SyMAP 3.2 Trouble Shoot  
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This guide is intended to aid in the installation and configuration of SyMAP.
Please send questions and suggestions to symap@agcol.arizona.edu.

Problems


Not Enough Memory

This problem can occur when running from a web page (see Web Use) or as a standalone application (see Standalone Use at bottom).

Web Use
When running SyMAP from a web page (i.e., as an applet): The default Java applet memory limit is very low, and memory may run out for large displays or for the 2D Base View. Increase the Java memory limit for your system using the instructions below:

On Windows:

  1. From the Start menu button, select Settings, then Control Panel to open the Control Panel. Or right click on the Java icon in the lower right of the task bar.
  2. Double click the Java icon to open the Java Control Panel.
  3. Select the Java tab.
  4. Click the View button under Java Applet Runtime Settings.
  5. For each row, click the Java Runtime Parameters column and type -Xmx512m and press enter.
  6. Click the OK button to close the Control Panel.
  7. Restart your browser.
On Mac:
  1. In the Finder, select Go then select Applications.
  2. In the new window select Utilities, then double-click Java Preferences to open the Java Control Panel.
  3. Select the top-most Java version in the list under Java Applet Plugin and click Options.
  4. Under Java Runtime Parameters enter -Xmx512m.
  5. Click the OK button and close the Control Panel.
  6. Restart your browser.
On Unix:
  1. Open a terminal and change to the Java installation directory (e.g., /usr/jre1.6.0_03).
  2. Execute bin/ControlPanel to open the Java Control Panel.
  3. Select the Java tab.
  4. Click the View button under Java Applet Runtime Settings.
  5. For each row, click the Java Runtime Parameters column and enter -Xmx512m.
  6. Click the OK button to close the Control Panel.
  7. Restart your browser.

Standalone Use
When running SyMAP as a standlone application: For very large projects the Project Manager may run out of memory. To fix this problem, run symap with the -m parameter to increase the maximum memory used from the default 2048 MB to 4096 MB.: 

     > ./symap -m 4096m
You will also need to be using a 64-bit processor. It should not be necessary to go any higher than this, unless you have set do_clustering=0 in the params file.

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"A database error occurred"

The message "A database error occurred" is shown when SyMAP cannot access the MySQL database. There are several possible causes.

Check the database privileges

The database user specified in the SyMAP params file (db_clientuser) may not have remote access to the database as specified in the mysql.user table.

As an example, to add remote access from all hosts for user named 'db_clientuser': 


    mysql> use mysql;
    mysql> insert into user values ('%','db_clientuser',PASSWORD('db_clientpasswd'),'Y','Y','Y','Y','Y','Y','N','N','N',
						'N','N','N','N','N','N','N','N','N','N','N','N','','','','',0,0,0);
    mysql> flush privileges;
Also try using the mysqlaccess script to show which entries in the mysql privilege tables are in use for a particular host/user/password.

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 doesn't make a connection then either the server isn't running, or the port is blocked by a firewall. Contact a system administrator. (Note, to get out of telnet type "^]".)

Perl error: "Can't locate ..."

The SyMAP web displays need some non-standard Perl modules. If any of these modules are missing, the install script will fail: 
     Can't locate Data/Page.pm in @INC (...)
     Can't locate DBI.pm in @INC (...)
     Can't locate GD.pm in @INC (...)
To install these modules on your server, execute the following commands: 
     > cpan Data::Page
     > cpan DBI
     > cpan GD
Note: CPAN is the Comprehensive Perl Archive Network.

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"No projects found" on the web display

If there are no projects to select in the main projects web page (projects.cgi), then either the demo was not run, or the demo projects were not properly loaded into the database. Re-run the demo and try again.

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"The built-in MySQL server cannot run..."

SyMAP comes with a MySQL server built in, but it does not run right if there is another MySQL server already running on the computer. There are two solutions: either stop the other server temporarily, or edit the parameters file to point SyMAP at that server (or another server) so it doesn't use the built-in MySQL.

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"Status window disappeared"

Occassionally the status window disappears when running an alignment. Clicking the top of the project manager sometimes brings it back. Otherwise, just check the output to the terminal, which tells you when it is done. You may have to restart the project manager to see the results.

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Email Comments To: symap@agcol.arizona.edu

Email Comments To: symap@agcol.arizona.edu