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# Project Tracker Status Priority Subject Assignee Updated Target version
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
3290 GROMACS Task Resolved Normal Require CMake >= 3.12 04/14/2020 02:45 PM GROMACS - 2021-refactoring
3297 GROMACS Task Resolved Normal Require gcc > 5 04/30/2020 11:00 AM GROMACS - 2021-infrastructure-stable
3300 GROMACS Task New Normal Abandon docs/OpenCLTODOList.txt? 01/15/2020 02:46 PM
3306 GROMACS Task New Normal Document gmx dos tool more clearly Christian Blau 01/20/2020 02:31 PM GROMACS - future
3308 GROMACS Task New Normal GPU update-constraints: Cycle counting for GPU launches 01/23/2020 11:54 AM GROMACS - 2021-infrastructure-stable
3312 GROMACS Task In Progress Normal Data type for coordinates, xyzq data, LJ parameters data to use for GPU buffers Artem Zhmurov 03/20/2020 09:54 AM GROMACS - 2021-refactoring
3314 GROMACS Task Resolved Normal Platform agnostic DeviceStream Artem Zhmurov 03/20/2020 09:55 AM GROMACS - 2021-refactoring
3315 GROMACS Task Resolved Normal Platform agnostic DeviceContext Artem Zhmurov 03/11/2020 04:15 PM GROMACS - 2021-refactoring
3316 GROMACS Task Accepted Normal Context and Stream manager Artem Zhmurov 01/22/2020 09:49 AM GROMACS - 2021-refactoring
3317 GROMACS Task Accepted Normal Improve testing of the GPU code Artem Zhmurov 01/22/2020 09:49 AM GROMACS - 2021-refactoring
3319 GROMACS Task In Progress Normal Use DeviceBuffer instead of native GPU types in NBNXM Artem Zhmurov 01/22/2020 09:49 AM GROMACS - 2021-refactoring
3320 GROMACS Task In Progress Normal Remove duplicating D2H/H2D wrappers in NBNXM Artem Zhmurov 01/22/2020 09:50 AM GROMACS - 2021-refactoring
3321 GROMACS Task Accepted Normal Add D2D wrapper Artem Zhmurov 01/22/2020 09:50 AM GROMACS - 2021-refactoring
3322 GROMACS Task Accepted Normal Add reallocate(...) function that does not care about the contents of the buffer Artem Zhmurov 01/22/2020 09:50 AM GROMACS - 2021-refactoring
3323 GROMACS Task In Progress Normal Rework the StatePropagatorDataGpu Artem Zhmurov 01/22/2020 09:50 AM GROMACS - 2021-refactoring
3324 GROMACS Task New Normal Rework CMake handling of GPU code 01/22/2020 09:52 AM GROMACS - 2021-refactoring
3325 GROMACS Task New Normal Allow complete re-initialization of a simulation 01/29/2020 05:13 PM GROMACS - 2021-refactoring
3326 GROMACS Task New Normal Allow changing task assignment 01/22/2020 09:44 AM GROMACS - 2021-refactoring
3327 GROMACS Task New Normal Refactor workload flags 01/22/2020 09:45 AM GROMACS - 2021-refactoring
3329 GROMACS Task New Normal Extend energy comparison testing framework 01/22/2020 09:51 AM GROMACS - 2021-refactoring
3330 GROMACS Task New Normal Compile list of codepaths for testing task assignment 01/22/2020 10:03 AM GROMACS - 2021-refactoring
3331 GROMACS Task New Low Run physical validation tests in Gitlab Paul Bauer 02/27/2020 11:09 PM GROMACS - future
3337 GROMACS Task New Normal GPU update-constraints: Merge Leap-Frog, LINCS and SETTLE kernels. Artem Zhmurov 01/23/2020 11:55 AM GROMACS - 2021-infrastructure-stable
3338 GROMACS Task New Normal GPU update-constraints: Do not save intermediate coordinates if there is no constraints Artem Zhmurov 01/23/2020 11:55 AM GROMACS - 2021-infrastructure-stable
3339 GROMACS Task New Normal GPU LINCS: Warp-level synchronization for coupled constraints Artem Zhmurov 01/23/2020 11:55 AM GROMACS - 2021-infrastructure-stable
3340 GROMACS Task New Normal GPU LINCS: Move more data to local/shared memory Artem Zhmurov 01/23/2020 11:56 AM GROMACS - 2021-infrastructure-stable
3341 GROMACS Task New Normal GPU LINCS: Use analytical solution for the matrix A inversion. Artem Zhmurov 01/23/2020 11:56 AM GROMACS - 2021-infrastructure-stable
3342 GROMACS Task New Normal GPU SETTLE: Read only one index per water molecule. Artem Zhmurov 01/23/2020 11:56 AM GROMACS - 2021-infrastructure-stable
3343 GROMACS Task New Normal GPU SETTLE: Use different ordering for matrices. Artem Zhmurov 01/23/2020 11:57 AM GROMACS - 2021-infrastructure-stable
3344 GROMACS Task New Normal GPU update-constraints: Better virial reduction. Artem Zhmurov 01/23/2020 11:57 AM GROMACS - 2021-infrastructure-stable
3345 GROMACS Task New Normal GPU update-constraints: Reconsider the naming of coordinates buffer in constraints. Artem Zhmurov 01/23/2020 11:57 AM GROMACS - 2021-infrastructure-stable
3346 GROMACS Task New Normal GPU SETTLE: Use the same parameters and parameters initialization in GPU and CPU versions of SETTLE. Artem Zhmurov 01/23/2020 11:58 AM GROMACS - 2021-infrastructure-stable
3348 GROMACS Task New Normal GPU LINCS and SETTLE: unify virial reduction Artem Zhmurov 01/23/2020 11:58 AM GROMACS - 2021-infrastructure-stable
3353 GROMACS Task New Normal Document gmx densmap output 01/23/2020 12:52 PM
3356 GROMACS Task New Normal Expose setting of random seed to API 01/29/2020 06:16 PM GROMACS - 2021
3357 GROMACS Task New Normal Make sure "colvars" interoperates stably and smoothly with gromacs 03/04/2020 11:25 AM
3360 GROMACS Task New Normal investigate the future of DD dynamic load balancing with GPU offload 01/29/2020 11:23 AM
3361 GROMACS Task New Normal Gitlab source archive contains files from build directory Paul Bauer 02/25/2020 10:13 AM GROMACS - 2020.2
3365 GROMACS Task New Low consider making GPU bonded work independent from nonbonded 03/01/2020 01:11 PM
3366 GROMACS Task New Normal Enforce compability of MdModules 02/28/2020 11:20 AM
3370 GROMACS Task New High Further improvements to GPU Buffer Ops and Comms 03/04/2020 01:38 PM
3382 GROMACS Task Accepted Normal Split up t_inputrec 02/17/2020 05:28 PM
3392 GROMACS Task New Low Unify box correction for modular simulator Pascal Merz 03/11/2020 05:20 PM GROMACS - 2021-infrastructure-stable
3415 GROMACS Task New Normal Port Pre-submit matrix to Gitlab CI Szilárd Páll 03/23/2020 10:09 AM GROMACS - 2021-refactoring
3416 GROMACS Task New Normal Port post-submit matrix to Gitlab CI Joe Jordan 03/16/2020 05:50 PM GROMACS - 2021-refactoring
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