[gmx-users] Gromacs compilation on AMD multicore

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 6 03:08:36 CEST 2011


On 6/07/2011 1:36 AM, Anthony Cruz Balberdi wrote:
> Thank you very much Mark. Another question, will be better if I 
> compile FFTW than use the one included in my linux distro?

Per the GROMACS installation instructions, you want the precision of 
FFTW to match the precision of GROMACS. You'll have to find out what 
precision of FFTW is available for your distro and then decide. Note 
that single-precision will often be labelled fftwf or fftws, and 
double-precision fftw or fftwd.

Mark

> Anthony
>
> On Tue, Jul 5, 2011 at 11:08 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 6/07/2011 12:28 AM, Matthew Zwier wrote:
>
>         Sorry about that.
>
>         The default options are nearly optimal, and the difference
>         between a
>         modern (4.4 or 4.5) series GCC and the Intel compilers are only a
>         couple of percent.  Just be sure to have FFTW available.
>
>
>     ... if planning to use PME. Also, Intel MKL is only a percent or
>     two faster than FFTW3, last I tested, but much more fiddly to link.
>
>     Mark
>
>
>         On Tue, Jul 5, 2011 at 10:26 AM, Matthew
>         Zwier<mczwier at gmail.com <mailto:mczwier at gmail.com>>  wrote:
>
>             Hi Anthony,
>
>             The default options are nearly optimal, and the difference
>             between a
>             modern (4.4 or 4.5) GCC
>
>             On Tue, Jul 5, 2011 at 10:01 AM, Anthony Cruz Balberdi
>             <anthony.cruz5 at upr.edu <mailto:anthony.cruz5 at upr.edu>>  wrote:
>
>                 Dear Users:
>
>                 We recently received our new computer.  This computer
>                 have 4 multicore
>                 Opteron AMD cpus and I am planning to install GROMAS.
>                 Which options I will
>                 need to use in order to achieve the best possible
>                 performance?
>                 Which compiler GNU or Intel?
>
>                 Thank you for all you help.
>
>                 Anthony
>
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