I have corrupt h5 files can I do anything to recover the data?

HDF5 Library
1

During a hardware move to a new location h5 files have become corrupt.

version 1 B-tree:Could not find B-tree signature at addr 3453606706
End of Error messages
Error
version 1 B-tree:Could not find B-tree signature at addr 36648953331
End of Error messages
Error
version 1 B-tree:Could not find B-tree signature at addr 65846640331
End of Error messages
Error
version 1 B-tree:Could not find B-tree signature at addr 66017886521
End of Error messages
Error
version 1 B-tree:Could not find B-tree signature at addr 125374209973
End of Error messages
Error
version 1 B-tree:Could not find B-tree signature at addr 3453503481
End of Error messages
Error
version 1 B-tree:Could not find B-tree signature at addr 36648822505
End of Error messages
Error
Version 1 B-tree:left & right keys are out of order at addr 62805794737
End of Error messages
Error
version 1 B-tree:Could not find B-tree signature at addr 65846521150
End of Error messages
Error
version 1 B-tree:Could not find B-tree signature at addr 125374100540
End of Error messages
Error
version 1 B-tree:Could not find B-tree signature at addr 51419310617
End of Error messages
Error
Version 1 B-tree:left & right keys are out of order at addr 67852021227
End of Error messages
Error
Version 1 B-tree:left & right keys are out of order at addr 108309900491
End of Error messages
Error
Version 1 B-tree:left & right keys are out of order at addr 108379266210
End of Error messages
Error
Version 1 B-tree:left & right keys are out of order at addr 131296087919
End of Error messages
Error
Version 1 B-tree:left & right keys are out of order at addr 151248051098
End of Error messages

Not all the error messages but received so far.

2

[quote=“jbaldwin, post:1, topic:13459”]
Hello, it sounded like the file had corrupted B-tree. You might have to use the tool h5debug to look and see if there is anything recoverable, but we don’t have any tool for recovering corrupted files at this time.

3

Thanks for this much appreciated. If I use the h5debug tool (I’ve got something called h5dump) if there’s anything recoverable how do I recover it?

4

If you have h5dump, you should also have the command line tool h5debug available as well. Unlike h5dump, h5debug only displays information about the file that might give you some idea whether the file is salvageable.

At this time, we don’t have a tool to recover the data from a corrupted file. If salvageable, it will be a manual process. If the data is valuable to you, then you might be interested in our paid Data Conversion Service, which can include rescuing corrupted files. However, that will be a manual and personalized service as there is no available generic solution.

5

Okay thanks. I’ve used h5dump and seen that there are maybe 15 errors in the file itself. Is there anything I can read anywhere on how to go about doing a manual recovery?

6

Hi @jbaldwin

Our executive director went over this concept in this Call the Doctor video, you might find your answers there. This link will jump you to the right timestamp:

It seems like it’s not particularly easy or fun to handle. We have some ideas for how we’d create a tool to do this, but funding the work is an issue.

(You can also hop on a Call the Doctor session for additional free discussion. More info on when and how is here: https://www.hdfgroup.org/weekly-hdf-clinic/)