SyMAP Trouble Shoot

  #!/bin/sh
  mem="8192m";
  echo ">>>> SyMAP build, query and view ($mem)     `date` <<<<"
  java -Xmx$mem -classpath java/jar/symap.jar symapCE.SyMAPmanager $@

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

Slow to load

Slow queries

Go to top

SyMAP prints out the values the important MySQL variables when a symap database is created.
Additionally, they will be printed if the following is executed: ./symap -sql

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 Problems

Database
connect
errors

MariaDB
cannot
connect

Does not
support
Innodb tables

Run mysqld
as root

Cannot
create table
(errno: 121)

MySQL
indices

Go to top

Database connect errors

On startup, error messages mentioning the database or SQL probably mean that the database connection could not be established or was lost. First, make sure your db_adminuser and db_adminpasswd are correct in the symap.config file.

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 user specified in symap.config may not have necessary access to the database.

If you running the read/write symap, then db_adminuser is used.
If you are running a read-only 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.

MySQL privileges are granted specifically to certain users on certain machines. You can check these by starting the mysql from the command line, and then using

SELECT User, Host FROM mysql.user;

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 "^]".)

If symap has been running and you get this message to the terminal:

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

** BEGIN NEXTED EXCEPTION **

Restart the program as the connection was dropped.

MariaDB cannot connect

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.

Run mysqld as root

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

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

Cannot 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.

General

Hangs on Load

Status window disappeared

Go to top

Hangs on Load

1. Other apps may cause it to hang, e.g. on Mac, downloaded apps, such as Bartender may interfere with SyMAP, which causes it to hang. When Bartender was removed, SyMAP no longer hung on load.

2. It occasionally hangs for no discernible reason (especially if I have been doing testing on MacOS, where I remove projects and reload over and over). If this happens, Cntl-C to stop the program (or kill it some other way). Restart ./symap, Remove project from database and Load Project again.

3. If in the middle of a Load Project, any of the following actions: Cancel, or Cntl-C to stop the program, or killing it from the command line, can leave the database in a non-repairable state. Unfortunately, it has be removed and rebuilt. (22-June-2025) I have not had this happen in a very long time.

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.

MacOS

Running external programs

MacOS Fonts

Go to top

Running external programs

MacOS will run symap but not MUMmer, MAFFT or MUSCLE until they have been authenticated by you. The following instructions use Sequoia v15.7.3 and MUMmer program mgaps:

Click the apple icon in the upper left, click System Settings, click Privacy & Security. Scroll down until you see Security. Leave this window open (see left image below).
Using the Finder, go to the symap_5/ext/mummer/mac directory.
Click mgaps. You will get a pop-up that will say:
"mgaps" Not Opened.
Select Done.
Back on the Privacy & Security window, you will see under Security:
"mgaps" was blocked to protect your Mac
Select Open Anyway
Then you will get another popup saying (see right image below):
Open "mgaps"
Select Open Anyway.
Then you will get another popup asking for your password;
Enter your Mac password.
A terminal window will popup.
You can close it.

Referring to the image on the left, the mummer near the bottom will change to mgaps on Done (step 2).

For running MUMmer, perform this on the following in symap_5/ext/mummer/mac:

  mummer
  mgaps
  show-coords
  aux_bin/prepro
  aux_bin/postpro
  aux_bin/prenuc
  aux_bin/postnuc

For running MUSCLE, perform this on symap_5/ext/muscle/mac/muscle:

After that, you should be able to run these via SyMAP, even if you move the symap_5 directory. In fact, it still worked even after downloading a new symap_5.tar.gz. So, even though this is a pain to do, its only necessary once (at least with Sonoma).

Update 27-Jan-26: I updated to Sequoia, and at first, symap would try to run mummer, which would give an error. I downloaded the latest symap_5.tar.gz, went through the above steps to verify the MUMmer programs, and was then able to move the /ext directory to other symap directories and have it work.

Versions of this worked with my previous Catalina, Monterey, and Sonoma. If it does not work for you, see Apple Help.

MacOS Fonts

If you get the following warning:

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.

Java Runtime Error

On rare occasions, Java crashes, SyMAP will quit and you will see:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGBUS (0xa) at pc=0x000000010a05a58e, pid=70813, tid=89091
etc

When searching online for this problem, it says: "This fatal error occurs when the Java Virtual Machine (JVM) crashes, typically due to issues in native code (outside the JVM), memory corruption, or hardware instability".

Searching native code, it says: "When a 'fatal error' occurs in native code, it means the crash happened in a non-Java component such as a shared library (.dll, .so), a system driver".

This was happening to me recently. I used CleanMyMac app to remove old files, then rebooted; it has not happened since.

Go to top

Email Comments To: cas1@arizona.edu