Fs2 open on Linux/Optimization

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The fs2_open on Linux Guide Optimization

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Warning: If you compile a debug build, don't use the -fomit-frame-pointer and -fno-ident compiler flags, as it will make debugging impossible.

Note: This step is only for those who want the bleeding-edge source code to compile on their own. You can skip this if you intend to use a provided binary executable.

Optimizing fs2_open might have little or no effect, or improve performance greatly, I honestly have no clue.
You can specify your compiler flags with the configure script, se below.

$ ./configure CFLAGS="<your desired flags>"

If you want to play it safe, a good set of CFLAGS would be

$ ./configure CFLAGS="-march=native -O3 -pipe -fomit-frame-pointer -fno-ident" CXXFLAGS="$CFLAGS"

Note: it seems that in GCC 4.7.0 (and higher until at least 4.7.2) the -ftree-vectorize flag (part of -O3) causes segfaults in FSO. Therefore you could instead use:

$ ./configure CFLAGS="-march=native -O2 -pipe -fomit-frame-pointer -fno-ident -finline-functions -funswitch-loops -fpredictive-commoning -fgcse-after-reload -fipa-cp-clone" CXXFLAGS="$CFLAGS"

You should read up on CFLAGS and what they do before trying anything. I recommend you read through these links (adjust the URL as required for your version of GCC).
http://gcc.gnu.org/onlinedocs/gcc-4.2.0/gcc/Optimize-Options.html
http://gentoo-wiki.com/Safe_Cflags