Dave,
I reproduced the issue with h5py and entered
HDFFV-10026<https://jira.hdfgroup.org/browse/HDFFV-10026> (for your reference)
into our JIRA database.
h5py reports: Unable to create attribute (Attribute creation index can't be
incremented)
h5debug tool reports suspicious number of attributes for that dataset ;-) See
below. We will need to investigate.
Thank you for your report!
Elena
[volga:~] epourmal% h5debug precip.V1.0.2016.nc 2482
Reading signature at address 2482 (rel)
Object Header...
Dirty: FALSE
Version: 2
Header size (in bytes): 12
Number of links: 1
Attribute creation order tracked: Yes
Attribute creation order indexed: Yes
Attribute storage phase change values: Default
Timestamps: Disabled
Number of messages (allocated): 7 (8)
Number of chunks (allocated): 1 (2)
Chunk 0...
Address: 2482
Size in bytes: 263
Gap: 0
Message 0...
Message ID (sequence number): 0x0001 `dataspace' (0)
Dirty: FALSE
Message flags: <none>
Chunk number: 0
Raw message data (offset, size) in chunk: (14, 52) bytes
Message Information:
Rank: 3
Dim Size: {310, 120, 300}
Dim Max: {UNLIM, 120, 300}
Message 1...
Message ID (sequence number): 0x0005 `fill_new' (0)
Dirty: FALSE
Message flags: <C>
Chunk number: 0
Raw message data (offset, size) in chunk: (72, 10) bytes
Message Information:
Space Allocation Time: Incremental
Fill Time: If Set
Fill Value Defined: User Defined
Size: 4
Data type: <dataset type>
Message 2...
Message ID (sequence number): 0x000b `filter pipeline' (0)
Dirty: FALSE
Message flags: <C>
Chunk number: 0
Raw message data (offset, size) in chunk: (88, 22) bytes
Message Information:
Number of filters: 2/2
Filter at position 0
Filter identification: 0x0002
Filter name: NONE
Flags: 0x0001
Num CD values: 1
CD value 0 4
Filter at position 1
Filter identification: 0x0001
Filter name: NONE
Flags: 0x0001
Num CD values: 1
CD value 0 2
Message 3...
Message ID (sequence number): 0x0008 `layout' (0)
Dirty: FALSE
Message flags: <C>
Chunk number: 0
Raw message data (offset, size) in chunk: (116, 27) bytes
Message Information:
Version: 3
Type: Chunked
Number of dimensions: 4
Size: {1, 120, 300, 4}
Index Type: v1 B-tree
B-tree address: 17919
Message 4...
Message ID (sequence number): 0x0015 `ainfo' (0)
Dirty: FALSE
Message flags: <DS>
Chunk number: 0
Raw message data (offset, size) in chunk: (149, 28) bytes
Message Information:
Number of attributes: 18446744073709551615
Track creation order of attributes: TRUE
Index creation order of attributes: TRUE
Max. creation index value: 65535
'Dense' attribute storage fractal heap address: 4671
'Dense' attribute storage name index v2 B-tree address: 4817
'Dense' attribute storage creation order index v2 B-tree address: 4855
Message 5...
Message ID (sequence number): 0x0003 `datatype' (0)
Dirty: FALSE
Message flags: <C>
Chunk number: 0
Raw message data (offset, size) in chunk: (183, 20) bytes
Message Information:
Type class: floating-point
Size: 4 bytes
Version: 1
Byte order: little endian
Precision: 32 bits
Offset: 0 bits
Low pad type: zero
High pad type: zero
Internal pad type: zero
Normalization: implied
Sign bit location: 31
Exponent location: 23
Exponent bias: 0x0000007f
Exponent size: 8
Mantissa location: 0
Mantissa size: 23
Message 6...
Message ID (sequence number): 0x0000 `null' (0)
Dirty: FALSE
Message flags: <none>
Chunk number: 0
Raw message data (offset, size) in chunk: (209, 62) bytes
Message Information:
<No info for this message>
On Nov 14, 2016, at 4:10 PM, Dave Allured - NOAA Affiliate
<[email protected]<mailto:[email protected]>> wrote:
HDF5 support,
My work group encounters rare failures when attempting to update collections of
HDF5 files. The usual symptom is that a previously valid file becomes
partially broken, such that it becomes impossible to add new attributes to one
particular data variable. The file otherwise reads and writes normally.
Attributes can be added to other variables, and data can still be written to
the suspect variable, including extending the unlimited dimension.
We normally operate on these files with the Netcdf-4 interface to HDF5, but I
think I isolated the failure to pure HDF5 functionality. You can examine one
of these broken files here (9 Mb):
ftp://ftp.cdc.noaa.gov/Public/dallured/hdf5/precip.V1.0.2016.nc
Diagnostics such as h5check, h5debug, h5dump, and h5stat all report this file
as valid. h5edit demonstrates the problem:
> ls -go precip.V1.0.2016.nc<http://precip.v1.0.2016.nc/>
-rw-r--r-- 1 9024497 Nov 9 15:02
precip.V1.0.2016.nc<http://precip.v1.0.2016.nc/>
> h5edit -c 'CREATE /precip/att12 { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE (
> 2 ) DATA { 777.0, 778.0 } } ;'
> precip.V1.0.2016.nc<http://precip.v1.0.2016.nc/>
failed to create attribute (null)
CREATE Attribute command failed
... and the data file is unchanged. It does not matter whether the added
attribute is scalar or array.
We are currently using the HDF5 library version 1.8.16 in combination with
Netcdf to read and write these data sets. The version of h5edit above is
1.3.1. The broken file behaves the same way on both Mac and Linux platforms,
and with several Netcdf-based attribute writers in addition to h5edit.
We are investigating, but we have not yet found a good way to isolate the exact
program or event that creates this broken file condition. We are suspicious
that NFS connected file servers may contribute to the problem, but no strong
evidence yet to back this up.
Today I have these questions:
1. Can someone identify exactly what is wrong with the above sample file?
2. Can h5check or another utility be updated to diagnose this condition?
3. Has anyone else experienced partially broken files with this symptom?
Thank you for any insights.
--Dave A.
NOAA/OAR/ESRL/PSD/CIRES
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