Forwarding to list. ~Josh.
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> From: pytables-users-boun...@lists.sourceforge.net
> Date: December 3, 2011 12:52:46 AM GMT+01:00
> To: pytables-users-ow...@lists.sourceforge.net
> Subject: Auto-discard notification
>
> The attached message has been automatically discarded.
> From: "Edward C. Jones" <edcjo...@comcast.net>
> Date: December 3, 2011 12:50:13 AM GMT+01:00
> To: pytables-users@lists.sourceforge.net
> Subject: Giant HDF5/PyTables error message
>
>
> The following gigantic (but hard to interpret) error message was generated
> by the line of code:
>
> self.h5.root.sortlist.cols.score.createCSIndex()
>
> Is there a document on how to interpret HDF5 error messages in a PyTables
> context? What kind of errors in my code create these error messages? Which
> styles of PyTables programming tends to lead to HDF5 errors? If I cannot
> figure out a way to analyze these messages, I will have to remove much of
> the PyTables from my code.
>
> (I wrapped long lines)
> HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 4148012736:
> #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 1733 in H5D_chunk_read():
> unable to read raw data chunk
> major: Low-level I/O
> minor: Read failed
> #003: ../../../src/H5Dchunk.c line 2742 in H5D_chunk_lock():
> data pipeline read failed
> major: Data filters
> minor: Filter operation failed
> #004: ../../../src/H5Z.c line 1017 in H5Z_pipeline():
> filter returned failure during read
> major: Data filters
> minor: Read failed
> #005: blosc/blosc_filter.c line 232 in blosc_filter():
> Blosc decompression error
> major: Data filters
> minor: Callback failed
> Traceback (most recent call last):
> File "./mrq.py", line 133, in <module>
> options.scoretask)
> File "/home/edcjones/imagedb/imgSeek/mrquery/DB.py", line 56, in __init__
> self.New(basename, topdirs, scoretask, excluded_dirs)
> File "/home/edcjones/imagedb/imgSeek/mrquery/DB.py", line 180, in New
> hashbin.HashBin(self)
> File "/home/edcjones/imagedb/imgSeek/mrquery/hashbin.py",
> line 74, in __init__
> self.mrq.reversesort_sortlist(self.quota)
> File "/home/edcjones/imagedb/imgSeek/mrquery/DB.py",
> line 951, in reversesort_sortlist
> self.h5.root.sortlist.cols.score.createCSIndex()
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 3437, in createCSIndex
> _blocksizes=_blocksizes, _testmode=_testmode, _verbose=_verbose)
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 3412, in createIndex
> tmp_dir, _blocksizes, _verbose)
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 360, in _column__createIndex
> self.pathname, 0, table.nrows, lastrow=True, update=False )
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2405, in _addRowsToIndex
> [self._read(startLR, self.nrows, 1, colname)],
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 1759, in _read
> self.row._fillCol(result, start, stop, step, field)
> File "tableExtension.pyx", line 1134,
> in tables.tableExtension.Row._fillCol (tables/tableExtension.c:10214)
> File "tableExtension.pyx",
> line 548, in tables.tableExtension.Table._read_records
> (tables/tableExtension.c:5400)
> tables.exceptions.HDF5ExtError: Problems reading records.
> Closing remaining open files: /extra/thumbs/BrianYoung_data/temp.h5... done
> /extra/thumbs/BrianYoung_data/pytables-HsQPfE.tmp... done
> /extra/thumbs/BrianYoung_data/mrq.h5...
> HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 4148012736:
> #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 1733 in H5D_chunk_read():
> unable to read raw data chunk
> major: Low-level I/O
> minor: Read failed
> #003: ../../../src/H5Dchunk.c line 2742 in H5D_chunk_lock():
> data pipeline read failed
> major: Data filters
> minor: Filter operation failed
> #004: ../../../src/H5Z.c line 1017 in H5Z_pipeline():
> filter returned failure during read
> major: Data filters
> minor: Read failed
> #005: blosc/blosc_filter.c line 232 in blosc_filter():
> Blosc decompression error
> major: Data filters
> minor: Callback failed
> Error in atexit._run_exitfuncs:
> Traceback (most recent call last):
> File "/usr/lib/python2.6/atexit.py", line 24, in _run_exitfuncs
> func(*targs, **kargs)
> File "/usr/local/lib/python2.6/dist-packages/tables/file.py",
> line 2337, in close_open_files
> fileh.close()
> File "/usr/local/lib/python2.6/dist-packages/tables/file.py",
> line 2141, in close
> self.root._f_close()
> File "/usr/local/lib/python2.6/dist-packages/tables/group.py",
> line 968, in _f_close
> self._g_closeDescendents()
> File "/usr/local/lib/python2.6/dist-packages/tables/group.py",
> line 918, in _g_closeDescendents
> lambda path: aliveNodes[path])
> File "/usr/local/lib/python2.6/dist-packages/tables/group.py",
> line 899, in closeNodes
> node._f_close()
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2764, in _f_close
> self.flush()
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2711, in flush
> self.reIndexDirty()
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2579, in reIndexDirty
> self._doReIndex(dirty=True)
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2548, in _doReIndex
> indexedrows = indexcol._doReIndex(dirty)
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 3459, in _doReIndex
> kind=kind, optlevel=optlevel, filters=filters))
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 3412, in createIndex
> tmp_dir, _blocksizes, _verbose)
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 360, in _column__createIndex
> self.pathname, 0, table.nrows, lastrow=True, update=False )
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2405, in _addRowsToIndex
> [self._read(startLR, self.nrows, 1, colname)],
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 1759, in _read
> self.row._fillCol(result, start, stop, step, field)
> File "tableExtension.pyx",
> line 1134, in tables.tableExtension.Row._fillCol
> (tables/tableExtension.c:10214)
> File "tableExtension.pyx",
> line 548, in tables.tableExtension.Table._read_records
> (tables/tableExtension.c:5400)
> HDF5ExtError: Problems reading records.
> Error in sys.exitfunc:
> Traceback (most recent call last):
> File "/usr/lib/python2.6/atexit.py", line 24, in _run_exitfuncs
> func(*targs, **kargs)
> File "/usr/local/lib/python2.6/dist-packages/tables/file.py",
> line 2337, in close_open_files
> fileh.close()
> File "/usr/local/lib/python2.6/dist-packages/tables/file.py",
> line 2141, in close
> self.root._f_close()
> File "/usr/local/lib/python2.6/dist-packages/tables/group.py",
> line 968, in _f_close
> self._g_closeDescendents()
> File "/usr/local/lib/python2.6/dist-packages/tables/group.py",
> line 918, in _g_closeDescendents
> lambda path: aliveNodes[path])
> File "/usr/local/lib/python2.6/dist-packages/tables/group.py",
> line 899, in closeNodes
> node._f_close()
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2764, in _f_close
> self.flush()
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2711, in flush
> self.reIndexDirty()
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2579, in reIndexDirty
> self._doReIndex(dirty=True)
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2548, in _doReIndex
> indexedrows = indexcol._doReIndex(dirty)
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 3459, in _doReIndex
> kind=kind, optlevel=optlevel, filters=filters))
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 3412, in createIndex
> tmp_dir, _blocksizes, _verbose)
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 360, in _column__createIndex
> self.pathname, 0, table.nrows, lastrow=True, update=False )
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 2405, in _addRowsToIndex
> [self._read(startLR, self.nrows, 1, colname)],
> File "/usr/local/lib/python2.6/dist-packages/tables/table.py",
> line 1759, in _read
> self.row._fillCol(result, start, stop, step, field)
> File "tableExtension.pyx",
> line 1134, in tables.tableExtension.Row._fillCol
> (tables/tableExtension.c:10214)
> File "tableExtension.pyx",
> line 548, in tables.tableExtension.Table._read_records
> (tables/tableExtension.c:5400)
> tables.exceptions.HDF5ExtError: Problems reading records.
>
>
>
>
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