[gmx-users] GROMACS 4.6 beta1 released!

Mark Abraham mark.j.abraham at gmail.com
Fri Nov 30 02:19:49 CET 2012

Now with email subject. Sorry all!


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

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