[gmx-users] Gromacs compilation on AMD multicore

[Szilárd Páll]

Additionally, if you care about a few percent extra performance, you
should use gcc 4.5 or 4.6 for compiling Gromacs as well as FFTW
(unless you have a bleeding-edge OS which was built with any of these
latest gcc versions). While you might not see a lot of improvement in
mdrun performance (wrt gcc >v4.5), as far as I remember, FFTW gets
slightly more boost form the new gcc versions.

I can't comment on other compilers, I haven't tried to run binaries
compiled with Intel Compiler on AMD lately.

--
Szilárd



On Wed, Jul 6, 2011 at 3:08 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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>
> 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>  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>  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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