- 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)
OBS-URL: https://build.opensuse.org/request/show/157462
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/gromacs?expand=0&rev=23
- 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)
OBS-URL: https://build.opensuse.org/request/show/150933
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/gromacs?expand=0&rev=22
- 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. (forwarded request 84299 from kwk)
OBS-URL: https://build.opensuse.org/request/show/84316
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/gromacs?expand=0&rev=16
dimstar_suse
maxlin_factory
Stephan Kulow
Ismail Dönmez
Sascha Peilicke
Lars Vogdt
darix
Ruediger Oertel