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# Project Tracker Status Priority Subject Assignee Updated Target version
3093 GROMACS Task In Progress High rework GPU direct halo-exchange related force reduction complexities 12/20/2019 08:19 AM 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
3132 GROMACS Task New Normal gmxapi testing support tools 10/31/2019 03:35 PM
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
3170 GROMACS Task New Low investigate GPU f buffer ops use cases 12/27/2019 04:13 PM GROMACS - 2021
3171 GROMACS Task New Normal schedule CPU H2D force contribution in separate stream 12/20/2019 08:33 AM 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
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
3212 GROMACS Task New Normal Update regression tests for new kernel flavours 11/21/2019 11:50 AM
3220 GROMACS Task New Normal change rolling pruning scheduling with GPU update 12/27/2019 04:11 PM GROMACS - 2020.1
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
3252 GROMACS Task New Normal Remove support for 32 bit architectures 01/09/2020 02:03 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
3262 GROMACS Task New High Trjconv - dimer protein-ligand 12/20/2019 09:26 PM
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 New Normal Adopt PEP-518 for Python package build system configuration. 12/27/2019 03:07 PM GROMACS - 2021-infrastructure-stable
3279 GROMACS Task New Normal Provide more advice for building client software 01/02/2020 01:04 PM
3287 GROMACS Task New Normal Deprecate make_ndx, use select instead 01/23/2020 01:16 PM
3290 GROMACS Task New Normal Require CMake >= 3.12 01/17/2020 10:29 AM GROMACS - 2021-refactoring
3297 GROMACS Task Accepted Normal Require gcc > 5 01/15/2020 05:58 PM GROMACS - 2021-infrastructure-stable
3300 GROMACS Task New Normal Abandon docs/OpenCLTODOList.txt? 01/15/2020 02:46 PM
3308 GROMACS Task New Normal GPU update-constraints: Cycle counting for GPU launches 01/23/2020 11:54 AM GROMACS - 2021-infrastructure-stable
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 01/22/2020 09:41 AM 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
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 01/24/2020 03:11 PM GROMACS - 2021
3357 GROMACS Task New Normal Make sure "colvars" interoperates stably and smoothly with gromacs 01/28/2020 11:04 AM
3106 GROMACS Task Fix uploaded Normal Implement multiple pulses with GPU communication Alan Gray 12/18/2019 10:32 AM GROMACS - future
3156 GROMACS Task Fix uploaded Normal move ddUsesGpuDirectCommunication and related conditionals into the workload data structures Alan Gray 01/20/2020 01:01 PM GROMACS - 2021-infrastructure-stable
3157 GROMACS Task New Normal separate PME x receive sync Alan Gray 10/17/2019 02:44 PM
2453 GROMACS Task Resolved High PME OpenCL porting effort Aleksei Iupinov 12/20/2019 12:18 PM GROMACS - 2021
2516 GROMACS Task New Low Support PME OpenCL execution width < 16 Aleksei Iupinov 06/05/2019 05:32 PM
2537 GROMACS Task New Normal Simplify PME solve reduction Aleksei Iupinov 12/20/2019 12:21 PM GROMACS - future
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
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
3236 GROMACS Task New Normal GPU update-constraints: Pulling support Artem Zhmurov 01/23/2020 11:53 AM GROMACS - 2021-infrastructure-stable
3258 GROMACS Task New Normal GPU update-constraints: Enable free energy perturbation Artem Zhmurov 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 01/24/2020 03:30 PM GROMACS - 2021-refactoring
3314 GROMACS Task Accepted Normal Platform agnostic DeviceStream Artem Zhmurov 01/22/2020 09:48 AM GROMACS - 2021-refactoring
3315 GROMACS Task Accepted Normal Platform agnostic DeviceContext Artem Zhmurov 01/22/2020 09:49 AM 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
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
2864 GROMACS Task New Normal Building incompatibilties Benson Muite 02/19/2019 02:00 PM
2071 GROMACS Task In Progress High Low accuracy default settings yield incorrect liquid densities Berk Hess 01/05/2018 03:32 PM
2238 GROMACS Task In Progress Normal GPU emulation mode support for rolling pruning missing Berk Hess 12/21/2017 03:21 PM
2452 GROMACS Task In Progress Normal Reduce data dependencies in mdrun algorithms Berk Hess 03/14/2018 08:47 PM
2822 GROMACS Task Accepted Normal Make nbnxn a module Berk Hess 12/18/2019 10:49 AM GROMACS - future
2875 GROMACS Task Accepted Normal SIMD version of the free-energy kernel Berk Hess 12/02/2019 01:44 PM GROMACS - 2021-infrastructure-stable
2908 GROMACS Task New Normal Renaming things in nbnxm Berk Hess 03/28/2019 10:10 AM
2017 GROMACS Task In Progress Normal Modularize simulation option storage and reading from mdp files Christian Blau 04/06/2018 06:07 PM GROMACS - future
2590 GROMACS Task New Normal Essential Dynamics as module providing forces Christian Blau 08/22/2018 05:03 PM GROMACS - future
2658 GROMACS Task New Normal Secondary structure assignment via DSSP as native gromacs code Christian Blau 10/09/2018 04:51 PM GROMACS - future
2834 GROMACS Task In Progress Normal C++ matrix classes Christian Blau 12/29/2019 10:32 AM GROMACS - 2021
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
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
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
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
3260 GROMACS Task New Low keep up to with mdspan reference implementation Christian Blau 12/20/2019 01:16 PM GROMACS - 2021-infrastructure-stable
3306 GROMACS Task New Normal Document gmx dos tool more clearly Christian Blau 01/20/2020 02:31 PM GROMACS - future
1323 GROMACS Task New Normal determine future of existing tools for David van der Spoel 12/04/2018 11:53 AM
2764 GROMACS Task New Normal gmxapi version updates for post release-2019 Eric Irrgang 11/21/2018 12:53 PM
3130 GROMACS Task New Normal Interim handling of gmxapi data references. Eric Irrgang 12/11/2019 11:26 AM GROMACS - 2021-infrastructure-stable
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
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
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