Different machines and MySQL installations can produce different results with these variables.
If the SyMAP demo-seq to demo-seq2 load and synteny computations seem slow,
try different combinations of these two variables to see what performs the fastest inserts.
Slow queries
Database connect errors
After startup, if the program is left idle for some time then its
database connection will close and it will show a complicated-looking error on
next usage, or it may say this:
com.mysql.jdbc.CommunicationsException: Communications link failure due to underlying exception:
** BEGIN NEXTED EXCEPTION **
In this case the solution is to restart the program.
On startup, error messages mentioning the database or SQL probably mean that the database connection
could not be established or was lost. A message at startup means SyMAP was not able
to connect to the database using the provided information in symap.config. First, make sure
your db_adminuser and db_adminpasswd are correct.
These days, the best way to find the MySQL problems is to search the internet. However,
the following are some things to check for connection problems on SyMAP startup:
Check the database privileges:
The database users specified in symap.config may not have necessary access to the database.
If you running the read/write symap, then the relevant user is db_adminuser. If
you are running a read-only session using viewSymap, it will use the
read-only db_clientuser or read-write db-adminuser. In either case the user needs
to have database access privileges from the machine where you are working.
Note that MySQL privileges are granted specifically to certain users on certain machines. You can test
the user access by using the MySQL command line client mysql, if it is installed
on your machine, or by looking at the privilege table using an administration interface
such as PHPMyAdmin. The mysqlaccess tool is also useful, if it is installed
on your machine.
Check the MySQL configuration:
The MySQL configuration file (/etc/my.cnf) should not contain any
of the following lines that prevent remote access to the database.
bind_address=127.0.0.1
skip_networking
Make sure the port is visible:
If the database is on a different computer, test that its port 3306 is visible
from your computer:
telnet <server address> 3306
If it does not make a connection then either the server is not running, or
it is set to run on a non-standard port, or the
port is blocked by a firewall. Contact a system administrator. (Note,
to get out of telnet type "^]".)
