Hi Jan,
You can use the h5clear -s utility to remove the flag.
I should have mentioned that!
-Barbara
On Fri, 16 Feb 2018, Kotanski, Jan wrote:
Hi Barbara,
Is there any way to rescue (i.e. unlock) the files broken by hdfview,
e.g. a script which unlocks the file?
If not we have to forbid our user to use the hdfview (or do not use SWMR).
They don't know a priori if the file was created with SWMR or not.
And if they cannot unlock broken files they loose their data.
Best regards,
Jan
----- Original Message -----
From: h...@hdfgroup.org
To: "Jan Kotanski" <jan.kotan...@desy.de>
Cc: debian-science-maintainers@lists.alioth.debian.org
Sent: Friday, 16 February, 2018 16:49:46
Subject: Re: hdfview 2.11 locks SWMR files
Hi Jan,
HDFView 2.11 is based on HDF5-1.8 with 32-bit object identifiers. SWMR is a new
feature in HDF5-1.10 (which has 64-bit object identifiers).
HDFView 3.0 (Beta) supports HDF5-1.10. However, even if you use it and select
"File->Open", it gets a lock on the file and it modifies it. We are working on
resolving this issue for the release version of HDFView 3.0 due out later this
year (after HDF5-1.10.2).
As a workaround, we believe you should be able to use HDFView 3.0 (Beta) to open
the file if you select "File->Open Read-Only".
-Barbara
========================================================
Barbara Jones, The HDF Group Helpdesk, h...@hdfgroup.org
Support Services: https://www.hdfgroup.org/solutions/
========================================================
On Fri, 16 Feb 2018, Jan Kotanski wrote:
Dear HDFView Maintainers,
I've just accounted problems in reading SWMR files with hdfview 2.11 on debian
stretch.
The hdfview 2.11 not only cannot read the SWMR files but it breaks them, i.e.
set a lock inside the files,
and the files are no more readable.
For example I create a file
http://www.desy.de/~jkotan/swmr/swmr.h5
with:
http://www.desy.de/~jkotan/swmr/writer2dattr.py
Normally, I can read it on stretch with:
http://www.desy.de/~jkotan/swmr/reader2d.py
But after I run:
jkotan@stretch-jk:~/sources/lavue/nxstest$ hdfview swmr.h5
I get:
jkotan@stretch-jk:~/sources/lavue/nxstest$ python reader2d.py
Traceback (most recent call last):
File "reader2d.py", line 4, in <module>
f = h5py.File("swmr.h5", 'r', libver='latest', swmr=True)
File "/usr/lib/python2.7/dist-packages/h5py/_hl/files.py", line 271, in
__init__
fid = make_fid(name, mode, userblock_size, fapl, swmr=swmr)
File "/usr/lib/python2.7/dist-packages/h5py/_hl/files.py", line 101, in
make_fid
fid = h5f.open(name, flags, fapl=fapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
(/build/h5py-b1xqNM/h5py-2.7.0/h5py/_objects.c:2842)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
(/build/h5py-b1xqNM/h5py-2.7.0/h5py/_objects.c:2800)
File "h5py/h5f.pyx", line 78, in h5py.h5f.open
(/build/h5py-b1xqNM/h5py-2.7.0/h5py/h5f.c:2127)
IOError: Unable to open file (File is not already open for swmr writing)
Thus, the hdfview breaks the file and the SWMR file is not more readable.
Is it possible to provide backports for the hdfview package with the version
which fix the above problem
(hope the newer version, e.g. 3.0.0 fix this problem)?
Best regards,
Jan
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