This error appears to show up sometimes when using MySQL 5 with --with-mysql=/usr.
There have been reports that changing it to --with-mysqli=/usr/bin/mysql_config will fix this, but when I tried it, the mysql client api in php was set to mysql 3, so it wasn't quite working. Â The solution I used was to have them both in the configure.php:
--with-mysql=/usr \
--with-mysqli=/usr/bin/mysql_config \
./build clean
./build php n
SSLRandomSeed startup builtin
SSLRandomSeed connect builtin
#SSLRandomSeed startup file:/dev/random  512
#SSLRandomSeed startup file:/dev/urandom 512
#SSLRandomSeed connect file:/dev/random  512
#SSLRandomSeed connect file:/dev/urandom 512
#SSLRandomSeed startup builtin
#SSLRandomSeed connect builtin
#SSLRandomSeed startup file:/dev/random  512
SSLRandomSeed startup file:/dev/urandom 512
#SSLRandomSeed connect file:/dev/random  512
SSLRandomSeed connect file:/dev/urandom 512
I also upgraded MySQL to 5.0.41 (this case, it was a 64-bit server):
http://files.directadmin.com/services/all/mysql/64-bit/