I see this too: 1.8.4 patch 1, using pytables. Command and output are below
My file size is ~1.1 GB. The table opens in HDFview, and as far as I can
tell is working in our applications.
----------------------------------------
>>> for i in bhdf.root.alignments.intergenic.refmap.iterrows(1,10): print i
...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 140665648559872:
#000: ../../../src/H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ../../../src/H5Dio.c line 404 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: ../../../src/H5Dchunk.c line 1715 in H5D_chunk_read(): error looking
up chunk address
major: Dataset
minor: Can't get value
#003: ../../../src/H5Dchunk.c line 2284 in H5D_chunk_get_info(): can't
query chunk address
major: Dataset
minor: Can't get value
#004: ../../../src/H5Dbtree.c line 1010 in H5D_btree_idx_get_addr(): can't
get chunk info
major: Dataset
minor: Can't get value
#005: ../../../src/H5B.c line 332 in H5B_find(): unable to load B-tree
node
major: B-Tree node
minor: Unable to load metadata into cache
#006: ../../../src/H5AC.c line 1831 in H5AC_protect(): H5C_protect()
failed.
major: Object cache
minor: Unable to protect metadata
#007: ../../../src/H5C.c line 6160 in H5C_protect(): can't load entry
major: Object cache
minor: Unable to load metadata into cache
#008: ../../../src/H5C.c line 10990 in H5C_load_entry(): unable to load
entry
major: Object cache
minor: Unable to load metadata into cache
#009: ../../../src/H5Bcache.c line 201 in H5B_load(): can't read B-tree
node
major: B-Tree node
minor: Read failed
#010: ../../../src/H5Fio.c line 113 in H5F_block_read(): read from
metadata accumulator failed
major: Low-level I/O
minor: Read failed
#011: ../../../src/H5Faccum.c line 196 in H5F_accum_read(): driver read
request failed
major: Low-level I/O
minor: Read failed
#012: ../../../src/H5FDint.c line 142 in H5FD_read(): driver read request
failed
major: Virtual File Layer
minor: Read failed
#013: ../../../src/H5FDsec2.c line 755 in H5FD_sec2_read(): file read
failed
major: Low-level I/O
minor: Read failed
#014: ../../../src/H5FDsec2.c line 755 in H5FD_sec2_read(): Bad file
descriptor
major: Internal error (too specific to document in detail)
minor: System error message
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "tableExtension.pyx", line 845, in tables.tableExtension.Row.__next__
File "tableExtension.pyx", line 955, in
tables.tableExtension.Row.__next__general
File "tableExtension.pyx", line 565, in
tables.tableExtension.Table._read_records
tables.exceptions.HDF5ExtError: Problems reading records.
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