[gmx-users] Re: GROMACS 4.6 beta1 released!

[Mark Abraham]

I should also add that we have newly updated
http://www.gromacs.org/Documentation/Installation_Instructions and pages
that discuss some of the technical details of running the different kinds
of simulations that use the new forms ofhttp://
www.gromacs.org/Documentation/Acceleration_and_parallelization techniques
and the new and old http://www.gromacs.org/Documentation/Cut-off_schemes

We know these will all need more work - but do let us know what you think
is priority content to fix/add!

Cheers,

Mark

On Fri, Nov 30, 2012 at 2:19 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Now with email subject. Sorry all!
>
> Mark
>
> On Fri, Nov 30, 2012 at 1:38 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> Hi GROMACS users!
>>
>> We've finally got the first beta release of GROMACS 4.6 ready for you to
>> try out! We've put a lot of very hard work into it, and we hope you'll like
>> the good things we've done. Things won't be perfect yet, so we'll be
>> looking forward to your help finding the things we haven't done well enough
>> yet! Remember, if you want the big performance gains that will be available
>> in 4.6, then you'll want to know things will build and work well on your
>> hardware, and the best way of doing that is helping us over the next few
>> weeks. At the same time, we discourage you from doing work with this code
>> whose scientific reliability you need to trust - this is very much a draft
>> version of the software!
>>
>> You can find the manual here
>> ftp://ftp.gromacs.org/pub/manual/gromacs-manual-4.6-beta1.pdf and the
>> source code here
>> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6-beta1.tar.gz.
>>
>> It would be great for us if some of you want to try out the new code on
>> lots of different hardware and operation systems and report build problems,
>> inconsistencies, strange or lacking documentation and in worst case pure
>> bugs. To tempt you to do so here's a bit of a carrot corresponding to the
>> new features:
>>
>> * A brand-new native GPU implementation layer. Gromacs now does
>> heterogeneous parallalization using both CPUs and modern NVIDIA GPUs at the
>> same time, the GPU port also works in parallel using both multiple cards in
>> a node or multiple nodes, and it's smoking fast. There's lots of heroic
>> work by Szilard Pall and Berk Hess here, and special thanks to NVIDIA and
>> Mark Berger for their assistance in making this happen.
>>
>> * Gromacs can now use OpenMP parallelization for better scaling inside
>> nodes, in particular when doing the FFT part on the CPU while the GPU does
>> the normal nonbonded interactions.
>>
>> * Automatic load balancing between direct-space and PME nodes, and lots
>> of improvements in domain decomposition load balancing and scaling.
>>
>> * We have a brand new set of classical nonbonded interaction kernels, and
>> Gromacs can now use either SSE2, SSE4.1, 128-bit AVX with FMA support (AMD)
>> or 256-bit AVX (Intel), all of them in both single and double precision.
>> The performance difference depends on your system and parallelization, but
>> it is quite large in many cases - we have seen >40% improvement on ion
>> channels running on modern AMD machines!  Did we mention that the classical
>> C kernels are faster too since we can now do force-only interactions for
>> most steps?
>>
>> * There are new kernels using analytical switch/shift functions that are
>> quite a bit faster, and a new CPU-implementation of verlet kernels that
>> guarantee buffered interactions (no atoms drifting in/out of the neighbor
>> list range) that conserve energy extremely well.
>>
>> * There is a large new module to do advanced free energy calculations,
>> thanks to Michael Shirts. Trust us, you need the full manual to decipher
>> all the possibilities…
>>
>> * Gromacs has switched completely to CMake for configuration and
>> building. To be honest, we do expect some hiccups from this, but it has
>> enabled us to provide much more automation and advanced features as part of
>> the setup - and Gromacs now works on Windows out-of-the-box. Please test as
>> many parts of the build system as you can!
>>
>> * All raw assembly has been replaced by machine intrinsics in C. This
>> does wonders for readability, but it means the compiler and compiler flags
>> matter. On x86, you will typically get 5-10% better performance from icc
>> than gcc.
>>
>> Happy simulating!
>>
>> The GROMACS development team
>>
>
>