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# Project Tracker Status Priority Subject Assignee Updated Target version
2657 GROMACS Bug New Normal Biphasic tutorial 09/28/2018 10:02 AM
2650 GROMACS Task New Normal revise OpenCL stack recommendations 12/31/2018 11:19 AM GROMACS - future
2649 GROMACS Bug New Normal Virial calculation necessary for correct energy calculation on GPU 12/17/2018 02:32 PM GROMACS - future
2645 GROMACS Bug New Normal Security 09/28/2018 01:16 PM
2643 GROMACS Feature New Low mdp options and/or docs for anisotropic aspects of implementations 09/12/2018 02:23 PM
2637 GROMACS Bug New High gmx solvate tears apart molecules 09/11/2018 07:43 PM
2632 GROMACS Task New Low make sure cmake defines proper hwloc versionc with cross-compilation enabled 12/03/2018 01:35 PM GROMACS - future
2628 GROMACS Bug Fix uploaded Normal GMXRC removes trailing colon from existing MANPATH 08/28/2018 03:13 PM
2624 GROMACS Bug New Normal GPU build system not robust enough 09/05/2018 02:00 AM
2623 GROMACS Task Resolved Normal Allow extensible MDModules and forceProviders. 10/15/2018 03:44 PM
2622 GROMACS Feature New Low Reduce severity of Berendsen warning 08/23/2018 11:16 PM GROMACS - future
2620 GROMACS Feature In Progress Normal MD signaling API 03/02/2019 01:24 AM
2616 GROMACS Task New Normal Model for MD state 09/14/2018 05:12 PM
2615 GROMACS Feature Accepted Normal Switch to Python3 07/05/2019 02:57 PM GROMACS - 2020
2611 GROMACS Bug New Normal issues with gpu_utils-test with GMX_BUILD_UNITTESTS=OFF and on OSX 08/14/2018 07:03 PM
2608 GROMACS Task New Normal Remove code duplication between OpenCL and CUDA 09/24/2018 12:47 PM
2607 GROMACS Bug New Normal Grompp becomes extremely slow when many pull groups are present 08/11/2018 08:54 AM
2606 GROMACS Bug New Normal Free Energy Calculation -- Function type Fourier Dih. Not implemented in ip_pert 08/10/2018 01:48 AM
2602 GROMACS Bug New Low build information gets outdated if build tree is reused 08/13/2018 09:04 PM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
2598 GROMACS Bug New Normal Tools using read_next_x cannot read TNG files with sanitzers 10/15/2018 01:16 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
2586 GROMACS Feature Resolved Normal Versioned libgmxapi target for build, install, headers, docs 03/02/2019 01:32 AM
2585 GROMACS Feature Resolved Normal Infrastructure supporting external API 03/31/2019 04:47 PM
2581 GROMACS Feature Accepted Normal User interface for hybrid Monte Carlo 10/15/2018 05:21 PM GROMACS - 2020
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
2579 GROMACS Feature New Normal Add dimensionality option to gmx trjconv -center 07/19/2018 04:53 PM GROMACS - future
2576 GROMACS Bug New Normal gmx potential -correct outputs the wrong potential 07/25/2018 02:58 PM
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
2570 GROMACS Feature New Normal Better string formatting and printing 05/02/2019 12:20 PM
2568 GROMACS Bug New Low gmx editconf -rotate does not rotate the box 07/10/2018 10:27 AM GROMACS - future
2567 GROMACS Bug New Normal make check fails at test 23 SIMD errors 07/10/2018 09:35 AM
2564 GROMACS Bug New Normal Result Summary Different For Jobs With Different Numbers of Nodes 07/05/2018 02:39 PM
2563 GROMACS Bug New Normal Windows 7 Compilation with GPU support 07/02/2018 09:58 AM
2555 GROMACS Bug New Low building GROMACS 2018.2 07/03/2018 11:41 PM
2535 GROMACS Task New Normal consider compiling opencl fft kernels once 05/31/2018 01:33 PM
2532 GROMACS Task New Normal enable queue priorities in OpenCL 05/29/2018 02:29 PM
2531 GROMACS Task New Low Consider optimizing tabulated data access on GPU 07/30/2018 12:31 PM
2530 GROMACS Task New Normal consider using CUDA Driver API 09/23/2018 11:47 PM GROMACS - future
2528 GROMACS Task New Normal PME GPU tuning 12/31/2018 11:18 AM GROMACS - future
2527 GROMACS Task New Normal Rename GpuEventSynchronizer to something more fitting (after mergin PME OpenCL) 10/30/2018 04:06 AM GROMACS - future
2526 GROMACS Bug New Normal Bug of gmx hbond 05/30/2018 03:12 PM
2524 GROMACS Task New Normal struct alignment/packing for OpenCL host & device code 10/30/2018 12:06 PM GROMACS - 2020
2522 GROMACS Task New Normal OpenCL context duplication 10/30/2018 12:07 PM GROMACS - 2020
2521 GROMACS Task New Normal Implement alternating PME/NB wait for OpenCL 10/15/2018 12:39 PM
2520 GROMACS Task New Normal Treat OpenCL kernel width more diligently 05/24/2018 06:21 PM
2519 GROMACS Task New High Improve/remove PME OpenCL kernel barriers 02/15/2019 06:34 PM
2518 GROMACS Task New Normal redesign task-assignment code for OpenCL 12/28/2018 12:38 PM GROMACS - 2020
2514 GROMACS Task New Normal PME OpenCL reductions with intrinsics 05/31/2018 12:27 AM GROMACS - future
2498 GROMACS Task New Normal OpenCL memory pinning/mapping 10/30/2018 12:07 PM GROMACS - 2020
2496 GROMACS Task New Low find system xdr properly 05/02/2018 02:19 PM
2488 GROMACS Task New Normal use MPI non-blocking collectives to overlap pull comm 04/25/2018 04:19 PM
2482 GROMACS Bug Feedback wanted Normal Atoms/molecules in freezegrps move and system crashes 05/18/2018 07:13 PM
2481 GROMACS Task New Low Update gmx report-methods to write more method information 09/20/2018 07:43 AM GROMACS - 2020
2478 GROMACS Task New Low avoid use of getenv in static initialization 04/13/2018 11:57 AM
2475 GROMACS Task New Normal make OpenCL 1st class-citizen in the build system 10/30/2018 12:01 PM GROMACS - 2020
2473 GROMACS Bug New Normal mdrun sometimes stalls due to large coordinates with no constraints 04/04/2018 10:15 PM
2469 GROMACS Task New Normal implement GPU timer reduction for reporting 03/27/2018 05:08 PM
2468 GROMACS Bug New Low incorrect GPU timing reported with OpenCL and domain decomposition 12/17/2018 01:28 PM GROMACS - future
2464 GROMACS Task New Normal GPU performance goals overview 03/26/2018 10:42 AM
2463 GROMACS Task New Low PME GPU decomposition 03/26/2018 10:42 AM
2462 GROMACS Task New Normal consider adding STL misuse tests 03/23/2018 01:23 AM
2460 GROMACS Bug New Normal Allow inclusion of user libraries through CMake cache variables 03/28/2018 08:47 PM
2456 GROMACS Task New Normal Add a pull module external potential tests 03/15/2018 03:02 PM
2448 GROMACS Task Accepted Normal should mdrun -multidir permit only one directory? 03/21/2018 12:10 PM
2445 GROMACS Task New Normal Decide if/how to check for incompatible user input to mdrun for bonds and vsites 03/13/2018 02:02 PM
2435 GROMACS Task New Normal identify and note about/tune task offload in GPU-bound runs 03/02/2018 04:08 PM
2429 GROMACS Feature New Normal Add option of periodic chain topology to pdb2gmx 03/10/2018 01:01 PM
2428 GROMACS Feature New Normal Add way of selecting interactive arguments of pdb2gmx by string rather than an index 02/27/2018 06:28 PM
2427 GROMACS Bug New Normal gmx select gives syntax error for selection involving evaluating simple arithmetic expression 02/27/2018 05:15 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
2422 GROMACS Task New Normal write C kernel for tables in Verlet scheme 02/26/2018 01:38 PM
2412 GROMACS Task New Normal attempt to do better FFTW planning 03/15/2018 05:01 PM
2402 GROMACS Task New Normal PME kernels general performance improvements 03/26/2018 10:41 AM GROMACS - future
2393 GROMACS Bug New Normal incorrect error message with omitted command line flag before its argument 01/24/2018 11:24 PM
2390 GROMACS Bug Feedback wanted Normal GROMACS build system should check for valid nvcc flags before use 01/30/2019 06:16 PM GROMACS - 2020
2382 GROMACS Task New Normal Simplify Doxygen guidelines 01/13/2018 12:40 AM
2380 GROMACS Bug New Low cycle counter issues with separate PME rank + GPUs 01/16/2018 10:21 PM
2376 GROMACS Task New Normal max_mpi_ranks has wrong name 02/10/2018 11:03 AM
2375 GROMACS Task New Normal Clarify execution phases for MD simulation 04/30/2019 12:59 PM
2373 GROMACS Bug New Low gmx -nice can't work 01/04/2018 11:17 AM
2371 GROMACS Task New Normal mtop searching needs reconsideration 01/04/2018 11:54 AM GROMACS - future
2367 GROMACS Task New Normal construct pbc_simd less often 09/24/2018 11:02 PM GROMACS - future
2362 TNG trajectory library Bug New Normal tng_*_of_particle_nr_get() functions return wrong result for structures with multiple molecule types 12/21/2017 11:51 AM
2360 GROMACS Bug New Low error at counter reset with PME-only rank 01/05/2018 12:43 PM GROMACS - future
2354 GROMACS Feature New Normal develop configuration file support for control of task layout 09/19/2018 03:01 PM GROMACS - future
2353 GROMACS Task New Normal improve on relative tolerance for constructing tables 10/30/2018 04:17 AM GROMACS - 2020
2351 GROMACS Task New Normal Avoid the SIMD module depending on non-trivial parts of Gromacs 12/14/2017 02:47 AM GROMACS - future
2341 GROMACS Task New Low assess the state of building and using GROMACS on Windows 07/29/2019 11:09 PM GROMACS - future
2310 GROMACS Feature Accepted Low Let mdrun dump coordinates with non-finite energy 10/03/2018 09:47 PM GROMACS - future
2304 GROMACS Task New Normal Document and propose tracking mdrun heuristics 10/03/2018 09:39 PM GROMACS - future
2294 GROMACS Task New Normal Require identical hardware on nodes on parallel runs 11/19/2017 08:54 PM
2289 GROMACS Feature New Normal gmx spatial add ability to perform over multiple reference structures 11/08/2017 12:31 AM
2288 GROMACS Feature Accepted Low gmx msd doesn't optimally handle missing input trajectory frames 11/10/2017 11:03 AM
2255 GROMACS Bug New Normal nstlist override stopped affecting the input parameter listing 12/17/2017 08:05 AM
2254 GROMACS Feature New Normal GPU extensions for Google Tests 09/19/2017 05:01 PM
2252 GROMACS Bug New Low Memory allocation failures with large page sizes during PME tuning 12/14/2017 04:27 AM
2248 GROMACS Feature New Normal Label all SIMD functions as pure/nodiscard 02/04/2019 04:49 AM
2241 GROMACS Bug New Low refdata can segfault when reading 09/07/2017 11:57 AM
2240 GROMACS Task Accepted Low GPU emulation mode support for PME missing 09/16/2017 10:02 PM
2239 GROMACS Feature New Normal split libgromacs into base and full 01/07/2019 01:47 AM
2233 GROMACS Bug Accepted Normal replica exchange and -append bugged? 03/05/2018 01:38 PM
2232 GROMACS Bug New Normal pdb2gmx can't form special bonds with terminal patched atoms 12/03/2017 01:35 PM
2231 GROMACS Bug New Normal convert-tpr aborts when saving subset of the system 01/12/2018 03:52 PM
2226 GROMACS Feature New Normal Harmonise commands for exit in make_ndx and distance 08/04/2017 12:24 PM
2221 GROMACS Task New Normal Avoid preprocessor for SIMD functions 02/21/2018 01:43 PM
2220 GROMACS Feature New Normal report relevant env var behaviour to console 07/31/2017 09:40 PM
2218 GROMACS Feature Feedback wanted Normal A tiny feature: damping for umbrella pull 08/16/2017 07:20 PM
2217 GROMACS Bug New Low GPU emulation and separate PME ranks doesn't work properly 12/12/2017 11:50 AM
2211 GROMACS Bug New Low gmx writes normal output to stderr 03/05/2018 02:00 PM GROMACS - future
2208 GROMACS Bug New Normal cuFFT linking 06/30/2017 01:58 PM
2207 GROMACS Feature New Normal solvent excluded volume of large molecule with periodic boundary condition 06/16/2017 10:37 AM
2194 GROMACS Feature Accepted Low xvg output requested as an output option in place of xpm files 05/31/2017 04:26 PM
2185 GROMACS Task New Normal add docs on MPI + CUDA w/wo MPS 05/24/2017 05:17 PM
2182 GROMACS Task New Low de-duplicate code in densorder and hydorder 05/16/2017 11:29 AM
2180 Support Platforms Feature Fix uploaded Low releng matrices would work better with a hint for execution 05/19/2017 01:02 AM
2178 GROMACS Task New Normal Move checks for specific warnings to source repo 05/12/2017 03:57 PM
2175 GROMACS Task New Normal improve clang static analyzer docs further 01/04/2018 04:13 PM GROMACS - future
2169 GROMACS Task New Normal remove 'continuation' mdp option 10/12/2018 10:36 PM GROMACS - 2020
2168 GROMACS Task Feedback wanted Normal Design for multiple comparisons against same test reference data 05/08/2017 02:45 PM GROMACS - future
2166 GROMACS Task Accepted Normal gmx trjconv functionality should check for mismatch between the tpr and the trajectory 05/05/2017 04:32 PM
2158 GROMACS Task New Normal consider adding post-submit test that runs PME with 2xNN kernels 04/19/2017 08:04 PM
2149 Support Platforms Bug New Normal gerrit server excessive CPU usage 04/05/2017 07:25 PM
2147 GROMACS Bug Feedback wanted Normal Parrinello-Rahman barostat not properly working 06/06/2017 07:53 AM
2139 GROMACS Feature New Normal More precise/explicit documentation conventions 01/07/2018 11:54 PM
2133 GROMACS Task New Low gmx traj needs reform 03/07/2017 02:02 PM
2132 GROMACS Feature New Normal Intermediate code for xvg handling 03/08/2017 05:12 PM GROMACS - future
2126 GROMACS Feature New Normal implement native CUDA support in CMake 10/29/2019 09:03 PM
2118 GROMACS Feature New Low More verbose comments requested in header of gmx distance -oxyz 02/08/2017 05:46 AM
2115 GROMACS Task New Normal trjconv does too many things, and combinations of them work poorly 10/02/2018 09:04 AM
2113 GROMACS Bug New Normal Google tests and execution order 03/05/2018 02:05 PM
2111 GROMACS Feature In Progress Normal Implement Gaussian screening of electrostatics 02/23/2019 12:33 PM
2107 GROMACS Task Accepted High Change to clang-format 08/02/2019 07:30 PM
2101 GROMACS Feature New Low warninp could print the offending line, as well as its number 01/20/2017 03:06 PM
2099 Support Platforms Feature New High sharing accounts/credentials 12/06/2017 08:11 PM
2097 GROMACS Feature New Low Move output of dhdl file entirely to edr, rather than having a separate text dhdl file 01/05/2017 05:21 PM GROMACS - future
2096 Support Platforms Bug New Normal Redmine internal error with special characters 05/31/2017 08:48 PM
2094 GROMACS Bug New Normal Solvation Consistency with MARTINI forcefield water across GROMACS versions with user-specified VDW size 01/20/2017 04:56 PM
2092 GROMACS Task New Normal Tests running on GPU, and hardware assignment 12/19/2017 05:27 PM GROMACS - future
2089 GROMACS Task New Normal Encourage code review 01/10/2017 12:03 AM
2084 GROMACS Task New Low MPI and stderr/log output 11/28/2016 06:37 PM
2080 GROMACS Feature New Normal add grompp warning for suitableness for domain decomposition 11/23/2016 03:03 PM
2069 GROMACS Task New Low Simple thread-parallelism inside routines 11/09/2016 06:06 PM
2068 GROMACS Feature New Normal Access to low level classes 03/02/2019 01:37 AM GROMACS - future
2065 GROMACS Bug New Normal thread-MPI internal errors 11/08/2018 03:43 PM
2060 GROMACS Feature New Normal Convert enum to enum class 10/17/2016 05:27 PM
2059 GROMACS Task In Progress Normal Separate different types of data in t_state 10/12/2018 10:36 PM GROMACS - 2020
2056 GROMACS Feature New Low rename "gmx select" 10/03/2016 08:24 PM
2055 GROMACS Task New Low Wiki registration is broken 01/20/2017 11:31 AM
2053 GROMACS Task New Normal refine notation in GPU code 09/04/2019 01:47 PM GROMACS - 2020
2048 GROMACS Task New Normal C++11: CUDA dependency on general headers 09/07/2016 10:30 PM
2039 GROMACS Bug New Normal mdrun -pinstride defaults are too confusing 12/13/2017 04:14 AM
2035 GROMACS Task New Normal A common trajectory analysis data exchange format 03/15/2017 05:46 PM GROMACS - future
2018 GROMACS Feature New Normal Pulling along a line between given points 07/27/2016 09:59 AM
2015 GROMACS Feature New Normal Auto recovery from dd communication error 07/28/2016 03:17 PM
2010 GROMACS Task New Normal Use size_t instead of int for indexing 07/01/2018 07:57 AM
2009 GROMACS Task New Normal improve command-line reporting of useful things 07/26/2016 12:54 PM
2003 GROMACS Task New Normal reconsider various simd flags 07/07/2016 11:23 PM
2001 GROMACS Feature New Normal add MPI info to the mdrun log header 07/06/2016 05:21 PM
1994 GROMACS Feature New Low explore using JIT for CUDA 07/11/2016 10:20 PM GROMACS - future
1985 GROMACS Bug Fix uploaded Low CUDA build system refactoring awaiting review 10/15/2018 05:21 PM GROMACS - 2020
1977 GROMACS Bug Feedback wanted Low warning: __WORDSIZE not defined 09/21/2018 06:19 PM GROMACS - 2020
1974 GROMACS Feature New Normal Report atom numbers and types in the error message about missed parameters 05/30/2016 09:24 AM
1973 GROMACS Task New Normal OpenCL implementation wish list 05/27/2016 03:42 PM
1972 GROMACS Feature New Normal external potential modules for refinement against experimental data 08/22/2018 05:03 PM GROMACS - future
1971 GROMACS Task New Normal Removing buggy features vs. keeping workflows 01/19/2018 01:36 PM GROMACS - future
1967 Support Platforms Bug Resolved Normal Documentation pages generated by Jenkins do not render properly 08/27/2016 02:04 AM
1966 GROMACS Feature New Low Hydrogen mass repartiniong 05/25/2016 06:04 PM GROMACS - future
1964 GROMACS Feature Accepted Normal "pull=no" should not produce warnings about "unknown" pull keywords 05/20/2016 02:37 PM
1953 GROMACS Feature New Low use more regular polymorphism for GPU code 05/06/2016 10:06 PM GROMACS - future
1948 GROMACS Feature New Low add warning when non-identical GPUs are used 06/12/2017 08:45 PM
1936 GROMACS Task New Normal treat default-able mdp fields as strings 04/02/2016 10:32 PM GROMACS - future
1934 GROMACS Bug New Normal QMMM with ORCA: memory leaks, buffer overflows and much more 07/10/2016 09:26 AM
1925 GROMACS Task In Progress Normal remove concept of unilateral global communication 07/15/2019 06:42 PM GROMACS - 2020
1919 GROMACS Bug Accepted Normal static linking issues cause by hwloc support 10/12/2018 10:49 PM GROMACS - future
1907 GROMACS Task Accepted Low keeping compile- and run-time CPU/arch detection consistent 08/01/2016 10:09 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
1900 GROMACS Feature New Normal Implement some new errors in grompp 06/22/2016 05:20 PM
1885 GROMACS Feature New Normal DPD Thermostat 01/26/2016 10:17 AM
1879 GROMACS Task In Progress Low make the GROMACS OpenCL kernel work on Gallium 11/30/2018 05:46 PM GROMACS - future
1876 GROMACS Task New Normal Reorganize vector input passed to core MD routines 06/01/2016 01:59 PM GROMACS - future
1867 GROMACS Feature New Normal make coupling implementations reversible 12/02/2015 07:43 AM
1862 GROMACS Task New Normal Fully replace t_topology by gmx_mtop_t 02/13/2019 04:53 PM
1855 GROMACS Task New Normal Convert preprocessor use so that symbols are always defined 06/28/2016 02:17 PM
1854 GROMACS Feature New Normal Remove all cyclic dependencies 05/25/2017 08:34 AM
1852 GROMACS Task New Normal Remove group scheme 09/27/2019 03:13 PM GROMACS - future
1842 GROMACS Feature New Normal Replace XML with JSON 01/18/2018 05:12 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
1836 Support Platforms Bug New Normal Support a way to retrigger part of matrix job 07/22/2017 12:30 AM
1829 GROMACS Task New Normal Future of thread level parallelism 11/18/2016 05:29 PM
1828 GROMACS Task New Normal Exception handling in mdrun 10/07/2015 11:36 AM
1827 GROMACS Bug New Low cmake multi-configuration generator support partly broken 12/11/2017 05:20 PM GROMACS - future
1815 Support Platforms Task In Progress Normal implement and execute plan for new releng machinery 10/15/2016 05:37 PM
1811 GROMACS Bug New Normal Extrae build issues 12/13/2017 03:43 AM
1785 GROMACS Task New Low no pV term written to energy file when pressure coupling is anisotropic 07/26/2015 01:47 PM GROMACS - future
1770 GROMACS Bug New Normal segmentation fault with free energy changes and multiple GPU's 07/14/2015 03:24 AM
1768 GROMACS Task New Normal decide future of command-line options vs env vars 11/03/2016 05:51 PM GROMACS - future
1745 GROMACS Task New Normal Moving to C++11 after Gromacs-5.1 06/01/2016 03:01 PM
1732 Support Platforms Bug New Normal review and extend jeknins tests setups, coverage 05/03/2016 05:30 AM
1731 Support Platforms Bug In Progress Normal document jenkins configuration and set up means to track changes 05/31/2017 06:13 PM
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