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2020

Due in 45 days (01/01/2020)

Annual major release

12%

140 issues   (14 closed — 126 open)

Issues by
Bug

8/27
Feature

3/34
Task

3/79
Related issues
Bug #1977: warning: __WORDSIZE not defined
Bug #1985: CUDA build system refactoring awaiting review
Bug #2192: grompp should read floats (e.g charge) from data files to double, to avoid accumulating round-off error
Bug #2390: GROMACS build system should check for valid nvcc flags before use
Bug #2480: pdb2gmx does not protonate correctly for united-atom Gromos
Bug #2553: Incorrect COM velocity correction with frozen atoms
Bug #2668: gmx anaeig entropy output are not consistent between runs
Bug #2728: Fix NB kernel picking
Bug #2767: grompp warns about md + FEP even for fully coupled states
Bug #2798: Default mpi rank number fails when there are 16 cores and 3 gpus
Bug #2815: gmx msd -mol broken
Bug #2832: PaddedVector move operations broken
Bug #2836: Travis-CI configuration file is broken and obstructive
Bug #2843: Building with GMX_BUILD_OWN_FFTW
Bug #2844: Test SEGV with -DGMX_DOUBLE due to LAPACK
Bug #2858: Group scheme C kernels fail in complext tests
Bug #2862: Division by zero in restrained dihedrals
Bug #2903: gmx wham doesn't compute profile with pull=angle-axis
Bug #2925: BasicVector addition operator yields unexpected result when adding scalar
Bug #2987: assess the bonded GPU task assignment default
Bug #3024: Bad logic for Sphinx detection CMake output
Bug #3050: Fix tests on Solaris
Bug #3071: complex.nbnxn-ljpme-LB-geometric failing with OpenCL timing debug mode assertions
Bug #3141: gmxapi File placeholders missing from beta release
Bug #3161: mdrun-test hangs with -ntmpi2
Feature #868: Implement parallelization support to analysis framework
Feature #1165: Multi-SIMD binaries
Feature #1975: grompp should warn if .mdp define does nothing
Feature #2054: PME on GPU
Feature #2070: Physical validation testing
Feature #2224: Proposed feature: conditional stop
Feature #2581: User interface for hybrid Monte Carlo
Feature #2615: Switch to Python3
Feature #2667: Suggested steps for calculating entropy in solution and binding
Feature #2710: Separate dvdl for each molecule (of couple-moltype) when running FEP
Feature #2715: Avoid requesting the user to recompile gromacs for Intel OpenCL support
Feature #2774: Refactor shell code into its own integrator
Feature #2806: SIMD algorithms for ARM SVE // nobnonded cluster and otheres
Feature #2816: GPU offload / optimization for update&constraits, buffer ops and multi-gpu communication
Feature #2885: CUDA version of LINCS
Feature #2886: CUDA version of SETTLE
Feature #2887: CUDA version of Leap Frog algorithm
Feature #2888: CUDA Update and Constraints module
Feature #2890: GPU Halo Exchange
Feature #2896: Python packaging
Feature #2901: Declare external Resources in mdp / tpr files.
Feature #2934: GPU X Buffer ops
Feature #2944: Roadmap for thermostats / barostats in new propagation/integration scheme
Feature #2957: add support for the Hygon Dhyana architecture
Feature #2985: Python package documentation
Feature #2994: Data flow topology in gmxapi 2020
Feature #2996: gmxapi execution model
Feature #3021: Completion of docs for GPU developments
Feature #3022: modernized naming for new GPU developments
Feature #3032: Clean up dev-manual structure
Feature #3034: Python gmxapi exception hierarchy
Feature #3038: Improvements to MD plugin development environment
Feature #3087: enable GPU peer to peer access
Feature #3140: Allow explicit input definition for gmxapi.operation function wrapper
Task #1587: improve the configurability of regression tests
Task #1781: re-design benchmarking functionality
Task #1925: remove concept of unilateral global communication
Task #1943: make sure releases are submitted early for Debian Experimental
Task #2053: refine notation in GPU code
Task #2059: Separate different types of data in t_state
Task #2169: remove 'continuation' mdp option
Task #2281: Represent data on regularly spaced N-dimensional grids.
Task #2353: improve on relative tolerance for constructing tables
Task #2391: re-enable TPI test
Task #2395: break up commrec
Task #2396: Refactor trajectoryanalysis module to allow handling of trajectory frame manipulation
Task #2425: testing multisim with multiple ranks per simulation
Task #2453: PME OpenCL porting effort
Task #2475: make OpenCL 1st class-citizen in the build system
Task #2481: Update gmx report-methods to write more method information
Task #2495: replace -noconfout with mdp option
Task #2498: OpenCL memory pinning/mapping
Task #2505: increase cmake reqirement for GROMACS 2020
Task #2518: redesign task-assignment code for OpenCL
Task #2522: OpenCL context duplication
Task #2524: struct alignment/packing for OpenCL host & device code
Task #2537: Simplify PME solve reduction
Task #2654: make more symbols always defined
Task #2660: rework OpenCL nbnxn kernel constants
Task #2671: replace constants like M_PI
Task #2675: bonded CUDA offload task
Task #2686: add tests for gpu bonded interactions
Task #2695: bonded GPU module timing
Task #2697: improve FFT library flavor/version reporting
Task #2699: Test POWER9
Task #2706: Rework classic QM/MM interface
Task #2723: Update mdrun-performance.rst to clearly express the nature of task
Task #2727: Move non-analysis functions out of gmxana
Task #2730: Add tests for gmx_genion
Task #2731: Add test support for modifiable inputs to command line tools
Task #2735: Allow gmx_genrestr to write correct position restraints for molecules after the first molecule
Task #2766: Improve hardware option selection
Task #2770: change branch maintenance policy
Task #2771: Size independent Hessian for normal mode analysis
Task #2773: improve GPU error handling and make such handling uniform across modules
Task #2795: Incorporate regressiontests into core gromacs
Task #2822: Make nbnxn a module
Task #2833: Update topology datastructures
Task #2834: C++ matrix classes
Task #2839: make module and file naming consistent
Task #2875: SIMD version of the free-energy kernel
Task #2877: use gmx::Options more
Task #2889: update grompp warnings for brevity, usefulness and actionability
Task #2893: Integrate gmxapi Python package
Task #2894: Wrap importable Python code.
Task #2895: gmxapi Output proxy establishes execution dependency.
Task #2936: introduce check that CPU-GPU transfers are made between arrays of compatible types
Task #2943: Rename Integrator
Task #2945: Give MdModules access to simulation resources (e.g. atom selection manager or communication infrastructure)
Task #2965: Performance of GPU direct communications
Task #2976: Basic math for Multidimensional arrays
Task #2988: clean up and refactor code to modern standards
Task #2992: Split hw_opt in const user options and dynamic settings
Task #2997: improve performance of alchemical free energy calculations
Task #3001: explore simplifying virial and shift force reduction
Task #3008: verify block size choice of CUDA bonded kernel
Task #3014: gmxapi example Python scripts
Task #3026: add flags for GPU force buffer op / reduction activation
Task #3031: evaluate the impact of particle order on PME
Task #3037: add missing cylcle counters related to buffer ops/reduction launches
Task #3057: re-enable fusion on Power8/9
Task #3062: add twin cut-off mdrun test
Task #3064: add test for perturbed bonded forces
Task #3082: move launch/synchronization points to clarify task dependencies
Task #3092: implement better receiver ready / notify in halo exchange
Task #3104: implement GPU DD cycle counting
Task #3105: implement GPU PME/PP comm cycle counting
Task #3119: clang-tidy coverage of parallelizaton codepaths
Task #3133: Cookiecutter for sample_restraint
Task #3143: move the non-force accumulation/accounting tasks out of the GPU wait functions
Task #3170: investigate GPU f buffer ops use cases
Task #3171: schedule CPU H2D force contribution in separate stream
Task #3188: re-enalble parallel spline calculation for #threads/atoms > 4