Hi,
I am trying to create a library to OpenFOAM (CFD toolbox from
www.openfoam.org) to write the solution field to HDF5 archives.
Creating the file and dataspace seems to go well, but the creation of
the dataset with H5Dcreate2 fails miserably. I have followed the
example/tutorial found on http://www.hdfgroup.org/HDF5/Tutor/pcrtaccd.html
The error message is:
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) MPI-process 0:
#000: ../../../src/H5D.c line 171 in H5Dcreate2(): unable to create
dataset
major: Dataset
minor: Unable to initialize object
#001: ../../../src/H5Dint.c line 428 in H5D_create_named(): unable to
create and link to dataset
major: Dataset
minor: Unable to initialize object
#002: ../../../src/H5L.c line 1639 in H5L_link_object(): unable to
create new link to object
major: Links
minor: Unable to initialize object
#003: ../../../src/H5L.c line 1862 in H5L_create_real(): can't insert
link
major: Symbol table
minor: Unable to insert object
#004: ../../../src/H5Gtraverse.c line 877 in H5G_traverse(): internal
path traversal failed
major: Symbol table
minor: Object not found
#005: ../../../src/H5Gtraverse.c line 776 in H5G_traverse_real():
component not found
major: Symbol table
minor: Object not found
and similar for other ranks. The source code is attached. When
meshInit();
meshWrite();
meshClose();
is called, the error occures (in H5DCreate2).
The following is in the h5Write.H header file:
#define H5T_SCALAR H5T_NATIVE_DOUBLE
(to include the possibility to compile with support for single precision).
The system is Ubuntu 12.04 with system OpenMPI and HDF5-OpenMPI
libraries installed. Compiler is GCC. I have tried to compile the same
code on another system with SLES 11sp1, Intel compilers and SGI-MPI.
Same error message occurs on that system.
Do you have any hints to help me? Thanks in advance.
Best regards,
Håkon Strandenes
Norway
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
OpenFOAM is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.
You should have received a copy of the GNU General Public License
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
\*---------------------------------------------------------------------------*/
#include "h5Write.H"
#include "Time.H"
#include "SortableList.H"
#include "OFstream.H"
#include "string.H"
#include "stringOps.H"
#define H5DATA_MESH_FILE_NAME "h5Data/h5DataMesh.h5"
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
/*
const Foam::label Foam::h5Write::foamToXDMFFaceAddr[4][6] =
{
{ 4, 5, 2, 3, 0, 1 }, // 11 = pro-STAR hex
{ 0, 1, 4, 5, 2, -1 }, // 12 = pro-STAR prism
{ 5, 4, 2, 0, -1, -1 }, // 13 = pro-STAR tetra
{ 0, 4, 3, 5, 2, -1 } // 14 = pro-STAR pyramid
};
*/
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
void Foam::h5Write::meshInit()
{
Info<< "h5Write::meshInit" << endl << endl;
// Set up file access property list with parallel I/O access
meshPlistID_ = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(meshPlistID_, MPI_COMM_WORLD, MPI_INFO_NULL);
// Create a new file collectively.
meshFileID_ = H5Fcreate
(
H5DATA_MESH_FILE_NAME,
H5F_ACC_TRUNC,
H5P_DEFAULT,
meshPlistID_
);
// Close the property list
H5Pclose(meshPlistID_);
}
void Foam::h5Write::meshClose()
{
Info<< "h5Write::meshClose" << endl << endl;
// Close the file.
H5Fclose(meshFileID_);
}
void Foam::h5Write::meshWrite()
{
meshWritePoints();
meshWriteCells();
}
void Foam::h5Write::meshWritePoints()
{
const pointField& points = mesh_.points();
// Create the dataspace for the dataset
hsize_t dimsf[] = {points.size(), 3};
hid_t fileSpace = H5Screate_simple(2, dimsf, NULL);
// Construct dataset name
char datasetName[80];
sprintf(datasetName, "/%f/points/processor%i", mesh_.time().value(), Pstream::myProcNo());
//if (debug)
{
Pout<< "Dataset name: "<< datasetName << endl;
}
// Create the dataset with default properties
hid_t dsetID = H5Dcreate2
(
meshFileID_,
datasetName,
H5T_SCALAR,
fileSpace,
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT
);
// Create property list for collective dataset write.
meshPlistID_ = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(meshPlistID_, H5FD_MPIO_COLLECTIVE);
//if (debug)
{
Pout<< "Writing " << points.size() << " points" << endl;
}
// Create a simple array of points (to pass on to H5Dwrite)
scalar pointList[points.size()][3];
// Fill the array
forAll(points, ptI)
{
pointList[ptI][0] = points[ptI].x();
pointList[ptI][1] = points[ptI].y();
pointList[ptI][2] = points[ptI].z();
}
// Do the actual write
meshStatus_ = H5Dwrite
(
dsetID,
H5T_SCALAR,
H5S_ALL,
H5S_ALL,
meshPlistID_,
pointList
);
// Close/release resources.
H5Dclose(dsetID);
H5Sclose(fileSpace);
H5Pclose(meshPlistID_);
}
void Foam::h5Write::meshWriteCells()
{
}
// ************************************************************************* //
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