[gmx-users] About Warnings in Mdrun

[Mirco Wahab]

On 28.05.2013 17:11, vidhya sankar wrote:
> As you Mailed Me I have compiled gromacs 4.6
> I have installed using the command As posted in mail
> But I have AMD 8 Core black Edition
> When I run the mdrun I saw a warning
> Note: file tpx version 73, software tpx version 83
> Using 8 MPI threads
> Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, which is better)
>
> What is the Meaning of the Above statement ?
> How to raise the Performance

1) The meaning of the above statement:
Your machine is a newer AMD FX with a FMA (fused multiply/add)
execution unit. Your Gromacs is compiled for "older" architectures
having SSE (streaming SIMD extensions) version 4.1.
But you cannt use the AVX unit properly unless you upgrade your
gcc compiler to 4.7.x (maybe 4.6.x will work too). The older
gcc is not able to not generate the AVX instructions properly.

2) How to raise the performance:
The performance difference between AVX and SSE4.1 on an
AMF FX 8350 is marginal (I have a 8350 too) and can be
ignored for most real world scenarios. The speedup would
be 3%-5% with 4.6.1 for now, depending on the scenario
(chosen integrator, system size, electrostatics).

Much higher performance gains are to be expected by
properly configuring your system (cut off, integration
method etc.). This is an advanced topic in itself, please
read this
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
and this
http://www.gromacs.org/Documentation/Cut-off_schemes

Regards

M.