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
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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