[BioSQL-l] " Lost connection to MySQL server" when I via biosql by using "find_by_unique_key" method

[shenyang]

Hello-
	I updated my mysql from "mysql-standard-4.0.20-sgi-irix6.5-mips" to
 "mysql-max-4.1.12-sgi-irix6.5-mips".

Then I failed to get richseq object from my sequence database which is biosql schema.
My perl scripte is "

$db = $db||Bio::DB::BioDB->new(-database   => "biosql",
                            -printerror => 0,	
                            -host       => "localhost",
                            -dbname     => $dbname,
                            -driver     => "mysql",
                            -user       => $dbuser,
                            -pass       => $dbpass,
                            );
$seq->namespace($namespace);
$seq->version($version);
my $adp = $db->get_object_adaptor($seq);
my $seqfactor=Bio::Seq::SeqFactory->new(-type=>"Bio::Seq::RichSeq");
$lseq = $adp->find_by_unique_key(
   			$seq,
   			-obj_factory =>$seqfactor,
);

The error message is "

------------- EXCEPTION  -------------

MSG: error while executing statement in Bio::DB::BioSQL::SeqAdaptor::find_by_unique_key: Lost connection to MySQL server during query
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/bioperl-db//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:952
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/bioperl-db//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856
STACK toplevel test_get_seq_embl_acc.pl:9

--------------------------------------

and the mysql log file indicated it's a innodb's problem, here is the mysql logs:

"
050620 16:32:47  mysqld restarted
050620 16:32:49  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
050620 16:32:50  InnoDB: Starting log scan based on checkpoint at
InnoDB: log sequence number 0 2237087117.
InnoDB: Doing recovery: scanned up to log sequence number 0 2237087117
InnoDB: Last MySQL binlog file position 0 79, file name ./biomed-bin.000022
050620 16:32:51  InnoDB: Flushing modified pages from the buffer pool...
050620 16:32:51  InnoDB: Started; log sequence number 0 2237087117
050620 16:32:51 [Warning] mysql.user table is not updated to new password format; Disabling new password usage until mysql_fix_privilege_tables is run
050620 16:32:51 [Warning] Can't open and lock time zone table: Table 'mysql.time_zone_leap_second' doesn't exist trying to live without them
/database/mysql/bin/mysqld: ready for connections.
Version: '4.1.12-max-log'  socket: '/tmp/mysql.sock'  port: 3306  MySQL Community Edition - Experimental (GPL)"


Thanks for any suggestions,
Yang Shen