@Richard and @DTest already have good advice in their answers, but I would like add a little as well.
RECOMMENDATION #1 : Check SUPER Privilege for all DB Users
Make sure all users do not have SUPER privilege. Once you hit max_connections, mysqld will only allow one more connection to itself, and that user must have SUPER privilege. If all users have SUPER privilege, no DBA or sysadmin can ever login to MySQL and do admin tasks. Please do an inventory of all users and make sure that only necessary users have SUPER privilege.
RECOMMENDATION #2 : Check MySQL Connections from the OS Point-of-View
If you cannot connect to mysqld, try running this in Linux on the DB Server
netstat | grep -i mysql | grep TIME_WAIT
This will show how many DB Connections have not completely closed, even if mysqld was told to close a connection via mysql_close. Keep your eyes open for TIME_WAIT state of netstat that are associated with mysql connections.
This would be good to look at if MATLAB is a Windows program hitting a MySQL DB. Note this excerpt from MySQL Website on TIME_WAIT:
C.220.127.116.11. Connection to MySQL Server Failing on Windows
When you're running a MySQL server on Windows with many TCP/IP
connections to it, and you're experiencing that quite often your
clients get a Can't connect to MySQL server error, the reason might be
that Windows does not allow for enough ephemeral (short-lived) ports
to serve those connections.
The purpose of TIME_WAIT is to keep a connection accepting packets
even after the connection has been closed. This is because Internet
routing can cause a packet to take a slow route to its destination and
it may arrive after both sides have agreed to close. If the port is in
use for a new connection, that packet from the old connection could
break the protocol or compromise personal information from the
original connection. The TIME_WAIT delay prevents this by ensuring
that the port cannot be reused until after some time has been
permitted for those delayed packets to arrive.
It is safe to reduce TIME_WAIT greatly on LAN connections because
there is little chance of packets arriving at very long delays, as
they could through the Internet with its comparatively large distances
Windows permits ephemeral (short-lived) TCP ports to the user. After
any port is closed it will remain in a TIME_WAIT status for 120
seconds. The port will not be available again until this time expires.
The default range of port numbers depends on the version of Windows,
with a more limited number of ports in older versions:
• Windows through Server 2003: Ports in range 1025–5000
• Windows Vista, Server 2008, and newer: Ports in range 49152–65535
With a small stack of available TCP ports (5000) and a high number of
TCP ports being open and closed over a short period of time along with
the TIME_WAIT status you have a good chance for running out of ports.
There are two ways to address this problem:
• Reduce the number of TCP ports consumed quickly by investigating
connection pooling or persistent connections where possible
• Tune some settings in the Windows registry (see below)