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. The solution I used was to have them both in the configure.php:

–with-mysql=/usr \
–with-mysqli=/usr/bin/mysql_config \

Then recompile php:

./build clean
./build php n

Then I edited the /etc/httpd/conf/httpd.conf and changed:

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

To

#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

Quite possibly, only the changes to the httpd.conf are actually required, but adding the extra functionality of mysqli probably won’t hurt any.
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/

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