Compiling NAMD

From: Marcel UJI (IMAP) (
Date: Fri Mar 09 2012 - 06:49:34 CST

Dear all,

I have been compiling NAMD for my exact machine, an Intel Xeon E5345
processor, to get the most of it. However I have found that using
-march=native (or -march=core2, which seems also correct) gets SLOWER
namd code!!

I'm using gcc compiler version 4.4.5 and introducing the option via a
configuration like this:

./config Linux-x86_64-g++ --charm-arch net-linux-x86_64 --with-cuda
--cuda-prefix /usr/local/cuda/ --cxx-opts "-march=native -mtune=native"
--cc-opts "-march=native -mtune=native"

The difference goes from about ~2.72 days/ns in a ~450.000 atoms MD-NVT
system with external field applied to 3.33 days/ns using the above
optimizations. charm++ was also compiled using gcc but without any

Do someone have an explanation for this??

Thank you in advance


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