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# Project Tracker Status Priority Subject Assignee Updated Target version
3370 GROMACS Task New High Further improvements to GPU Buffer Ops and Comms 02/21/2020 05:57 PM
3266 GROMACS Bug New High gmx density show wrong symmetrize density profile using -symm? Super duper 12/24/2019 01:49 PM GROMACS - 2019.6
3262 GROMACS Task New High Trjconv - dimer protein-ligand 12/20/2019 09:26 PM
3210 GROMACS Bug New High rerun does not reproduce dVcoul/dl 12/27/2019 10:45 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
3160 GROMACS Feature Fix uploaded High implement direct comm for different src/target memory spaces Alan Gray 02/14/2020 11:28 AM GROMACS - 2021-infrastructure-stable
3159 GROMACS Bug Fix uploaded High eliminate regression due to moving gmx_pme_send_coordinates() Alan Gray 02/14/2020 11:31 AM GROMACS - 2020.1
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
3082 GROMACS Task New High move launch/synchronization points to clarify task dependencies 12/27/2019 04:21 PM GROMACS - 2021
2915 GROMACS Feature In Progress High GPU direct communications 02/14/2020 12:48 PM
2792 GROMACS Task New High Improvement of PME gather and spread CUDA kernels 12/28/2019 10:36 AM
2637 GROMACS Bug New High gmx solvate tears apart molecules 09/11/2018 07:43 PM
2600 GROMACS Bug New High coul-lambdas turns off all coulombic interactions in system instead of the molecule specificed in the couple-moltype 08/07/2018 06:50 PM
2580 GROMACS Bug Feedback wanted High sc-coul option yields different free energy estimate on a ligand with zero partial charge 09/11/2018 08:10 AM
2573 GROMACS Bug New High Different mdp files describing the same change yield different free energy on the same trajectory 07/19/2018 06:52 PM
2519 GROMACS Task New High Improve/remove PME OpenCL kernel barriers 02/15/2019 06:34 PM
2453 GROMACS Task Resolved High PME OpenCL porting effort Aleksei Iupinov 12/20/2019 12:18 PM GROMACS - 2021
2229 GROMACS Feature New High Full Object Oriented Modularization of GROMACS MDRUN Codebase Mark Abraham 08/22/2018 05:03 PM GROMACS - future
2071 GROMACS Task In Progress High Low accuracy default settings yield incorrect liquid densities Berk Hess 01/05/2018 03:32 PM
2054 GROMACS Feature Accepted High PME on GPU Aleksei Iupinov 12/20/2019 12:18 PM GROMACS - future
2935 Support Platforms Bug New High redmine issue updates about gerrit uploads stopped working 06/11/2019 01:42 PM Support Platforms - current
2099 Support Platforms Feature New High sharing accounts/credentials 12/06/2017 08:11 PM
2188 TNG trajectory library Feature Resolved High Masses missing from TNG specification Magnus Lundborg 06/13/2017 05:08 PM
1106 Benchmark suite Feature New Normal publish benchmark numbers 06/19/2014 12:08 PM
1105 Benchmark suite Feature New Normal produce a benchmark suite 09/13/2016 10:31 PM
3398 GROMACS Bug New Normal Intermittent failure of non-bonded kernels when run using nvprof 02/25/2020 12:14 PM
3397 GROMACS Bug Fix uploaded Normal Gmxapi stopsignaler test is too strict Pascal Merz 02/25/2020 08:16 AM GROMACS - 2020.1
3395 GROMACS Feature Feedback wanted Normal Consider scripted composition of Dockerfiles 02/25/2020 06:46 PM
3394 GROMACS Feature New Normal improve gmxapi error handling Eric Irrgang 02/24/2020 11:45 AM GROMACS - 2021-infrastructure-stable
3393 GROMACS Feature Resolved Normal Allow gmxapi.commandline_operation to use STDIN Eric Irrgang 02/25/2020 05:15 PM GROMACS - 2021-infrastructure-stable
3391 GROMACS Bug Resolved Normal Integer overflow in dispersion correction 02/25/2020 04:15 PM GROMACS - 2020.1
3389 GROMACS Bug Fix uploaded Normal Catch need for t_graph in modular simulator more gracefully Pascal Merz 02/24/2020 05:14 PM GROMACS - 2020.1
3387 GROMACS Bug New Normal Death test bug 02/20/2020 05:39 PM
3385 GROMACS Bug New Normal FindLibStdCpp.cmake - wrong sanity check for clang 02/24/2020 11:18 AM
3382 GROMACS Task Accepted Normal Split up t_inputrec 02/17/2020 05:28 PM
3380 GROMACS Bug New Normal IBM VSX checks fail with gcc-10 Paul Bauer 02/24/2020 05:23 PM GROMACS - 2019.6
3379 GROMACS Feature New Normal C++ API for simulation input and output 02/15/2020 01:03 PM GROMACS - 2021-infrastructure-stable
3378 GROMACS Feature New Normal genion usage without stdin (facilitates use in gmx python api) 02/13/2020 12:04 PM
3376 GROMACS Bug Resolved Normal gmxapi.commandline_operation is not helpful when an invalid executable is provided Eric Irrgang 02/24/2020 01:45 PM
3374 GROMACS Feature New Normal SimulationInput abstraction 02/25/2020 11:52 AM GROMACS - 2021-refactoring
3372 GROMACS Bug In Progress Normal Re-enable RVec and float3 compatibility tests Artem Zhmurov 02/22/2020 11:44 PM GROMACS - 2021-refactoring
3371 GROMACS Feature New Normal Control FEP using AWH Magnus Lundborg 02/06/2020 02:20 PM GROMACS - 2021
3369 GROMACS Feature New Normal Add quote about "the truth" 02/05/2020 05:08 PM
3368 GROMACS Bug New Normal Erroneous interplay between gmx rms command and atommass.dat: Can not find mass in database for atom MG in residue Vedat Durmaz 02/05/2020 04:51 PM GROMACS - future
3366 GROMACS Task New Normal Enforce compability of MdModules 02/03/2020 03:32 PM
3365 GROMACS Task New Normal consider making GPU bonded work independent from nonbonded 02/12/2020 05:54 PM
3363 GROMACS Feature New Normal Improve FEP testing Pascal Merz 01/30/2020 05:06 AM GROMACS - 2021-infrastructure-stable
3362 GROMACS Feature New Normal gmx traj: add an option to plot each component in a separate file 01/29/2020 06:18 PM
3361 GROMACS Task New Normal Gitlab source archive contains files from build directory Paul Bauer 02/25/2020 10:13 AM GROMACS - 2020.2
3360 GROMACS Task New Normal investigate the future of DD dynamic load balancing with GPU offload 01/29/2020 11:23 AM
3357 GROMACS Task New Normal Make sure "colvars" interoperates stably and smoothly with gromacs 02/07/2020 01:04 PM
3356 GROMACS Task New Normal Expose setting of random seed to API 01/29/2020 06:16 PM GROMACS - 2021
3355 GROMACS Feature Accepted Normal New PME parallel (GPU) scheme Jonathan Vincent 02/12/2020 11:58 AM
3354 GROMACS Bug Resolved Normal release-2020 nightly gpuupdte matrix failing 02/25/2020 06:00 PM
3353 GROMACS Task New Normal Document gmx densmap output 01/23/2020 12:52 PM
3352 GROMACS Feature New Normal GPU update-constraints feature support Artem Zhmurov 01/23/2020 11:59 AM GROMACS - 2021
3351 GROMACS Feature New Normal GPU update-constraints code organization and integration Artem Zhmurov 01/23/2020 11:59 AM GROMACS - 2021
3350 GROMACS Feature New Normal GPU update-constraints performance Artem Zhmurov 01/23/2020 11:59 AM GROMACS - 2021
3348 GROMACS Task New Normal GPU LINCS and SETTLE: unify virial reduction Artem Zhmurov 01/23/2020 11:58 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
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
3344 GROMACS Task New Normal GPU update-constraints: Better virial reduction. Artem Zhmurov 01/23/2020 11:57 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
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
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
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
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
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
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
3334 GROMACS Bug New Normal Check for DD when increasing rlist is broken Berk Hess 02/25/2020 03:28 PM GROMACS - 2020.2
3333 GROMACS Bug New Normal Assertion failure when trying to get unit test help Paul Bauer 02/25/2020 10:16 AM GROMACS - 2021-infrastructure-stable
3332 GROMACS Feature New Normal gmx helixorient doesn't have a -tu option to change time unit 01/22/2020 11:57 AM
3331 GROMACS Task New Normal Run physical validation tests in Gitlab Paul Bauer 01/22/2020 10:06 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
3329 GROMACS Task New Normal Extend energy comparison testing framework 01/22/2020 09:51 AM GROMACS - 2021-refactoring
3328 GROMACS Feature New Normal Testing framework for task assignment 01/22/2020 09:48 AM GROMACS - 2021-refactoring
3327 GROMACS Task New Normal Refactor workload flags 01/22/2020 09:45 AM GROMACS - 2021-refactoring
3326 GROMACS Task New Normal Allow changing task assignment 01/22/2020 09:44 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
3324 GROMACS Task New Normal Rework CMake handling of GPU code 01/22/2020 09:52 AM GROMACS - 2021-refactoring
3323 GROMACS Task In Progress Normal Rework the StatePropagatorDataGpu 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
3321 GROMACS Task Accepted Normal Add D2D wrapper Artem Zhmurov 01/22/2020 09:50 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
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
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
3317 GROMACS Task Accepted Normal Improve testing of the GPU code 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
3315 GROMACS Task In Progress Normal Platform agnostic DeviceContext Artem Zhmurov 02/01/2020 04:45 PM GROMACS - 2021-refactoring
3314 GROMACS Task Accepted Normal Platform agnostic DeviceStream Artem Zhmurov 01/22/2020 09:48 AM GROMACS - 2021-refactoring
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
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
3311 GROMACS Feature In Progress Normal GPU infrastructure development 01/23/2020 12:12 PM GROMACS - 2021-refactoring
3309 GROMACS Bug New Normal -reprod: checkpoint reading bug and general considerations 01/22/2020 02:00 PM
3308 GROMACS Task New Normal GPU update-constraints: Cycle counting for GPU launches 01/23/2020 11:54 AM GROMACS - 2021-infrastructure-stable
3307 GROMACS Feature New Normal General interface for communication between simulation ranks 01/22/2020 03:22 PM GROMACS - 2021-refactoring
3306 GROMACS Task New Normal Document gmx dos tool more clearly Christian Blau 01/20/2020 02:31 PM GROMACS - future
3305 GROMACS Bug New Normal Case gives FPE with Debug build when GPU update is enabled 01/21/2020 05:44 PM
3304 GROMACS Bug New Normal Failure in Log Output for Expanded Ensemble Weights using Simulated Tempering in GROMACS 2019.5 Michael Shirts 01/16/2020 04:46 PM GROMACS - 2019.6
3302 GROMACS Bug Fix uploaded Normal source tarball modified flag does not get updated in an existing build tree Paul Bauer 01/16/2020 02:32 PM GROMACS - 2020.1
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