The snapshot h5diff fixes the slowness I reported.
Thanks,
--Greg
On 10/29/12 10:29 AM, Barbara Jones wrote:
Hello Greg and Xavier,
We created a development snapshot with a fix for the h5diff
performance issue that you reported (described by Elena below).
You can get to the snapshot from either The HDF Group Downloads
page,
http://www.hdfgroup.org/downloads/
or directly from here:
http://www.hdfgroup.uiuc.edu/ftp/pub/outgoing/hdf5/snapshots/v18/
Scroll down and you will find the "hdf5-1.8.11-snap0" snapshot files
containing the fix:
- hdf5-1.8.11-snap0-RELEASE.txt
- hdf5-1.8.11-snap0.tar.bz2
- hdf5-1.8.11-snap0.tar.gz
- hdf5-1.8.11-snap0.tar.md5
- hdf5-1.8.11-snap0_docs.tar
Please let us know whether or not this resolves the issue for
you.
Thanks!
-Barbara
[email protected]
On Thu, 18 Oct 2012, Elena Pourmal wrote:
Hello,
I would like to give a status update on the h5diff slowness issue.
Background: 1.8.6 and earlier versions of h5diff had a bug in the
attributes comparison. In some cases attributes were not compared at all
;-) When the bug was removed in 1.8.7, a performance issue in HDF5 was
exposed. The performance deficiencies in the h5diff code were also not
ruled out.
We are actively working on the problem, but unfortunately will not be
able to provide a fix in the upcoming 1.8.10 release. We will inform the
FORUM as soon as the root(s) of the problem and the possible solutions
are identified.
Thank you!
Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Oct 16, 2012, at 3:44 PM, Jonathan Kim wrote:
Hi Gregory,
We've identified the issue and put it in the bug tracking system.
We will look into the issue.
If it's possible to send us your HDF5 file, we'd appreciate.
Thanks for your input!
Jonathan
On 10/16/2012 12:50 PM, Gregory Sjaardema wrote:
We are also seeing this slowdown. I did a little looking and some
of the issue seems to be in H5O_attr_find_opened_attr. There is a
call to "num_open_attr = H5F_get_obj_count(loc->file, H5F_OBJ_ATTR
| H5F_OBJ_LOCAL, FALSE);"
On hdf5 >= 1.8.7, the num_open_attr count keeps increasing on each
call. For one particular problem I am running, it returns 21153 at
the end of execution. However, in hdf5 < 1.8.7, the num_open_attr
is always 0.
Hope this helps track down the issue; h5diff is unusable for us at
the current time.
--Greg
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Hdf-forum is for HDF software users discussion.
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_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
