Thanks, Mike. I'll try your recommendations and post back what I find out.
Cheers,
Christopher Curry
Assistant Technical Librarian / Assistant IT Officer
American Philosophical Society
105 South Fifth Street
Philadelphia, PA 19106-3386
Tel. (215) 599-4299
[email protected] <mailto:[email protected]>
Main Library number: (215)440-3400
APS website: http://www.amphilsoc.org
On 09/21/2010 10:11 AM, Mike Hafen wrote:
It could still be memory, because MySQL keeps indexes and such in
memory. It could also be a bad sector on the disk, because MySQL
caches query results to disk when they are bigger than the space
allocated in memory for query results.
The only character I can think of that would cause trouble in the dump
would be an unescaped single quote, or maybe half of a UTF16 character
that happens to have the same value as an ASCII single quote. It
seems unlikely to me though that mysqldump wouldn't spot such a
character as it was dumping.
Have you tried something like 'select * from biblioitems limit
41537,1'. That should pull the specific row that has the error, and
you could visually examine it, or see if MySQL throws an error on the
row. That could tell you if the problem is in the data file
specifically, or if it's somewhere else (memory or disk spaced used to
cache the result).
I doubt it's the disk overrunning what it can physically allocate,
since as you say the query results can't be more than a few
gigabytes. Unless the disk is already nearly full, which I'm sure
you've already checked.
I think MySQL could try to allocate memory beyond what it can, beyond
the 3.x GB addressable by a 32bit app, but the error message indicates
it's a problem with the disk drive. Assuming the error message is
accurate I'd start with a bad block scan on the host's hard drive.
That's what I recommend.
Good luck.
On Tue, Sep 21, 2010 at 7:39 AM, Christopher Curry
<[email protected] <mailto:[email protected]>> wrote:
Mike,
Thanks for the reply. I did try querying individual records
around that row; in fact, I used "limit 41536,1" to find out the
specific biblioitemnumber. I checked the record in Koha and found
no problems with it or adjacent records and I had no problem
querying these individual records with select statements.
I did try a few queries like "select * from biblioitems limit
1,41537" and did get the same 2013 error when querying large
datasets, but not when querying smaller data sets. "limit
1,41535" also threw the error, but "limit 1,20,000" did not. I
thought this might indicate a memory issue, but the syslog error:
"InnoDB: Database page corruption on disk or a failed file read of
page 58164" led me to think there was corrupted data in the database.
The VM has 120 GB of dynamically expanding storage and the vdi is
housed on a filesystem with 108GB free, so there shouldn't be a
problem with with running out of disk space. The dump is less
than 2GB, so the database itself can't be much larger than that,
can it?
The VM currently has 1.5 GB allocated for memory, and I tried
increasing this to 2GB, which did not prevent the error. The host
is 32-bit and is maxed out at 4GB of memory, so I can't go much
higher than this without destabilizing my host.
I had another theory that there might be an offending character in
one of the MARCXML records that is messing with the format of the
SQL commands in the .sql file. Anyone know if this is a
possibility? I'm no SQL expert, so I'm not sure what characters
to look for.
Cheers,
Christopher Curry
Assistant Technical Librarian / Assistant IT Officer
American Philosophical Society
105 South Fifth Street
Philadelphia, PA 19106-3386
Tel. (215) 599-4299
[email protected] <mailto:[email protected]>
Main Library number: (215)440-3400
APS website: http://www.amphilsoc.org
On 09/20/2010 06:17 PM, Mike Hafen wrote:
Sorry to hear you are having problems with your failover server.
I've had problems with failovers servers and backups before, it's
not fun.
Have you checked the memory and hard drive of the failover
server? (the host) That would be my first guess. Also, it may
be the filesystem on either the host or the guest, but I'm not up
on file systems so I can't say for sure.
There's a good chance the row number in the error message relates
to the biblioitemnumber. You could try just querying the
database for rows around that. Something like 'select * from
biblioitems where biblioitemnumber > 41470 and biblioitemnumber <
41600. If you see the error it could be data, disk, or
filesystem related. If you don't it's probably memory related,
but maybe filesystem related.
Good luck.
2010/9/17 Christopher Curry <[email protected]
<mailto:[email protected]>>
Hello all,
I'm trying to create a mirrored failover server with data
from our live Koha. In order to do so, I'm using *mysqldump*
and *mysql* for backup and restore.
I've discovered a troubling problem and I can't determine the
cause.
I run this command to backup the live server:
*mysqldump --single-transaction -ukoha -p koha >
/home/koha/KohaServerBackups/koha.`/bin/date
+\%Y\%m\%d\%H\%M\%S`.sql*
This seems to work correctly (and very quickly! 1.7 GB
database exports in 2 min)
Then, I run this command:
*mysql -v -ukoha -p koha <
/home/koha/KohaServerBackups/backupFileName.sql*
This also seems to work, as I receive no warnings or error
messages.
I'm exporting from a 3.00.05.001 system and importing to a
3.00.05.003 system, so I then run the
*$KOHA_SOURCE/installer/data/mysql/updatedatabase.pl
<http://updatedatabase.pl>* script.
Relevant specs:
MySQL version: mysql Ver 14.12 Distrib 5.0.51a, for
debian-linux-gnu (i486) using readline 5.2
OS: Debian Lenny
Failover server is virtual, running on VirtualBox 3.2.8, on
an Ubuntu 10.4 host.
All GUI functions of the Koha failover server seem to operate
correctly, but when I run *mysqlcheck -ukoha -p koha* the
check fails on koha.biblioitems with the following error message:
mysqlcheck: Got error: 2013: Lost connection to MySQL server
during query when executing 'CHECK TABLE ... '
If I try mysqldump, I get the same error, but it is more
specific, reporting that it falls on row 41536.
If I check /var/log/syslog, I see this
http://pastebin.com/YuuFBHry
"InnoDB: Database page corruption on disk or a failed file
read of page 58164", etc.
Both mysqlcheck & mysqldump work without error on the live
server, so I'm thinking that something must be happening to
the data during the export or import that corrupts the InnoDB
data, but this is speculation, since I'm not a MySQL expert.
Has anyone seen behavior like this? Any suggestions for
further troubleshooting/resolution?
--
Cheers,
Christopher Curry
Assistant Technical Librarian / Assistant IT Officer
American Philosophical Society
105 South Fifth Street
Philadelphia, PA 19106-3386
Tel. (215) 599-4299
[email protected] <mailto:[email protected]>
Main Library number: (215)440-3400
APS website: http://www.amphilsoc.org
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