Charm++ parallel programming system

[Gengbin Zheng <gzheng AT illinois.edu>]

I think this is rather a NAMD specific compiling issue, since in any
case I understand Charm++ is built without extra -march and -mtune
flags. The performance difference was due to the different ways of
compiling NAMD.

I believe if you choose --cc-opts and  --cxx-opts when configure NAMD,
 it completely overrides the default optimization flags which were
already set in NAMD config files (for example:   -O3
-fexpensive-optimizations -ffast-math)
You may want to include these flags in your cc-opts and cxx-opts too.

Gengbin

On Fri, Mar 9, 2012 at 7:43 AM, Chris Harrison 
<charris5 AT gmail.com>
 wrote:
> Marcel,
>
> I am forwarding you question to the charm++ list for further help.
>
> Best,
> Chris
>
>
> ---------- Forwarded message ----------
> From: Marcel UJI (IMAP) 
> <arzo AT uji.es>
> Date: Fri, Mar 9, 2012 at 6:49 AM
> Subject: namd-l: Compiling NAMD
> To: 
> namd-l AT ks.uiuc.edu
>
>
> 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
> optimization.
>
> Do someone have an explanation for this??
>
> Thank you in advance
>
> Marcel
>
>
>
> --
> Chris Harrison, Ph.D.
> NIH Center for Macromolecular Modeling and Bioinformatics
> Theoretical and Computational Biophysics Group
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> http://www.ks.uiuc.edu/Research/namd       Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char                          Fax: 217-244-6078
>
>
>