Yes!  I ran into this on 5.0.0 due to my odd use of symlinks (bug #321, 
fixed!), the workaround is:

Open up /usr/lib/s3ql/s3ql/database.py.  Go to around line 540, and comment 
out these two lines (shown here commented out):
#            if params.db_md5 != digest:
 #               raise DatabaseChecksumError(db_file, params.db_md5, digest)

This simply supresses the error and causes it to continue, essentially your 
only good copy of the database at that point is in your cache.  So be 
careful! But in my case it definitely let me go ahead with the local 
metadata, both for running fsck and for mounting the filesystem.  

Then to restoring your filesystem to full functionality!  (Assuming your 
internet provider and storage provider problems have cleared up)....   

s3ql now sends the database incrementally, sends 64KB chunks that have 
changed rather than the entire database.  By default this upload is done 
when you unmount the filesystem or every 6 hours when it's mounted.  It's 
slick, instead of uploading a potentially 100MB-1GB+ database, it uploads 
like a couple hundred KB that have actually changed. If fsck finds any 
errors, it will do a full database upload instead which does not rely on 
any previous snapshots.   And I note fsck checks the last 5 available 
snapshots, so once you get your "bad" snapshots 6 back from the current 
one, you can undo that patch.  (It does delete the old snapshots after like 

So, do that patch, run fsck, let it correct some error and it'll do a full 
database upload.  Then you can either mount it and use it for at least 30 
hours (since it does an automatic metadata backup every 6 hours, it'll have 
made 5 good snapshots).  Or do 5 cycles of mount the file system, make some 
change to it (like add or remove 1 file,), unmount it, so the last 5 
snapshots are good.  Then remove that patch.    There is code in s3ql to 
remove those 64KB blocks when they're no longer needed for any recent 
snapshots.

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