"Peter P." <peterparker at fastmail.com> writes:> I ran xapian-check on ~/.notmuch/xapian and include its messages below at the > end of this mail. Everyone please forgive me for pasting 1121 there. :) >H'mm. It doesn't look familiar to me, but I will check with xapian experts to see if the failure mode is known/fixable. I'd guess probably not fixable.>> 2) Move the database out of the way, re-run notmuch new, >> and restore your state using "notmuch restore < notmuch-db.txt" > > I'd be fine regenerating the entire database without a backup dump even, > I don't think there is anything in there that can't be regernerated, > no?The main thing that would be lost is tags that are not synched to maildir flags. In the "standard" workflow "inbox" is such a tag.> How could I move the existing database out of the way? I have the > following files in notmuch's directory: > > ~/.notmuch/xapian$ ls -1 > docdata.glass > flintlock > iamglass > position.glass > postlist.glass > termlist.glassjust $ mv ~/.notmuch/xapian ~/.notmuch/xapian.bak (assuming that partition has space)
David Bremner <david at tethera.net> writes:> "Peter P." <peterparker at fastmail.com> writes: > >> I ran xapian-check on ~/.notmuch/xapian and include its messages below at the >> end of this mail. Everyone please forgive me for pasting 1121 there. :) >> > > H'mm. It doesn't look familiar to me, but I will check with xapian > experts to see if the failure mode is known/fixable. I'd guess probably > not fixable.Sorry, I changed my mind about CCing the xapian list, but not the headers. In case someone is curious, here is the xapian-check output under discussion. docdata: blocksize=8K items=161 firstunused=1 revision=1 levels=0 root=0 B-tree checked okay docdata table structure checked OK termlist: blocksize=8K items=267730 firstunused=23171 revision=1 levels=2 root=746 B-tree checked okay Size of wdf out of range in termlist termlist_size != # of entries in termlist doclen != sum(wdf) termlist table errors found: 3 postlist: blocksize=8K items=2437844 firstunused=22023 revision=1 levels=2 root=567 B-tree checked okay document id 63805: length 325 doesn't match 0 in the termlist table document id 89028: length 404416 doesn't match 359353 in the termlist table collfreq 29 != sum wdf 25 termfreq 5 != # of entries 1 docid 3536 > last docid 3534 docid 3538 > last docid 3534 collfreq 15055 != sum wdf 15059 First did in this chunk is <= last in prev chunk termfreq 8544 != # of entries 8555 collfreq 331831 != sum wdf 334753 termfreq 11793 != # of entries 11800 collfreq 24971 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> last docid 261935 docid 2991140 > last docid 261935 docid 2991256 > last docid 261935 docid 2991371 > last docid 261935 docid 2991483 > last docid 261935 docid 2991588 > last docid 261935 docid 2991699 > last docid 261935 docid 2991701 > last docid 261935 docid 3261338 > last docid 261935 termfreq 1 != # of entries 423 collfreq 1 != sum wdf 5430479 lastdid 261935 != last did 3261338 collfreq 24746 != sum wdf 24750 collfreq 65388 != sum wdf 65392 termfreq 66671 != # of entries 66685 collfreq 1936000 != sum wdf 1937849 termfreq 486 != # of entries 592 collfreq 8681 != sum wdf 27243 Failed to unpack wdf No last chunk for term 'Zreo' collfreq 179379 != sum wdf 179383 termfreq 392 != # of entries 395 collfreq 21293 != sum wdf 21301 collfreq 55 != sum wdf 59 collfreq 261223 != sum wdf 261227 collfreq 1 != sum wdf 5 collfreq 1071706 != sum wdf 1071710 docid 2080 > last docid 2076 collfreq 51416 != sum wdf 51420 termfreq 2055 != # of entries 2061 collfreq 53739 != sum wdf 53759 collfreq 1080 != sum wdf 1084 collfreq 2 != sum wdf 6 termfreq 6860 != # of entries 6876 collfreq 51054 != sum wdf 51657 termfreq 1093 != # of entries 1116 collfreq 35366 != sum wdf 35408 collfreq 9504 != sum wdf 9508 collfreq 19438 != sum wdf 19442 collfreq 70 != sum wdf 74 collfreq 10148080 != sum wdf 10148084 collfreq 250 != sum wdf 254 collfreq 898103 != sum wdf 898107 termfreq 299 != # of entries 300 collfreq 4276 != sum wdf 4279 collfreq 70165 != sum wdf 70169 termfreq 5 != # of entries 423 collfreq 11 != sum wdf 3529494 collfreq 90939 != sum wdf 90943 postlist table errors found: 962 position: blocksize=8K items=19047625 firstunused=46353 revision=1 levels=2 root=520 B-tree checked okay Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms position table: Junk after position data Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms position table: Junk after position data Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms Position list entry for document 63805 which doesn't exist or has no terms position table errors found: 129 spelling: Lazily created, and not yet used. synonym: Lazily created, and not yet used.
On Mon, Jul 03, 2023 at 02:26:03PM +0200, David Bremner wrote:> "Peter P." <peterparker at fastmail.com> writes: > > > I ran xapian-check on ~/.notmuch/xapian and include its messages > > below at the end of this mail. Everyone please forgive me for > > pasting 1121 there. :) > > H'mm. It doesn't look familiar to me, but I will check with xapian > experts to see if the failure mode is known/fixable. I'd guess probably > not fixable.Currently we don't have a database fixing tool for glass databases (the "fix" mode in xapian-check can recreate base files for the older chert database format, but glass doesn't have these base files which eradicated the failure mode of them sometimes getting truncated to zero size on power failure or OS crash). Some of the problems reported have an obvious fix, but we don't have existing code to fix them, and some look like they are probably due to data being overwritten so fixing everything to be consistent probably wouldn't actually give a database that entirely matches your email anyway. Was this database originally created by Xapian < 1.4.22? It looks like it could be the result of the bug fixed in 1.4.22 with handling commit() failure on disk full.> >> 2) Move the database out of the way, re-run notmuch new, > >> and restore your state using "notmuch restore < notmuch-db.txt" > > > > I'd be fine regenerating the entire database without a backup dump even, > > I don't think there is anything in there that can't be regernerated, > > no? > > The main thing that would be lost is tags that are not synched to > maildir flags. In the "standard" workflow "inbox" is such a tag.If there's tag data in the database which isn't backed up or synced to maildir flags, you may be able to rescue it using: https://git.xapian.org/?p=xapian;a=blob;f=README.notmuch;hb=refs/heads/notmuch-tag-rescue-hack This creates a file with the tag data in the format `notmuch restore` expects. I'd expect this would work for your database as the termlist table is mostly OK. Cheers, Olly