Changelog for
gromacs-debuginfo-4.6.1-16.7.i586.rpm :
Tue Mar 5 13:00:00 2013 kkaempfAATTsuse.com
- Update to 4.6.1
Bugfix release
- increased shared object major version to 8, #1147
- updates to HTML manual, install guide, PDF manual, shell completions
copious minor bug fixes
- various build system upgrades and fixes #1143
- new and enhanced error messages
- fixes for AdResS bugs (neighbour list construction, flop accounting,
multiple tf tables)
- fixed PME timing counter issues #1125
- fixed PME load balance reporting
- fixed forcerec to work with tools like genion and g_disre #1136
- various GPU performance enhancements
- fixed sd integrator with OpenMP threading #1138
- various minor fixes for interacting with CUDA for GPUs
- fixes for g_tune_pme to cope with new mdrun behaviour and changed
command-line options (for both g_tune_pme and mdrun)
- more checks for system support for setting thread affinities
- removed inter-flag dependency in g_order
- fixed issues with free-energy pertubation soft-core and cut-offs #1146
- fixed issues with md-vv + nose-hoover + (nstcalcenergy > nsttcouple)
[#1129]
- incorporated new changes from release 4.5.x branch
- prevented building with icc 11.1 and SSE4.1 because of known problems
[#1126]
- adding warning about not building with icc version < 12 #1126
- fixed bug sorting atoms with GPUs introduced since 4.6 #1153
- fixed issues with automated download of regression tests #1150
- fixed bug with DD cut-off check and PME dynamic load balancing #1169
Mon Feb 4 13:00:00 2013 kkaempfAATTsuse.com
- Update to 4.6
New features
- New Verlet non-bonded scheme which, by default, uses exact cut-off\'s
and a buffered pair-list.
- Multi-level hybrid parallelization (MPI + OpenMP + CUDA):
full OpenMP multithreading with the Verlet scheme;
- OpenMP mulitthreading for PME-only nodes with the group scheme;
native GPU acceleration using CUDA (supporte NVIDIA hardware).
- New x86 SIMD non-bonded kernels for the usual cut-off scheme, called
group scheme and the new verlet scheme, use x86 SIMD intrinsics (no
more assembly code):
SSE2
SSE4.1
AVX-128-FMA (for AMD Bulldozer/Piledriver)
AVX-256 (for Intel Sandy/Ivy Bridge)
- Automated OpenMP thread count choice to use all available cores.
- Automated CPU affinity setting: locking processes or threads to cores.
- Automated PP-PME (task) load-balancing: balancing non-bonded force and
PME mesh workload when the two are executed on different
compute-resources (i.e CPU and GPU or different CPUs). This enables
GPU-CPU and PP-PME process load balancing by shifting work from the
mesh to the non-bonded calculation.
- PPPM/P3M with analytical derivative at the same cost and with the same
features as PME.
- New, advanced free energy sampling techniques.
- AdResS adaptive resolution simulation support.
- Enforced rotation (\"rotational pulling\")
- Build configuration now uses CMake, configure+autoconf/make no longer
supported. (The CMake build system features with a lot of automation
and cleverness under the hood and we know that the it might not always
prove to be as rock-solid as the old one. However, far more advanced
and complex, so bear with us while we iron out issues that come up
along the way.)
- g_hbond now utilizes OpenMP.
Plus plenty of bug fixes.
Mon Jun 4 14:00:00 2012 toddrme2178AATTgmail.com
- Clean up spec file
Wed Sep 21 14:00:00 2011 kkaempfAATTsuse.com
- Clean up spec file
- Update to 4.5.5
- Improved pdb2gmx -chainsep option and reintroduced the -merge option.
- Fixed mdrun file appending truncating files to 0 bytes when
continuation runs stopped before writing new output.
- Fixed COM pulling with multiple constraints checking the
convergence of one constraint instead of all.
- Fixed some dihedrals in sugars in Gromos53a5/6 working on the
wrong atoms.
- AmberGS force field is now based on Amber94 instead of Amber96.
- Moved hydrogens in Charmm27 protein termini to separate charge
groups and added ACE and CT3 residue types.
- Many small fixes which avoid termination with fatal errors or
crashes in mdrun and tools.
- Many small updates to the manual pages of programs.
Tue Mar 22 13:00:00 2011 kkaempfAATTnovell.com
- Update to 4.5.4
- Fixed pdb2gmx picking up force field from local instead of
library directory
- Made pdb2gmx vsite generation work again for certain His
namings.
- Fixed incorrect virial and pressure averages with certain
nst... values (instantaneous values correct)
- Fixed incorrect cosine viscosity output
- New -multidir alternative for mdrun -multi option
- Several minor fixes in analysis tools
- Several updates to the program documentation
Wed Nov 10 13:00:00 2010 kkaempfAATTnovell.com
- Update to 4.5.3
- Double precision energy file reading
- CHARMM and GB issues
- Support for Altivec (PowerPC) with CMake
- Running binaries within the CMake build tree is now possible
- Various other fixes
Thu Oct 7 14:00:00 2010 kkaempfAATTnovell.com
- Update to 4.5.1
- fix bnc#642828 (CVE-2010-4001: Insecure use of LD_LIBRARY_PATH)
See http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5
for a full list of changes
- 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 thread-
based parallelization.
- 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
Sat May 22 14:00:00 2010 cristian.rodriguezAATTopensuse.org
- read \"/dev/urandom\" instead of /dev/random
Sat Jun 20 14:00:00 2009 cooloAATTnovell.com
- fix build with automake 1.11
Fri Jan 9 13:00:00 2009 crrodriguezAATTsuse.de
- remove static libraries and \"la\" files
Tue Oct 7 14:00:00 2008 kkaempfAATTsuse.de
- Fix buffer overflow (gcc static detection) in calcmu.c
Sun Oct 15 14:00:00 2006 schwabAATTsuse.de
- Use install-exec-hook instead of install-hook.
- Use AM_PROG_AS.
Wed Jul 19 14:00:00 2006 kkaempfAATTsuse.de
- update to 3.3.1
see http://www.gromacs.org for a complete list of changes.
