Trying to delete tuples containing invalid timestamps with
DELETE FROM comments WHERE date > '1 Jan 9999' OR date < '1 Jan 2000' OR date_found > '1 Jan 9999' OR date_found < '1 Jan 2000';
ERROR: attempted to delete invisible tuple
There is a mailing list from 2009 discussing the exact same error message, where OP had it fixed, but I find no explanation of how he did it or what might have led to this error.
I am helpless due to lack of hits on Google and to my limited knowledge of PostgreSQL.
What led to corruption
I've had a PostgreSQL 9.5.5 server (~4TB data, all the default settings, except for upped memory limits) running on Debian 8, when OS kernel panicked – probably while rebuilding /dev/md1 where swap was located. Prior to that, PostgreSQL ate up almost all of the disk space with a 400GB log file. OS never booted again, disk checks were OK, so I have booted from a LiveCD and backed up each block device to images, just in case. I have successfully rebuilt / directory from /dev/md2, fsck showed a clean filesystem, and I have backed up the PGDATA folder on to an external HDD.
What I did to attempt recovery
After I've formatted md devices and reinstalled the OS along with a fresh postgresql-9.5, I have stopped the PostgreSQL server, moved and chowned the PGDATA folder to postgres user, and started the server – everything seemed fine, there were no errors.
As soon as I've started
pg_dumpall, it died with
Error message from server: ERROR: timestamp out of range
I have naturally tried to delete the offending tuples, only to end up with the same
invisible tuple error over and over again.
Things I tried
First off, DELETE queries failed because of damaged pages, so I've set following settings:
zero_damaged_pages = on ignore_system_indexes = on enable_indexscan = off enable_bitmapscan = off enable_indexonlyscan = off
Now I've noticed that when I run the same queries again, the server zeros out same pages over and over again, not sure what it means:
invalid page in block 92800 of relation base/16385/16443; zeroing out page
I've tried following in an undefined order:
pg_resetxlog -D $PGDATAdid its job without any errors or messages
- Deleted all indexes including pkey constraints
CREATE TABLE aaa AS (SELECT * FROM comments);leads to
heap_deform_tuple (tuple=tuple@entry=0x7f0d1be29b08, tupleDesc=tupleDesc@entry=0x7f0d1a35abe0, values=values@entry=0x7ffd57a5beb0, isnull=isnull@entry=0x7ffd57a65af0 "\001\001")It is reproducible and leaves a ~9GB core dump.
SELECT COUNT(*) from comments;allowed
VACUUM comments;to complete, same trick doesn't work on other tables.
SELECT COUNT(*) from photos;and
VACUUM photos;now dies with
ERROR: MultiXactId 302740528 has not been created yet -- apparent wraparound– this one haunts every table, where other errors don't pop up anymore.
DB was getting hammered by lots of (possibly duplicate) writes withDB was doing a
VACUUMwhen kernel panic occured, I believe it is what's left of it that is causing trouble with
- Data was collected with crawler throughout a span of 2+ years, and I am totally okay with losing some of it
- Now I do backups
- There were no relational constraints between tables nor any triggers
Here is the pg_controldata output as of now:
pg_control version number: 942 Catalog version number: 201510051 Database system identifier: 6330224129664261958 Database cluster state: in production pg_control last modified: Thu 08 Dec 2016 01:06:22 AM EET Latest checkpoint location: 1562/8F9F8A8 Prior checkpoint location: 1562/8F7F460 Latest checkpoint's REDO location: 1562/8F9F8A8 Latest checkpoint's REDO WAL file: 000000010000156200000008 Latest checkpoint's TimeLineID: 1 Latest checkpoint's PrevTimeLineID: 1 Latest checkpoint's full_page_writes: on Latest checkpoint's NextXID: 0/40781255 Latest checkpoint's NextOID: 67798231 Latest checkpoint's NextMultiXactId: 1 Latest checkpoint's NextMultiOffset: 0 Latest checkpoint's oldestXID: 615 Latest checkpoint's oldestXID's DB: 1 Latest checkpoint's oldestActiveXID: 0 Latest checkpoint's oldestMultiXid: 1 Latest checkpoint's oldestMulti's DB: 1 Latest checkpoint's oldestCommitTsXid:0 Latest checkpoint's newestCommitTsXid:0 Time of latest checkpoint: Thu 08 Dec 2016 01:06:22 AM EET Fake LSN counter for unlogged rels: 0/1 Minimum recovery ending location: 0/0 Min recovery ending loc's timeline: 0 Backup start location: 0/0 Backup end location: 0/0 End-of-backup record required: no wal_level setting: minimal wal_log_hints setting: off max_connections setting: 100 max_worker_processes setting: 8 max_prepared_xacts setting: 0 max_locks_per_xact setting: 64 track_commit_timestamp setting: off Maximum data alignment: 8 Database block size: 8192 Blocks per segment of large relation: 131072 WAL block size: 8192 Bytes per WAL segment: 16777216 Maximum length of identifiers: 64 Maximum columns in an index: 32 Maximum size of a TOAST chunk: 1996 Size of a large-object chunk: 2048 Date/time type storage: 64-bit integers Float4 argument passing: by value Float8 argument passing: by value Data page checksum version: 0
- (9 december 2016) While reading about nonexistent MultiXactIds, I have remembered that my database was not under operational load at the moment of the crash, but it was processing a manual
VACUUMrequest. I have taken the webservers and crawlers offline after I realized that there was only 3% space left on disks. I should have checked
/var/logfor large files, but I have mistakenly blamed PostgreSQL and tried
VACUUM FULL, only to find it aborted due to little space left on device. So I've started ordinary VACUUM and left it at that.
- (14 december 2016) Downloaded a 9.5 branch of PostgreSQL sources from Github, commented out blocks in heapam.c and multixact.c and compiled it with hopes that it won't throw these errors. But the server wouldn't start, because it had to be configured with the same flags used in one I had from APT. There were around 47 flags, each requiring a dependency with non-obvious name, so I gave up on that idea.
(16 december 2016) I have found a way to get rid of tuples with invalid timestamps by zeroing out relevant pages. I first set following options in
\set FETCH_COUNT 1 \pset pager off
I then do
SELECT ctid, * FROM comments;. That way it spits out the
ctidof a bad tuple before the query dies. I then proceed to fill that page with zeros:
dd if=/dev/zero of=/var/lib/postgresql/9.5/main/base/16385/16443 bs=8K seek=92803 count=1 conv=notruncBut each page, zeroed out this way, breaks the previous page, resulting in page
16442now having a tuple with invalid timestamp. Not sure what I am doing wrong here.
(16 december 2016) Attempting
pg_dump -Fc --table photos vw > photos.bakresults in segmentation fault after 1.3GB (out of probably 800GB) written. Here is the server log:
2016-12-16 18:48:05 EET [19337-2] LOG: server process (PID 29088) was terminated by signal 11: Segmentation fault 2016-12-16 18:48:05 EET [19337-3] DETAIL: Failed process was running: COPY public.photos (id, owner_id, width, height, text, date, link, thumb, album_id, time_found, user_id, lat, long) TO stdout; 2016-12-16 18:48:05 EET [19337-4] LOG: terminating any other active server processes 2016-12-16 18:48:05 EET [19342-2] WARNING: terminating connection because of crash of another server process 2016-12-16 18:48:05 EET [19342-3] DETAIL: The postmaster has commanded this server process to roll back the current transaction and exit, because another server process exited abnormally and possibly corrupted shared memory. 2016-12-16 18:48:05 EET [19342-4] HINT: In a moment you should be able to reconnect to the database and repeat your command. 2016-12-16 18:48:05 EET [19337-5] LOG: all server processes terminated; reinitializing 2016-12-16 18:48:06 EET [29135-1] LOG: database system was interrupted; last known up at 2016-12-14 22:58:59 EET 2016-12-16 18:48:07 EET [29135-2] LOG: database system was not properly shut down; automatic recovery in progress 2016-12-16 18:48:07 EET [29135-3] LOG: invalid record length at 1562/A302F878 2016-12-16 18:48:07 EET [29135-4] LOG: redo is not required 2016-12-16 18:48:07 EET [29135-5] LOG: MultiXact member wraparound protections are now enabled 2016-12-16 18:48:07 EET [19337-6] LOG: database system is ready to accept connections 2016-12-16 18:48:07 EET [29139-1] LOG: autovacuum launcher started
Here is a short stacktrace:
#0 pglz_decompress (source=source@entry=0x7fbfb6b99b13 "32;00/0ag4d/Jnz\027QI\003Jh3A.jpg", slen=<optimized out>, dest=dest@entry=0x7fbf74a0b044 "", rawsize=926905132) #1 0x00007fc1bf120c12 in toast_decompress_datum (attr=0x7fbfb6b99b0b) #2 0x00007fc1bf423c83 in text_to_cstring (t=0x7fbfb6b99b0b)
I have no idea how to work around that.
(29 december 2016) I have written a utility which does
SELECT * FROM tablename LIMIT 10000 OFFSET 0, incrementing the offset and narrowing down around dead tuples, and it has successfully duplicated data on my local machine except the tuples (I hope the only ones) I have manually corrupted. It is also supposed to wait if the server restarts. However I did not have enough space left on my RAID, and I have created a tablespace
slowdiskon an 8TB HDD. When I attempt to
CREATE DATABASE vwslow WITH TABLESPACE slowdisk, it won't do so with errors:
2016-12-29 02:34:13 EET [29983-1] LOG: request to flush past end of generated WAL; request 950412DE/114D59, currpos 1562/A3030C70 2016-12-29 02:34:13 EET [29983-2] CONTEXT: writing block 58368001 of relation base/16385/16473 2016-12-29 02:34:13 EET [29983-3] ERROR: xlog flush request 950412DE/114D59 is not satisfied --- flushed only to 1562/A3030C70 2016-12-29 02:34:13 EET [29983-4] CONTEXT: writing block 58368001 of relation base/16385/16473 2016-12-29 02:34:13 EET [30005-44212] postgres@vw ERROR: checkpoint request failed 2016-12-29 02:34:13 EET [30005-44213] postgres@vw HINT: Consult recent messages in the server log for details. 2016-12-29 02:34:13 EET [30005-44214] postgres@vw STATEMENT: CREATE DATABASE vwslow WITH TABLESPACE slowdisk;
CHECKPOINTresulted in the same errors.
A server restart has made the checkpoint error go away and let me run my tool. Will answer my question and publish the code if it works.