Re: hdfview 2.11 locks SWMR files

2018-02-19 Thread Jan Kotanski 
Dear HDF5-tools Maintainers,

is it possible to provide the h5clear tool in the hdf5-tools package for 
stretch, (e.g. backports).
Since hdfview brakes SWMR files it would be good to have a script which fix 
them back.

Best regards,
Jan



On 02/16/18 19:16, h...@hdfgroup.org wrote:
> 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
>>

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: hdfview 2.11 locks SWMR files

2018-02-19 Thread Jan Kotanski 
Hello Frederic,

Thanks for your answer. Yes, indeed. Since even hdfview 3.0.0 has problems with 
SWMR files it is better to use other browser, e.g. silx.


cheers,
Jan

On 02/16/18 10:28, PICCA Frederic-Emmanuel wrote:
> Hello Jan,
> 
> just as a work around, you can use the silx package which is available as a 
> stretch-backports in order to explore your hdf5 file.
> 
> cheers
> 
> Frederic
> 

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

hdfview 2.11 locks SWMR files

2018-02-16 Thread Jan Kotanski 
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 
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

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers