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

Hi all,

This is more information about an HDF5 bug that I alluded to recently.

This bug is farther-reaching than I realized, and may affect people
who are using NCL V5.1.1 *or* NCL 5.2.0-beta to write NetCDF files on
big-endian machines (IBM/AIX,
Sun/Solaris, Mac PPC, for example).

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.

I'm going to do some testing on this to see if I can recreate the bug
with a simple NCL script. I then plan to rebuild V5.1.1 on our big-
endian systems and provide a new binary if necessary.

If you think you are affected by this bug and want a new version of
V5.1.1, 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 14:30:08 2010