[gmx-users] template parallelization

[Erik Marklund]

Do you really mean compile time? If so, issue make -j X (where x is  
the number of jobs used for building).

If you mean runtime then the easiest thing is to split your trajectory  
in parts and run the processes in parallel, then patch the results  
together. That's if the calculations can be done on a per-frame basis  
(i.e. embarrassingly parallelizable problems). Next in line is to wrap  
some performance critical loop(s) in OpenMP pragmas and link to the  
OpenMP libraries on your system. If you want others to benefit from  
the code you should adhere to the parallelization framework in  
gromacs, e.g. use gromacs' wrappers and preprocessor directives for  
OpenMP and MPI magic. The latter may be more trouble than it's worth  
if your analysis is only for a limited userbase. There is a framework  
underway in gromacs for parallel analysis tools, but as far as I know  
it's not finalized yet.

Erik

On Mar 14, 2013, at 2:22 PM, subhadipdas wrote:

> First, here my system :
> Cent Os 64 bits
> gcc : 4.4.6
> fftw : 3.3.2 including SSE 2
>
> I am writing a code to find out the number of five and six membered  
> rings in
> structure I of hydrate . My code takes long time to compile for my  
> 500ps
> trajectory . So my query is that can the template file be made to  
> run in
> parallel fashion ? If so ,how
>
>
>
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