Please excuse the simplicity of this question.
I would like to take advantage of the multiple processors of my Mac running Mac OSX. Following the instructions for installation, I have changed the makefile to read “CC = g++ -arch x86_64”. Next, I have been instructed to re-run the “make” command. When I do so, I get the reply “make: ‘mothur’ is up to date”. I have the feeling that I have changed nothing. Can anyone lend a hand?
Thanks
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First, run “make clean” and then run “make” again with your edited makefile. This should hopefully do the trick.
You can also add these flags for better CPU optimization:
if running Intel Mac : -O3 -fast -ftree-vectorize -ffast-math -arch x86_64
if running G5 : -O3 -fast -mcpu=G5 -mtune=G5 -ftree-vectorize -ffast-math
if running a G4 : -03 -fast -mcpu=G4 -mtune=G4 -ftree-vectorize -ffast-math
Turns on SSE and Altivec depending on your CPU. There is no need to explicitly use the -arch x86_64 as the Apple Xcode compiler auto detects this for you. But I could be wrong… even I state this explicitly. 
I think -ffast-math is turned on by the -fast flag… but you never know when they may change things so I also add that as well.
Check these links out:
http://developer.apple.com/mac/library/releasenotes/DeveloperTools/RN-GCC4/index.html
http://gcc.gnu.org/onlinedocs/gcc-4.1.1/gcc/Optimize-Options.html
Hope this helps!