[Dock-fans] Speed-Optimization for your DOCK

Sheng-Hung Wang gentamicin5 at yahoo.com.tw
Mon Oct 31 06:48:56 PST 2005


Dear docker,

I'd like to share some strategies for improve performance of DOCK in
compiling level.
Some test can be find in:
http://home.pchome.com.tw/team/gentamicin/mol/mol.htm
It can improve performance about 35% compared to -O2 option only.

-------------------------------------------------------------
Suggestions of optimization options for gcc:

Makefile.linux:

CXX=            g++
CFLAGS= -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O3 -march=pentium4
-mfpmath=sse -msse2 -malign-double -funroll-loops -fomit-frame-pointer
-fschedule-insns2 -fexpensive-optimizations -w
......
-------------------------------------------------------
This is just an example for gcc in linux, and for pentium 4 processor
with sse2 function.
You should change your cpu-type indicated in -march option.
For other cpu-type, you can visit this article and also see gcc
manpage.
http://www.linuxjournal.com/node/7269/print

Note:
1. Some optimization options work only when your cpu supports it, and
some options should be used carefully (for example, -ffast-math,
-mno-ieee-fp...etc).  It is possible to give you the wrong calculating
results in some programs.
2. For higher level(newer) pentium processors, you can consider to use
Inter C++ compiler. But in my case, gcc-3.2.2 seems still better than
icc-9.0 in performance(P4 2.0 AG, single CPU).
3. You should re-compile and re-install DOCK after modifying CFLAGS.



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