void MapEpetra::importFromHDF5 ( std::string const& fileName, std::string const& mapName )
{
ASSERT (M_commPtr.get()!=0, "Error! The stored communicator pointer is not valid.\n");
EpetraExt::HDF5 HDF5 ( *M_commPtr );
// Open an existing file
HDF5.Open ( ( fileName + ".h5" ).data() );
// Check if the file is created
if ( !HDF5.IsOpen () )
{
std::cerr << "Unable to open " + fileName + ".h5";
abort();
}
// Read the unique map from the file
Epetra_Map* importedMap ( 0 );
HDF5.Read ( ( mapName + "Unique" ).c_str(), importedMap );
// Copy the loaded map to the member object
M_uniqueMapEpetra.reset ( new map_Type ( *importedMap ) );
// Read the repeated map from the file
HDF5.Read ( ( mapName + "Repeated" ).c_str(), importedMap );
// Copy the loaded matrix to the member object
M_repeatedMapEpetra.reset ( new map_Type ( *importedMap ) );
// Close the file
HDF5.Close();
} // importFromHDF5
void MapEpetra::exportToHDF5 ( std::string const& fileName, std::string const& mapName, bool const truncate )
{
ASSERT (M_commPtr.get()!=0, "Error! The stored communicator pointer is not valid.\n");
ASSERT (M_uniqueMapEpetra.get()!=0 && M_repeatedMapEpetra.get()!=0, "Error! One (or both) the map pointers are not valid.\n");
EpetraExt::HDF5 HDF5 ( *M_commPtr );
if ( truncate )
{
// Create and open the file / Truncate and open the file
HDF5.Create ( ( fileName + ".h5" ).data() );
}
else
{
// Open an existing file without truncating it
HDF5.Open ( ( fileName + ".h5" ).data() );
}
// Check if the file is created
if ( !HDF5.IsOpen () )
{
std::cerr << "Unable to create " + fileName + ".h5";
abort();
}
// Save the maps into the file
HDF5.Write ( ( mapName + "Unique" ).c_str(), *M_uniqueMapEpetra );
HDF5.Write ( ( mapName + "Repeated" ).c_str(), *M_repeatedMapEpetra );
// Close the file
HDF5.Close();
} // exportToHDF5
int main (int argc, char **argv)
{
#ifdef HAVE_MPI
MPI_Init(&argc, &argv);
Epetra_MpiComm Comm(MPI_COMM_WORLD);
#else
Epetra_SerialComm Comm;
#endif
try
{
// This is the HDF5 file manager
EpetraExt::HDF5 HDF5(Comm);
// creates a new file. To open an existing file, use Open("myfile.h5")
// This file contains:
// - a sparse (diagonal) matrix, whose group name is "speye"
// - a multivector, whose group name is "x"
// - a map for 2-processor run, whose group name is "map-2"
HDF5.Open("matlab.h5");
if (Comm.MyPID() == 0)
cout << endl;
cout << "*) Reading Epetra_CrsMatrix from HDF5 file matlab.h5..." << endl;
cout << endl;
// first query for matrix properties:
int NumGlobalRows, NumGlobalCols, NumGlobalNonzeros;
int NumGlobalDiagonals, MaxNumEntries;
double NormOne, NormInf;
HDF5.ReadCrsMatrixProperties("speye", NumGlobalRows, NumGlobalCols,
NumGlobalNonzeros, NumGlobalDiagonals,
MaxNumEntries, NormOne, NormInf);
if (Comm.MyPID() == 0)
{
cout << "Matrix information as given by ReadCrsMatrixProperties()";
cout << endl << endl;
cout << "NumGlobalRows = " << NumGlobalRows << endl;
cout << "NumGlobalCols = " << NumGlobalCols << endl;
cout << "NumGlobalNonzeros = " << NumGlobalNonzeros << endl;
cout << "NumGlobalDiagonals = " << NumGlobalDiagonals << endl;
cout << "MaxNumEntries = " << MaxNumEntries << endl;
cout << "NormOne = " << NormOne << endl;
cout << "NormInf = " << NormInf << endl;
}
// the reading the actual matrix, with a linear map, since no map
// has been specified.
Epetra_CrsMatrix* Matrix = 0;
HDF5.Read("speye", Matrix);
cout << *Matrix;
if (Comm.MyPID() == 0)
{
cout << endl;
cout << "*) Reading Epetra_MultiVector from HDF5 file matlab.h5..." << endl;
cout << endl;
}
Epetra_MultiVector* x;
HDF5.Read("x", x);
cout << *x;
if (Comm.NumProc() == 2)
{
if (Comm.MyPID() == 0)
{
cout << endl;
cout << "*) Reading Epetra_Map from HDF5 file matlab.h5..." << endl;
cout << endl;
}
Epetra_Map* Map;
HDF5.Read("map-2", Map);
cout << *Map;
}
// We finally close the file. Better to close it before calling
// MPI_Finalize() to avoid MPI-related errors, since Close() might call MPI
// functions.
HDF5.Close();
// delete memory
if (Matrix) delete Matrix;
}
catch(EpetraExt::Exception& rhs)
{
rhs.Print();
}
catch (...)
{
cerr << "Caught generic exception" << endl;
}
#ifdef HAVE_MPI
MPI_Finalize();
#endif
return(EXIT_SUCCESS);
}
int main (int argc, char **argv)
{
#ifdef HAVE_MPI
MPI_Init(&argc, &argv);
Epetra_MpiComm Comm(MPI_COMM_WORLD);
#else
Epetra_SerialComm Comm;
#endif
if (Comm.MyPID() == 0)
{
cout << "Converter from MatrixMarket files to HDF5 files" << endl;
cout << "For notes on the usage, execute" << endl;
cout << " ./HDF5Converter.exe --help" << endl;
cout << endl;
}
// Creating an empty command line processor looks like:
Teuchos::CommandLineProcessor CLP;
string MapFileName = "not-set";
string XFileName = "not-set";
string BFileName = "not-set";
string MatrixFileName = "not-set";
string HDF5FileName = "myfile.f5";
string MapHDF5Name = "map";
string XHDF5Name = "X";
string BHDF5Name = "B";
string MatrixHDF5Name = "matrix";
CLP.setOption("in-map", &MapFileName, "map file name");
CLP.setOption("in-matrix", &MatrixFileName, "matrix file name");
CLP.setOption("in-x", &XFileName, "x vector file name");
CLP.setOption("in-b", &BFileName, "b vector file name");
CLP.setOption("output", &HDF5FileName, "name of HDF5 file");
CLP.setOption("out-map", &MapHDF5Name, "map name in HDF5 file");
CLP.setOption("out-matrix", &MatrixHDF5Name, "matrix name in HDF5 file");
CLP.setOption("out-x", &XHDF5Name, "x vector name in HDF5 file");
CLP.setOption("out-b", &BHDF5Name, "b vector name in HDF5 file");
CLP.throwExceptions(false);
CLP.parse(argc,argv);
Epetra_Map* Map = 0;
Epetra_CrsMatrix* Matrix = 0;
Epetra_MultiVector* X = 0;
Epetra_MultiVector* B = 0;
if (MapFileName != "not-set")
{
if (Comm.MyPID() == 0)
cout << "Reading map from " << MapFileName << endl;
EpetraExt::MatrixMarketFileToMap(MapFileName.c_str(), Comm, Map);
}
else
{
cerr << "You need to specify a map, sorry" << endl;
#ifdef HAVE_MPI
MPI_Finalize();
#endif
exit(EXIT_SUCCESS);
}
if (XFileName != "not-set")
{
if (Comm.MyPID() == 0)
cout << "Reading vector from " << XFileName << endl;
EpetraExt::MatrixMarketFileToMultiVector(XFileName.c_str(), *Map, X);
}
if (BFileName != "not-set")
{
if (Comm.MyPID() == 0)
cout << "Reading vector from " << BFileName << endl;
EpetraExt::MatrixMarketFileToMultiVector(BFileName.c_str(), *Map, B);
}
if (MatrixFileName != "not-set")
{
if (Comm.MyPID() == 0)
cout << "Reading matrix from " << MatrixFileName << endl;
EpetraExt::MatrixMarketFileToCrsMatrix(MatrixFileName.c_str(), *Map, Matrix);
}
// ================================= //
// Open HDF5 file and append data in //
// ================================= //
EpetraExt::HDF5 HDF5(Comm);
HDF5.Create(HDF5FileName);
if (Map)
HDF5.Write(MapHDF5Name + EpetraExt::toString(Comm.NumProc()), *Map);
if (Matrix)
HDF5.Write(MatrixHDF5Name, *Matrix);
if (X)
HDF5.Write(XHDF5Name, *X);
if (B)
HDF5.Write(BHDF5Name, *B);
HDF5.Close();
if (Map) delete Map;
if (Matrix) delete Matrix;
if (X) delete X;
if (B) delete B;
#ifdef HAVE_MPI
MPI_Finalize();
#endif
return(EXIT_SUCCESS);
}
