Appendix B. Troubleshooting

Table of Contents

B.1. MySQL-Related Errors
B.1.1. ERROR 2013 (HY000): Lost connection to MySQL server during query
B.2. AppArmor
B.3. Other Errors

When running Mychem, you may encounter certain errors that prevent the Mychem software to run perfectly. The purpose of this chapter is to help you to diagnose and correct some of these errors.

B.1. MySQL-Related Errors

This section describes the errors encounter with MySQL when running Mychem.

B.1.1. ERROR 2013 (HY000): Lost connection to MySQL server during query

The following examples show an error messages you may encounter when using the SMILES_TO_MOLECULE function.

mysql> SELECT SMILES_TO_MOLECULE('CCOCC');
ERROR 2013 (HY000): Lost connection to MySQL server during query

This problem has been observed with version of Mychem earlier to 0.6.0. To avoid this error, set the thread_stack parameter of MySQL to 192K. The thread_stack parameter is defined in the MySQL server configuration file.