[gmx-users] GROMACS 5.1-beta1 released

Mark Abraham mark.j.abraham at gmail.com
Thu Apr 23 17:28:27 CEST 2015

Hi GROMACS users,

The first beta release of GROMACS 5.1 is available! We are making this
available to you to get an early taste of how GROMACS 5.1 will look and
work, and most importantly to get feedback from you about how well things
work. While we try our hardest to keep the quality of GROMACS as high as
possible, we’re human, we overlook things while doing other things, and we
need your many pairs of eyes to help build a tool that we can all use to do
good science! We really need you to test your kinds of simulation on your
hardware, both for correctness and performance. This is particularly
important if you are using older hardware or compilers, because we don’t
test much on them.

Please do not use this version for doing science you plan to publish - it
needs more testing before it’s reliable enough for that. Similarly, please
don’t use this version as a base for a project that bundles or forks

What new things can you expect? (See the release notes for details)
* no more symlinks from grompp to gmx grompp, etc. (as forecast in GROMACS
* updated support and functionality for running on CUDA GPUs (see below)
* new unified documentation, including new User Guide (see below)
* several improved analysis tools
* some minor improvements to simulation performance
* enhancements to the pull code

Still in the pipeline
* OpenCL support from our friends at StreamComputing
* more minor improvements to simulation performance
* more enhancements to pull code
* improvements to multi-simulation performance
* more documentation
* perhaps a few other things

On the CUDA front
*support for the NVIDIA Tesla K80 and Maxwell architecture GeForce GPUs
like GTX 9x0 (compute capability 3/7 and 5.x)
* built-in support for checking and adjusting GPU application clocks
* improved intra-GPU load balancing
* improved multi-level heterogenous load balancing
* improved performance with pressure coupling
* the option to compile for just one target architecture, to speed up

The new documentation is aimed at bringing together all of our
documentation together with the source code, and making it easier to update
alongside the code, be in a common reStructuredText format, and deploy as a
coherent webpage that can match a single code version. There's definitely
rough edges, and we still need to bring more content in from the wiki. Any
help would be most welcome here. Which bits do you find most useful, or in
need of improvement? What’s hard to understand about the new organization?
How can we improve it?

Just so you know, a fair bit of the work done since 5.0 has been
re-organizational, rather than new features or faster performance. The
payoff is yet to come...

There’s lots of other new things, and old things removed - please see the
link to the release notes. All the content of GROMACS 5.0.4 (plus several
yet-to-be-released bug fixes) is present, apart from features that have
been removed.

If all goes to plan, we hope to ship the final 5.1 release in the next
month or two, but that relies on people joining in and helping us test! We
hope you will consider making that contribution, so that we can continue to
deliver high-quality free simulation software that will be useful to you on
day 1.

You can find the code, manual, release notes, installation instructions and
suite at the links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1-beta1.tar.gz
Documentation: http://manual.gromacs.org/documentation/5.1-beta1/index.html
(includes install guide, user guide, reference manual)
Release Notes:
Test Suite:

Happy testing!

Mark Abraham
GROMACS Development Manager

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