Revisions of gromacs

Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 536517 from Klaus Kämpf's avatar Klaus Kämpf (kwk) (revision 36)
fixed build failure caused by openmpi
Stephan Kulow's avatar Stephan Kulow (coolo) accepted request 256827 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 28)
Automatic submission by obs-autosubmit
Adrian Schröter's avatar Adrian Schröter (adrianSuSE) committed (revision 26)
Split 13.2 from Factory
Stephan Kulow's avatar Stephan Kulow (coolo) accepted request 221759 from Klaus Kämpf's avatar Klaus Kämpf (kwk) (revision 25)
 (forwarded request 221740 from cjunghans)
Adrian Schröter's avatar Adrian Schröter (adrianSuSE) committed (revision 24)
Split 13.1 from Factory
Stephan Kulow's avatar Stephan Kulow (coolo) accepted request 157462 from Matthias Mailänder's avatar Matthias Mailänder (Mailaender) (revision 23)
- 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 (forwarded request 157461 from kwk)
Stephan Kulow's avatar Stephan Kulow (coolo) accepted request 150933 from Dmitry Roshchin's avatar Dmitry Roshchin (Dmitry_R) (revision 22)
- 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 (forwarded request 150931 from kwk)
Adrian Schröter's avatar Adrian Schröter (adrianSuSE) committed (revision 21)
Split 12.3 from Factory
Ismail Dönmez's avatar Ismail Dönmez (namtrac) accepted request 134106 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 20)
Automatic submission by obs-autosubmit
Displaying revisions 21 - 40 of 59
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