Fwd: HDF Bulletin: HDF5 1.8 Corruption Problem 2/26/10

This is more information about an HDF5 bug that I alluded to
recently. Even if you are not a user of PyNIO, if you have used HDF5
V1.8.0 through V1.8.4 you should read the bulletin below.

It may affect people who are using a version of PyNIO newer than
1.3.0b1 to write NetCDF files on big-endian machines (IBM/AIX, Sun/
Solaris, Mac PPC, for example).

I believe of the recent 1.3.0b4 binaries I mentioned yesterday, only
the PPC one (PyNIO-1.3.0b4.macos-10.5-ppc-py255-gcc401.tar.gz) will
be affected by this. I've removed this binary from the website.

I don't have a test script yet that demonstrates the problem. I hope
to create one soon.

Please read the bulletin below from the HDF5 group about when this
bug shows up, and how to determine if you might have written a NetCDF
file affected by this.

If you think you are affected by this bug and want a new version of
PyNIO, send me an email offline.

--Mary

>
>
> Begin forwarded message:
>
>> From: Barbara Jones <bljones@hdfgroup.org>
>> Date: February 26, 2010 1:06:13 PM MST
>> To: news@hdfgroup.org
>> Subject: [News] HDF Bulletin: HDF5 1.8 Corruption Problem 2/26/10
>> Reply-To: Moderated mailing list to disseminate HDF news and
>> information <news@hdfgroup.org>
>>
>>
>> ( http://www.hdfgroup.org/newsletters/bulletin20100226.html )
>>
>> ===================================================
>> HDF Bulletin: HDF5 1.8 Corruption Problem 02/26/10
>> ===================================================
>>
>> A corruption problem was found in the HDF5 1.8 release, which affects
>> versions 1.8.0 through 1.8.4. The problem has been fixed in
>> HDF5 1.8.4 Patch 1.
>>
>> The HDF5 1.8.4 Patch 1 release can be obtained from here:
>>
>> http://www.hdfgroup.org/HDF5/release/obtain5.html
>>
>>
>> What Causes The Problem
>> -----------------------
>>
>> Files that have this corruption problem meet *all* of the following
>> circumstances:
>>
>> - The version of HDF5 was before the HDF5 1.8.4 Patch 1 release
>> (which
>> includes the 1.8.4 release).
>>
>> - The file was created on a big-endian platform (SPARC/Solaris,
>> POWER/AIX, etc).
>>
>> - NetCDF-4 was used to create the file, OR the H5Pset_libver_bounds
>> (fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) call was made, OR shared
>> object header messages were enabled with
>> H5Pset_shared_mesg_nindexes()
>> when creating the file.
>>
>> - More than 8 attributes were added to an object in the file (in the
>> case of using netCDF-4 or calling H5Pset_libver_bounds), OR if
>> messages
>> of the type specified to be shared were stored in the file (in the
>> case
>> of calling H5Pset_shared_mesg_nindexes).
>>
>> If your data matches these criteria, then you may have generated
>> files
>> that have incorrectly encoded IDs for attributes and shared object
>> header messages.
>>
>>
>> How To Determine If Your Files Are Corrupted
>> --------------------------------------------
>>
>> There is no foolproof way to detect a file with these IDs incorrectly
>> encoded, but if the h5dump tool reports an error message similar
>> to the
>> following when displaying information about the file, it is likely
>> that
>> you have a file with this problem:
>>
>> h5dump error: error getting attribute information
>>
>> For files created with netCDF-4, this message will generally
>> display when
>> dumping information about the root group. If your application is
>> generating
>> an error stack similar to this, it is also likely that the file
>> has this
>> problem:
>> .
>> .
>> .
>> #008: ../../hdf5_v1.8/src/H5B2int.c line 1951 in
>> H5B2_iterate_node():
>> iterator function failed major: B-Tree node minor: Unable to
>> list node
>> #009: ../../hdf5_v1.8/src/H5Adense.c line 1076 in
>> H5A_dense_iterate_bt2_cb(): heap op callback failed major:
>> Attribute minor:
>> Can't operate on object
>> #010: ../../hdf5_v1.8/src/H5HF.c line 680 in H5HF_op():
>> can't operate on
>> object from fractal heap major: Heap minor: Can't operate on
>> object
>> #011: ../../hdf5_v1.8/src/H5HFman.c line 462 in H5HF_man_op
>> (): unable to
>> operate on heap object major: Heap minor: Can't operate on object
>> #012: ../../hdf5_v1.8/src/H5HFman.c line 276 in
>> H5HF_man_op_real():
>> fractal heap object offset too large major: Heap minor: Out of
>> range
>>
>>
>> Fixing The Problem
>> ------------------
>>
>> A tool is being developed that can be run on a corrupted file to
>> correct it.
>> Please contact the HDF Helpdesk if you are unable to wait for this
>> tool.
>>
>>
>>
>>
>> _______________________________________________
>> News is for news regarding HDF.
>> News@hdfgroup.org
>> http://mail.hdfgroup.org/mailman/listinfo/news_hdfgroup.org
>
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Received on Fri Feb 26 14:43:05 2010