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File gromacs.changes of Package gromacs (Revision a8f5411323452d57ee59bcbe9485566b)

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Tue Mar  5 21:02:02 UTC 2013 - kkaempf@suse.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

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Mon Feb  4 09:20:09 UTC 2013 - kkaempf@suse.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.

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Mon Jun  4 16:09:35 UTC 2012 - toddrme2178@gmail.com

- Clean up spec file

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Wed Sep 21 13:32:02 UTC 2011 - kkaempf@suse.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.

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Tue Mar 22 08:37:59 UTC 2011 - kkaempf@novell.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

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Wed Nov 10 08:07:38 UTC 2010 - kkaempf@novell.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

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Thu Oct  7 07:24:01 UTC 2010 - kkaempf@novell.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

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Sat May 22 19:29:07 UTC 2010 - cristian.rodriguez@opensuse.org

- read "/dev/urandom" instead of /dev/random

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Sat Jun 20 14:07:02 CEST 2009 - coolo@novell.com

- fix build with automake 1.11

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Fri Jan  9 18:33:46 CET 2009 - crrodriguez@suse.de

- remove static libraries and "la" files

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Tue Oct  7 20:32:58 CEST 2008 - kkaempf@suse.de

- Fix buffer overflow (gcc static detection) in calcmu.c

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Mon Oct 16 01:24:15 CEST 2006 - schwab@suse.de

- Use install-exec-hook instead of install-hook.
- Use AM_PROG_AS.

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Wed Jul 19 10:11:29 CEST 2006 - kkaempf@suse.de

- update to 3.3.1
  see http://www.gromacs.org for a complete list of changes.

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Mon Jun 19 13:09:31 CEST 2006 - schwab@suse.de

- Set datadir.

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Wed Jan 25 21:36:21 CET 2006 - mls@suse.de

- converted neededforbuild to BuildRequires

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Mon Dec 19 15:00:36 CET 2005 - ro@suse.de

- added .so symlink to filelist

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Wed Aug 11 20:11:06 CEST 2004 - kkaempf@suse.de

- bugfix update to 3.2.1

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Mon Feb 23 18:34:10 CET 2004 - kkaempf@suse.de

- rename 'disco' to 'g_disco' to avoid nameclash with package mono
- build with -fno-strict-aliasing
- return value from main()

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Tue Feb 17 18:42:05 CET 2004 - kkaempf@suse.de

- remove obsolete libtool from "configure.ac".
- use proper automake syntax in "acinclude.m4".
- add missing FF.dat as advised on gromacs-users mailing list.

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Tue Feb  3 10:13:09 CET 2004 - kkaempf@suse.de

- update to 3.2

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Sat Jan 10 11:51:34 CET 2004 - adrian@suse.de

- add %run_ldconfig

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Fri Jun 13 13:51:26 CEST 2003 - kukuk@suse.de

- Add missing directories to filelist and fix permissions

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Thu Nov 21 00:34:18 CET 2002 - ro@suse.de

- work around automake problem

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Fri Nov 15 11:42:59 CET 2002 - uli@suse.de

- removed lesstif from neededforbuild (not used)

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Mon Nov 11 23:49:54 CET 2002 - ro@suse.de

- changed neededforbuild <xf86 xshared xdevel> to <x-devel-packages>

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Tue Oct 29 12:55:11 CET 2002 - ro@suse.de

- removed own libtool hacks from acinclude.m4

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Mon Jul 29 10:46:44 CEST 2002 - kkaempf@suse.de

- Initial version 3.1.4

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