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Re: [vox-tech] Need your help in recovering database.
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Re: [vox-tech] Need your help in recovering database.

On Wed, 23 Apr 2003, Soumyadeep nandi wrote:

> Thank you All,
> Thankyou very much for your cooperation. I doubt if I
> am able to present you properly.

Your "present" is getting better, but you are talking to the wrong people.

I have a few comments below, but you need to go ask the InnoDB experts at
http://www.innodb.com or http://www.mysql.com if you want authoritative

> Replying to Tim:-
> > > Didn't find any fields in table 'blast_genescan'
> > Does "describe blast_genescan;" return the correct
> > columns? If so, maybe the perl script needs a       
> > closer look.
> > >
> > > This for all the tables.
> > Do you mean that "describe table2;", "describe      
> > table3;", and "describe table4;" all return no     >
> columns?
> This is after the command "use Entamoeba".
> After searching the solution in
> "http://www.innodb.com/ibman.html";
> I could get I must have specified "max" size. I've
> specified the max size along with some server
> variables viz. 
> set-variable = key_buffer=256M
> set-variable = max_allowed_pack = 40M
> ...
> set-variable = myisam_sort_buffer_size = 64M
> set-variable = thread_cache = 8
> set-variable = thread_concurrency = 4
> ...
> innodb_data_file_path =
> /ibdata/ibdata1:100M:autoextend:max:2000M

Once the database is corrupt, recovery is unlikely.  (Let this be a
reminder that mysqldump should be used periodically to create a
recoverable backup.)

You will probably need to eliminate the "autoextend" option when you build
a new database configuration to prevent the same problem from
re-occurring.  Review the documentation... you can specify multiple files
in the innodb_data_file_path.

> But then I could once get into the database
> i.e. by command "use Entamoeba"
> It flushed nothing only "database changed"
> As I tried to select the rows from one of the four
> tables it flushed
> "Didn't find any fields in table 'blast_genescan'"
> and was same for all other tables.
> But after that I cant start server anymore its showing
> error:
> ERROR 2002: Can't connect to local MySQL server
> through socket '/var/lib/mysql/mysql.sock' (2)

I don't know much about the specific messages that may arise due to
database corruption, but the Behavior of most software when presented with
corrupt data may be unpredictable.

> Replying to Jeff:-
> > The fact that this exceeds 2GB is certainly         
>    > suspicious.  There is a warning in the InnoDB    
>  > documentation [1] to beware of OS filesize
> > limitations. They don't seem to be specific about  >
> the consequences, but I would not be surprised if  >
> the file was corrupt by now.  I suspect that
> > using multiple data files rather than the          >
> autoextend option will be necessary if you are     >
> dealing with large databases.
> How would I do this if I have to rebuild the database.

Read the manual... you just need to specify multiple innodb files in the
configuration.  I don't know if you can add files whenever you want to,
but I think you can do it whenever you restart the server.

> > There are kernel patches (options by now?) that    >
> support large file sizes, but they require          
> But mine is 32 bit processor could I reconfigure the
> kernel for 64-bit

No... the Large File Size kernel patch supports an alternative set of
system calls that the calling software may be configured to use if the
programmers have set it up to support that option. [1]

> > some cooperation on the part of the application    >
> (mysql compile options) before they will take      >
> effect.
> How would I do this?

I don't know... details vary for different software.  Download a
precompiled version set up to support the option? Recompile from source,
following instructions provided with the source?

> Is there any way I can recover or take back up of the
> database "Entamoeba".

I already said I am not an expert at this... go ask the InnoDB people.
I think you will most likely have to rebuild the database from external


[1] http://www.linuxgazette.com/issue67/tag/13.html

Jeff Newmiller                        The     .....       .....  Go Live...
DCN:<jdnewmil@dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live Go...
                                      Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...2k

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