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# Project Tracker Status Priority Subject Assignee Updated Target version
2874 GROMACS Task New Normal Refactor Gromacs (cluster) neighborlist into separate module Erik Lindahl 02/28/2019 11:36 AM
2875 GROMACS Task Accepted Normal SIMD version of the free-energy kernel Berk Hess 12/02/2019 01:44 PM GROMACS - 2021-infrastructure-stable
2877 GROMACS Task New Normal use gmx::Options more Mark Abraham 12/20/2019 01:22 PM GROMACS - 2021
2882 GROMACS Task New Normal evaluate different storage layouts for GPU coordinates/changes/forces Szilárd Páll 03/07/2019 06:21 PM
2889 GROMACS Task New Normal update grompp warnings for brevity, usefulness and actionability Mark Abraham 12/27/2019 04:38 PM GROMACS - future
2898 GROMACS Task New Low Naming common variables 03/26/2019 11:46 PM
2905 GROMACS Task New Normal Add a Jenkins configuration with std library assert 08/24/2019 05:22 PM
2908 GROMACS Task New Normal Renaming things in nbnxm Berk Hess 03/28/2019 10:10 AM
2909 GROMACS Task New Normal consider implementing mechanisms to ensure pair lists are not used past their max lifetime 04/03/2019 05:14 PM
2916 GROMACS Task New Normal Decide future of symtab Paul Bauer 09/06/2019 02:35 PM GROMACS - 2021-infrastructure-stable
2919 GROMACS Task New Normal C++ style guidelines for namespace use 04/15/2019 01:21 PM
2925 GROMACS Task New Normal BasicVector addition operator yields unexpected result when adding scalar Christian Blau 12/17/2019 10:04 AM GROMACS - 2021-infrastructure-stable
2933 GROMACS Task New Normal Convert walls to a ForceProvider 04/25/2019 02:43 PM
2936 GROMACS Task New Normal introduce check that CPU-GPU transfers/assignments are made between compatible types 02/05/2020 03:57 PM GROMACS - 2021
2947 GROMACS Task Accepted Normal make an end to end test for membed 09/24/2019 03:22 PM GROMACS - future
2965 GROMACS Task In Progress Normal Performance of GPU direct communications 02/14/2020 12:38 PM GROMACS - 2021
2976 GROMACS Task New Normal Basic math for Multidimensional arrays 12/27/2019 04:37 PM GROMACS - 2021
2983 GROMACS Task New Normal better suited data-types for bonded GPU kernels 07/11/2019 04:32 PM
2988 GROMACS Task In Progress Low clean up and refactor code to modern standards 12/27/2019 04:37 PM GROMACS - future
2992 GROMACS Task New Normal Split hw_opt in const user options and dynamic settings 12/27/2019 04:31 PM GROMACS - future
2997 GROMACS Task New Normal improve performance of alchemical free energy calculations 12/27/2019 04:31 PM GROMACS - 2021
2998 GROMACS Task Resolved Normal Update Python detection 04/23/2020 04:45 PM GROMACS - 2021-infrastructure-stable
2999 GROMACS Task New Normal Move all logging in core library and tools to use MDLogger 09/06/2019 02:36 PM GROMACS - 2021-infrastructure-stable
3001 GROMACS Task New Normal explore simplifying virial and shift force reduction 12/27/2019 04:30 PM GROMACS - 2021
3002 GROMACS Task New Normal consider splitting bonded work into local/nonlocal 06/25/2019 04:06 PM
3003 GROMACS Task New Normal implement heuristic fallback to CPU when there is too little work for GPU offload 06/25/2019 04:10 PM
3004 GROMACS Task New Normal Move trajectory analysis logging to MDLogger 06/26/2019 09:59 AM
3005 GROMACS Task New Normal Move logging in gmx preprocess to MDLogger 06/26/2019 10:01 AM
3008 GROMACS Task New Normal verify block size choice of CUDA bonded kernel 12/27/2019 04:30 PM GROMACS - 2021
3010 GROMACS Task In Progress Normal upgrade OpenCL stack on bs-gpu01 12/20/2019 08:25 AM GROMACS - 2021-infrastructure-stable
3013 GROMACS Task New Normal Extend logging levels in MDLogger 09/06/2019 02:34 PM GROMACS - 2021-infrastructure-stable
3014 GROMACS Task In Progress Normal gmxapi example Python scripts 01/03/2020 11:00 AM GROMACS - 2021-infrastructure-stable
3015 GROMACS Task New Normal Create central log handle for calls to gmx_fatal 09/06/2019 02:34 PM GROMACS - 2021-infrastructure-stable
3016 GROMACS Task New Normal intermittent failure of essentialdynamics test 07/18/2019 05:23 PM
3031 GROMACS Task New Normal evaluate the impact of particle order on PME 12/27/2019 04:29 PM GROMACS - 2021
3033 GROMACS Task In Progress Normal Clean up and modernize googletest bundling and usage 01/16/2020 04:50 PM GROMACS - 2021-refactoring
3035 GROMACS Task New Normal Provide central logger in wrapper binary Paul Bauer 09/06/2019 02:34 PM GROMACS - 2021-infrastructure-stable
3040 GROMACS Task New Normal Refactor Restraint module 07/18/2019 03:59 PM
3041 GROMACS Task Resolved Normal Remove workaround for gcc bug 58265 06/19/2020 04:45 PM
3047 GROMACS Task Feedback wanted Normal Set required versions for GROMACS 2021 02/20/2020 11:42 AM
3057 GROMACS Task New Normal re-enable fusion on Power8/9 Szilárd Páll 12/27/2019 04:22 PM GROMACS - 2021
3062 GROMACS Task New Normal add twin cut-off mdrun test 12/27/2019 04:22 PM GROMACS - 2021
3064 GROMACS Task New Normal add test for perturbed bonded forces 12/27/2019 04:22 PM GROMACS - 2021
3072 GROMACS Task New Normal Use gmx::index for indexing instead of int Christian Blau 09/03/2019 04:23 PM GROMACS - 2021-infrastructure-stable
3076 GROMACS Task New Normal Selectively activate MdModules during simulation instead of instantiating all of them Christian Blau 01/17/2020 02:40 PM GROMACS - 2021-infrastructure-stable
3077 GROMACS Task Feedback wanted Normal PME/PP GPU Comms unique pointer deletion causes seg fault when CUDA calls exist in destructor 11/01/2019 06:56 PM
3078 GROMACS Task New Normal Allow MD modules to register energy output fields themselves 09/06/2019 11:36 AM
3082 GROMACS Task New High move launch/synchronization points to clarify task dependencies 12/27/2019 04:21 PM GROMACS - 2021
3093 GROMACS Task In Progress High rework GPU direct halo-exchange related force reduction complexities 02/14/2020 11:35 AM GROMACS - 2021-infrastructure-stable
3096 GROMACS Task New Normal Multiple time-stepping: correct coupling algorithms, virial calculation and energy output Christian Blau 09/18/2019 02:18 PM GROMACS - 2021-infrastructure-stable
3104 GROMACS Task New Normal implement GPU DD cycle counting 12/27/2019 04:21 PM GROMACS - 2021
3105 GROMACS Task New Normal implement GPU PME/PP comm cycle counting 12/27/2019 04:20 PM GROMACS - 2021
3119 GROMACS Task New Normal clang-tidy coverage of parallelizaton codepaths 12/27/2019 04:20 PM GROMACS - 2021
3123 GROMACS Task New Normal address sanitizer coverage of parallelization code-paths 10/05/2019 12:32 AM
3130 GROMACS Task New Normal Interim handling of gmxapi data references. Eric Irrgang 12/11/2019 11:26 AM GROMACS - 2021-infrastructure-stable
3131 GROMACS Task New Normal support ccache with clang-tidy Mark Abraham 12/20/2019 08:20 AM GROMACS - 2021-infrastructure-stable
3132 GROMACS Task New Normal gmxapi testing support tools 10/31/2019 03:35 PM
3133 GROMACS Task In Progress Normal Cookiecutter for sample_restraint Eric Irrgang 12/10/2019 01:59 PM GROMACS - 2021-infrastructure-stable
3139 GROMACS Task New Normal gmxapi Futures should be subscribable Eric Irrgang 10/15/2019 03:56 PM
3143 GROMACS Task New Normal move the non-force accumulation/accounting tasks out of the GPU wait functions Szilárd Páll 12/27/2019 04:16 PM GROMACS - 2021
3145 GROMACS Task New Normal gmxapi.mdrun needs improved (and public) interface for attaching an MD extension. Eric Irrgang 01/16/2020 04:31 PM GROMACS - 2021-refactoring
3153 GROMACS Task New Low Let CMake process module directories earlier to support more modern CMake idioms. 10/17/2019 10:40 AM GROMACS - 2021-infrastructure-stable
3154 GROMACS Task Resolved Low Update use of Python subprocess for >=3.5 04/09/2020 10:15 PM
3155 GROMACS Task Accepted Normal Unify DD and CPU-GPU gather & scatter Artem Zhmurov 10/17/2019 03:50 PM GROMACS - 2021-infrastructure-stable
3162 GROMACS Task New Normal Add virtual site support to GPU version of update-constraints. Artem Zhmurov 01/23/2020 11:52 AM GROMACS - 2021-infrastructure-stable
3171 GROMACS Task New Normal schedule CPU H2D force contribution in separate stream 12/20/2019 08:33 AM GROMACS - 2021-infrastructure-stable
3174 GROMACS Task Feedback wanted Low Proposed gmxapi syntax update: "input" and "output" key word arguments -> "inputs" and "outputs" Eric Irrgang 10/23/2019 06:34 PM
3180 GROMACS Task New Normal Remove extra D2H and H2D copies of coordinates when the COM motion is compensated. Artem Zhmurov 02/14/2020 12:45 PM GROMACS - 2021-infrastructure-stable
3181 GROMACS Task New Normal consolidate task assignment and workload data initialization 10/28/2019 02:53 PM
3183 GROMACS Task Accepted Normal enable bonded interactions on GPU 12/20/2019 08:32 AM GROMACS - 2021-infrastructure-stable
3185 GROMACS Task New Normal Update PME CUDA kernels to allow a different number of threads per atom in the gather and spread kernels. 10/30/2019 11:18 AM
3186 GROMACS Task In Progress Normal Update Constant/Variable naming in the PME GPU kernels. 10/30/2019 11:23 AM
3187 GROMACS Task New Normal Template updated PME kernels using threads per atom 10/30/2019 11:33 AM
3189 GROMACS Task In Progress High implement heuristics for switching between different spread/gather kernel layouts Jonathan Vincent 01/29/2020 04:18 PM GROMACS - 2021-infrastructure-stable
3194 GROMACS Task New Normal consider passing GPU dependency list to both dependency producers and consumers 11/01/2019 07:10 PM
3201 GROMACS Task In Progress Normal Convert mdp parameters to key value tree 11/06/2019 06:06 PM
3203 GROMACS Task Accepted Normal Tools should check that input is valid when first using it Paul Bauer 12/03/2019 05:26 PM GROMACS - 2021-infrastructure-stable
3212 GROMACS Task New Normal Update regression tests for new kernel flavours 11/21/2019 11:50 AM
3216 GROMACS Task New Normal improve CPU force reductions Szilárd Páll 12/04/2019 09:24 PM
3220 GROMACS Task New Normal change rolling pruning scheduling with GPU update 02/25/2020 03:41 PM GROMACS - 2021-infrastructure-stable
3224 GROMACS Task New Normal add regression test case large enough to miscalculated GPU grid launch cases 12/20/2019 01:18 PM GROMACS - 2021
3229 GROMACS Task New Normal Move checkpointing to the beginning of the MD step 01/16/2020 04:31 PM GROMACS - 2021-infrastructure-stable
3235 GROMACS Task New Normal Run mdrun-test in parallel and make sure they tests test critical quantities like energy conservation Christian Blau 12/12/2019 03:46 PM GROMACS - 2021-infrastructure-stable
3236 GROMACS Task New Normal GPU update-constraints: Pulling support Artem Zhmurov 01/23/2020 11:53 AM GROMACS - 2021-infrastructure-stable
3252 GROMACS Task New Normal Remove support for 32 bit architectures 03/01/2020 02:05 PM
3254 GROMACS Task New Normal Remove support for generation of virtual sites to replace aromatic rings in standard residues 12/19/2019 12:13 PM
3255 GROMACS Task New Normal Move benchmarking options from mdrun to a dedicated tool 12/19/2019 01:21 PM
3256 GROMACS Task New Normal Remove -nsteps option from mdrun 12/19/2019 12:12 PM
3258 GROMACS Task New Normal GPU update-constraints: Enable free energy perturbation Artem Zhmurov 01/23/2020 11:54 AM GROMACS - 2021-infrastructure-stable
3260 GROMACS Task New Low keep up to with mdspan reference implementation Christian Blau 12/20/2019 01:16 PM GROMACS - 2021-infrastructure-stable
3262 GROMACS Task New High Trjconv - dimer protein-ligand 12/20/2019 09:26 PM
3264 GROMACS Task New Normal Break up MdrunMpiTests Paul Bauer 12/23/2019 11:44 AM GROMACS - 2021-infrastructure-stable
3267 GROMACS Task New Normal Document tools 12/26/2019 03:20 PM GROMACS - future
3268 GROMACS Task New Normal add more Intel driver recommendations 12/26/2019 04:39 PM
3271 GROMACS Task Resolved Normal Adopt PEP-518 for Python package build system configuration. 04/09/2020 10:15 PM GROMACS - 2021-infrastructure-stable
3272 GROMACS Task New Normal Port complete CI testing to Gitlab Paul Bauer 02/27/2020 11:04 AM GROMACS - 2021-infrastructure-stable
3275 GROMACS Task New Normal Document Gitlab CI instead of Jenkins and releng Paul Bauer 03/09/2020 05:55 PM GROMACS - 2021-infrastructure-stable
3279 GROMACS Task New Low Provide more advice for building client software 03/02/2020 11:54 AM
3287 GROMACS Task New Normal Deprecate make_ndx, use select instead 01/23/2020 01:16 PM
3289 GROMACS Task New Normal Distinguish identifying and non-identifying inputs to API operations. Eric Irrgang 01/10/2020 11:30 AM
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