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# Project Tracker Status Priority Subject Assignee Updated Target version
2537 GROMACS Task New Normal Simplify PME solve reduction Aleksei Iupinov 12/20/2019 12:21 PM GROMACS - future
2546 GROMACS Task New Normal Add more assertions to AWH code Viveca Lindahl 06/06/2018 11:20 AM GROMACS - future
2590 GROMACS Task New Normal Essential Dynamics as module providing forces Christian Blau 08/22/2018 05:03 PM GROMACS - future
2595 GROMACS Task New Normal Reusable Utilities for Schedules Prashanth Kanduri 02/22/2019 03:48 PM GROMACS - future
2603 GROMACS Task New Normal Add ability to properly check coordinate files during testing Paul Bauer 10/15/2018 01:16 PM GROMACS - future
2621 GROMACS Task New Normal Fine-Grained API to Describe Force Calculation and Neighbourhood Search Prashanth Kanduri 08/22/2018 11:36 AM GROMACS - future
2632 GROMACS Task New Low make sure cmake defines proper hwloc versionc with cross-compilation enabled 12/03/2018 01:35 PM GROMACS - future
2644 GROMACS Task New Normal Replace compute_globals Mark Abraham 09/24/2018 05:51 PM GROMACS - future
2650 GROMACS Task New Normal revise OpenCL stack recommendations 12/31/2018 11:19 AM 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
2660 GROMACS Task New Low rework OpenCL nbnxn kernel constants Szilárd Páll 12/28/2019 10:53 AM GROMACS - future
2671 GROMACS Task New Normal replace constants like M_PI 12/20/2019 01:17 PM GROMACS - future
2672 GROMACS Task New Normal check & document execution width requirements in OpenCL 12/31/2018 11:20 AM GROMACS - future
2697 GROMACS Task New Normal improve FFT library flavor/version reporting 12/27/2019 04:40 PM GROMACS - future
2735 GROMACS Task New Normal Allow gmx_genrestr to write correct position restraints for molecules after the first molecule Joe Jordan 12/11/2019 09:26 AM GROMACS - future
2758 GROMACS Task New Low Modernize genconf 11/15/2018 07:38 AM GROMACS - future
2771 GROMACS Task New Normal Size independent Hessian for normal mode analysis 12/28/2019 10:50 AM GROMACS - future
2889 GROMACS Task New Normal update grompp warnings for brevity, usefulness and actionability Mark Abraham 12/27/2019 04:38 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
3267 GROMACS Task New Normal Document tools 12/26/2019 03:20 PM GROMACS - future
3306 GROMACS Task New Normal Document gmx dos tool more clearly Christian Blau 01/20/2020 02:31 PM GROMACS - future
3331 GROMACS Task New Low Run physical validation tests in Gitlab Paul Bauer 02/27/2020 11:09 PM GROMACS - future
1197 TNG trajectory library Feature New Normal Rework the molecule descriptions 03/18/2013 04:16 PM TNG trajectory library - version 2
1199 TNG trajectory library Feature New Normal residue numbering Magnus Lundborg 04/24/2013 09:33 AM TNG trajectory library - version 2
1200 TNG trajectory library Feature New Normal Field for the PDB format 'segment identifier' Magnus Lundborg 04/24/2013 09:32 AM TNG trajectory library - version 2
1202 TNG trajectory library Feature New Normal Other hash types 06/25/2013 10:02 PM TNG trajectory library - version 2
1206 TNG trajectory library Feature New Low XTC Compression 10/25/2013 03:43 PM TNG trajectory library - version 2
3313 GROMACS Feature Accepted Normal Introduce and use opaque types for the DeviceStream and DeviceContext Artem Zhmurov 01/23/2020 12:00 PM GROMACS - 2021-refactoring
3316 GROMACS Task Accepted Normal Context and Stream manager Artem Zhmurov 01/22/2020 09:49 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
3071 GROMACS Bug Accepted Normal complex.nbnxn-ljpme-LB-geometric failing with OpenCL timing debug mode assertions Szilárd Páll 02/25/2020 03:39 PM GROMACS - 2020.2
3246 GROMACS Bug Accepted Normal GPU code misses settle error check, simulation crashes with segfault without any further output Artem Zhmurov 12/20/2019 09:52 AM GROMACS - 2021-infrastructure-stable
2706 GROMACS Task Accepted Normal Rework classic QM/MM interface 12/02/2019 01:45 PM GROMACS - 2021-infrastructure-stable
2875 GROMACS Task Accepted Normal SIMD version of the free-energy kernel Berk Hess 12/02/2019 01:44 PM GROMACS - 2021-infrastructure-stable
3155 GROMACS Task Accepted Normal Unify DD and CPU-GPU gather & scatter Artem Zhmurov 10/17/2019 03:50 PM GROMACS - 2021-infrastructure-stable
3183 GROMACS Task Accepted Normal enable bonded interactions on GPU 12/20/2019 08:32 AM GROMACS - 2021-infrastructure-stable
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
2192 GROMACS Bug Accepted Low grompp should read floats (e.g charge) from data files to double, to avoid accumulating round-off error Berk Hess 12/20/2019 12:11 PM GROMACS - 2021
1943 GROMACS Task Accepted Low make sure releases are submitted early for Debian Experimental Szilárd Páll 12/20/2019 12:05 PM GROMACS - 2021
2495 GROMACS Task Accepted Normal replace -noconfout with mdp option Mark Abraham 12/28/2019 10:39 AM GROMACS - 2021
2233 GROMACS Bug Accepted Normal replica exchange and -append bugged? 03/05/2018 01:38 PM
2702 GROMACS Bug Accepted Normal PME gather reduction race in OpenCL (and CUDA) 03/28/2019 03:14 PM
3234 GROMACS Bug Accepted Normal Signal: Floating point exception Signal code: Floating point divide-by-zero Erik Lindahl 12/16/2019 03:40 PM
3405 GROMACS Bug Accepted Normal intermitted OpenCL regressiontest failures 03/02/2020 11:01 AM
3442 GROMACS Bug Accepted Normal continuing mdrun with -deffnm and pulling does not work 03/15/2020 08:33 AM
1192 GROMACS Feature Accepted Normal Add support for Verlet scheme with Buckingham Berk Hess 07/11/2016 08:19 PM
1328 GROMACS Feature Accepted Normal Names for selection positions 07/11/2016 08:15 PM
1511 GROMACS Feature Accepted Normal add PDBx (ie mmcif) support 10/05/2018 07:14 PM
1902 GROMACS Feature Accepted Low Add grompp check that non-excluded atoms are not too close to each other in the starting structure 02/15/2016 01:34 PM
1964 GROMACS Feature Accepted Normal "pull=no" should not produce warnings about "unknown" pull keywords 05/20/2016 02:37 PM
2194 GROMACS Feature Accepted Low xvg output requested as an output option in place of xpm files 05/31/2017 04:26 PM
2288 GROMACS Feature Accepted Low gmx msd doesn't optimally handle missing input trajectory frames 11/10/2017 11:03 AM
3355 GROMACS Feature Accepted Normal New PME parallel (GPU) scheme Jonathan Vincent 02/12/2020 11:58 AM
1056 GROMACS Task Accepted Normal status of fft5d_threads and fftw3_threads functionality Mark Abraham 07/11/2016 08:21 PM
1907 GROMACS Task Accepted Low keeping compile- and run-time CPU/arch detection consistent 08/01/2016 10:09 PM
2166 GROMACS Task Accepted Normal gmx trjconv functionality should check for mismatch between the tpr and the trajectory 05/05/2017 04:32 PM
2240 GROMACS Task Accepted Low GPU emulation mode support for PME missing 09/16/2017 10:02 PM
2448 GROMACS Task Accepted Normal should mdrun -multidir permit only one directory? 03/21/2018 12:10 PM
3382 GROMACS Task Accepted Normal Split up t_inputrec 02/17/2020 05:28 PM
1839 GROMACS Bug Accepted Low pdb2gmx: Failure to rename non-standard hydrogen atom names after generating missing hydrogens in pdb2gmx 07/09/2016 07:27 PM GROMACS - future
1919 GROMACS Bug Accepted Normal static linking issues cause by hwloc support 10/12/2018 10:49 PM GROMACS - future
720 GROMACS Feature Accepted Low permit pdb2gmx to choose a kind of HIS based on proton position 11/17/2016 03:51 PM GROMACS - future
907 GROMACS Feature Accepted Normal Add tests for verifying installed headers 03/11/2014 09:15 PM GROMACS - future
1165 GROMACS Feature Accepted Low Multi-SIMD binaries 12/20/2019 12:00 PM GROMACS - future
1221 GROMACS Feature Accepted Normal More generic position mapping for selections 06/10/2014 02:58 PM GROMACS - future
2054 GROMACS Feature Accepted High PME on GPU Aleksei Iupinov 12/20/2019 12:18 PM GROMACS - future
2310 GROMACS Feature Accepted Low Let mdrun dump coordinates with non-finite energy 10/03/2018 09:47 PM GROMACS - future
2581 GROMACS Feature Accepted Normal User interface for hybrid Monte Carlo 12/20/2019 12:24 PM GROMACS - future
1781 GROMACS Task Accepted Normal re-design benchmarking functionality Mark Abraham 12/20/2019 12:03 PM GROMACS - future
2674 GROMACS Task Accepted Normal Improve domain decomposition for bilayer systems 12/07/2018 04:03 PM GROMACS - future
2822 GROMACS Task Accepted Normal Make nbnxn a module Berk Hess 12/18/2019 10:49 AM GROMACS - future
2947 GROMACS Task Accepted Normal make an end to end test for membed 09/24/2019 03:22 PM GROMACS - future
3311 GROMACS Feature In Progress Normal GPU infrastructure development 03/20/2020 09:54 AM GROMACS - 2021-refactoring
3318 GROMACS Feature In Progress Normal Use wrappers for the GPU buffer copy/allocations Artem Zhmurov 01/23/2020 12:01 PM GROMACS - 2021-refactoring
2756 GROMACS Task In Progress Normal gmxapi integration testing 01/16/2020 05:12 PM GROMACS - 2021-refactoring
3033 GROMACS Task In Progress Normal Clean up and modernize googletest bundling and usage 01/16/2020 04:50 PM GROMACS - 2021-refactoring
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
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
3323 GROMACS Task In Progress Normal Rework the StatePropagatorDataGpu Artem Zhmurov 01/22/2020 09:50 AM GROMACS - 2021-refactoring
2996 GROMACS Feature In Progress Normal gmxapi execution model Eric Irrgang 12/10/2019 01:57 PM GROMACS - 2021-infrastructure-stable
2395 GROMACS Task In Progress Normal break up commrec Mark Abraham 12/15/2019 11:51 AM GROMACS - 2021-infrastructure-stable
2698 GROMACS Task In Progress Normal gmxapi documentation integration 01/29/2020 03:59 PM GROMACS - 2021-infrastructure-stable
3010 GROMACS Task In Progress Normal upgrade OpenCL stack on bs-gpu01 12/20/2019 08:25 AM GROMACS - 2021-infrastructure-stable
3014 GROMACS Task In Progress Normal gmxapi example Python scripts 01/03/2020 11:00 AM GROMACS - 2021-infrastructure-stable
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
3133 GROMACS Task In Progress Normal Cookiecutter for sample_restraint Eric Irrgang 12/10/2019 01:59 PM GROMACS - 2021-infrastructure-stable
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
3244 GROMACS Bug In Progress Normal center of mass motion removal with position restraints can lead to artifacts Berk Hess 12/27/2019 10:40 AM GROMACS - 2021
868 GROMACS Feature In Progress Normal Implement parallelization support to analysis framework Kevin Boyd 12/20/2019 11:59 AM GROMACS - 2021
2890 GROMACS Feature In Progress Normal GPU Halo Exchange 02/14/2020 12:41 PM GROMACS - 2021
1925 GROMACS Task In Progress Normal remove concept of unilateral global communication 12/29/2019 10:35 AM GROMACS - 2021
2059 GROMACS Task In Progress Normal Separate different types of data in t_state 12/27/2019 04:42 PM GROMACS - 2021
2675 GROMACS Task In Progress Normal bonded CUDA offload task 02/12/2020 05:54 PM GROMACS - 2021
2766 GROMACS Task In Progress Normal Improve hardware option selection Kevin Boyd 12/20/2019 02:34 PM GROMACS - 2021
2834 GROMACS Task In Progress Normal C++ matrix classes Christian Blau 12/29/2019 10:32 AM GROMACS - 2021
2965 GROMACS Task In Progress Normal Performance of GPU direct communications 02/14/2020 12:38 PM GROMACS - 2021
1618 GROMACS Bug In Progress Normal g_protonate segfaults unconditionally Erik Lindahl 08/17/2015 02:10 PM
1843 GROMACS Bug In Progress Normal pbc=xy with 2 walls floating point exception with the verlet scheme Berk Hess 10/31/2016 11:35 AM
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