Elena, Thank you for reproducing the issue, and for showing me how to display the object structure. h5debug versions 1.8.16 and 1.10.0 are both showing ridiculous values for number of attributes, for known good Netcdf-4 files, even trivial examples. There might be a problem in h5debug, independent from this broken file problem.
--Dave On Mon, Nov 14, 2016 at 10:54 PM, Elena Pourmal <[email protected]> wrote: > 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]> 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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