[gmx-users] GROMACS-4.5-beta1 is out!

[Roland Schulz]

Hi,

what is the error message? Look at stdout/stderr and log file.

Roland

On Tue, Aug 3, 2010 at 11:21 AM, Da-Wei Li <lidawei at gmail.com> wrote:

> Hello
>
> I tried the Gromacs 4.5 beta. However, my MPI  mdrun died. Here it is
> the output. The Gromacs-4.0.7 work fine for the same system. It is
> "protein in water" system.  There are about 22000 atoms.
>
> ***************************************************************************************
> Will use 9 particle-particle and 7 PME only nodes
> This is a guess, check the performance at the end of the log file
> Making 1D domain decomposition 9 x 1 x 1
>
> Steepest Descents:
>   Tolerance (Fmax)   =  1.00000e+03
>   Number of steps    =        50000
> rank 9 in job 1  hpc-8-16.local_53455   caused collective abort of all
> ranks
>  exit status of rank 9: killed by signal 9
> ************************************************************
>
>
>
> dawei
>
> On Fri, Jul 30, 2010 at 3:20 PM, Rossen Apostolov
> <rossen.apostolov at cbr.su.se> wrote:
> >
> > After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is
> > out!
> >
> > It is full of many new and exciting features, please try them out!
> >
> > If something is not working as expected, please send a mail or file a
> > bugzilla report.
> >
> > For developers: there is a new branch for stable releases called
> > "release-4-5-patches". Bugfixes should be applied there *first*, and if
> > needed, merged from that branch into the master after the fix. See
> > http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more
> > information.
> >
> >
> > New features:
> >
> > 2D decomposition support for PME: improved load balancing with up to 40%
> > overall performance improvement for large systems.
> > Memory usage is improved for very large systems, allowing simulations of
> >>100 million atoms.
> > Running on multi-core nodes now automatically uses threads for domain
> > decomposition through the built-in threaded MPI library
> > GPU computing support
> > Check-pointing is made more secure:MD5sum are used to verify that all
> files
> > are correctly in-place before a simulation is appended. Output file
> > appending at continuation is turned on by default
> > Full Cmake support. Autoconf/automake will be deprecated after the final
> 4.5
> > release!
> > Full support for 7 AMBER force fields
> > Support for CHARMM27, including cmap for dihedrals
> > Efficient Generalized-Born implicit solvent support including the
> > Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating
> > the generalized Born-interaction formula for greater speed, and optimized
> > SSE-routines for both cut-off and all-vs-all simulations.
> > Support for nucleic acid simulations
> > Support for Velocity-Verlet integrators for reversible T- and P-coupling;
> > MTTK pressure control integrators; Nose-Hoover chains
> > Support for Bennett acceptance ratio (BAR) free energy calculations
> > Decoupling group setup for free energy
> > File formats: All GROMACS tools can now read any VMD supported trajectory
> > format, without converting trajectory first. (VMD is required)
> > g_rdf was a little bit enhanced that structure factors can be calculated
> for
> > any system, by supplying the necessary data via sfactor.dat. Most of the
> > common atomtypes are already contained, but everybody who needs more
> freedom
> > can enhance the table
> > Library support for "dynamic index groups" based on textual selections
> > (experimental feature). See the tool g_select, the included template.c,
> or
> > Doxygen documentation for information on how to write analysis tools
> using
> > the library. Existing tools have not (yet) been converted.
> > g_tune_pme: For a given number of processes or threads this tool
> > systematically times mdrun with various numbers of PME-only nodes and
> > determines which setting is fastest. It also checks whether performance
> can
> > be enhanced by shifting load between the real and the reciprocal space
> part
> > of the Ewald sum.
> > g_membed: a very convenient utility for embedding membrane proteins into
> > equilibrated lipid bilayers
> >
> > Big thanks to all developers, contributors and users!
> >
> > --
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