AGCoL SyMAP Trouble Shooting UA
BIO5
SyMAP Home | Download | Docs | System Guide | User Guide | Tour
Please send questions and suggestions to symap@agcol.arizona.edu.
SyMAP cannot be improved or problems fixed without user feedback!

Contents

Memory

Not enough memory

If SyMAP gives an out of memory error, you need to increase the memory. The symap script has the following lines: 
#!/bin/sh
mem="8192m";
echo ">>>> SyMAP build, query and view ($mem)     `date` <<<<"
java -Xmx$mem -classpath java/jar/symap.jar symapCE.ProjectManagerFrame $@
Change the number after mem=. The viewSyMAP script also requests 8192m memory, which you can also edit.

If your machine does not have much memory, you can reduce the amount of memory requested, but beware, you probably will not have enough memory to process large genomes.

For memory issues related to running MUMmer, see MUMmer.

MySQL suggested settings

Go to top

Slow to load sequence and annotation

Two MySQL settings are especially important for SyMAP performance (and generally for InnoDB table performance).

innodb_buffer_pool_size The default is too low for most purposes. You should set this to around 1Gb if possible (note that the units are bytes).
innodb_flush_log_at_trx_commit=0 The default setting is 1, which results in very slow loading of data to the database.

To check the values, start mysql and type: 

show variables like "innodb_buffer_pool_size";
show variables like "innodb_flush_log_at_trx_commit";
To change the variables, then type: 
set global innodb_buffer_pool_size=1073741824;
set global innodb_flush_log_at_trx_commit=0;
Alternatively, You can set these in the MySQL configuration file my.cnf and restart MySQL. Note that my.cnf is typically located at /etc/my.cnf, on both Linux and Mac.

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

max_allowed_packet This should be at least 500M if possible (the units are bytes).

To check the value, start mysql and type: 

show variables like "max_allowed_packet";
To change this variable, then type: 
set global max_allowed_packet=1073741824;

MySQL

Go to top

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 "^]".)

MariaDB cannot connect

Go to top
If you are using MariaDB (post version 10.4.12) and get the error: 
Unable to connect to the mysql database on localhost; are username and password correct?
Try adding the following lines to the /etc/my.cnf: 
[mysqld]
character-set-server=utf8mb4
And restart MariaDB with systemctl restart mariadb.

Thanks to Lori for this solution!

The database does not support Innodb tables

This can happen in a couple of ways ways. Look in the mysql log for clues.
  • MySQL started with the "skip-innodb" flag. Solution is to remove this.
  • InnoDB log file problems. This can happen if you change the log file size, without deleting the log file. Solution: shut down mysql, remove the innodb log file, and restart mysql.

Please read "Security" section of the manual to find out how to run mysqld as root

You are launching SyMAP as the unix root user, which is blocked by MySQL as a security hazard. Solution is simply to use a regular non-root user account.

Can't create table (errno: 121)

This can occur if you try to create a SyMAP database whose name differs only by case from an existing database, e.g. "symapTest" when "symaptest" already exists.

MySQL indices

Most records in MySQL have an index. The Hit# shown in SyMAP (queries and 2d) is one such index. If you have many alignments in the database, this number will get very large. Also, if you add alignments and delete them, the index can keep growing. Solution: once you determine the set of alignments you want, delete the database and just reload what you want for the final database.

Alignment

Go to top
Status window disappeared Occasionally 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 symap to see the results.

No anchors loaded This message indicates that SyMAP could not parse the MUMmer or BLAT output files to load the anchors. For MUMmer, see MUMmer.

MacOS and external programs

Go to top
MacOS 10.15 has made it difficult to run programs downloaded from the web unless its been authenticated by Apple. Running external programs from SyMAP, you will either get popup that states "xxx cannot be opened because developer cannot be verified", or the program will just fail. Do the following:
  • Using the Finder, select the program and Open With "Terminal" or "iTerm".
  • You will get a pop-up, select "Open".
For Promer, perform this on the following: 
mummer
promer
mgaps
show-coords
aux_bin/postpro
aux_bin/prepro
After that, you should be able to run it via SyMAP. This worked with my previous Catalina and current Monterery, but if it does not work for you, see Apple Help, section If you want to open an app that has not been notarized or is from an unidentified developer.

MacOS Monterey

Since SyMAP is compiled with v8 (pre-v5.5.0) to be upward compatible, it produces the following warning on MacOS Monterey: 
Warning: the fonts "Times" and "Lucida Bright" are not available for the Java logical font "Serif",
 which may have unexpected appearance or behavior. Re-enable the "Times" font to remove this warning.
It does not hurt anything, but its tiresome. Do the following:
  • Download Lucida Bright.zip and Times.zip from LengionFonts.
  • Double click to unzip into Times.tff. Double click Times.tff, which brings up the FontBook, then install.
  • Do the same for Lucida Bright.zip.
  • Note: after OS updates, you may have to install again.

Go to top

Email Comments To: symap@agcol.arizona.edu