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# Project Tracker Status Priority Subject Assignee Updated Target version
1105 Benchmark suite Feature New Normal produce a benchmark suite 09/13/2016 10:31 PM
1106 Benchmark suite Feature New Normal publish benchmark numbers 06/19/2014 12:08 PM
3117 GROMACS Feature New Normal Coulomb FEP PME on GPU Magnus Lundborg 02/17/2020 09:52 AM GROMACS - 2021-infrastructure-stable
3370 GROMACS Task New High Further improvements to GPU Buffer Ops and Comms 02/16/2020 09:15 PM
2440 GROMACS Bug Accepted Normal Multidir simulations can stop at different times when using mdrun -maxh Berk Hess 02/15/2020 04:56 PM GROMACS - 2019.6
3374 GROMACS Feature New Normal SimulationInput abstraction 02/15/2020 01:03 PM GROMACS - 2021-refactoring
3379 GROMACS Feature New Normal C++ API for simulation input and output 02/15/2020 01:03 PM GROMACS - 2021-infrastructure-stable
3380 GROMACS Bug New Normal IBM VSX checks fail with gcc-10 Paul Bauer 02/15/2020 03:54 AM
3377 GROMACS Bug Resolved High Parrinello-Rahman checkpoint restart fails using modular simulator Pascal Merz 02/14/2020 08:45 PM GROMACS - 2020.1
2915 GROMACS Feature In Progress High GPU direct communications 02/14/2020 12:48 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
3021 GROMACS Feature Feedback wanted Normal Completion of docs for GPU developments 02/14/2020 12:43 PM GROMACS - 2020.1
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
2965 GROMACS Task In Progress Normal Performance of GPU direct communications 02/14/2020 12:38 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
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
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
3373 GROMACS Bug Resolved Normal checkNumberOfBondedInteractions not exiting on failure Pascal Merz 02/13/2020 06:00 PM GROMACS - 2020.1
3378 GROMACS Feature New Normal genion usage without stdin (facilitates use in gmx python api) 02/13/2020 12:04 PM
3376 GROMACS Bug New Normal gmxapi.commandline_operation is not helpful when an invalid executable is provided Eric Irrgang 02/12/2020 07:20 PM
2675 GROMACS Task In Progress Normal bonded CUDA offload task 02/12/2020 05:54 PM GROMACS - 2021
3365 GROMACS Task New Normal consider making GPU bonded work independent from nonbonded 02/12/2020 05:54 PM
3375 GROMACS Bug New Normal Orires consistency check too strict David van der Spoel 02/12/2020 02:53 PM GROMACS - 2019.6
3355 GROMACS Feature Accepted Normal New PME parallel (GPU) scheme Jonathan Vincent 02/12/2020 11:58 AM
3114 GROMACS Feature New Normal Improve GPU update-constraints module Artem Zhmurov 02/10/2020 04:30 PM GROMACS - 2021
2601 GROMACS Feature New Normal Free energy calculations, soft-core potential Vytautas Gapsys 02/10/2020 11:29 AM GROMACS - future
3372 GROMACS Bug New Normal Re-enable RVec and float3 compatibility tests Artem Zhmurov 02/08/2020 10:08 AM GROMACS - 2021-refactoring
3357 GROMACS Task New Normal Make sure "colvars" interoperates stably and smoothly with gromacs 02/07/2020 01:04 PM
1166 GROMACS Bug New Low g_order is incorrect for unsaturated carbons David van der Spoel 02/06/2020 02:32 PM GROMACS - future
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
2936 GROMACS Task New Normal introduce check that CPU-GPU transfers/assignments are made between compatible types 02/05/2020 03:57 PM GROMACS - 2021
3366 GROMACS Task New Normal Enforce compability of MdModules 02/03/2020 03:32 PM
3315 GROMACS Task In Progress Normal Platform agnostic DeviceContext Artem Zhmurov 02/01/2020 04:45 PM GROMACS - 2021-refactoring
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
3285 GROMACS Feature New Normal Run simulations from the same tpr file with different random seeds 01/29/2020 06:18 PM GROMACS - 2021
3356 GROMACS Task New Normal Expose setting of random seed to API 01/29/2020 06:16 PM GROMACS - 2021
3361 GROMACS Task New Normal Gitlab source archive contains files from build directory Paul Bauer 01/29/2020 05:28 PM GROMACS - 2020.1
3325 GROMACS Task New Normal Allow complete re-initialization of a simulation 01/29/2020 05:13 PM GROMACS - 2021-refactoring
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
2045 GROMACS Task New Normal API design and language bindings Peter Kasson 01/29/2020 03:59 PM
2698 GROMACS Task In Progress Normal gmxapi documentation integration 01/29/2020 03:59 PM GROMACS - 2021-infrastructure-stable
3360 GROMACS Task New Normal investigate the future of DD dynamic load balancing with GPU offload 01/29/2020 11:23 AM
3124 GROMACS Bug New Normal significant performance loss due to DLB auto-off when PP/PME load >1 01/28/2020 02:44 PM GROMACS - 2021
2798 GROMACS Bug Feedback wanted Normal Default mpi rank number fails when there are 16 cores and 3 gpus Berk Hess 01/28/2020 02:42 PM GROMACS - 2020.1
3283 GROMACS Feature New Normal Support for the string method with swarms of trajectories in GROMACS 01/28/2020 11:04 AM GROMACS - 2021
3125 GROMACS Bug New Normal OpenCL on Volta and Turing borken 01/27/2020 04:48 PM GROMACS - 2020.1
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
3354 GROMACS Bug New Normal release-2020 nightly gpuupdte matrix failing 01/24/2020 12:02 PM
3336 GROMACS Bug Resolved Normal DD error can't be avoided with the suggested manual decomposition option Berk Hess 01/23/2020 05:50 PM GROMACS - 2020.1
3334 GROMACS Bug New Normal Check for DD when increasing rlist is broken Berk Hess 01/23/2020 03:58 PM GROMACS - 2020.1
3287 GROMACS Task New Normal Deprecate make_ndx, use select instead 01/23/2020 01:16 PM
3353 GROMACS Task New Normal Document gmx densmap output 01/23/2020 12:52 PM
2967 GROMACS Feature New Normal GPU reallocateDeviceBuffer improvements 01/23/2020 12:15 PM GROMACS - 2021-refactoring
3311 GROMACS Feature In Progress Normal GPU infrastructure development 01/23/2020 12:12 PM 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
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
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
3308 GROMACS Task New Normal GPU update-constraints: Cycle counting for GPU launches 01/23/2020 11:54 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
3236 GROMACS Task New Normal GPU update-constraints: Pulling support Artem Zhmurov 01/23/2020 11:53 AM 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
3333 GROMACS Bug New Normal Assertion failure when trying to get unit test help Paul Bauer 01/22/2020 04:37 PM GROMACS - 2020.1
3307 GROMACS Feature New Normal General interface for communication between simulation ranks 01/22/2020 03:22 PM GROMACS - 2021-refactoring
3309 GROMACS Bug New Normal -reprod: checkpoint reading bug and general considerations 01/22/2020 02:00 PM
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
3294 GROMACS Bug New Normal multiple tests fail on fedora 31 Paul Bauer 01/22/2020 09:55 AM
3324 GROMACS Task New Normal Rework CMake handling of GPU code 01/22/2020 09:52 AM GROMACS - 2021-refactoring
3329 GROMACS Task New Normal Extend energy comparison testing framework 01/22/2020 09:51 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
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
3328 GROMACS Feature New Normal Testing framework for task assignment 01/22/2020 09:48 AM GROMACS - 2021-refactoring
3314 GROMACS Task Accepted Normal Platform agnostic DeviceStream Artem Zhmurov 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
3310 GROMACS Bug New Low Thread affinity on Mac OS 01/22/2020 12:02 AM
3305 GROMACS Bug New Normal Case gives FPE with Debug build when GPU update is enabled 01/21/2020 05:44 PM
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