if you're using putty, means the logs will appear during ./configure, make clean, make sql, make server in your putty terminal.
to keep the log in your vps, you can try ./athena-start start >log1 >log2 so the logs will be saved in log1 and log2 which you can find inside rathena folder.
about map crash, you can use gdb and view the core file when the process crash.
https://github.com/rathena/rathena/wiki/GDB