HDF5 I/O crashing

Question

Hi

The following code compiles fine but crashes when run. First, I run it without commenting the "OUTPUT" so as to generate the h5 output file; this works fine but it crashes when I try to read in the generated h5 file.

UFL File:

element = FiniteElement("Lagrange", "triangle", 1)

v       = TestFunction( element )
u       = TrialFunction( element )

main.cpp

#include <dolfin.h>
#include "HDF5_TEST.h"

using namespace dolfin;

int main()
{
/*  
    // OUTPUT
    UnitSquareMesh mesh_out(5, 5);
    HDF5_TEST::FunctionSpace V(mesh_out);

    HDF5File f("u.h5", "w");

    Function materials_out(V);
    Constant tmp(11);
    materials_out.interpolate( tmp );

    f.write( mesh_out, "mesh" );
    f.write( materials_out, "materials" );
    //f.close();
*/  

    // INPUT
    HDF5File g( "u.h5", "r" );
    Mesh mesh_in;
    HDF5_TEST::FunctionSpace Vin(mesh_in);
    g.read( mesh_in, "mesh" );

    Function materials_in(Vin);
    g.read( materials_in, "materials" );
    //g.close();

    plot( materials_in );
    interactive();
}

After generating the output h5 file, I comment out the "OUTPUT" section as in the code above and attempt to read it but it crashes with the following error:

HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000:
../../../src/H5L.c line 824 in H5Lexists(): unable to get link info
major: Symbol table
minor: Object not found #001: ../../../src/H5L.c line 2765 in H5L_exists(): path doesn't exist
major: Symbol table
minor: Object already exists #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found #003: ../../../src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
major: Symbol table
minor: Object not found HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000: ../../../src/H5L.c line 824 in H5Lexists():
unable to get link info
major: Symbol table
minor: Object not found #001: ../../../src/H5L.c line 2765 in H5L_exists(): path doesn't exist
major: Symbol table
minor: Object already exists #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found #003: ../../../src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
major: Symbol table
minor: Object not found HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000: ../../../src/H5D.c line 334 in H5Dopen2(): not
found
major: Dataset
minor: Object not found #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find object
major: Symbol table
minor: Object not found #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found #003: ../../../src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
major: Symbol table
minor: Object not found HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000: ../../../src/H5D.c line 437 in H5Dget_space():
not a dataset
major: Invalid arguments to routine
minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000: ../../../src/H5S.c line 794 in
H5Sget_simple_extent_ndims(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc [shortqt:25078]
*** Process received signal *** [shortqt:25078] Signal: Aborted (6) [shortqt:25078] Signal code: (-6) [shortqt:25078] [ 0]
/lib/x86_64-linux-gnu/libc.so.6(+0x36ff0) [0x2b81df3b3ff0]
[shortqt:25078] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)
[0x2b81df3b3f77] [shortqt:25078] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148) [0x2b81df3b75e8]
[shortqt:25078] [ 3]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9gnu_cxx27verbose_terminate_handlerEv+0x155)
[0x2b81deec36e5] [shortqt:25078] [ 4]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e856) [0x2b81deec1856]
[shortqt:25078] [ 5]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e883) [0x2b81deec1883]
[shortqt:25078] [ 6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5eaae) [0x2b81deec1aae]
[shortqt:25078] [ 7]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xafde2) [0x2b81def12de2]
[shortqt:25078] [ 8]
/usr/lib/libdolfin.so.1.3(_ZN6dolfin13HDF5Interface16get_dataset_sizeEiSs+0x159)
[0x2b81de59ee69] [shortqt:25078] [ 9]
/usr/lib/libdolfin.so.1.3(_ZNK6dolfin8HDF5File4readERNS_4MeshESs+0x307)
[0x2b81de541617] [shortqt:25078] [10] ./main(main+0x166) [0x404816]
[shortqt:25078] [11]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)
[0x2b81df39ede5] [shortqt:25078] [12] ./main() [0x404af6]
[shortqt:25078] *** End of error message *** Aborted (core dumped)

Answer 1

You have to read in mesh before you initialize function space

g.read( mesh_in, "mesh" );
HDF5_TEST::FunctionSpace Vin(mesh_in);

Comments

Thanks Jan.

I've stared at the code over and over again and didn't spot that. It's amazing how such inconspicuous and silly errors go undetected.