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Old 09-10-2013, 08:46 AM   #21
amaruquyllur
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Thank you, i will check that.
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Old 09-10-2013, 09:01 AM   #22
SES
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Quote:
Originally Posted by amaruquyllur View Post
Thank you, i will check that.
You can check that at the command line:
Code:
mysql -u orthomcl -P 3307
That will let you know if you can connect via port 3307, but I don't think that is the issue. That database connection string does not look correct, which would indicate there is something wrong with your configuration file for the user to be interpreted as the host.
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Old 09-10-2013, 09:07 AM   #23
amaruquyllur
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$ cat orthomcl.config
# this config assumes a mysql database named 'orthomcl'. adjust according
# to your situation.
dbVendor=mysql
dbConnectString=dbi:mysqlrthomcl:3307
dbLogin=orthomcl
dbPassword=*** (i'm sure it is right)
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-5
oracleIndexTblSpc=NONE

and:


mysql> show databases;
+--------------------+
| Database |
+--------------------+
| information_schema |
| orthomcl |
| test |
+--------------------+
3 rows in set (0.00 sec)


So the database exists. I have all the grants for `orthomcl' on this database, and the .config file should be ok...
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Old 09-10-2013, 09:15 AM   #24
SES
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Try dropping the port from the "dbConnectString" (i.e., try just dbi:mysqlrthomcl).
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Old 09-10-2013, 09:17 AM   #25
amaruquyllur
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YAY! Wait three minutes. I will jump off a bridge and then come back to celebrate this. I think it worked :-)

Thank you!

Last edited by amaruquyllur; 09-10-2013 at 09:20 AM.
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Old 09-10-2013, 09:24 AM   #26
amaruquyllur
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USEFUL TIP
(for other users)

Actually I had already tried to modify that line, putting port 3306 instead of 3307. Didn't work. But deleted the whole line allowed the connection... THROUGH PORT 3306!

A bit crazy, but i have to process some data and not time to ask why.

Thanks again.
:-)
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Old 09-10-2013, 09:34 AM   #27
SES
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Quote:
Originally Posted by amaruquyllur View Post
USEFUL TIP
(for other users)

Actually I had already tried to modify that line, putting port 3306 instead of 3307. Didn't work. But deleted the whole line allowed the connection... THROUGH PORT 3306!

A bit crazy, but i have to process some data and not time to ask why.

Thanks again.
:-)
Glad you got things working.

For other users, it may not be necessary to specify the port. However, it is important to correctly specify the host, user, password, and database. If you combine those parameters into a string it may cause parsing/connection issues.
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Old 09-10-2013, 09:38 AM   #28
GenoMax
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Default port for MySQL connections is 3306. Hope you are allowing connects only from localhost (or have appropriate firewall rules set).
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Old 10-11-2014, 11:41 PM   #29
dnajuice
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Unhappy DBI can't connect to local MySQL server (orthoMCL)

Dear friends,

I encountered similar situation (and this is the closest error message I could find), but could not work it out with the methods discussed here. I would appreciate very much if you can help diagnose and advise some troubleshooting tricks. Please forgive me for this long post as I am a newby for mysql.

DESCRIPTION: I installed mysql 5.6.21 to ubuntu 14.04 as a non-root user. I set up the default mysql database using the special configuration file mysql.cnf from the orthoMCL package (socket=/tmp/mysql_2.sock, port=3307, ...):
./scripts/mysql_install_db --defaults-file=mysql.cnf

and started mysql server like this:
./bin/mysqld_safe --defaults-file=mysql.cnf &

The mysql database seemed running fine. when I typed ps -e|grep -i 'mysqld', I got
23388 pts/0 00:00:00 mysqld_safe
23553 pts/0 00:00:00 mysqld

I logged in to this mysql server as root, and created a database called orthomcl that I will use for OrthoMCL. Then I logged out (ctrlD)
./bin/mysql --defaults-file=mysql.cnf -u root -p
mysql> CREATE DATABASE orthomcl;
mysql> GRANT SELECT,INSERT,UPDATE,DELETE,CREATE VIEW,CREATE, INDEX, DROP on orthomcl.* TO [email protected];
mysql> set password for [email protected] = password('yourpassword');

According to the UserGuide, I also created an orthomcl.config file, the first few lines look like this:
dbVendor=mysql
dbConnectString=dbi:mysqlrthomcl:localhost:3307
dbLogin=orthomcl
dbPassword=***(I'm sure it's the right password)

Then I run the orthomclInstallSchema with the command
./bin/orthomclInstallSchema ./my_orthomcl_dir/orthomcl.config ./my_orthomcl_dir/sql_log_file table_suffix

and I got the following error message:
DBI connect('orthomcl:localhost:3307','orthomcl',...) failed: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) at /home/mylogin/orthomclSoftware-v2.0.9/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56.

I assume this may be due to the dbConnectString, so I changed it to
dbConnectString=dbi:mysqlrthomcl
and executed the orthomclInstallSchema command again, but I still got the same error:
DBI connect('orthomcl','orthomcl',...) failed: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) at /home/mylogin/orthomclSoftware.......

I even tried dbConnectString=dbi:mysqlrthomcl:3307 and got this:
DBI connect('orthomcl:3307','orthomcl',...) failed: Can't connect to MySQL server on '3307' (22) at /home/mylogin/orthomclSoftware......

QUESTIONS:
1) As long as the mysql database was running, it is not necessary to login as orthomcl, right? Because the orthomcl.config file will be used to automatically login to the database.

2) What's the difference between these two? Which one should I use? Is the orthomcl a centrally installed mysql server if it was created by root?
dbi:mysqlrthomcl (for a centrally installed mysql server with a database called 'orthomcl')
dbi:MySqlrthomcl:localhost:3307 (for a user installed mysql server on port 3307 with a database called 'orthomcl')

3) I already specified the socket=/tmp/mysql_2.sock in mysql,cnf when I started the mysql server, why was the socket '/var/run/mysqld/mysqld.sock' called later?

4) Did I install the DBI and DBD::mysql modules correctly? I am not sure. I installed them using CPAN as root.
$ perl -MCPAN -e shell
cpan> o conf makepl_arg "mysql_config=/path_to_mysql_dir/bin/mysql_config"
cpan> install Data:umper
cpan> install DBI
cpan> force install DBD::mysql

I didn't see error when I check with
$ perl -MDBI -e 1
$ perl -MDBD::mysql -e 1

but I received the same DBI error as above when I installed DBD:mysql, such as
t/32insert_error.t ................... skipped: ERROR: DBI connect('test','root',...) failed: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) at t/32insert_error.t line 14.

Sorry about the long text, hope it helps.
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Old 10-12-2014, 05:28 AM   #30
GenoMax
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Your problem is related to mysql install.

See these two threads for possible solutions: http://stackoverflow.com/questions/1...un-mysqld-mysq

http://www.tech-recipes.com/rx/762/s...-tmpmysqlsock/
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Old 09-05-2017, 08:47 AM   #31
agali
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For those who struggle with the error 'DBI connect('orthomcl7','root',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)' while running OrthoMCL, I might have found a simple solution.
When connecting to a MySQL server located on the local system, the mysql client connects through a socket which is typically located in /tmp/mysql.sock. However, the socket can be placed elsewhere, in my case it was /var/run/mysql/mysql.sock.
You need to:
1) Find the right location of the socket and replace it in the mysql.cnf e.g.

Code:
socket=/var/run/mysqld/mysqld.sock
2) In the config_file (needed for the orthomcl modules like orthomclInstallSchema) you need to specify the socket for the dbConnectString like so:

Code:
dbConnectString=dbi:mysql:orthomcl;mysql_socket=/var/run/mysqld/mysqld.sock
Hope this helps!

Last edited by GenoMax; 09-05-2017 at 08:58 AM.
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