Connection timed out

[rgauss]

Hope I didn't miss this one in the forums, I did quite a bit of searching.

Can't get Tomcat to come up all the way.  It doesn't seem to crash or produce a core dump and there's no exceptions in the logs.

I've turned up debugging everywhere I can think of, and catalina.out or alfresco.log just stop at:

19:50:51,213 DEBUG [hibernate.cfg.Configuration] processing native query and ResultSetMapping mappings
19:50:51,213 DEBUG [hibernate.cfg.Configuration] processing association property references
19:50:51,213 DEBUG [hibernate.cfg.Configuration] processing foreign key constraints
19:50:51,213 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.domain.hibernate.NodeImpl
19:50:51,214 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.domain.hibernate.NodeImpl
19:50:51,214 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.security.permissions.impl.hibernate.RecipientImpl
19:50:51,214 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.domain.hibernate.StoreImpl
19:50:51,214 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.domain.hibernate.NodeStatusImpl
19:50:51,214 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.domain.hibernate.NodeImpl
19:50:51,214 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.domain.hibernate.NodeImpl
19:50:51,214 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.domain.hibernate.NodeImpl
19:50:51,214 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.security.permissions.impl.hibernate.PermissionReferenceImpl
19:50:51,214 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.security.permissions.impl.hibernate.NodePermissionEntryImpl
19:50:51,215 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.security.permissions.impl.hibernate.RecipientImpl
19:50:51,215 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.domain.hibernate.NodeImpl
19:50:51,215 DEBUG [hibernate.cfg.Configuration] resolving reference to class: org.alfresco.repo.domain.hibernate.NodeImpl
19:50:51,871 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.StoreKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,897 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,900 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,901 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,920 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.StoreKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,922 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,923 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,924 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.StoreKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,925 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,926 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,927 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,928 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,930 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,931 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,932 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,933 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:51,934 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:52,020 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.PropertyValue, NullPointerException: null
19:50:52,021 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:52,022 DEBUG [hibernate.util.ReflectHelper] reflection optimizer disabled for: org.alfresco.repo.domain.NodeKey, BulkBeanException: Property is private (property setProtocol)
19:50:52,030 INFO  [hibernate.connection.ConnectionProviderFactory] Initializing connection provider: org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍

Just sits right there forever.  Tomcat never comes all the way up so going to the address:8080 just times out but netstat shows the port in use.

Steps I've taken:
Many, many clean installs of Tomcat.
Dropping in war with Tomcat off and starting and dropping in while running.
Manually expanding the war then starting Tomcat
Tried the alfresco-tomcat bundle
jdk1.5.0_05 and 1.5.0_06
Verified the alfresco user can connect to the mysql db

This is on:
Fedora Core 5
Either jdk1.5.0_05 or 1.5.0_06
MySQL 5.0.18
MySQL Connector 3.1.12
Tomcat 5.5.17
Alfresco 1.2.1

Thanks for any help.

[rgauss]

OK, I may have lied about 'forever'.  Looks like it times out after 45 minutes with:

Caused by: com.mysql.jdbc.CommunicationsException: Communications link failure due to underlying exception: 

** BEGIN NESTED EXCEPTION ** 

java.net.SocketException
MESSAGE: Connection timed out

STACKTRACE:

java.net.SocketException: Connection timed out
        at java.net.SocketInputStream.socketRead0(Native Method)
        at java.net.SocketInputStream.read(SocketInputStream.java:129)
        at com.mysql.jdbc.util.ReadAheadInputStream.fill(ReadAheadInputStream.java:113)
        at com.mysql.jdbc.util.ReadAheadInputStream.readFromUnderlyingStreamIfNecessary(ReadAheadInputStream.java:160)
        at com.mysql.jdbc.util.ReadAheadInputStream.read(ReadAheadInputStream.java:188)
        at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1902)‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍

But again, I've verified the alfresco user can connect to db over 127.0.0.1, localhost, localhost.localdomain, and the public domain address and IP.

[rgauss]

Since last post I've tried:

Reverting to 3.0 connector
Specifying INNODB and utf8 per this post http://forums.alfresco.com/viewtopic.php?t=667
Other versions of mysql server
Setting the old-passwords flag

What's interesting is that when I pointed repository.properties to a 4.1 mysql server on a totally different server it worked fine which makes me think it's got to do with the mysql server config itself.

In the mysql log I see:

060508 16:22:30       3 Connect     alfresco@localhost on alfresco
                      3 Query       SET NAMES utf8
                      3 Query       SET character_set_results = NULL
                      3 Query       SHOW VARIABLES‍‍‍‍

then nothing further.

When I log in via mysql client as alfresco and run those commands the response seems to come back fine.

Nothing special in /etc/my.cnf:

[mysqld]
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
# Default to using old password format for compatibility with mysql 3.x
# clients (those using the mysqlclient10 compatibility package).
old_passwords
log
default-character-set=utf8 
default-storage-engine=INNODB
    
[mysql.server]
user=mysql
basedir=/var/lib

[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍

Any thoughts?  Any where else I should be looking for debugging info?

Thanks

[rgauss]

Never figured out what the problem was.

Had the host rebuild the box with FC4 and MySQL 4.1, everything seems fine now.

Maybe there was something I was supposed to change in alfresco's config to use MySQL 5.0?