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

Da-Wei Li lidawei at gmail.com
Tue Aug 3 17:21:42 CEST 2010


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


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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