Revisions of gromacs
fixed build failure caused by openmpi
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(forwarded request 221740 from cjunghans)
- 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)
- 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)
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