$db_port for non-standard ports

That will not be enough: you'll need to overhaul the frontend (which means the db_server node form and the db_server table schema) so that this can be changed by the user. I'm marking this as minor since it's fairly uncommon to see a mysqld on a different port (why would you do that anyways?).

Feel free to provide a patch for this functionality.

(as for the grant issue, the behavior likely didn't change in the d6 upgrade, so may as well open a bug about this if you think it's one)

Has there been any progress on this? UC Berkeley hosts db accounts separate ports, one per account. So, for me it is a major issue :)

Ok, to fix this, in provision_mysql.drush.inc, in the function provision_mysql_drush_init()

replace:
drush_set_default('master_db_host', $db['host']);
drush_set_default('db_host', $db['host']);

with:
$host = $db['host'];
if ($db['port']) {
$host .= ':'. $db['port'];
}
drush_set_default('master_db_host', $host);
drush_set_default('db_host', $host);

Of course, it is not that simple.
The next bit I found is in provision_drupal_settings.tpl.php.
The db_host needs to be urldecoded in the $db_url, or the colon gets munged.
Here is one way to do it:

   $db_host = urldecode($_SERVER['db_host']);

  $databases['default']['default'] = array(
    'driver' => urldecode($_SERVER['db_type']),
    'database' => urldecode($_SERVER['db_name']),
    'username' => urldecode($_SERVER['db_user']),
    'password' => urldecode($_SERVER['db_passwd']),
    'host' => $db_host,
  );
  $db_url = "<?php print strtr("%db_type://%db_user:%db_passwd@%db_host/%db_name", arr\
ay(
    '%db_type' => '$_SERVER[db_type]',
    '%db_user' => '$_SERVER[db_user]',
    '%db_passwd' => '$_SERVER[db_passwd]',
    '%db_host' => '$db_host',
    '%db_name' => '$_SERVER[db_name]')); ?>";

More as I figure it out.

Ok, this is getting a little ugly. Here is the code to get backups working with the port in the host, from db_server/backup.provision.inc/drush_provision_mysql_pre_provision_backup

  $db_host = explode(':', drush_get_option('db_host'));
  $db_port = isset($db_host[1]) ? $db_host[1] : '3306'; // Default mysqld port.
  $mycnf = sprintf('[client]
host=%s
port=%s
user=%s
password=%s
', $db_host[0], $db_port, drush_get_option('db_user'), drush_get_option('db_passwd'));

And, of course, we need to do almost the same thing in db_server/provision_mysql.drush.inc/_provision_mysql_import_dump

  $db_host = explode(':', $db_host);
  $db_port = isset($db_host[1]) ? $db_host[1] : '3306'; // Default mysqld port.
  $mycnf = sprintf('[client]
host=%s
port=%s
user=%s
password=%s
', $db_host[0], $db_port, $db_user, $db_passwd);

And, of course, to clone you need backup and import, so
platform/drupal/import_6.inc

if ($parts = @parse_url($db_url)) {
  $db_host = urldecode($parts['host']);
  if ($parts['port']) {
    $db_host .= ':'. urldecode($parts['port']);
  }
  drush_set_option('db_host', $db_host, 'site');

Just to be clear, I am not actually recommending this path. It would be better to break the db port out into it's own UI field and cached option. This is the quick and dirty approach, and it has only one advantage, and that is that it seems to be working.

This will help with that :
#836136: Simplify ports support.

This is partially implemented in HEAD now.

The front end is there, all that's remaining is adding the value to the mysql db credentials.

Committed to HEAD.

you configure it on the server, and the configs will generate for it

I took a quick look at this in alpha12 a few days ago and was going down this path:

$ diff  .drush/provision/install.hostmaster.inc .drush_orig/provision/install.hostmaster.inc
25,26d24
<   $aegir_db_host = drush_get_option('aegir_db_host', 'localhost', 'options');
<   $aegir_db_port = drush_get_option('aegir_db_port', '3306', 'options');
29c27
<   $data['master_db'] = sprintf("mysql://%s:%s@%s:%d",$aegir_db_user, $aegir_db_pass, $aegir_db_host, $aegir_db_port);
---
>   $data['master_db'] = sprintf("mysql://%s:%s@%s",$aegir_db_user, $aegir_db_pass, $aegir_host);

The reason I added 'aegir_db_host' is that without that install.hostmaster, seems to be assuming that mysql will be running locally on the webserver, which is not the case for me.

$data['master_db'] is the db url that the frontend (hostmaster) server uses (I think).

If I want to use --backend-only, does the webserver I'm setting up need $data['master_db']? (I think that $data['master_db'] might need to go in one of the drush alias files created on the backend (webserver).)

Does the backend (webserver) need to connect to the frontend (hostmaster)'s database? (I think that it probably does not need to...)

I'll be coming back to this early next week.

(I'm trying to step through the new code using eclipse + xdebug working on my ubuntu 10.04 laptop. I've got it working basically, but if there are any notes on the best way to debug drush/provision that you can point me too, let me know!)

Any luck? I also got this far in the code before seeing your post, but I still get the dreaded "Fatal error: Call to a member function quote() on a non-object", meaning the database connection didn't work.

In my use case, I only need to change the port, not the host, as MAMP picks its own port number and I don't want to change it for several reasons. I'm surprised that an assumed port number would be hardwired into an install script, especially since "db_port" already appears deep down in some included code.

(Based on the error message, it looks like there are two errors here:
1. the wrong sort of mysql db connection parameters.
2. the script itself is not recovering from error #1.

It seems the script has support to show a diagnostic about the database problem, but that logic is wrong and gives the "object-oriented" error. Can that be fixed by someone familiar with it? Then the rest of us can fix our own database connections as we see fit.)

I'm fairly certain that Aegir now supports this.

Related: #2069387: Support nonstandard ports on hostmaster-install command