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# Project Tracker Status Priority Subject Assignee Updated Target version
2818 GROMACS Task In Progress Normal bonded GPU kernel fusion Magnus Lundborg 07/03/2019 09:01 PM
2822 GROMACS Task Accepted Normal Make nbnxn a module Berk Hess 01/03/2019 03:07 PM GROMACS - 2020
2833 GROMACS Task New Normal Update topology datastructures Paul Bauer 12/02/2019 01:43 PM GROMACS - 2021-infrastructure-stable
2834 GROMACS Task New Normal C++ matrix classes Christian Blau 01/23/2019 12:19 PM GROMACS - 2020
2835 GROMACS Task New Normal Matrix class constraint to upper or lower triangle 02/07/2019 02:44 PM
2839 GROMACS Task New Normal make module and file naming consistent 04/09/2019 04:27 PM GROMACS - 2020
2850 GROMACS Task In Progress Normal assess Raptor Talos for testing Szilárd Páll 02/12/2019 01:14 PM
2851 Support Platforms Task New Normal uninstall redmine checklist plugin 01/30/2019 03:33 PM
2855 GROMACS Task New Normal Allow compiling GROMACS without C compiler 01/31/2019 08:44 PM
2857 GROMACS Task New Normal Clarify recommended function specifies (constexpr, noexcept, pure) 02/04/2019 04:48 AM
2859 GROMACS Task Fix uploaded Normal Change ArrayRef iterator type from pointer to std::iterator 02/08/2019 11:00 PM
2863 GROMACS Task New Normal improve PBC handling 03/11/2019 04:28 PM
2864 GROMACS Task New Normal Building incompatibilties Benson Muite 02/19/2019 02:00 PM
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 04/02/2019 06:14 PM GROMACS - 2020
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 03/11/2019 02:15 PM GROMACS - 2020
2893 GROMACS Task Resolved Normal Integrate gmxapi Python package Eric Irrgang 10/23/2019 09:16 AM GROMACS - 2020
2894 GROMACS Task Resolved Normal Wrap importable Python code. Eric Irrgang 05/09/2019 11:30 AM GROMACS - 2020
2895 GROMACS Task Resolved Normal gmxapi Output proxy establishes execution dependency. Eric Irrgang 03/29/2019 05:18 PM GROMACS - 2020
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
2912 GROMACS Task Resolved Normal C++ extension module for Python bindings Eric Irrgang 07/05/2019 09:00 AM
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
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 are made between arrays of compatible types 05/13/2019 09:23 AM GROMACS - 2020
2943 GROMACS Task New Normal Rename Integrator Pascal Merz 05/23/2019 08:04 PM GROMACS - 2020
2945 GROMACS Task New Normal Give MdModules access to simulation resources (e.g. atom selection manager or communication infrastructure) Christian Blau 05/19/2019 01:26 PM GROMACS - 2020
2947 GROMACS Task Accepted Normal make an end to end test for membed 09/24/2019 03:22 PM GROMACS - future
2965 GROMACS Task New Normal Performance of GPU direct communications 11/22/2019 12:39 PM GROMACS - 2020
2976 GROMACS Task New Normal Basic math for Multidimensional arrays 08/04/2019 09:44 PM GROMACS - 2020
2979 GROMACS Task Accepted Normal Reconsider default 1 OpenMP thread per thread-MPI rank Berk Hess 11/01/2019 03:24 PM GROMACS - 2020-rc1
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 06/20/2019 02:14 PM GROMACS - 2020
2992 GROMACS Task New Normal Split hw_opt in const user options and dynamic settings 09/24/2019 03:23 PM GROMACS - 2020
2997 GROMACS Task New Normal improve performance of alchemical free energy calculations 06/24/2019 03:07 PM GROMACS - 2020
2998 GROMACS Task In Progress Normal Update Python detection 12/02/2019 09:58 AM 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 06/25/2019 04:03 PM GROMACS - 2020
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 06/26/2019 08:38 PM GROMACS - 2020
3010 GROMACS Task In Progress Normal upgrade OpenCL stack on bs-gpu01 10/29/2019 05:41 PM GROMACS - 2020-rc1
3013 GROMACS Task New Normal Extend logging levels in MDLogger 09/06/2019 02:34 PM GROMACS - 2021-infrastructure-stable
3014 GROMACS Task New Normal gmxapi example Python scripts 06/28/2019 11:07 AM GROMACS - 2020
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
3026 GROMACS Task New Normal add flags for GPU force buffer op / reduction activation 08/01/2019 04:46 PM GROMACS - 2020
3031 GROMACS Task New Normal evaluate the impact of particle order on PME 08/21/2019 06:08 PM GROMACS - 2020
3033 GROMACS Task In Progress Normal Clean up and modernize googletest bundling and usage 08/24/2019 05:23 PM GROMACS - 2021-infrastructure-stable
3035 GROMACS Task New Normal Provide central logger in wrapper binary Paul Bauer 09/06/2019 02:34 PM GROMACS - 2021-infrastructure-stable
3037 GROMACS Task New Normal add missing cylcle counters related to buffer ops/reduction launches 11/27/2019 03:33 PM GROMACS - 2020-rc1
3040 GROMACS Task New Normal Refactor Restraint module 07/18/2019 03:59 PM
3041 GROMACS Task New Normal Remove workaround for gcc bug 58265 07/23/2019 12:27 PM
3047 GROMACS Task New Normal Set required versions for GROMACS 2021 08/24/2019 05:25 PM GROMACS - 2021-infrastructure-stable
3057 GROMACS Task New Normal re-enable fusion on Power8/9 Szilárd Páll 08/12/2019 11:41 AM GROMACS - 2020
3062 GROMACS Task New Normal add twin cut-off mdrun test 08/19/2019 06:21 PM GROMACS - 2020
3064 GROMACS Task New Normal add test for perturbed bonded forces 08/22/2019 06:34 PM GROMACS - 2020
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 09/05/2019 11:36 AM 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 10/11/2019 05:53 PM GROMACS - 2020
3092 GROMACS Task New Normal implement better receiver ready / notify in halo exchange 09/18/2019 02:47 AM GROMACS - 2020
3093 GROMACS Task In Progress High rework GPU direct halo-exchange related force reduction complexities 12/02/2019 02:17 PM GROMACS - 2020-rc1
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 09/24/2019 03:19 PM GROMACS - 2020
3105 GROMACS Task New Normal implement GPU PME/PP comm cycle counting 09/24/2019 03:19 PM GROMACS - 2020
3106 GROMACS Task New Normal Implement multiple pulses with GPU communication Alan Gray 11/01/2019 11:05 AM GROMACS - future
3114 GROMACS Task New Low Possible improvements to update-constraints Artem Zhmurov 11/14/2019 06:06 PM
3119 GROMACS Task New Normal clang-tidy coverage of parallelizaton codepaths 10/04/2019 12:17 PM GROMACS - 2020
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 12/05/2019 02:12 PM GROMACS - 2020-rc1
3131 GROMACS Task New Normal support ccache with clang-tidy Mark Abraham 10/29/2019 05:41 PM GROMACS - 2020-rc1
3132 GROMACS Task New Normal gmxapi testing support tools 10/31/2019 03:35 PM
3133 GROMACS Task New Normal Cookiecutter for sample_restraint Eric Irrgang 11/20/2019 04:36 PM GROMACS - 2020
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 10/14/2019 05:14 PM GROMACS - 2020
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 New Low Update use of Python subprocess for >=3.5 10/17/2019 01:46 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
3156 GROMACS Task New Normal move ddUsesGpuDirectCommunication and related conditionals into the workload data structures Alan Gray 12/02/2019 01:57 PM GROMACS - 2021-infrastructure-stable
3157 GROMACS Task New Normal separate PME x receive sync Alan Gray 10/17/2019 02:44 PM
3158 GROMACS Task In Progress Normal use MPI_Isend() in sendFToPpCudaDirect and receiveCoordinatesFromPpCudaDirect Alan Gray 11/07/2019 05:26 PM
3159 GROMACS Task In Progress High eliminate regression due to moving gmx_pme_send_coordinates() Alan Gray 12/02/2019 01:59 PM GROMACS - 2020-rc1
3167 GROMACS Task New High GPU update path user documentation Paul Bauer 12/02/2019 10:00 AM GROMACS - 2020-rc1
3170 GROMACS Task New Low investigate GPU f buffer ops use cases 10/22/2019 12:14 AM GROMACS - 2020
3171 GROMACS Task New Normal schedule CPU H2D force contribution in separate stream 11/29/2019 12:14 AM GROMACS - 2020-rc1
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 12/06/2019 01:15 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 12/02/2019 01:14 PM GROMACS - 2020-rc1
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
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