+    MPI_Barrier(MPI_COMM_WORLD);
+}
+
+#endif

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

@@ -83,31 +83,11 @@ namespace
     TEST_F(RDataset_test, Read)
     {
 	RFile h5f(mFilename, false);
-	h5f.open();
+	auto dat = h5f.open().getGroup("dir")->open().get("dat", [](const String& name, const ContentBase* par, auto& i)
-	//h5f.addGroup("dir");
+	{ (*i)->close(); auto dset = std::make_shared<SRDataset<Double>>(name, par); *i = dset;
-	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{} )();

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(name,this,*i);
+	    return f(name,this,i);
 	}
 	
 	template <typename... Ts>

src/opt/hdf5/lib/h5_group.cc

@@ -100,7 +100,6 @@ namespace CNORXZ
 		const String next = name.substr(delimpos+1);
 		auto g = getGroup(thisname);
 		g->open();
-		CHECK;
 		return g->get(next);
 	    }
 	    auto i = this->getIndexTo(thisname);
@@ -170,8 +169,8 @@ namespace CNORXZ
 	{
 	    const hid_t id = H5Dopen(loc_id, name, H5P_DEFAULT);
 	    if(not H5Aexists(id, "CLASS")){
-		return false;
 		H5Dclose(id);
+		return false;
 	    }
 	    hid_t attrid = H5Aopen(id, "CLASS", H5P_DEFAULT);
 	    const hid_t atype = H5Aget_type(attrid);