Thread: Detecting DB corruption
I'm looking for ways to detect DB index and any other type of corruption in DB. It looks like there is no tool to verify if Postgres DB is corrupted or not.
I would like to detect some of the following DB corruptions:
- corruption in DB indexes
- detect duplicate primary keys in a table (noticed in couple of instances where duplciates keys were found becuase of corrupted indexes)
- any page or block is corrupted
Planning to do the following on every restart of Postgres DB. Can someone suggest if this is the write approach? Or, suggest better and faster approach to detect the corruption.
- reindex database <dbname>
- for each table run : select count(*) from <table name> //to ensure no rows are corrupted
- for each table run update: begin; update <table name> set <col_name> = "value" ; rollback; //to update whole table and then rollback the transactions
- run "vacuum analyze"
If indexes are corrupted then it will be re-built. For other types of corruption, pg_dump will be restored from last known good backup.
How do I write a generic SQL script to detect the corruption, remove duplicate rows etc.?
Using Postgres 8.3.18 on Linux. Database has around 100 tables with average rows in a table are 500.
Thanks in advance for your help.
On 11/01/2012 08:01 AM, Raj Gandhi wrote: > > I'm looking for ways to detect DB index and any other type of corruption > in DB. It looks like there is no tool to verify if Postgres DB is > corrupted or not. There is no database verifier tool. One would be quite nice to have for testing and development purposes, though I question whether corruption should be a concern in production. If you face the realistic risk of database corruption, you need to urgently address the problems in your setup that make that possible. I wrote a bit about that a while ago: http://blog.ringerc.id.au/2012/10/avoiding-postgresql-database-corruption.html Seriously, if you're facing DB corruption then something is already horribly wrong with your setup. PostgreSQL isn't like MySQL with MyISAM; corruption is not routine and part of life. It's a sign of a very bad problem, one you should diagnose and fix not paper over. Do you expect ext3 file system corruption routinely? No? PostgreSQL should be the same. > I would like to detect some of the following DB corruptions: > - corruption in DB indexes A query that scans the whole index (say, to sort on it) should generally find damaged pages in indexes. "Corruption" can cover many different things, though, and some damage would not be detected by simply using the index. > - detect duplicate primary keys in a table (noticed in couple of > instances where duplciates keys were found becuase of corrupted indexes) A REINDEX will find that. Alternately, you might be able to formulate queries that ignore the indexes and do duplicate searches by grouping by the primary key with `enable_indexscan = off`, `enable_indexonlyscan = off`, etc etc. > - any page or block is corrupted I'd want to use the `pageinspect' extension to scan the table manually. Create some artificially damaged blocks in a just-for-testing table and make sure that doing so actually finds them. > Using Postgres 8.3.18 on Linux. Database has around 100 tables with > average rows in a table are 500. Well, you're on an old version, but not one with any known serious issues AFAIK. -- Craig Ringer
On Oct 31, 2012, at 8:50 PM, Craig Ringer wrote: > Seriously, if you're facing DB corruption then something is already > horribly wrong with your setup. True, but. In a past life, complaints from the db (it was a db that stored a checksum with every block) were the very firstsymptom when something went horribly wrong with the hardware. (Partial short between wires of an internal SCSI cable;eventually we determined that about every 1MB, 1 bit would get flipped between the controller & disk.) So, if there were an official db verifier tool for PG, I for one would have it run periodically. -- Scott Ribe scott_ribe@elevated-dev.com http://www.elevated-dev.com/ (303) 722-0567 voice
On 11/01/2012 01:10 PM, Scott Ribe wrote: > On Oct 31, 2012, at 8:50 PM, Craig Ringer wrote: > >> Seriously, if you're facing DB corruption then something is already >> horribly wrong with your setup. > True, but. In a past life, complaints from the db (it was a db that stored a checksum with every block) were the very firstsymptom when something went horribly wrong with the hardware. (Partial short between wires of an internal SCSI cable;eventually we determined that about every 1MB, 1 bit would get flipped between the controller & disk.) > > So, if there were an official db verifier tool for PG, I for one would have it run periodically. If there were a way to reliably detect corruption, so would I. As things stand there are no block checksums, so if a bit gets flipped in some random `text` field you're never going to know, corruption-checker or no. Some forms of random corruption - like bad blocks on disks causing I/O errors, zeroed blocks, truncated files, etc - will become apparent with general checking, but others won't be detectable unless you know what the expected vs actual data is. If page checksumming or any other reliable method of detecting possible incipient corruption were available I'd quite likely want to use it for much the same reason you outlined. For that matter, if there were a general "sanity check my tables and indexes" tool I'd probably use that too. However, no such tool exists - and in a good setup, none should be needed. I'd want to use one anyway purely out of paranoia. -- Craig Ringer
Am 01.11.2012 06:47, schrieb Craig Ringer: > On 11/01/2012 01:10 PM, Scott Ribe wrote: >> On Oct 31, 2012, at 8:50 PM, Craig Ringer wrote: >> >>> Seriously, if you're facing DB corruption then something is already >>> horribly wrong with your setup. "Horribly" is not strong enough a word IMHO when we're discussing double primary key values... except if Raj is not using sequences to generate them. Although on the other hand, in that case, it's in turn an even more horrible setup; questionable DB design on unreliable hardware. Raj, would you mind pasting your schema somewhere, at least of the tables you experienced the corruption? >> True, but. In a past life, complaints from the db (it was a db that stored a checksum with every block) were the veryfirst symptom when something went horribly wrong with the hardware. (Partial short between wires of an internal SCSIcable; eventually we determined that about every 1MB, 1 bit would get flipped between the controller & disk.) >> >> So, if there were an official db verifier tool for PG, I for one would have it run periodically. > If there were a way to reliably detect corruption, so would I. As things > stand there are no block checksums, so if a bit gets flipped in some > random `text` field you're never going to know, corruption-checker or > no. Some forms of random corruption - like bad blocks on disks causing I think checksums are currently being worked on and are to be expected for 9.3. Might be interesting to scan -hackers for that once more... > I/O errors, zeroed blocks, truncated files, etc - will become apparent > with general checking, but others won't be detectable unless you know > what the expected vs actual data is. > > If page checksumming or any other reliable method of detecting possible > incipient corruption were available I'd quite likely want to use it for > much the same reason you outlined. For that matter, if there were a > general "sanity check my tables and indexes" tool I'd probably use that > too. However, no such tool exists - and in a good setup, none should be > needed. I'd want to use one anyway purely out of paranoia. > > -- > Craig Ringer > > On a side note, Raj, you might want to read the descriptions of MVCC and WAL once more, then re-think about your idea of updating all rows and rolling back the transaction. That would potentially produce the effect you're looking for with InnoDB or Oracle, but not with PG. Cheers, -- Gunnar "Nick" Bluth RHCE/SCLA Mobil +49 172 8853339 Email: gunnar.bluth@pro-open.de __________________________________________________________________________ In 1984 mainstream users were choosing VMS over UNIX. Ten years later they are choosing Windows over UNIX. What part of that message aren't you getting? - Tom Payne
Re-sending to correct addresses.
>>Seriously, if you're facing DB corruption then something is already
>>horribly wrong with your setup.
>"Horribly" is not strong enough a word IMHO when we're discussing double primary key values... except if Raj is not using sequences to generate them. Although on the other hand, in that case, it's in turn >an even more horrible setup; questionable DB design on unreliable hardware.
>Raj, would you mind pasting your schema somewhere, at least of the tables you experienced the corruption?
Each DB table has primary key that is populated using DB-sequence. There is a UNIQUE constraint created on natural keys.
The problem on the test setup was because disk cache was enabled. Indexes were corrupted when powering down the host. I have noticed that integrity of both PK and UNIQUE constraint were violated - Table had rows with duplicate primary keys and in other case there were rows with duplicate unique key constraint.
We are now evaluating to turn off the disk cache to avoid this kind of corruption.
I would still like to have some mechanism to detect any kind of corruption in Postgres. As Craig pointed out I am planning to run "reindex database <dbname>" which will detect any duplicates and will also remove any corruption as indexes are recreated.
About the corruption in table - will running "VACUUM FULL" on all tables detect the corruption?
I see 8.4 and later version has param 'vacuum_freeze_table_age' which by setting to 0 will force regular "vacuum" to run on whole database and will check every block. I don't see that param in 8.3 though so I guess "vacuum full" is the only option.
If "vacuum full" is not going to detect the corruption then I am also thinking to run "pg_dump" which should catch the corruption.
On Thu, Nov 1, 2012 at 4:06 AM, Gunnar "Nick" Bluth <gunnar.bluth@pro-open.de> wrote:
Am 01.11.2012 06:47, schrieb Craig Ringer:"Horribly" is not strong enough a word IMHO when we're discussing double primary key values... except if Raj is not using sequences to generate them. Although on the other hand, in that case, it's in turn an even more horrible setup; questionable DB design on unreliable hardware.On 11/01/2012 01:10 PM, Scott Ribe wrote:On Oct 31, 2012, at 8:50 PM, Craig Ringer wrote:Seriously, if you're facing DB corruption then something is already
horribly wrong with your setup.
Raj, would you mind pasting your schema somewhere, at least of the tables you experienced the corruption?I think checksums are currently being worked on and are to be expected for 9.3. Might be interesting to scan -hackers for that once more...True, but. In a past life, complaints from the db (it was a db that stored a checksum with every block) were the very first symptom when something went horribly wrong with the hardware. (Partial short between wires of an internal SCSI cable; eventually we determined that about every 1MB, 1 bit would get flipped between the controller & disk.)If there were a way to reliably detect corruption, so would I. As things
So, if there were an official db verifier tool for PG, I for one would have it run periodically.
stand there are no block checksums, so if a bit gets flipped in some
random `text` field you're never going to know, corruption-checker or
no. Some forms of random corruption - like bad blocks on disks causingOn a side note, Raj, you might want to read the descriptions of MVCC and WAL once more, then re-think about your idea of updating all rows and rolling back the transaction. That would potentially produce the effect you're looking for with InnoDB or Oracle, but not with PG.I/O errors, zeroed blocks, truncated files, etc - will become apparent
with general checking, but others won't be detectable unless you know
what the expected vs actual data is.
If page checksumming or any other reliable method of detecting possible
incipient corruption were available I'd quite likely want to use it for
much the same reason you outlined. For that matter, if there were a
general "sanity check my tables and indexes" tool I'd probably use that
too. However, no such tool exists - and in a good setup, none should be
needed. I'd want to use one anyway purely out of paranoia.
--
Craig Ringer
Cheers,
--
Gunnar "Nick" Bluth
RHCE/SCLA
Mobil +49 172 8853339
Email: gunnar.bluth@pro-open.de
__________________________________________________________________________
In 1984 mainstream users were choosing VMS over UNIX. Ten years later
they are choosing Windows over UNIX. What part of that message aren't you
getting? - Tom Payne
Am 01.11.2012 16:10, schrieb Raj Gandhi: > > Each DB table has primary key that is populated using DB-sequence. > There is a UNIQUE constraint created on natural keys. That does sound decent. > The problem on the test setup was because disk cache was enabled. > Indexes were corrupted when powering down the host. I have noticed > that integrity of both PK and UNIQUE constraint were You should have mentioned that in the beginning. "Powering down" meant "remove from the power line" in this case, right? That is a situation that certainly can lead to corruption. > violated - Table had rows with duplicate primary keys and in other > case there were rows with duplicate unique key constraint. > > We are now evaluating to turn off the disk cache to avoid this kind of > corruption. Never too late ;-) > About the corruption in table - will running "VACUUM FULL" on all > tables detect the corruption? > I see 8.4 and later version has param 'vacuum_freeze_table_age' which > by setting to 0 will force regular "vacuum" to run on whole database > and will check every block. I don't see that param in 8.3 though so I > guess "vacuum full" is the only option. CLUSTER will probably be the better approach here. Shouldn't take too long on 500 record tables. > > If "vacuum full" is not going to detect the corruption then I am also > thinking to run "pg_dump" which should catch the corruption. <pun>In your current situation, pg_restore sounds more reasonable</pun> I've luckily never been in your situation, but I'd guess pg_dump will just happily dump what it sees. It's not like a seq scan will realize "oh, I've seen that value before" and bail out. The _restore_ will bring it to light though... Good luck anyway. -- Gunnar "Nick" Bluth RHCE/SCLA Mobil +49 172 8853339 Email: gunnar.bluth@pro-open.de __________________________________________________________________________ In 1984 mainstream users were choosing VMS over UNIX. Ten years later they are choosing Windows over UNIX. What part of that message aren't you getting? - Tom Payne