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# Project Tracker Status Priority Subject Assignee Updated Target version
3418 GROMACS Task New Normal Infrastructure improvements for modular simulator Pascal Merz 03/10/2020 10:24 PM GROMACS - 2021-infrastructure-stable
3419 GROMACS Task New Normal Reduce / remove use of legacy t_state objects throughout modular simulator Pascal Merz 03/10/2020 10:24 PM GROMACS - 2021-infrastructure-stable
3420 GROMACS Task New Normal Unify force and shellfc elements for modular simulator Pascal Merz 03/10/2020 09:50 PM GROMACS - 2021-infrastructure-stable
3421 GROMACS Task New Normal Implement client system for global reduction Pascal Merz 03/11/2020 03:31 PM GROMACS - 2021-infrastructure-stable
3437 GROMACS Task New Normal Use builders to prepare modules Pascal Merz 03/11/2020 07:05 AM GROMACS - 2021-infrastructure-stable
3445 GROMACS Task New Normal create heuristic for c_skipNeutralAtoms Jonathan Vincent 03/17/2020 12:12 PM
3446 GROMACS Task New Normal apply maintainability updates across all GPU kernels Jonathan Vincent 03/19/2020 03:31 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
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
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
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
3234 GROMACS Bug Accepted Normal Signal: Floating point exception Signal code: Floating point divide-by-zero Erik Lindahl 12/16/2019 03:40 PM
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
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
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
1192 GROMACS Feature Accepted Normal Add support for Verlet scheme with Buckingham Berk Hess 07/11/2016 08:19 PM
1221 GROMACS Feature Accepted Normal More generic position mapping for selections 06/10/2014 02:58 PM GROMACS - future
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
2054 GROMACS Feature Accepted High PME on GPU Aleksei Iupinov 12/20/2019 12:18 PM GROMACS - future
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
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
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
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
1781 GROMACS Task Accepted Normal re-design benchmarking functionality Mark Abraham 12/20/2019 12:03 PM GROMACS - future
1907 GROMACS Task Accepted Low keeping compile- and run-time CPU/arch detection consistent 08/01/2016 10:09 PM
1943 GROMACS Task Accepted Low make sure releases are submitted early for Debian Experimental Szilárd Páll 12/20/2019 12:05 PM GROMACS - 2021
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
2495 GROMACS Task Accepted Normal replace -noconfout with mdp option Mark Abraham 12/28/2019 10:39 AM GROMACS - 2021
2674 GROMACS Task Accepted Normal Improve domain decomposition for bilayer systems 12/07/2018 04:03 PM GROMACS - future
2706 GROMACS Task Accepted Normal Rework classic QM/MM interface 12/02/2019 01:45 PM GROMACS - 2021-infrastructure-stable
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
2947 GROMACS Task Accepted Normal make an end to end test for membed 09/24/2019 03:22 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
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
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
3382 GROMACS Task Accepted Normal Split up t_inputrec 02/17/2020 05:28 PM
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
2734 GROMACS Bug In Progress Normal regressiontests/kernel core dumps on ppc64le Paul Bauer 06/15/2019 04:12 PM GROMACS - future
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
3249 GROMACS Bug In Progress Low cmake bad tests for avx512 on AMD Erik Lindahl 02/26/2020 05:00 PM
438 GROMACS Feature In Progress Low New tool: g_correl Alexey Shvetsov 06/20/2014 10:38 AM GROMACS - future
868 GROMACS Feature In Progress Normal Implement parallelization support to analysis framework Kevin Boyd 12/20/2019 11:59 AM GROMACS - 2021
895 GROMACS Feature In Progress Normal g_rmsf previous frame as reference 04/29/2013 07:39 PM GROMACS - future
1053 GROMACS Feature In Progress Normal L-BFGS doesn't use constraints or call do_em_step Berk Hess 01/18/2013 11:00 AM GROMACS - future
1083 GROMACS Feature In Progress Normal Improve collective error/warning/note handling in mdrun 07/11/2016 08:21 PM
1168 GROMACS Feature In Progress Low g_density does not do what users think it does, given PBC over z and constant pressure simulation Erik Lindahl 10/20/2018 12:49 AM GROMACS - future
1332 GROMACS Feature In Progress Normal Supporting multiple end states instead of just A and B Michael Shirts 06/05/2018 03:58 PM
1627 GROMACS Feature In Progress Normal DPD integrator 07/11/2016 08:08 PM
2070 GROMACS Feature In Progress Normal Physical validation testing Michael Shirts 01/03/2020 09:36 PM GROMACS - future
2111 GROMACS Feature In Progress Normal Implement Gaussian screening of electrostatics 02/23/2019 12:33 PM
2426 GROMACS Feature In Progress Normal Trajectory analysis tool for functional mode analysis by partial least squares fitting (PLS-FMA) 10/03/2018 11:31 PM GROMACS - future
2587 GROMACS Feature In Progress Normal Provide Context (e.g. to runner code) to manage client and runtime environment 10/15/2018 03:34 PM
2791 GROMACS Feature In Progress Normal Implement a module for lambda-dynamics simulations (lambda_site module) Thomas Ullmann 03/01/2019 01:36 AM GROMACS - future
2890 GROMACS Feature In Progress Normal GPU Halo Exchange 02/14/2020 12:41 PM GROMACS - 2021
2891 GROMACS Feature In Progress Normal PME/PP GPU communications 02/14/2020 12:40 PM
2915 GROMACS Feature In Progress High GPU direct communications 02/14/2020 12:48 PM
2996 GROMACS Feature In Progress Normal gmxapi execution model Eric Irrgang 12/10/2019 01:57 PM GROMACS - 2021-infrastructure-stable
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
867 GROMACS Task In Progress Normal Update Doxygen documentation for C++ code Teemu Murtola 07/11/2016 08:28 PM
869 GROMACS Task In Progress Normal Make analysis data histogramming and multipoint data easier to use in parallel Teemu Murtola 07/11/2016 08:28 PM
920 GROMACS Task In Progress Normal Add test framework for trajectory analysis modules Teemu Murtola 07/11/2016 08:27 PM
1010 GROMACS Task In Progress Normal Better support for multiple AnalysisData datasets Teemu Murtola 07/11/2016 08:23 PM
1879 GROMACS Task In Progress Low make the GROMACS OpenCL kernel work on Gallium 11/30/2018 05:46 PM GROMACS - future
1925 GROMACS Task In Progress Normal remove concept of unilateral global communication 12/29/2019 10:35 AM GROMACS - 2021
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
2059 GROMACS Task In Progress Normal Separate different types of data in t_state 12/27/2019 04:42 PM GROMACS - 2021
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
2368 GROMACS Task In Progress Normal update implementation of gmx msd Kevin Boyd 11/03/2018 07:43 PM GROMACS - future
2395 GROMACS Task In Progress Normal break up commrec Mark Abraham 12/15/2019 11:51 AM GROMACS - 2021-infrastructure-stable
2452 GROMACS Task In Progress Normal Reduce data dependencies in mdrun algorithms Berk Hess 03/14/2018 08:47 PM
2675 GROMACS Task In Progress Normal bonded CUDA offload task 02/12/2020 05:54 PM GROMACS - 2021
2696 GROMACS Task In Progress Normal ensure PME queue is flushed Szilárd Páll 12/31/2018 11:21 AM GROMACS - future
2698 GROMACS Task In Progress Normal gmxapi documentation integration 01/29/2020 03:59 PM GROMACS - 2021-infrastructure-stable
2756 GROMACS Task In Progress Normal gmxapi integration testing 01/16/2020 05:12 PM GROMACS - 2021-refactoring
2766 GROMACS Task In Progress Normal Improve hardware option selection Kevin Boyd 12/20/2019 02:34 PM GROMACS - 2021
2818 GROMACS Task In Progress Normal bonded GPU kernel fusion Magnus Lundborg 07/03/2019 09:01 PM
2834 GROMACS Task In Progress Normal C++ matrix classes Christian Blau 12/29/2019 10:32 AM GROMACS - 2021
2850 GROMACS Task In Progress Normal assess Raptor Talos for testing Szilárd Páll 02/12/2019 01:14 PM
2965 GROMACS Task In Progress Normal Performance of GPU direct communications 02/14/2020 12:38 PM GROMACS - 2021
2988 GROMACS Task In Progress Low clean up and refactor code to modern standards 12/27/2019 04:37 PM GROMACS - future
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