Greetings,
From time to time I have a problem with reading hdf5 file created with 1.8.2 api. After several updates it occasionally becomes unusable.
When I try h5ls -v <file name> it gives me: unable to open file. Strangely enough, but when I try to open it in HDFViewer it opens and I can view the content.
Is there a way to restore the file? It contains about 500M of data and it's rather painful to recreate it.
In general, can you give any instructions on how to restore a corrupted hdf5 file?
Thanks,
Slava Mazur
···
From: Slava Mazur
Sent: Tuesday, February 12, 2013 2:22 PM
To: 'help@hdfgroup.org'
Subject: h5ls: unable to open file
try h5repack with "-L", use latest version of file format.
did you try h5dump -H to see if you can open the file?
Thanks
--pc
···
On 2/12/2013 2:49 PM, Slava Mazur wrote:
*From:*Slava Mazur
*Sent:* Tuesday, February 12, 2013 2:22 PM
*To:* 'help@hdfgroup.org'
*Subject:* h5ls: unable to open file
Greetings,
From time to time I have a problem with reading hdf5 file created with 1.8.2 api. After several updates it occasionally becomes unusable.
When I try h5ls -v <file name> it gives me: unable to open file. Strangely enough, but when I try to open it in HDFViewer it opens and I can view the content.
Is there a way to restore the file? It contains about 500M of data and it's rather painful to recreate it.
In general, can you give any instructions on how to restore a corrupted hdf5 file?
Thanks,
Slava Mazur
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Hello Barbara and Peter,
Thank you for a quick response.
I tried what Peter suggested. Specifically:
h5repack -L -f NONE 20120921.h5 /data/tmp/20120921.h5
h5repack error: <20120921.h5>: unable to open file
h5dump -H 20120921.h5
h5dump error: unable to open file "20120921.h5"
Then I tried to open it again in HDFView 2.9 to confirm it opens fine.
The HDF version I'm using is 1.8.10-patch1.
Thanks again,
Slava Mazur
···
-----Original Message-----
From: help@hdfgroup.org [mailto:help@hdfgroup.org]
Sent: Wednesday, February 13, 2013 2:42 PM
To: Slava Mazur
Subject: Re: h5ls: unable to open file
Hello Slava,
From time to time I have a problem with reading hdf5 file created
with 1.8.2
api. After several updates it occasionally becomes unusable.
When I try h5ls -v <file name> it gives me: unable to open file.
Strangely
enough, but when I try to open it in HDFViewer it opens and I can view the content.
Is there a way to restore the file? It contains about 500M of data and
it's
rather painful to recreate it.
In general, can you give any instructions on how to restore a
corrupted hdf5
file?
I saw that Peter responded to your same question on the HDF-Forum.
We do not provide a way to restore a corrupted HDF5 file. You might be able to salvage parts of a file. What you can do is try avoiding corruption, by flushing data from memory to disk frequently. (See H5Fflush)
However, it is not clear that your file is corrupted if HDFView can view it.
Did you try Peter's suggestions?
Early versions of HDF5-1.8 had some issues. Could you use the current release?
-Barbara
====================
Barbara Jones
The HDF Helpdesk
Slava,
Could you please try
h5ls -V
to see which version of the HDF5 library is used? (I think h5ls is linked with the old version of the library that cannot read the file).
Elena
···
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Feb 13, 2013, at 1:59 PM, Slava Mazur wrote:
Hello Barbara and Peter,
Thank you for a quick response.
I tried what Peter suggested. Specifically:
h5repack -L -f NONE 20120921.h5 /data/tmp/20120921.h5
h5repack error: <20120921.h5>: unable to open file
h5dump -H 20120921.h5
h5dump error: unable to open file "20120921.h5"
Then I tried to open it again in HDFView 2.9 to confirm it opens fine.
The HDF version I'm using is 1.8.10-patch1.
Thanks again,
Slava Mazur
-----Original Message-----
From: help@hdfgroup.org [mailto:help@hdfgroup.org]
Sent: Wednesday, February 13, 2013 2:42 PM
To: Slava Mazur
Subject: Re: h5ls: unable to open file
Hello Slava,
From time to time I have a problem with reading hdf5 file created
with 1.8.2
api. After several updates it occasionally becomes unusable.
When I try h5ls -v <file name> it gives me: unable to open file.
Strangely
enough, but when I try to open it in HDFViewer it opens and I can view the content.
Is there a way to restore the file? It contains about 500M of data and
it's
rather painful to recreate it.
In general, can you give any instructions on how to restore a
corrupted hdf5
file?
I saw that Peter responded to your same question on the HDF-Forum.
We do not provide a way to restore a corrupted HDF5 file. You might be able to salvage parts of a file. What you can do is try avoiding corruption, by flushing data from memory to disk frequently. (See H5Fflush)
However, it is not clear that your file is corrupted if HDFView can view it.
Did you try Peter's suggestions?
Early versions of HDF5-1.8 had some issues. Could you use the current release?
-Barbara
====================
Barbara Jones
The HDF Helpdesk
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
