[DAS] mysql.sock trouble

[Lincoln Stein]

Urrrgh.  I bet that the RedHat RPM wants my.cnf to be in 
some weird place like /usr/etc.

Lincoln

On Monday 20 May 2002 16:04, Steve Chervitz wrote:
> Thanks for the replies. The symlink trick works. The /etc/my.cnf file
> didn't work. I stopped mysqld, created the /etc/my.cnf file, re-started
> mysqld, but ldas_load.pl still throws a DBI->connect error complaining that
> it can't connect via /tmp/mysql.sock. If I then create symlink and re-try,
> it's happy.
>
> I also tried uninstalling and re-installing mysql (from rpms) with the
> /etc/my.cnf file in place. Still no go.
>
> Steve
>
> --- Lincoln Stein <lstein@cshl.org> wrote:
> > I think this has been addressed already (I'm reading my e-mail
> > backwards), but the best of all solution to is set the socket path
> > correctly in /etc/my.cnf:
> >
> > [client]
> > port            = 3306
> > socket          = /var/lib/mysql/mysql.sock
> >
> > [mysqld]
> > datadir=/var/lib/mysql
> > socket=/var/lib/mysql/mysql.sock
> >
> > These two stanzas tell both the client and the server to use the same
> > socket.
> >
> > Lincoln
> >
> > On Saturday 18 May 2002 00:01, Leonardo Marino-Ramirez wrote:
> > > Steve,
> > >
> > > I think that I found something that could be useful to you:
> > >
> > > http://www.mysql.com/doc/C/a/Can_not_connect_to_server.html and
> > > http://www.mysql.com/doc/P/r/Problems_with_mysql.sock.html
> > >
> > > in synthesis you can try to symlink it: "ln -s
> > > /var/lib/mysql/mysql.sock /tmp"
> > >
> > > I hope it works for you.
> > >
> > > Leonardo
> > >
> > > On Fri, 17 May 2002, Steve Chervitz wrote:
> > > > DAS folks,
> > > >
> > > > This may be more of a mysql issue than a DAS issue, and is more of an
> > > > FYI since I have a mostly satisfactory resolution, but I was getting
> > > > a connection error when using the ldas_load.pl script:
> > > >
> > > > $ ldas_load.pl --create --database dicty test.das
> > > > DBI->connect(dicty) failed: Can't connect to local MySQL server
> > > > through socket '/tmp/mysql.sock' (111) at
> > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > >i/ca ching_handle.pm line 140
> > > > ------------- EXCEPTION: Bio::Root::Exception -------------
> > > > MSG: Can't connect to database: Can't connect to local MySQL server
> > > > through socket '/tmp/mysql.sock' (111)
> > > > STACK: Error::throw
> > > > STACK: Bio::Root::Root::throw
> > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/Root/Root.pm:315
> > > > STACK: Bio::DB::GFF::Adaptor::dbi::caching_handle::new
> > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > >i/ca ching_handle.pm:90 STACK: Bio::DB::GFF::Adaptor::dbi::new
> > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > >i.pm
> > > >
> > > >:74 STACK: Bio::DB::GFF::Adaptor::dbi::mysql::new
> > > >
> > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > >i/my sql.pm:253 STACK: Bio::DB::GFF::Adaptor::dbi::mysqlopt::new
> > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > >i/my sqlopt.pm:149 STACK: Bio::DB::GFF::new
> > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF.pm:550
> > > > STACK: /usr/local/bin/ldas_load.pl:50
> > > > -----------------------------------------------------------
> > > >
> > > > I could succesfully connect to the dicty database using mysql on the
> > > > command-line, so my mysql setup appeared OK.
> > > >
> > > > My /tmp/mysql.sock was apparently defunct, probably from an old mysql
> > > > install that I did over a year ago. The real socket from the latest
> > > > mysql installation was at /var/lib/mysql/mysql.sock and wasn't been
> > > > recognized. I tried deleting /tmp/mysql.sock and re-installing
> > > > LDasServer, but still no go.
> > > >
> > > > Problem was solved by restarting mysqld with --socket=/tmp/mysql.sock
> > > >
> > > > This however created another annoyance in that the mysqladmin now
> > > > requires that I specify the --socket, since it defaults to
> > > > /var/lib/mysql/mysql.sock.
> > > >
> > > > So it seems I have to use /tmp/mysql.sock to appease the LDasServer,
> > > > but it complicates my mysql installation. Any suggestions from the
> > > > mysql jocks out there?
> > > >
> > > > Here's my version info:
> > > > mysqladmin  Ver 8.23 Distrib 3.23.49a, for pc-linux-gnu on i686
> > > >
> > > > Steve
> > > >
> > > >
> > > > =====
> > > > Steve Chervitz
> > > > sac@bioperl.org
> > > >
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> =====
> Steve Chervitz
> sac@bioperl.org
>
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