Re: hdfview 2.11 locks SWMR files
On 02/19/2018 10:08 AM, Jan Kotanski wrote: > 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. h5clear is not provided by hdf5-tools in testing/unstable either. Also a backport of hdf5 is unlikely. Please file a wishlist bug to enable building of h5client in hdf5. Once that's available you can install hdf5-tools in a Debian unstable chroot and use that to fix your file. Kind Regards, Bas -- 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
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
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
Re: hdfview 2.11 locks SWMR files
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
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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Re: hdfview 2.11 locks SWMR files
Hi Barbara,
Ah ok. Thanks.
Jan Oryginalna wiadomość Od: h...@hdfgroup.org Data: 16.02.2018
19:16 (GMT+01:00) Do: "Kotanski, Jan" <jan.kotan...@desy.de> DW:
debian-science-maintainers@lists.alioth.debian.org Temat: Re: hdfview 2.11
locks SWMR files
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
>> 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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Re: hdfview 2.11 locks SWMR files
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
>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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--
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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
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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hdfview 2.11 locks SWMR files
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
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