[RNABuilder-help] Re: MMB to quad-core computer

[Samuel Flores]

kalispera Vasili,

What forum did you post your question on?  I would like to answer on there but I can't find it.

To answer, MMB is currently still a single-processor code.  You will unfortunately get no speedup from using a quad core machine.

I can perhaps provide advice on how to speed up your calculation though.  You will want to reduce degrees of freedom, and make sure you have no fast oscillations in your system that might force a small time step size. Let me know if you want help with this.



Sam



> Hello sam,
> 
> The following is an e-mail sent to you by fadoulog via your account on
> "Simtk.org Forums". If this message is spam, contains abusive or other
> comments you find offensive please contact the webmaster of the board at
> the following address:
> 
> Simtk.org Forums <noreply at simtk.org>
> 
> Include this full e-mail (particularly the headers). Please note that the
> reply address to this e-mail has been set to that of fadoulog.
> 
> Message sent to you follows
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> Dear Dr Flores,
> 
> I use MMB 2.13 in a quad-core computer (8GB RAM) and Ubuntu 13.04 64bit for
> folding an RNA.
> However, the job uses just one of the four available cores.
> I am wondering if I could share it to all four of them.
> 
> Many thanks.
> Vasiliki