[Hdf-forum] read fail, error diagnosis?

[Elena Pourmal]

John,

Can you try h5dump to read the hyperslab on which your MPI program fails? (to check if sequential indeed can read the file and file is OK).

Sub-setting parameters can now be expressed as --dataset="/foo/mydataset[START;STRIDE;COUNT;BLOCK]"

Elena
On Jan 13, 2010, at 6:52 AM, Biddiscombe, John A. wrote:

> Can anyone tell from this error stack (below) what might have gone wrong. The file is a single dataset of approx 32GB it looks like this "h5dump -HA ..."
> 
> HDF5 "/project/csvis/biddisco/xdmf_test/ringRe25k_omegaI01500.h5" {
> GROUP "/" {
>   DATASET "00000__Node__omega" {
>      DATATYPE  H5T_IEEE_F32LE
>      DATASPACE  SIMPLE { ( 3521, 881, 881, 3 ) / ( 3521, 881, 881, 3 ) }
>   }
> }
> }
> 
> Smaller versions of the same file work ok when I try to read hyperslabs (note parallel read is enabled, so mpiio is being used), but the big one fails. the final message about " can't convert from size to size_i" makes me suspicious that there's something fishy going on with long ints etc. 
> 
> thanks
> 
> JB
> 
> HDF5-DIAG: Error detected in HDF5 (1.8.4) MPI-process 1:
>  #000: /workspace/hdf5-1.8/src/H5Dio.c line 174 in H5Dread(): can't read data
>    major: Dataset
>    minor: Read failed
>  #001: /workspace/hdf5-1.8/src/H5Dio.c line 405 in H5D_read(): can't read data
>    major: Dataset
>    minor: Read failed
>  #002: /workspace/hdf5-1.8/src/H5Dcontig.c line 520 in H5D_contig_read(): contiguous read failed
>    major: Dataset
>    minor: Read failed
>  #003: /workspace/hdf5-1.8/src/H5Dselect.c line 275 in H5D_select_read(): read error
>    major: Dataspace
>    minor: Read failed
>  #004: /workspace/hdf5-1.8/src/H5Dselect.c line 210 in H5D_select_io(): read error
>    major: Dataspace
>    minor: Read failed
>  #005: /workspace/hdf5-1.8/src/H5Dcontig.c line 838 in H5D_contig_readvv(): block write failed
>    major: Low-level I/O
>    minor: Write failed
>  #006: /workspace/hdf5-1.8/src/H5Fio.c line 117 in H5F_block_read(): driver read request failed
>    major: Low-level I/O
>    minor: Read failed
>  #007: /workspace/hdf5-1.8/src/H5FDint.c line 142 in H5FD_read(): driver read request failed
>    major: Virtual File Layer
>    minor: Read failed
>  #008: /workspace/hdf5-1.8/src/H5FDmpio.c line 1445 in H5FD_mpio_read(): can't convert from size to size_i
>    major: Internal error (too specific to document in detail)
>    minor: Out of range
> 
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